[{"hash":"1093672786903404586","title":"Platelet-vascular signaling and cytoskeletal regulation","description":"This cluster centers on platelet aggregation and angiogenesis, with related enrichment for membrane trafficking and cytoskeletal control (Rho signaling, SNARE regulation, and plasma membrane localization). The mixture suggests proteins involved in membrane-associated signaling pathways important for platelet function and vascular development, with broader roles in cell polarity and signaling. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":2},{"id":"GO:0035544","count":2},{"id":"GO:0035751","count":2},{"id":"GO:0072659","count":2},{"id":"GO:0045765","count":2}]},{"hash":"2129304405737291185","title":"Retroviral infection and proviral latency","description":"Based on the top GO terms, this cluster centers on steps of the retroviral life cycle: entry into the host, reverse transcription (RNA-templated DNA synthesis), genome integration, and establishment of integrated proviral latency, with additional hints of host transcriptional regulation and apoptosis modulation by a symbiont/virus. These collectively support a cohesive theme around retroviral infection and provirus dynamics.","confidence":"High","size":29,"edges":45,"triangles":35,"max_degree":12,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0045944","count":5},{"id":"GO:0075732","count":5},{"id":"GO:0006278","count":5},{"id":"GO:0006310","count":5},{"id":"GO:0015074","count":5}]},{"hash":"1542841119569202428","title":"DNA Replication and Repair","description":"This cluster is dominated by GO terms related to DNA replication (replication, unwinding, primer synthesis) and DNA damage response (SOS response, transcription-coupled nucleotide-excision repair). While there are some RNA processing terms (spliceosomal changes, nonsense-mediated decay) present, the strongest and most frequent signals point to genome maintenance\u2014replication and repair processes. Confidence: High","confidence":"","size":29,"edges":117,"triangles":209,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0006268","count":10},{"id":"GO:0006269","count":10},{"id":"GO:0045944","count":9}]},{"hash":"736013197978745066","title":"Developmental gene regulation and stress responses","description":"The GO terms cluster around developmental processes (neural tube closure, forebrain development, multicellular organism development) and transcriptional control (DNA-templated transcription, regulation of gene expression by genomic imprinting), with additional signals related to cell cycle (mitotic cell cycle) and signaling (positive regulation of GTPase activity). Stress-related terms (defense response to Gram-positive bacteria, cellular response to cadmium ion) suggest ancillary regulatory layers. The mix points to a group of proteins involved in development via transcriptional regulation, with some stress and signaling roles; the lack of network edges in this dataset means the label reflects shared functional themes rather than a single interaction module.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":5},{"id":"GO:0001843","count":4},{"id":"GO:0001403","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1132866348579595621","title":"Chromatin remodeling and transcription regulation in development","description":"This cluster centers on chromatin remodeling and transcription control (chromatin remodeling; regulation of DNA-templated transcription; transcription). Developmental signals (multicellular development; neural crest cell migration; ureteric bud morphogenesis) imply a program where chromatin state modulates gene expression during development, with DNA maintenance/repair signals (telomeric D-loop disassembly; replication-born DSB repair) reflecting genome maintenance during these processes. Overall, the group appears to function as a chromatin-regulated transcription module active in developmental contexts.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043044","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0061820","count":4},{"id":"GO:1990414","count":4},{"id":"GO:0006351","count":4}]},{"hash":"726646271736254586","title":"Ribosome Biogenesis and Translation Initiation","description":"The dominant GO terms cluster around ribosome assembly and RNA processing (maturation of rRNA, ITS1 cleavage, ribosome biogenesis) and the formation of the translation preinitiation complex and translation reinitiation, indicating a core role in ribosome production and early protein synthesis. A few development-related terms appear, but the central theme is ribosome biogenesis and translation initiation rather than a developmental program. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007275","count":8},{"id":"GO:0000463","count":8},{"id":"GO:0000447","count":8},{"id":"GO:0001731","count":8},{"id":"GO:0042254","count":8}]},{"hash":"958414311423932439","title":"Developmental signaling and neural growth","description":"The cluster shows strong enrichment for multicellular development, axonogenesis, long-term synaptic potentiation, and angiogenesis, plus regulation of phosphorylation and cell-cycle transitions. This points to a broader developmental and signaling program with neural differentiation/neuronal signaling components, rather than a single pathway. ","confidence":"Medium","size":29,"edges":47,"triangles":28,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":29},{"id":"GO:0007121","count":29},{"id":"GO:0010800","count":29},{"id":"GO:0000086","count":29},{"id":"GO:0009738","count":29}]},{"hash":"2181381270689428012","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster's top GO terms emphasize ribosome biogenesis, ribosomal subunit biogenesis, rRNA maturation, and translation initiation/reinitiation, indicating a core function in assembling the protein synthesis machinery. While cilium assembly and bone marrow development appear among the terms, the dominant signal is ribosome- and translation-related processes, supporting a label focused on ribosome assembly and initiation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0060271","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1251344830290129887","title":"Central carbon metabolism and amino acid catabolism","description":"The cluster is driven by terms for the TCA cycle, glycolysis, gluconeogenesis, and various amino acid catabolic pathways (alanine, kynurenine, lysine). These point to core energy production and amino acid turnover as the unifying theme. Notch signaling and vitamin B6 response appear but are less dominant, suggesting possible cross-talk or annotation noise rather than a primary function. Overall, this cluster most strongly reflects central carbon metabolism and amino acid catabolism.","confidence":"Medium","size":29,"edges":363,"triangles":2926,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006099","count":10},{"id":"GO:0042853","count":8},{"id":"GO:0007219","count":8},{"id":"GO:0097053","count":8},{"id":"GO:0006096","count":7}]},{"hash":"1397172507969921777","title":"Neuronal vesicle trafficking and synaptic signaling","description":"These terms cluster around vesicle transport (ER-to-Golgi and endosome-to-Golgi) and neuronal signaling (excitatory postsynaptic potential, dendrite development, GPCR signaling). This suggests a cohesive role in neuronal vesicle trafficking and synaptic communication, with some non-neuronal development terms likely representing broader developmental annotations in the dataset.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0021762","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0001889","count":3}]},{"hash":"125020517764499154","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0008211","count":2},{"id":"GO:0003139","count":2},{"id":"GO:0010873","count":2},{"id":"GO:0043044","count":2}]},{"hash":"1239245921121410756","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":406,"triangles":3654,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0055114","count":3},{"id":"GO:1900865","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0090617","count":2}]},{"hash":"1139434065695896879","title":"Embryonic Development and Proteolysis","description":"Most terms cluster around embryonic development events (neural tube closure, blastocyst development, germ-line sex determination, myoblast fusion). The autoprocessing/self-proteolysis and digestion terms suggest proteolytic maturation mechanisms accompanying development. Together, these points indicate a cluster centered on developmental processes with proteolytic regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016540","count":3},{"id":"GO:0007520","count":3},{"id":"GO:0006886","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1380214417568632332","title":"Nucleolar ribosome biogenesis and RNA processing","description":"The top GO terms cluster around ribosome biogenesis, rRNA maturation, and mRNA export from the nucleus, which are hallmark nucleolar RNA-processing activities involved in ribosome assembly. Additional terms for translation and transcription regulation align with broader nuclear RNA metabolism, but the core signal is ribosome production and RNA maturation. Overall, this cluster seems best described by nucleolar ribosome biogenesis and RNA processing.","confidence":"High","size":29,"edges":403,"triangles":3575,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0000463","count":3}]},{"hash":"456385088461592718","title":"RNA transcription and processing cluster","description":"This cluster is dominated by GO terms pointing to transcription initiation and elongation (RNA polymerase II), snRNA transcription (both RNA Pol II and III), and spliceosomal snRNP assembly, along with chromatin remodeling and protein ubiquitination. These suggest a core theme of transcription and RNA processing machinery, with keratinization, spermatid differentiation, and chorio-allantoic fusion appearing as less directly connected or broader developmental signals. Overall, the label captures the central function of the proteins as transcription/RNA processing factors, with some peripheral differentiation-related terms.","confidence":"Medium","size":29,"edges":17,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":4},{"id":"GO:0000387","count":2},{"id":"GO:0007289","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0048096","count":1}]},{"hash":"649419912826947611","title":"Centromere-Chromatin Assembly and DNA Repair","description":"The dominant signals come from centromere/chromatin assembly (CENP-A containing chromatin assembly) and key mitotic processes such as cell division, microtubule dynamics, and Okazaki fragment processing during mitotic DNA replication, plus homologous recombination repair. These collectively point to chromosome maintenance during cell division. Some trafficking-related terms appear, but the core theme remains chromatin assembly and DNA replication/repair in mitosis.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061641","count":6},{"id":"GO:0006888","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0051013","count":5},{"id":"GO:0051301","count":5}]},{"hash":"494793002545972881","title":"Rho/GTPase-regulated actin remodeling","description":"The top terms point strongly to actin cytoskeleton dynamics (actin filament organization, actin crosslink formation, cortical patch assembly) and regulation by Rho signaling and GTPases, with supporting input from PI signaling and Wnt/calcium pathways. This suggests a cohesive cluster centered on cytoskeletal remodeling controlled by Rho/GTPase signaling, with some peripheral terms related to neural development and visual processes reflecting broader roles in plasticity and morphogenesis.","confidence":"Medium","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0060291","count":2},{"id":"GO:0000147","count":2},{"id":"GO:0007223","count":2},{"id":"GO:0007507","count":2}]},{"hash":"214432681058509271","title":"Unknown","description":"The top GO terms are highly heterogeneous, including transcription regulation and chromatin remodeling terms as well as cellulose catabolic, proteolysis, antibiotic biosynthesis, and redox-related processes. There is no clear single functional theme that ties all proteins together, making it not possible to assign a concise, representative label.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0030245","count":4},{"id":"GO:0006508","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0098869","count":3}]},{"hash":"723219449399131886","title":"Transcriptional Regulation in Immune and Developmental Contexts","description":"Top GO terms indicate a shared emphasis on transcriptional control (DNA-templated transcription; regulation of transcription by RNA polymerase II) coupled with various differentiation programs across immune and developmental lineages (T cell receptor recombination, inflammatory response, mammary gland, endocardial, skeletal muscle, myoblast differentiation). These patterns suggest the proteins collectively participate in gene expression regulation during development and immune-related processes, with incidental associations like glucose transport. Confidence: Medium.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033153","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0002437","count":2},{"id":"GO:0030879","count":2},{"id":"GO:0006351","count":2}]},{"hash":"413492273755726655","title":"Developmental gene regulation and stress responses","description":"This cluster shows enrichment in gene expression regulation and developmental processes (DNA-templated transcription, multicellular organism development, forebrain development) alongside cellular stress responses (ER stress\u2013related apoptotic signaling, cadmium ion response). The diverse GO terms point to proteins involved in coordinating development with general stress-response pathways rather than a single, specific function.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0006349","count":2}]},{"hash":"684013642622178563","title":"Mitotic Cytoskeleton and Contractile Ring Assembly","description":"The cluster shows multiple GO terms tied to mitosis and cytokinesis, including actin filament bundles and contractile ring assembly/localization, centrosome maintenance, and neuroblast division, indicating a coherent theme around mitotic cytoskeleton dynamics and cell division. Peripheral terms like exocytosis and GTPase regulation may be secondary but do not outweigh the central mitotic/cytoskeletal signal.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:1902405","count":2},{"id":"GO:1903478","count":2},{"id":"GO:0021873","count":2},{"id":"GO:1903477","count":2}]},{"hash":"1624595037490098801","title":"Immune signaling and cell migration","description":"The GO terms point to diverse signal transduction pathways (GPCR, NOD2, Rho signaling) along with immune-related processes (GM-CSF response, B cell homeostasis) and cytoskeletal/membrane dynamics (SNARE regulation, cell migration, muscle contraction). This suggests a broad theme of communication and movement coordination in immune and cellular contexts.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0070431","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0032088","count":2}]},{"hash":"959137619651875628","title":"Cell Architecture and Neural Development","description":"The terms cluster around cell architecture and polarity (actin cytoskeleton reorganization, establishment of cell shape/polarity) and neural development (nervous system development, substantia nigra development), with supporting signals for trafficking and division (Golgi to plasma membrane transport, mitotic spindle assembly); a few broader terms (xenobiotic response, oxidative phosphorylation, respiratory burst, ossification) are less central.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031532","count":7},{"id":"GO:0006893","count":6},{"id":"GO:0090324","count":6},{"id":"GO:0043931","count":6},{"id":"GO:0090307","count":6}]},{"hash":"198636574743498524","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0021510","count":8},{"id":"GO:0000447","count":8},{"id":"GO:0000472","count":8},{"id":"GO:0007568","count":8}]},{"hash":"380376944062788393","title":"Redox Homeostasis and Lipid Modification","description":"The top GO terms cluster around oxidative stress management (cellular oxidant detoxification, cell redox homeostasis, response to heat) and lipid-related processes (phospholipid dephosphorylation, GPI anchor biosynthesis), suggesting a shared theme of redox balance linked to membrane lipid remodeling and secretory pathway processing, despite a few outliers like insulin processing.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0046839","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0009408","count":2}]},{"hash":"1349499330498733907","title":"Spliceosome-driven mRNA splicing and translation initiation","description":"This cluster is dominated by GO terms on mRNA splicing via the spliceosome (including cis and alternative splicing) and its regulation, plus related RNA processing and regulatory processes such as ncRNA-mediated gene silencing and translation initiation/stability under stress. The common thread is post-transcriptional RNA processing and translation control centered on spliceosome activity.","confidence":"High","size":28,"edges":102,"triangles":121,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":11},{"id":"GO:0048026","count":11},{"id":"GO:0000398","count":10},{"id":"GO:1901407","count":10},{"id":"GO:0001731","count":9}]},{"hash":"798786647699606531","title":"Transcriptional Regulation of Metabolism and Growth","description":"The cluster centers on DNA-templated transcription and regulation of transcription linked to metabolic pathways (cellular respiration, leucine biosynthesis, glyoxylate cycle, gluconeogenesis) and cell division, with evidence of nutrient-responsive transcriptional control (e.g., regulation of transcription by carbon source). Despite several obsolete terms, the coherent theme is transcriptional regulation coordinating metabolism and growth.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0051301","count":3},{"id":"GO:0061415","count":3},{"id":"GO:0043457","count":3},{"id":"GO:0035948","count":3}]},{"hash":"110301372760025847","title":"Unknown","description":"The top terms cover diverse processes\u2014from phosphatidylinositol signaling and calcineurin-NFAT pathways to sporulation membrane formation, cell morphogenesis, ribosomal RNA maturation, and ER-to-cytosol proteolysis\u2014spanning signaling, development, ribosome biogenesis, and protein trafficking. Because there is no single cohesive function tying these terms together for this protein cluster, a unified label cannot be confidently assigned.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1202465805541123005","title":"Developmental transcription and stress response","description":"Most top GO terms point to gene regulation (DNA-templated transcription) and developmental processes (multicellular organism development, forebrain development). Additional terms indicate roles in ER-to-Golgi transport, ER stress\u2013induced apoptosis, and cell cycle, suggesting a broad module of transcriptional control linked to development with accompanying cellular stress signaling. The cluster does not map to a single pathway but rather to a development-focused gene regulation cluster with stress responsiveness.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006888","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0050830","count":3}]},{"hash":"872013358116226768","title":"Pheromone signaling and yeast cell-cycle control","description":"Top GO terms include response to pheromone and positive regulation of GTPase activity, with concurrent links to cell division, mitotic cell cycle, and budding. This suggests a cohesive theme around pheromone-triggered signaling that governs yeast cell-cycle progression and morphogenesis, despite some outlier terms that may reflect annotation noise.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":19},{"id":"GO:0043547","count":19},{"id":"GO:0051301","count":13},{"id":"GO:0007601","count":13},{"id":"GO:0000278","count":13}]},{"hash":"1314747349886737968","title":"Unknown","description":"The GO terms are a mosaic of metabolic and signaling processes across different systems (strigolactone and alkaloid metabolism, triglyceride and phospholipid processing, redox detoxification, endocannabinoid signaling, antibiotic biosynthesis) with no dominant shared function. There are no protein\u2013protein interactions (edges) linking a common pathway, and several terms are obsolete, so a coherent cluster label cannot be derived.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019380","count":9},{"id":"GO:0055114","count":9},{"id":"GO:0019433","count":9},{"id":"GO:2000124","count":9},{"id":"GO:0017000","count":8}]},{"hash":"264364245497877711","title":"Transcriptional Regulation and Metabolism","description":"Most of the top GO terms center on DNA-templated transcription and its regulation (RNA polymerase II), with additional terms tying transcriptional control to metabolic processes (cellular respiration, gluconeogenesis), and even secondary metabolism (aflatoxin biosynthesis). This suggests a coherent cluster of proteins involved in transcriptional regulation influenced by metabolic state.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0002098","count":4},{"id":"GO:0045793","count":4}]},{"hash":"2241184405255028265","title":"Oocyte Maturation and Meiotic Spindle Regulation","description":"This cluster centers on processes related to oocyte maturation and meiosis I spindle assembly, with supporting signals from microtubule dynamics and SCF-dependent ubiquitin-proteasome\u2013mediated protein degradation, indicating tight regulation of the meiotic spindle and cell-cycle control in female germ cells; some embryonic development terms may reflect broader developmental contexts but do not override the meiosis-focused core.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":9},{"id":"GO:0070544","count":7},{"id":"GO:0006516","count":7},{"id":"GO:0007057","count":7},{"id":"GO:0021993","count":7}]},{"hash":"2286025703009329162","title":"Cell cycle and neural development regulators","description":"The top terms cluster around mitotic cell cycle control, signaling regulation (JNK cascade), and neural development processes (axon/dendrite morphogenesis, axon extension), along with transcription and focal adhesion regulation. This pattern suggests a group of regulatory proteins that influence cell division and neural morphogenesis, rather than a single enzymatic function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":25},{"id":"GO:0046330","count":24},{"id":"GO:0043304","count":24},{"id":"GO:0050771","count":24},{"id":"GO:0033138","count":24}]},{"hash":"76756774099364368","title":"Developmental morphogenesis and cytoskeletal regulation","description":"The terms cluster around developmental processes (brain and spinal cord development, multicellular organism development, gastrulation) and cytoskeletal dynamics (actin filament depolymerization, GTPase activity regulation), with supporting signals from cell cycle and redox homeostasis. This suggests proteins involved in growth, morphogenesis, and cytoskeletal remodeling during development, rather than a single specific pathway. Confidence: Medium","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0007275","count":3}]},{"hash":"41070153923668007","title":"Stress-Response and Transcription Regulation","description":"This cluster centers on broad stimulus- and stress-related responses (lipopolysaccharide, xenobiotic, corticosterone, selenium), with accompanying DNA-templated transcription activity and regulatory functions, plus some metabolic biosynthesis terms. The lack of a single cohesive pathway and zero edges suggest a collection of genes involved in general stress responses and transcriptional regulation rather than one specific function. Medium","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032496","count":8},{"id":"GO:0006351","count":5},{"id":"GO:2000648","count":5},{"id":"GO:0043046","count":5},{"id":"GO:0014063","count":5}]},{"hash":"2228842922328265080","title":"Retroviral entry, genome integration, and latency","description":"This cluster is dominated by GO terms tied to viral infection and genome integration, including entry into host cells, viral penetration into the nucleus, RNA-templated DNA synthesis (reverse transcription), DNA integration into the host genome, establishment of proviral latency, and subsequent DNA replication/recombination. The combination of entry, reverse transcription, integration, and latency points to a retroviral/proviral life cycle as the unifying theme, with some related DNA remodeling steps accompanying replication. ","confidence":"High","size":27,"edges":40,"triangles":27,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0075713","count":4},{"id":"GO:0007131","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1467071823213875896","title":"LPS and O-antigen Biosynthesis","description":"This cluster is dominated by GO terms for lipopolysaccharide and related polysaccharide biosynthesis, including LPS biosynthetic, O antigen, and colanic acid pathways, plus dTDP-rhamnose and galactose metabolism, indicating enzymes involved in bacterial cell envelope polysaccharide assembly.","confidence":"High","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":10},{"id":"GO:0055114","count":9},{"id":"GO:0097171","count":8},{"id":"GO:0009243","count":7},{"id":"GO:0006012","count":7}]},{"hash":"1242579095006014078","title":"Translation initiation and regulation","description":"Most terms center on translation initiation and its control: formation of the translation preinitiation complex, translation reinitiation, regulation of translational initiation, and IRES-dependent viral translation. There is also a term for miRNA-mediated silencing by inhibiting translation, reinforcing a translational control theme. While a few GO terms relate to transcription and histone methylation, the dominant signal across the cluster is regulation of translation initiation, including viral contexts, justifying a label focused on translation initiation and its regulation.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":8},{"id":"GO:0002188","count":8},{"id":"GO:0035278","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0051568","count":5}]},{"hash":"1614126551755359017","title":"Transcriptional Regulation and Neuronal Development","description":"This cluster centers on DNA-templated transcription and dendrite morphogenesis, with additional signaling-related terms (Wnt pathway, prostaglandin response, GM-CSF stimulus) and cell-cycle/DNA replication processes. The pattern suggests proteins that regulate gene expression and signaling important for neuronal differentiation and development, rather than a single metabolic function. Therefore the label emphasizes transcriptional control coupled with neuronal development.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":14},{"id":"GO:0043552","count":13},{"id":"GO:0048813","count":13},{"id":"GO:0097011","count":13},{"id":"GO:0006813","count":13}]},{"hash":"948744909514265989","title":"DNA replication and repair with stress response","description":"The top GO terms cluster around DNA replication and DNA repair (including UV-damage excision repair) and cellular stress responses (oxidative stress and antibiotic response), suggesting a core function in genome maintenance under stress. Some terms such as chaperone-assisted refolding, ERAD, and vesicle transport appear less directly connected and may reflect annotation noise or multi-functional proteins, but the dominant theme points to DNA metabolism and stress response. ","confidence":"Medium","size":27,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0030420","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0006888","count":3}]},{"hash":"1758815592840820882","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by ribosome-related processes: ribosome biogenesis, translation, and ribosomal large subunit export from the nucleus, plus tRNA modification. These indicate a coherent theme around assembling and using ribosomes for protein synthesis, with some connection to cell growth and division. Thus, the label captures the core function of the cluster with high confidence.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000055","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0006412","count":4}]},{"hash":"1460862203349735551","title":"Ubiquitin-Proteasome\u2013Mediated Degradation","description":"Most top GO terms are centered on ubiquitin-dependent protein catabolic processes and proteasomal degradation (SCF-dependent ubiquitin-proteasome pathway, polyubiquitination). While developmental terms like neural tube closure and oocyte maturation appear, the dominant signal is protein turnover via ubiquitination and proteasomal breakdown, suggesting this cluster mainly groups components of the ubiquitin\u2013proteasome system with ties to cell-cycle\u2013related processes.","confidence":"Medium","size":27,"edges":7,"triangles":0,"max_degree":5,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":15},{"id":"GO:0042787","count":11},{"id":"GO:0000209","count":10},{"id":"GO:0006516","count":9},{"id":"GO:0021678","count":9}]},{"hash":"2104880730115291484","title":"Neural Development and Signaling","description":"Top GO terms collectively point to neural development and signaling processes (retinal cone development, neuronal tangential migration, dopamine receptor signaling, Wnt signalosome assembly), with supporting roles for cellular trafficking and signaling modulation (endocytic recycling, Cvt pathway targeting, CAMKK-AMPK). This combination suggests proteins involved in neural development and receptor-mediated signaling rather than a non-neural function, making the label representative of the cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046549","count":4},{"id":"GO:0048873","count":3},{"id":"GO:0032258","count":3},{"id":"GO:0032456","count":3},{"id":"GO:1903125","count":3}]},{"hash":"289287557424273590","title":"ER-Golgi Vesicle Transport","description":"This cluster shows strong enrichment for GO terms related to vesicle trafficking within the secretory pathway, including ER-to-Golgi transport, Golgi-to-plasma membrane transport, retrograde Golgi-ER transport, and vesicle fusion with the Golgi. While a few terms touch on other processes, the dominant theme is intracellular protein/vesicle transport in the Golgi network, justifying this label.","confidence":"High","size":27,"edges":5,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":9},{"id":"GO:0043001","count":7},{"id":"GO:0090316","count":7},{"id":"GO:0071701","count":6},{"id":"GO:0060789","count":6}]},{"hash":"77149229344673436","title":"Oocyte meiosis and spindle assembly proteins","description":"The top GO terms cluster around meiotic progression in oocytes, including oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, pointing to a core role in meiosis-related spindle dynamics. Additional terms for SCF-dependent ubiquitin-proteasome\u2013mediated protein catabolism and negative regulation of cell proliferation support tightly regulated cell-cycle control during meiosis. A broader transcriptional term also appears, suggesting coordinated gene expression with these processes. Overall, this cluster is best described as proteins involved in oocyte meiosis and spindle assembly, with related proteostasis and transcriptional regulation. ","confidence":"High","size":27,"edges":25,"triangles":0,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0031146","count":5},{"id":"GO:0006516","count":4},{"id":"GO:0001556","count":4},{"id":"GO:0021678","count":4}]},{"hash":"1891041971284591580","title":"Bacterial fatty acid metabolism and biosynthesis","description":"The cluster\u2019s top GO terms are dominated by fatty acid metabolic processes, including medium- and long-chain acyl-CoA catabolism and palmitic acid biosynthesis, as well as regulation of fatty acid biosynthesis. While there are also terms for translation and enterobactin biosynthesis, the recurring fatty acid\u2013related functions suggest proteins involved in lipid metabolism in bacteria, including both the production and breakdown of fatty acids and their regulation.","confidence":"Medium","size":27,"edges":34,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0036114","count":2},{"id":"GO:0009239","count":2},{"id":"GO:0045892","count":2},{"id":"GO:0036116","count":2}]},{"hash":"2169988053726508728","title":"Unknown","description":"The terms span multiple distinct biological areas (glycosylation modifications, insect cuticle development, neurotransmitter secretion regulation, and various sensory and homeostatic processes) with no clear, single shared function tying them together, so a cohesive label cannot be assigned.","confidence":"","size":27,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035269","count":3},{"id":"GO:0008363","count":2},{"id":"GO:0097370","count":2},{"id":"GO:0046929","count":2},{"id":"GO:0003026","count":2}]},{"hash":"463821563564981053","title":"Cell Cycle and Protein Turnover Regulation","description":"This cluster is dominated by GO terms for the mitotic cell cycle, cell division, and DNA-templated transcription, alongside roles in translation initiation and ubiquitin-proteasome\u2013mediated protein turnover (including ERAD). The convergence of cell-cycle processes with transcriptional control and protein degradation suggests a coherent theme of coordinating cell growth and proteome quality during division. A few terms such as defense response to Gram-positive bacteria and cellular response to dopamine appear less directly connected and may reflect pleiotropy or annotation noise, but do not detract from the main signal.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0030433","count":3}]},{"hash":"233824993607669012","title":"RNA methylation and mRNA capping","description":"The top GO terms cluster around RNA modification\u2014RNA guanine-N7 methylation, tRNA methylation, wobble uridine modification, and 7-methylguanosine mRNA capping\u2014pointing to a core function in RNA methyltransferases and processing. While a few cofactor biosynthesis terms are present, the dominant theme is RNA modification activity.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":4},{"id":"GO:0042220","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0006370","count":3},{"id":"GO:0030488","count":3}]},{"hash":"463229600197195028","title":"Rac\u2011Mediated Cytoskeleton Remodeling and Cell Adhesion","description":"The cluster shows strong enrichment for actin cytoskeleton\u2013related processes: positive regulation of stress fiber and filopodium assembly, Rac protein signal transduction, and substrate adhesion\u2013dependent cell spreading, plus mitotic spindle assembly. This points to proteins coordinating cytoskeletal dynamics and cell\u2013substrate interactions with Rac signaling at the center. Some terms also touch on trafficking and metabolism, but the dominant theme is cytoskeletal remodeling and adhesion.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051496","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0046847","count":4},{"id":"GO:1900026","count":4},{"id":"GO:0016601","count":4}]},{"hash":"1029965257563143150","title":"Actin Cytoskeleton Remodeling in Muscle","description":"Most top GO terms describe actin filament network formation, sarcomere organization, and skeletal muscle tissue development, plus actin filament dynamics. This suggests a cluster centered on actin cytoskeleton remodeling important for muscle structure, with other terms like B cell receptor signaling or spliceosomal processes appearing less central.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:0007519","count":3},{"id":"GO:0033138","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0051639","count":2}]},{"hash":"1062810423016114872","title":"Cellular stress response and proteostasis","description":"The prominent GO terms point to proteasomal ubiquitin-dependent protein catabolism (proteostasis) and various stress responses (heavy metal exposure, oxidative stress, and neuron-specific apoptotic signaling), along with cell cycle/DNA replication regulation and circadian rhythm. This suggests a cluster centered on how cells manage protein turnover and genome integrity under stress, rather than a single precise pathway; hence a general label of cellular stress response and proteostasis fits best.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0000083","count":8},{"id":"GO:0031571","count":7},{"id":"GO:0042752","count":7},{"id":"GO:1903378","count":7}]},{"hash":"1082770711908337088","title":"DNA-Templated Transcription Regulation","description":"This cluster is best described by transcriptional control terms, with GO:0006355 and GO:0006351 appearing prominently, suggesting a core theme around regulation of DNA-templated transcription. However, the presence of disparate terms (cocaine response, placenta development, light detection, plant signaling, etc.) and otherwise no network connectivity imply heterogeneous annotations and limited functional cohesion beyond transcription regulation. Therefore, the label reflects the strongest recurring function but with only moderate confidence due to diverse annotations.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042220","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0045793","count":2}]},{"hash":"321871188933857250","title":"Ubiquitin-Dependent Protein Degradation","description":"The prominent GO terms describe ubiquitin-dependent proteolysis and proteasomal degradation (including SCF-dependent pathways and protein polyubiquitination), indicating these proteins cluster around ubiquitin-mediated protein turnover; occasional terms about cell-cycle and oocyte maturation align with regulatory roles of degradation in those processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0000083","count":5},{"id":"GO:2000620","count":4},{"id":"GO:0085020","count":4}]},{"hash":"2091532109311213305","title":"Multi-tissue differentiation and regeneration","description":"The top GO terms predominantly point to differentiation across multiple tissues (fat, skeletal muscle, endothelium, dendritic cells) with some regeneration (muscle) and supportive signaling. While there are a few generic signaling terms, the common thread is lineage specification and tissue remodeling rather than a single pathway, justifying a label around differentiation and regeneration across tissues.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007253","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0035994","count":2},{"id":"GO:0002268","count":2},{"id":"GO:0060843","count":2}]},{"hash":"2161464856301103069","title":"Mitosis and Cell Cycle","description":"This cluster centers on cell division and mitosis: terms for mitotic DNA replication, spindle assembly, chromatid cohesion, APC/C-dependent proteolysis, actin remodeling during cytokinesis, and related growth signaling, suggesting a cohesive set of mitotic machinery proteins.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:1903461","count":3},{"id":"GO:0007064","count":3},{"id":"GO:0090344","count":3},{"id":"GO:0070306","count":3}]},{"hash":"506322154824971485","title":"Mitochondrial Transport and Metabolic Regulation","description":"These proteins cluster around mitochondrial transport and membrane permeability, with multiple GO terms for transmembrane transport of ATP, NAD, ornithine, and thiosulfate, and regulation of mitochondrial membrane permeability. They also include apoptosis-related mitochondrial changes and necroptosis regulation, plus metabolic signaling linked to insulin and fatty acids and a liver regeneration context. The unifying theme is mitochondria-driven transport/metabolism coupled to cell survival. ","confidence":"High","size":26,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":13},{"id":"GO:0032869","count":13},{"id":"GO:1990544","count":13},{"id":"GO:0000066","count":13},{"id":"GO:0035352","count":13}]},{"hash":"375204305238433232","title":"Mitotic cell cycle and cytoskeletal dynamics","description":"This cluster centers on mitosis and cell division (mitotic cell cycle, mitotic intra-S checkpoint, cell division) and includes signals of cytoskeletal remodeling (stress fiber assembly) and GTPase regulation, plus vesicle trafficking components (COPII-coated vesicle budding). The presence of hypoxia response and autophosphorylation regulation suggests broader stress-adaptive and signaling roles, but the dominant theme appears to be mitotic control coupled with cytoskeletal and trafficking dynamics.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0031573","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051260","count":2}]},{"hash":"1401800074307966428","title":"Lipid and pigment biosynthesis pathways","description":"This cluster is dominated by biosynthetic terms related to lipids and isoprenoid derivatives: fatty acid elongation, very long-chain fatty acids, sphingolipid biosynthesis, C21-steroid hormone metabolism, and phylloquinone turnover, along with melanin biosynthesis. A couple of stress-response terms (response to antibiotic, response to methotrexate) are present but do not define the main theme. Overall, the recurring theme is lipid- and pigment-related metabolism, with associated isoprenoid/pigment pathways linking the proteins.","confidence":"High","size":26,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0042619","count":8},{"id":"GO:0046677","count":6},{"id":"GO:0031427","count":5},{"id":"GO:0042438","count":5}]},{"hash":"1519609994097371364","title":"Neuronal spine development and Rac signaling","description":"The cluster is strongly aligned with neuronal development and cytoskeletal remodeling: enriched terms include positive regulation of dendritic spine development, brain and hippocampus development, Rac protein signal transduction, and lamellipodium/ruffle assembly, which together point to neurons remodeling their synaptic connections via Rac-driven actin dynamics. Trafficking terms like Golgi to plasma membrane transport also fit spine maturation processes that require targeted protein delivery. Overall, the dominant theme is neuronal spine formation and cytoskeletal regulation.","confidence":"Medium","size":26,"edges":77,"triangles":17,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":7},{"id":"GO:0010796","count":7},{"id":"GO:0031384","count":7},{"id":"GO:0007420","count":6},{"id":"GO:0010592","count":6}]},{"hash":"310535024708870764","title":"Golgi-centered vesicle trafficking","description":"This cluster centers on Golgi- and vesicle-related transport and organization, with top GO terms covering retrograde Golgi-to-ER transport, Golgi organization, and Golgi-to-plasma membrane trafficking, plus endomembrane pathways like the Cvt pathway and MVB-associated processes. The convergence on Golgi function and intracellular trafficking suggests a cohesive theme of Golgi-centered vesicle transport, with occasional neuronal development terms reflecting trafficking\u2019s role in morphogenesis. Overall, the label captures the dominant function of the proteins in this cluster.","confidence":"High","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":11},{"id":"GO:0060999","count":11},{"id":"GO:0051301","count":11},{"id":"GO:0010796","count":11},{"id":"GO:0031384","count":11}]},{"hash":"422074813459640014","title":"Intracellular trafficking and protein regulation","description":"The top GO terms cluster around internal cellular logistics: ER-to-Golgi vesicle transport, ubiquitin-dependent protein degradation, dephosphorylation, and cytoskeletal actin capping, with additional signals touching transcription and signaling pathways. While some terms are diverse, the strongest common theme is regulation of intracellular trafficking and protein turnover, with auxiliary links to cytoskeleton and signaling. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0070262","count":2},{"id":"GO:2000060","count":2}]},{"hash":"1589556950018689301","title":"Symbiont-driven host immune signaling suppression","description":"Based on the top GO terms, the cluster shows multiple entries about symbiont-mediated perturbation or suppression of host immune functions, including ISG15 modification/conjugation and IRF3 signaling. This suggests the proteins collectively participate in modulating host immunity in the presence of a symbiont. Although there are ancillary terms related to phosphorylation and chromatin regulation, the clearest common theme is immune signaling suppression driven by symbiotic interactions.","confidence":"High","size":26,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":4},{"id":"GO:0051572","count":3},{"id":"GO:0039648","count":3},{"id":"GO:0033128","count":3},{"id":"GO:0039579","count":3}]},{"hash":"787727029430518368","title":"Neural development and cell cycle regulation","description":"The top terms point to nervous system\u2013related processes (axonogenesis, Schwann cell development, long-term potentiation) and general development, alongside cell cycle control (G2/M transition, negative regulation of cyclin-dependent kinase activity) and nuclear/transcriptional regulation. This combination suggests a cluster centered on neural development with coordinated cell cycle regulation, rather than unrelated processes. ","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045736","count":15},{"id":"GO:0034501","count":15},{"id":"GO:0007409","count":13},{"id":"GO:0006351","count":13},{"id":"GO:0046826","count":13}]},{"hash":"850757887027344404","title":"Ribosome biogenesis and translation","description":"Proteins show strong enrichment for translation and ribosome assembly\u2014translation (GO:0006412), ribosome biogenesis (GO:0042254), and ribosomal subunit export from nucleus (GO:0000055)\u2014plus tRNA modification, all pointing to a ribosome-centric cluster. Additional terms like cell cycle and Golgi\u2013ER transport may reflect growth coordination with protein synthesis, rather than a separate trafficking role. Overall, the cluster centers on ribosome production and protein synthesis.","confidence":"High","size":26,"edges":4,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0042254","count":9},{"id":"GO:0051301","count":8},{"id":"GO:0000055","count":8},{"id":"GO:0007049","count":7}]},{"hash":"395379666555435735","title":"Ribosome Biogenesis and ER-Golgi Trafficking","description":"This cluster is enriched for genes involved in ribosome biogenesis and rRNA maturation (SSU/LSU maturation, 5.8S processing, large subunit assembly) as well as vesicle trafficking between the endoplasmic reticulum and Golgi (including clathrin-coated vesicle cargo loading) and vacuole organization, suggesting a combined role in ribosome assembly alongside cellular trafficking and storage pathways.","confidence":"Medium","size":26,"edges":35,"triangles":0,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0006890","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0070262","count":4}]},{"hash":"1636197374943610289","title":"Lipid and Steroid Metabolism","description":"The top GO terms converge on lipid biosynthesis and modification, including fatty acid elongation, very long-chain fatty acid biosynthesis, sphingolipid biosynthesis, and C21-steroid hormone metabolism, suggesting a cohesive lipid/steroid metabolic function for this cluster. Other terms (melanin biosynthesis, phylloquinone catabolic process) point to broader pigment/quinone-related metabolism, but the dominant signal is lipid and steroid pathways; regulation of transcription and a methotrexate response may reflect broader cellular context rather than defining activity.","confidence":"High","size":26,"edges":223,"triangles":960,"max_degree":24,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0031427","count":24},{"id":"GO:0042438","count":24},{"id":"GO:0008207","count":24},{"id":"GO:0042619","count":24},{"id":"GO:0042761","count":24}]},{"hash":"2242868376198074371","title":"DNA Repair and Genome Maintenance","description":"Most of the top GO terms cluster around DNA processing and repair (DNA recombination, base-excision repair, RNA phosphodiester bond hydrolysis), suggesting a core function in genome maintenance. Additional terms indicate broader stress-response and cell-cycle signaling (xenobiotic response, positive regulation of G1/S transition), which can accompany DNA damage responses and proliferation in differentiating tissues. A couple of terms (corneocyte development, renal water transport) are less directly tied, but don\u2019t override the central theme of DNA repair/maintenance.","confidence":"Medium","size":26,"edges":48,"triangles":19,"max_degree":11,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":12},{"id":"GO:0090502","count":10},{"id":"GO:0007568","count":8},{"id":"GO:0042493","count":8},{"id":"GO:0006284","count":8}]},{"hash":"98642687794067686","title":"Ribosome biogenesis and translation","description":"This cluster aggregates proteins involved in ribosome production and protein synthesis: translation, rRNA maturation (SSU rRNA processing), ribosome biogenesis, translational initiation, and mRNA export, indicating a core role in ribosome assembly and function. The presence of antibiotic response signals may reflect ribosome-targeting pathways, but the dominant theme is ribosome biogenesis and translation.","confidence":"High","size":26,"edges":168,"triangles":525,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0042254","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0043547","count":4}]},{"hash":"1271912555704495441","title":"Unknown","description":"The top terms span a broad mix of cellular signaling (GTPase activity regulation and tyrosine kinase regulation), stress/antibiotic response, vesicle trafficking, cell cycle, developmental processes (brain/spinal cord), and ribosome biogenesis. With no observed interactions among the 26 proteins (Edges and Triangles are zero), there is no clear shared function or pathway tying them together. Therefore, a coherent, specific label cannot be assigned; Unknown is appropriate with no confidence.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0061099","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1729601371509089269","title":"Ribosome Biogenesis and Translation","description":"Explanation: The dominant GO terms are translation, cytoplasmic translation, ribosome biogenesis, and ribosomal large subunit export from the nucleus, with accompanying cell cycle and cell division terms. This indicates a cohesive cluster focused on ribosome production and protein synthesis driving cell growth and division, with ancillary links to related cellular fusion and septum assembly processes.","confidence":"High","size":26,"edges":39,"triangles":14,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0000747","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0002181","count":5}]},{"hash":"745774306207871828","title":"Cardiac contraction regulation and heart development","description":"The top GO terms cluster around heart-related functions: positive and negative regulation of cardiac muscle contraction, negative regulation of striated muscle contraction, and secondary heart field specification, plus a heart development signal. Other terms like epidermal growth factor response and cytoplasmic translation appear less central, but the dominant theme is cardiac muscle regulation and heart formation, guiding a label focused on cardiac contraction control and heart development.","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071364","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0022400","count":1},{"id":"GO:0070602","count":1},{"id":"GO:0045988","count":1}]},{"hash":"1999291505401168034","title":"Skin development and pigmentation signaling","description":"The top GO terms are strongly skewed toward skin development and pigmentation (GO:0043588, GO:0043473), supported by broader developmental signaling (GO:0007275, GO:0043547, GO:0071902). Additional terms like mRNA transport, hypoxia response, and cell cycle suggest broader regulatory roles, but the dominant theme points to skin- and pigment-related developmental signaling.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0007275","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0071902","count":4},{"id":"GO:0051028","count":4}]},{"hash":"672441172509469666","title":"Cell growth, development, and stress responses","description":"The top GO terms include mitotic cell cycle and multicellular development, plus DNA-templated transcription, suggesting growth and gene-expression regulation. Other terms point to stress and immune responses (defense against Gram-positive bacteria, response to antibiotic, cadmium exposure) and signaling (positive regulation of GTPase activity). Taken together, the cluster appears to reflect a broad regulatory program governing development, proliferation, and adaptive responses, rather than a single, narrow function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0048240","count":6},{"id":"GO:0046677","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0001403","count":4}]},{"hash":"1836163286552412882","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0048833","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0032968","count":2}]},{"hash":"376848186504955493","title":"GPCR Signaling with cAMP/cGMP","description":"Proteins cluster around GPCR-mediated signaling and cyclic nucleotide production; GO terms include receptor guanylyl cyclase signaling, adenosine and adrenergic receptor pathways, adenylate cyclase activation, cAMP/cGMP biosynthesis, and forskolin response, indicating a GPCR-second-messenger module. A hypoxia detection term appears but does not define the cluster.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035556","count":6},{"id":"GO:0007168","count":5},{"id":"GO:0070483","count":5},{"id":"GO:0030828","count":5},{"id":"GO:0006171","count":5}]},{"hash":"1961260619008985008","title":"Cardiac muscle contraction and heart development","description":"This cluster shows GO terms centered on cardiac biology: positive regulation of cardiac muscle contraction, negative regulation of cardiac muscle hypertrophy, and negative regulation of striated muscle contraction, plus heart development signals such as secondary heart field specification. While a few terms like intramembranous ossification and opsin signaling are less directly related, the dominant theme is regulation of cardiac muscle function and heart development.","confidence":"Medium","size":25,"edges":37,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001957","count":3},{"id":"GO:0032461","count":2},{"id":"GO:0022400","count":2},{"id":"GO:0070602","count":2},{"id":"GO:0045988","count":2}]},{"hash":"1024692625002678583","title":"Neural development and cell-cycle regulation","description":"This cluster is enriched for neural development terms (nervous system development, hippocampus development, axon extension) along with core regulatory processes (DNA-templated transcription, mitotic cell cycle, spindle orientation checkpoint signaling, JNK cascade regulation). The combination suggests a cohesive theme where neural development is coordinated with cell-cycle control and signaling pathways. Some terms (e.g., T cell receptor signaling) are less directly connected and may reflect annotation breadth or noise, but the dominant pattern supports neural development with proliferation and signaling regulation.","confidence":"Medium","size":25,"edges":10,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0031578","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0045773","count":2},{"id":"GO:0031532","count":2}]},{"hash":"368795785769057120","title":"Apoptosis, Differentiation, and Polarity","description":"The set of GO terms shows a core of programmed cell death signals across multiple cell types (apoptotic signaling, myeloid/hepatocyte apoptosis) alongside differentiation processes (spermatid nucleus differentiation) and cellular organization (spindle assembly, establishment of epithelial cell polarity). Additional terms point to regulatory mechanisms (GTPase activity, ubiquitination) that can modulate these processes, suggesting a cohesive theme around regulated cell fate decisions involving apoptosis, development, and cell polarity. Given the diversity but related functional threads, this label captures the broad functional theme without overfitting to a single process.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007289","count":5},{"id":"GO:0051225","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0097190","count":4},{"id":"GO:0090162","count":4}]},{"hash":"566803045172122428","title":"ER-Golgi Trafficking and Mitosis in Development","description":"The cluster shows strong representation for ER-to-Golgi and COPII vesicle trafficking, including retrograde Golgi-ER transport, as well as mitotic processes (cell division, mitotic cell cycle, spindle assembly) and developmental growth (brain development, multicellular organism growth). This combination points to a coherent theme of vesicle transport linked to cell division and development.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0090114","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0043547","count":4}]},{"hash":"1523526647722844455","title":"Unknown","description":"The Top Terms include lipid A biosynthesis (bacterial), ER-to-Golgi vesicle transport, DNA replication, brassinosteroid signaling, Schwann cell development, cocaine response, and several obsolete terms. Such variety across metabolism, trafficking, development, and signaling suggests there is no single cohesive functional theme tying these proteins together. The cluster likely reflects annotation noise or incidental shared features rather than a specific biological module.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009245","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0006260","count":5},{"id":"GO:1902660","count":5},{"id":"GO:0051343","count":4}]},{"hash":"2277187661532357054","title":"Pheromone Signaling and Growth Control","description":"This cluster centers on pheromone-responsive signaling, with strong representation of signaling regulation (positive regulation of GTPase activity, Ran signaling) and growth-related processes (cell division, budding). Additional terms link to secretion and synaptic assembly, suggesting coordinated control of growth and secretory pathways in response to pheromone cues. Some terms (tRNA wobble modification, visual perception) are less directly connected but do not override the dominant signaling/growth theme.","confidence":"Medium","size":25,"edges":10,"triangles":1,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":25},{"id":"GO:0043547","count":25},{"id":"GO:0002098","count":22},{"id":"GO:0051301","count":22},{"id":"GO:0007117","count":22}]},{"hash":"1335262123695275820","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":177,"triangles":680,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002098","count":25},{"id":"GO:0051301","count":25},{"id":"GO:0007117","count":25},{"id":"GO:1905608","count":25},{"id":"GO:0006547","count":25}]},{"hash":"1768414170981983699","title":"Unknown","description":"The top GO terms span immune response, redox/metabolic processes, transcription regulation, and development, with no single dominant function tying the cluster together, so a cohesive label cannot be confidently assigned.","confidence":"","size":25,"edges":41,"triangles":4,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0032496","count":6},{"id":"GO:0021983","count":5},{"id":"GO:0045648","count":5},{"id":"GO:0006355","count":4}]},{"hash":"1028349076513447665","title":"Presynaptic vesicle maturation and neurotransmitter release","description":"This cluster is dominated by GO terms for synaptic vesicle maturation, neurotransmitter secretion, and presynaptic dense core vesicle exocytosis, which together define neuronal presynaptic secretory machinery. The brain development term corroborates a neural context. A few immune-related terms are present but do not override the central synaptic theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0016188","count":6},{"id":"GO:0007269","count":6},{"id":"GO:0099525","count":6},{"id":"GO:0010796","count":6},{"id":"GO:0007420","count":6}]},{"hash":"19096018651986407","title":"LDLR Regulation and Cholesterol Transport","description":"The top GO terms cluster around regulation and processing of LDL receptor\u2013mediated cholesterol transport (negative regulation of LDL receptor catabolic process, receptor-mediated endocytosis in cholesterol transport, LDL particle receptor catabolic process, etc.), suggesting a cohesive theme of lipid uptake and receptor regulation. Some terms related to nerve growth factor production and embryonic/spore development appear, but they are less represented and do not override the lipid transport signal.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032902","count":3},{"id":"GO:1905596","count":3},{"id":"GO:1905601","count":3},{"id":"GO:0032805","count":3},{"id":"GO:0010989","count":3}]},{"hash":"491176500991793166","title":"Nuclear DNA Repair and Transcription","description":"The top GO terms are dominated by nuclear processes: nucleotide-excision repair and DNA repair, plus transcription by RNA polymerase II and phosphorylation, suggesting a theme around genome maintenance and transcriptional regulation. Other terms (molybdate/taurine transport, xenobiotic export, fatty acid catabolism) are less cohesive with this core, so they may reflect broader annotation or multifunctionality rather than a single cohesive pathway. Overall, the cluster appears to center on nuclear DNA repair and transcription, consistent with a DNA damage response context.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006366","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0042993","count":2}]},{"hash":"471965523745175590","title":"DNA Damage Response and Innate Immunity","description":"Top GO terms indicate both DNA repair (nucleotide-excision repair; cellular response to ionizing radiation) and transcriptional regulation within the nucleus, alongside strong innate immune signaling (innate immune response; dsRNA response; interferon-beta production; LPS signaling; defense against Gram-positive bacteria). This pattern suggests proteins that participate in maintaining genome integrity while also modulating immune pathways, reflecting crosstalk between DNA damage responses and innate immunity.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071479","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0045087","count":3}]},{"hash":"156164252932124054","title":"Intracellular signaling and vesicle trafficking","description":"This cluster\u2019s top GO terms are dominated by intracellular signal transduction and membrane trafficking processes, including recycling endosome to Golgi transport, regulation of vesicle fusion, and retrograde transport. Although a few terms relate to specific developmental contexts (fat cell differentiation, lens fiber morphogenesis) and note NF-kappaB-related regulation (obsolete entries), the common thread appears to be coordination between signaling pathways and vesicle trafficking machinery.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007253","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0035526","count":1}]},{"hash":"657717650393091423","title":"RNA processing and developmental differentiation","description":"The cluster is dominated by GO terms related to RNA processing, such as spliceosome assembly and regulatory ncRNA-mediated gene silencing, suggesting RNA-level regulation. Additional terms point to development and differentiation processes (cardiac and hematopoietic lineages), implying the proteins may participate both in RNA regulation and developmental pathways.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000349","count":1},{"id":"GO:0000387","count":1},{"id":"GO:2000672","count":1},{"id":"GO:0070286","count":1},{"id":"GO:1904059","count":1}]},{"hash":"2134285278202389085","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":131,"triangles":374,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0010586","count":4},{"id":"GO:1903265","count":4},{"id":"GO:1902187","count":4},{"id":"GO:0061158","count":4},{"id":"GO:2000637","count":4}]},{"hash":"2172578940560634698","title":"Neural development and dendritic spine formation","description":"Dominant signals are nervous system and brain development, neuron maturation, and dendritic spine formation, indicating a neural development and synapse-formation cluster. Some terms are obsolete or general, but the core theme remains neuronal differentiation and dendritic/synaptic maturation.","confidence":"High","size":24,"edges":168,"triangles":470,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":10},{"id":"GO:0031384","count":10},{"id":"GO:0060999","count":9},{"id":"GO:0034629","count":9},{"id":"GO:0051301","count":9}]},{"hash":"441393348438085228","title":"Nuclear transport and cell-cycle regulation","description":"The terms show strong ties to nuclear trafficking (NLS-bearing protein import into nucleus; mRNA export from nucleus) and mitotic/kinetochore functions, alongside signals that control growth, apoptosis, and cell fate (GTPase regulation, Wnt signaling, proliferation). These together suggest a theme of coordinating nuclear transport with cell-cycle decisions and growth-regulatory pathways, even though a few terms (like proton transport) are peripheral. ","confidence":"Medium","size":24,"edges":20,"triangles":5,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0006607","count":9},{"id":"GO:0043065","count":7},{"id":"GO:0016477","count":7},{"id":"GO:0090090","count":7}]},{"hash":"280137189526902822","title":"ERAD and Protein Trafficking","description":"The top GO terms point to ubiquitin-dependent ER-associated degradation, protein polyubiquitination, and ER-to-Golgi vesicle transport, with additional terms related to translation initiation/reinitiation that can be linked to ER-associated ribosome function. This suggests a core theme of ER quality control and intracellular trafficking, though a few terms (defense response, meiosis) appear less related, indicating a somewhat mixed cluster with a central ER/trafficking focus.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0051754","count":3}]},{"hash":"2044352836212649849","title":"Stimulus-Response Signaling","description":"The top GO terms point to cellular responses to various stimuli (mechanical, chemical, temperature), including muscle stretch and salicylic acid stimulus, with ubiquitination indicating regulatory control. Although some terms relate to differentiation, the dominant theme is sensing and reacting to external cues, so a broad Stimulus-Response Signaling label best captures this cluster.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0090394","count":3},{"id":"GO:0050955","count":2},{"id":"GO:0035994","count":2}]},{"hash":"2286553422220430303","title":"Developmental regulators and xenobiotic response","description":"The top GO terms point to development across multiple tissues (pituitary, retina, osteoblast) and to transcriptional control (DNA-templated transcription, regulation of transcription) plus regulation of stem cell proliferation. There are also terms tied to xenobiotic response, indicating environmental or chemical stimulus handling. Together, these suggest a cohesive theme of developmental regulation and transcriptional control with a component of detox/chemical response, making this cluster best described as developmental regulators with xenobiotic responsiveness.","confidence":"Medium","size":24,"edges":122,"triangles":322,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0042493","count":7},{"id":"GO:2000648","count":6},{"id":"GO:0002087","count":6},{"id":"GO:0002076","count":6}]},{"hash":"993439278595287297","title":"Bacterial lipid and secondary metabolite biosynthesis","description":"The list shows strong representation of lipid-associated biosynthesis (lipoteichoic acid, very long-chain fatty acids, medium-chain acyl-CoA), plus central and secondary metabolite pathways (menaquinone, malonate catabolism, siderophore and nonribosomal peptide biosynthesis). These patterns point to microbial metabolism and production of small molecule metabolites rather than a single plant pathway; a few GO terms like seed coat development may be annotation noise or broader host interactions.","confidence":"Medium","size":24,"edges":83,"triangles":115,"max_degree":13,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0070395","count":10},{"id":"GO:0019654","count":8},{"id":"GO:0043041","count":8},{"id":"GO:0009234","count":8},{"id":"GO:0019290","count":8}]},{"hash":"1990116085042142545","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000472","count":3}]},{"hash":"1602486586955798970","title":"Carbon-source\u2013regulated transcription","description":"This cluster centers on transcriptional regulation tied to carbon source availability and metabolism. The top GO terms include DNA-templated transcription and, specifically, regulation of transcription from RNA Pol II promoter by a nonfermentable carbon source, along with regulation of cellular respiration. Some terms pertain to fungal secondary metabolism (e.g., aflatoxin biosynthesis), but the common theme is transcriptional control linked to nutrient/carbon status. Thus, a concise label is carbon-source\u2013regulated transcription.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0061415","count":4},{"id":"GO:0043457","count":4},{"id":"GO:0035948","count":4},{"id":"GO:0045122","count":4}]},{"hash":"1407846651659557964","title":"Developmental and cell cycle regulation","description":"The GO terms point to embryonic development and morphogenesis (embryo, liver morphogenesis, dendrite morphogenesis, stem cell division) along with regulation of cell cycle transitions (G1/S, G2/M) and related processes like spindle elongation and DNA repair. This suggests a theme of coordinating development with cell proliferation and genome maintenance, rather than a single, narrow function.","confidence":"Medium","size":24,"edges":31,"triangles":0,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":2},{"id":"GO:0050775","count":1},{"id":"GO:0000086","count":1},{"id":"GO:1900087","count":1},{"id":"GO:2000819","count":1}]},{"hash":"1500800361597980510","title":"Filopodium formation and cytoskeletal remodeling","description":"This cluster is dominated by GO terms for filopodium assembly and its regulation, small GTPase-mediated signaling, and actin cytoskeleton dynamics (with related processes like cell spreading and vesicle trafficking). Together, these point to a core theme of actin-based cytoskeleton remodeling driving filopodium formation and cell motility, with supportive signaling and vesicle trafficking connections. ","confidence":"Medium","size":24,"edges":33,"triangles":0,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046847","count":5},{"id":"GO:0051301","count":5},{"id":"GO:1900026","count":5},{"id":"GO:0007264","count":5},{"id":"GO:0090263","count":4}]},{"hash":"1475503017004761123","title":"Mitochondrial Transport and Metabolic Regulation","description":"Several top GO terms point to mitochondrial transport across membranes (ATP, NAD, ornithine, thiosulfate) and regulation of mitochondrial membrane permeability, as well as apoptotic mitochondrial changes. Additional terms for insulin response, fatty-acid response, and liver regeneration suggest a metabolic, liver-associated mitochondrial function cluster. The common theme is mitochondria-centered transport and regulation of metabolism and apoptosis.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":7},{"id":"GO:0008637","count":7},{"id":"GO:0070542","count":7},{"id":"GO:0097421","count":6},{"id":"GO:1990544","count":6}]},{"hash":"638492710259473127","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning keratinization, transcription regulation, GTPase activity, various transport processes (molybdate, taurine, thiamine), xenobiotic export, very long-chain fatty acid catabolism, and bacterial secretion, with no clear shared function. This suggests the cluster lacks a cohesive biological theme or may reflect mixed annotations.","confidence":"","size":24,"edges":54,"triangles":4,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0031424","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0015689","count":1}]},{"hash":"1438639434321464663","title":"Diverse biosynthesis and xenobiotic detoxification","description":"Top GO terms cluster around multiple biosynthetic processes (antibiotic, biotin, cobalamin, cholesterol, poly-hydroxybutyrate) and stress responses to xenobiotics/toxic substances, plus oxidant detoxification, suggesting the proteins participate in diverse metabolism and chemical defense rather than a single pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0042493","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0006695","count":3}]},{"hash":"1977137958579856639","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010586","count":2},{"id":"GO:1903265","count":2},{"id":"GO:1902187","count":2},{"id":"GO:0061158","count":2},{"id":"GO:2000637","count":2}]},{"hash":"824386025229905532","title":"Ubiquitin-Proteasome Proteolysis and Stress Response","description":"This cluster centers on ubiquitin-dependent proteolysis and proteasomal degradation (SCF ligase activity, polyubiquitination), suggesting proteostasis as the core function. Additional GO terms reflect cellular stress responses (cadmium/arsenic exposure, oxidative stress) and DNA damage signaling, indicating a broader link between protein turnover and stress-regulated cell-cycle control.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0071276","count":7},{"id":"GO:0000209","count":6},{"id":"GO:0031571","count":6}]},{"hash":"797280298328261723","title":"Organic Compound Metabolism and Metal Ion Response","description":"The proteins cluster around diverse organic-molecule metabolism (camphor, kaurene, isoquinoline alkaloids, carbazole, prostaglandin biosynthesis, lipid hydroxylation) plus cellular responses to metal ions (copper and potassium). This suggests a unifying theme of xenobiotic/secondary metabolite processing coupled with stress-response pathways, rather than a single specific function.","confidence":"Medium","size":24,"edges":33,"triangles":14,"max_degree":19,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071280","count":12},{"id":"GO:0001516","count":12},{"id":"GO:0019383","count":11},{"id":"GO:0010760","count":11},{"id":"GO:0010241","count":11}]},{"hash":"58275400644868267","title":"Unknown","description":"The top GO terms span nuclear membrane organization, various signaling pathways, Schwann cell development, DNA repair, mitotic spindle attachment, metabolism, and even organism-specific responses, with some terms marked obsolete. There is no single coherent function that ties these proteins together, so a confident, specific label isn\u2019t warranted.","confidence":"","size":24,"edges":13,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071763","count":1},{"id":"GO:0051343","count":1},{"id":"GO:0042220","count":1},{"id":"GO:0014044","count":1},{"id":"GO:0009742","count":1}]},{"hash":"1314252342102780275","title":"Skeletal muscle development and redox response","description":"The cluster\u2019s GO terms cluster around skeletal muscle biology (myoblast proliferation, skeletal muscle fiber development) plus metabolism (triglyceride metabolism) and oxidative stress/redox regulation (negative regulation of oxidative stress-induced apoptotic signaling, responses to hydroperoxide, protein oxidation, selenium ion). The mix suggests proteins involved in muscle growth/maintenance with redox and metabolic regulation, and some vascular/temperature aspects linked to muscle function. Despite no reported interactions, the shared themes support a muscle-development with redox/metabolic emphasis cluster.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902176","count":1},{"id":"GO:0018158","count":1},{"id":"GO:0051450","count":1},{"id":"GO:0002862","count":1},{"id":"GO:0006641","count":1}]},{"hash":"96017357695531797","title":"Developmental and Immune Signaling Regulators","description":"The Top Terms show involvement in signaling regulation (Rho), transcription, innate immunity, B cell signaling, and broad developmental processes (nervous system and muscle development) plus cell growth and proliferation. This pattern suggests proteins with broad regulatory roles across signaling and development, rather than a single cohesive pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0045773","count":3},{"id":"GO:0050853","count":3}]},{"hash":"622271021046792948","title":"Ubiquitin-Proteasome Mediated Innate Immunity","description":"The prominent GO terms are innate immune response and ubiquitin-dependent proteolysis, including defense against virus, SCF-dependent proteasomal ubiquitin-dependent catabolic processes, and NLRP3 inflammasome assembly. This suggests a cluster of proteins involved in antiviral innate signaling regulated by ubiquitin-proteasome turnover, with some links to NF-kappaB modulation and inflammatory cytokine production.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0051607","count":7},{"id":"GO:0032088","count":6},{"id":"GO:0042787","count":6}]},{"hash":"289345714855546427","title":"Golgi\u2013Endosome Trafficking Regulators","description":"This cluster is marked by GO terms for vesicle transport between the plasma membrane, Golgi, and endosomes (retrograde transport to Golgi, recycling endosome to Golgi, regulation of vesicle fusion) and GTPase activation, which points to Rab/Rho\u2013type regulators of trafficking. While there are some transcription-related terms present, the trafficking signals are the clearest common theme, justifying a label focused on Golgi\u2013endosome transport.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0035526","count":1}]},{"hash":"2164754621766869242","title":"DNA Transcription Regulation and DNA Repair","description":"The cluster centers on DNA-templated transcription and DNA metabolism, with terms for transcription regulation, replication initiation, UV-damage repair, and translesion synthesis, plus ubiquitin-dependent protein degradation. These common themes point to genome maintenance and gene expression control, despite some diverse terms (muscle differentiation, sporulation) that may reflect broad GO annotations. The lack of edges suggests functional association is inferred from shared GO terms rather than direct interactions.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0030435","count":2}]},{"hash":"273739665834540384","title":"Neuronal development and axonogenesis","description":"These terms cluster around neural development and neurite morphogenesis, including positive regulation of axonogenesis and axon extension, dendrite morphogenesis, and hippocampus development, along with calcium-dependent exocytosis relevant to synaptic signaling. While a few terms touch on broader signaling or immune-related exocytosis (mast cell degranulation, focal adhesion regulation), the dominant theme is neurons\u2014neurite outgrowth, synaptic vesicle release, and hippocampal development.","confidence":"High","size":23,"edges":51,"triangles":28,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046330","count":21},{"id":"GO:0043304","count":21},{"id":"GO:0050771","count":21},{"id":"GO:0033138","count":21},{"id":"GO:0045956","count":21}]},{"hash":"450093221134339772","title":"Membrane Transporters for Nutrients and Xenobiotics","description":"This cluster is dominated by transport-related GO terms: uptake/transport of nutrients (molybdate, taurine, thiamine, methionine), xenobiotics and drugs (xenobiotic export, doxorubicin transport), and a secretion system term, suggesting a group of membrane transporters and associated export machinery. The presence of regulatory GO terms like positive regulation of GTPase activity hints at trafficking/regulation of these transport processes. An anomalous term about antigen processing via MHC I appears to be an outlier rather than core to the cluster's theme. Overall, the common thread is substrate transport and export across membranes.","confidence":"Medium","size":23,"edges":23,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0015689","count":3},{"id":"GO:0015734","count":3},{"id":"GO:0046618","count":3},{"id":"GO:0042760","count":3}]},{"hash":"624901154903327845","title":"Cardiac GPCR Signaling and Heart Contraction Regulation","description":"These GO terms cluster around G protein-coupled receptor signaling with emphasis on heart-related processes: desensitization of GPCR signaling, GPCR internalization, acetylcholine and tachykinin receptor pathways, and negative regulation of heart contraction and cardiac hypertrophy, plus heart development. A minor visual perception term appears but is likely incidental. Thus, the cluster is best described as Cardiac GPCR signaling and contraction regulation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018107","count":3},{"id":"GO:0002029","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0045988","count":2},{"id":"GO:0010614","count":2}]},{"hash":"413338204594950123","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":11,"triangles":0,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0006446","count":5},{"id":"GO:0006406","count":4},{"id":"GO:0006888","count":4}]},{"hash":"2271861410041338881","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":54,"triangles":50,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0002098","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0007117","count":1},{"id":"GO:1905608","count":1}]},{"hash":"570704863189577041","title":"Innate Immune Signaling and Inflammation","description":"This cluster centers on innate immune sensing and inflammatory signaling, with prominent terms for TLR/MyD88 and NOD2 pathways, NF-kB regulation, TNF production, and NLRP3 inflammasome assembly. Additional terms point to antigen processing via proteasomal degradation and actin remodeling linked to immune cell migration, supporting a cohesive theme of immune activation and inflammation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0070431","count":7},{"id":"GO:0002755","count":7},{"id":"GO:0051014","count":7},{"id":"GO:0032088","count":7}]},{"hash":"1554614869833695474","title":"Meiosis-associated nuclear architecture and chromosome tethering","description":"Top GO terms focus on meiotic chromosome dynamics (homologous pairing, telomere attachment to the nuclear envelope, centromere clustering) and nuclear organization (nuclear envelope/matrix anchoring, centrosome localization, nucleokinesis, and nuclear migration). The cluster likely contains proteins coordinating chromosome movement and structure during meiosis and related spermatogenesis processes, with an emphasis on telomere-nuclear envelope interactions and nuclear dynamics.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072766","count":1},{"id":"GO:0045669","count":1},{"id":"GO:0007129","count":1},{"id":"GO:0034398","count":1},{"id":"GO:0090292","count":1}]},{"hash":"1114731272997008352","title":"mRNA Splicing and Processing Regulators","description":"The terms are dominated by spliceosome-mediated mRNA processing, including cis and alternative splicing, plus regulatory roles in splicing, mRNA export, and polyadenylation, indicating a cluster of proteins that regulate RNA maturation and processing.","confidence":"High","size":23,"edges":233,"triangles":1408,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0031047","count":5},{"id":"GO:0006378","count":5},{"id":"GO:1900363","count":5},{"id":"GO:0006446","count":5}]},{"hash":"1627117732117470027","title":"Chromatin maintenance and transcription regulation","description":"The top GO terms cluster around chromatin-centric processes, including negative regulation of transcription by RNA Pol II, chromatin assembly during DNA replication, subtelomeric heterochromatin formation, and establishment of protein localization to chromatin. This suggests a shared role in chromatin state control and nuclear gene expression; there is also support from terms related to nuclear mRNA decay, reinforcing a nuclear/chromatin-focused theme. A few terms (growth, fertilization) are broader but don\u2019t negate the central chromatin signal.","confidence":"Medium","size":23,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0071169","count":5},{"id":"GO:0031509","count":4},{"id":"GO:0035264","count":4},{"id":"GO:0051572","count":4}]},{"hash":"632892743907261354","title":"Mitosis and Vesicle Trafficking","description":"The top GO terms span mitotic processes (mitotic sister chromatid separation, spindle organization, cell division) and vesicle/trafficking pathways (Golgi vesicle transport, SNARE disassembly, intralumenal vesicle formation) plus autophagy-related maturation and mitochondrial assembly. This suggests a broad theme of cell division coupled with membrane trafficking and organelle dynamics, rather than a single narrow function. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051306","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007051","count":2},{"id":"GO:0097352","count":2},{"id":"GO:0048219","count":2}]},{"hash":"2045481017073143778","title":"Actin remodeling and vesicle transport","description":"The dominant terms point to actin cytoskeleton remodeling (actin polymerization, Arp2/3-mediated nucleation, barbed-end capping) and associated vesicle trafficking (ER-to-Golgi and intracellular transport). Some other terms (transcription, development) are peripheral, but the core cluster centers on actin-driven remodeling and transport.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030041","count":2},{"id":"GO:0034314","count":2},{"id":"GO:0060982","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0051016","count":2}]},{"hash":"327394251439502091","title":"Unknown","description":"These 23 proteins have top GO terms spanning diverse processes (plant ABA signaling, nitric oxide biosynthesis, cell cycle regulation, actin nucleation, peripheral nervous system myelination, defense against Gram-positive bacteria, protein autophosphorylation and kinase activity, mRNA transport, and angiogenesis) across different systems. There isn\u2019t a clear, single unifying theme linking them, so a generic label is most appropriate.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0051770","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0034314","count":2},{"id":"GO:0022011","count":2}]},{"hash":"1688877303005399335","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006207","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0002098","count":2},{"id":"GO:0006559","count":2}]},{"hash":"1638858328082634613","title":"Ciliary transport and left-right symmetry development","description":"The terms point to motor-driven vesicle transport in cilia and neurons (intraciliary retrograde transport, inner dynein arm assembly, minus-end-directed transport, anterograde neuronal dense core vesicle transport) and to embryonic patterning linked to nodal cilia (left/right symmetry determination, ventricular system development). These together suggest a cluster centered on ciliary/neuronal transport linked to developmental symmetry cues, with other terms being less central. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031914","count":2},{"id":"GO:1990048","count":1},{"id":"GO:0051568","count":1},{"id":"GO:0035721","count":1},{"id":"GO:1902176","count":1}]},{"hash":"2082158953888024389","title":"Signal transduction and gene expression regulation","description":"The terms emphasize signaling (kinase activity, autophosphorylation, GTPase regulation) alongside transcriptional and post-transcriptional control (DNA-templated transcription, RNA methylation, mRNA transport), with additional context from hypoxia/thermoception responses and cell-cycle processes. This suggests a theme where signaling pathways coordinate gene expression and RNA processing, including cell-cycle considerations.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071456","count":2}]},{"hash":"1292076667309593972","title":"Unknown","description":"The top GO terms are highly diverse, spanning transcription regulation, ion transport, adipogenesis, hepatocyte apoptosis, actin cytoskeleton remodeling, innate immune signaling, kidney morphogenesis, and ubiquitination. There is no single coherent function linking these proteins, so a specific representative label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0051017","count":2}]},{"hash":"44619684524072036","title":"Synaptic spine formation and receptor trafficking","description":"The cluster\u2019s top GO terms center on neuronal synapse development and function\u2014dendritic spine regulation, ruffle assembly, and transport of neurotransmitter receptors to the postsynaptic membrane\u2014indicating a core theme of actin-driven membrane remodeling and receptor trafficking in synaptic formation and signaling. Some terms (endothelial lumen extension, mating projection growth, glucan biosynthesis) are less directly related and may reflect broader or cross-species annotations, but the dominant signal is neuronal synaptic organization.","confidence":"Medium","size":22,"edges":16,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060999","count":5},{"id":"GO:0097178","count":5},{"id":"GO:0098887","count":5},{"id":"GO:0045859","count":5},{"id":"GO:0097498","count":5}]},{"hash":"1714155431451983148","title":"Membrane signaling and trafficking in sensory and metabolic systems","description":"The terms are dominated by membrane-associated signaling and transport processes: GPCR signaling, GTPase activity regulation, protein kinase activity regulation, Golgi-to-plasma membrane transport, calcium transporter activity, and ciliary membrane localization. Visual perception and ciliary context point toward retina/sensory biology, while fat cell differentiation and leptin signaling suggest metabolic tissue involvement. Together they indicate a theme of membrane-centric signaling and trafficking across diverse tissues, though with mixed specific functions.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0098907","count":2},{"id":"GO:1901896","count":2},{"id":"GO:0007205","count":2}]},{"hash":"1241782025768038767","title":"Xenobiotic and steroid metabolism","description":"Proteins in this cluster show a pattern of oxidative metabolism across diverse organic substrates, including terpenoids (camphor, ent-kaurene), alkaloids (isoquinoline alkaloids), and aromatic compounds (carbazole), as well as lipid hydroxylation and cortisol biosynthesis. This points to a shared role in the detoxification and modification of xenobiotics and steroid-related substrates. Some terms like cell cycle regulation or macrophage chemotaxis appear peripheral and do not define the core theme. ","confidence":"Medium","size":22,"edges":32,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":3},{"id":"GO:0010760","count":3},{"id":"GO:0010241","count":3},{"id":"GO:0002933","count":3},{"id":"GO:1900087","count":3}]},{"hash":"1128104905192068010","title":"Meiotic Chromosome Cohesion and Spindle Dynamics","description":"The top GO terms center on meiosis-specific chromosome behaviors: cohesion of sister chromatids, spindle elongation and separation, and DNA replication-dependent chromatin assembly. While some terms relate to broader signaling (TORC1, kinase activity) or other processes (ciliary docking, morphogenesis), the dominant signals point to meiosis-related chromosome dynamics and chromatin organization, justifying this label.","confidence":"High","size":22,"edges":21,"triangles":0,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051754","count":4},{"id":"GO:0038202","count":4},{"id":"GO:0051232","count":4},{"id":"GO:0000060","count":4},{"id":"GO:0051306","count":4}]},{"hash":"1622369585531006580","title":"Chaperone-assisted folding and stress signaling","description":"This cluster is anchored by chaperone-mediated protein folding and peptidyl-prolyl isomerization, with multiple terms pointing to stress responses (hydrogen peroxide and metal ion exposure) and a link to glucocorticoid receptor signaling, suggesting a cohesive theme of folding/chaperone regulation under stress that can influence receptor signaling pathways.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:2000324","count":7},{"id":"GO:1903646","count":7},{"id":"GO:0000413","count":7},{"id":"GO:0010288","count":7},{"id":"GO:0007091","count":7}]},{"hash":"2271656955409303454","title":"Unknown","description":"The GO terms are highly diverse, spanning xenobiotic response, cocaine response, plant brassinosteroid signaling, Schwann cell development, calcium signaling cascades, mitotic spindle attachment, DNA repair, and energy metabolism. This lack of a clear, shared function or pathway indicates no coherent cluster-level theme, so Unknown with None confidence.","confidence":"","size":22,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035690","count":6},{"id":"GO:0061587","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0051343","count":4},{"id":"GO:0014044","count":4}]},{"hash":"1473423727266845350","title":"Vesicle trafficking and organelle assembly","description":"This cluster is dominated by GO terms tied to intracellular membrane transport and organelle biogenesis, including inter-Golgi cisterna vesicle-mediated transport, intralumenal vesicle formation, SNARE complex disassembly, autophagosome maturation, and mitochondrial complex III assembly, suggesting a cohesive theme of membrane trafficking and organelle assembly processes. Some terms like cell division or blastocyst development are more general contexts and less directly defining the cluster\u2019s core function.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0001824","count":5},{"id":"GO:1903715","count":5},{"id":"GO:0097352","count":4},{"id":"GO:0048219","count":4}]},{"hash":"847131650155966433","title":"Mitochondrial translation and translation regulation","description":"The top GO terms are dominated by translation, especially mitochondrial translation and initiation, with several entries for mitochondrial protein synthesis and general translation regulation. This points to a cluster enriched for protein synthesis machinery centered on mitochondria, with some ancillary associations to broader cellular processes such as immune signaling and development. Overall, the label captures the core function suggested by the most represented terms, though a few scattered terms indicate additional roles. ","confidence":"Medium","size":22,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0070124","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0045727","count":2},{"id":"GO:0071357","count":2}]},{"hash":"2098771261162692553","title":"Unknown","description":"The top GO terms span immune responses (granuloma formation, TNF regulation), lipid biosynthesis (sphingolipid, phosphatidylethanolamine), membrane and vesicle processes (ER membrane organization, vesicle fusion), autophagy (ribophagy), and even synaptic regulation, showing no single cohesive function for the group. There isn\u2019t a clear common theme to assign a meaningful label, so Unknown is appropriate.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002432","count":2},{"id":"GO:1904468","count":2},{"id":"GO:0090153","count":2},{"id":"GO:0010793","count":2},{"id":"GO:0032228","count":2}]},{"hash":"2177827972381567473","title":"Unknown","description":"The Top Terms show a broad mix of processes including calcium signaling (release of Ca2+ into the cytosol; calcineurin-NFAT signaling), transcription-related events (RNA Pol II termination), DNA repair, transposable element silencing, and even osteoclast differentiation. Several GO terms are obsolete, which reduces interpretability. Because there is no single, coherent functional theme across the cluster, there is no convincing label beyond Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0051533","count":2},{"id":"GO:0006378","count":1},{"id":"GO:0051209","count":1},{"id":"GO:0006379","count":1}]},{"hash":"229575596140518549","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007252","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006370","count":2},{"id":"GO:1902570","count":2},{"id":"GO:0000390","count":2}]},{"hash":"273051302767203853","title":"TLR-driven innate immune signaling and inflammation","description":"Most terms point to innate immune signaling via Toll-like receptors (TLRs), including MyD88-dependent pathways, dsRNA/LPS sensing, interferon and chemokine production, and general innate/inflammatory responses. This suggests a coherent module of TLR-mediated immune activation rather than metabolic or structural roles. Therefore the label reflects a pathway-focused cluster of innate immune signaling and inflammation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:0032741","count":4},{"id":"GO:0050729","count":4},{"id":"GO:0043330","count":4},{"id":"GO:0034134","count":4}]},{"hash":"133764524521849085","title":"Fungal sterol and ubiquinone biosynthesis","description":"The dominant GO terms point to ergosterol biosynthetic process and regulation of ubiquinone biosynthesis, alongside lipid homeostasis and links to aerobic respiration. This suggests a cohesive cluster around fungal lipid/isoprenoid metabolism and mitochondrial cofactor (CoQ) biosynthesis. The presence of an outlier term for Purkinje cell layer morphogenesis likely reflects annotation noise rather than a shared function. Overall, a fungal sterol/CoQ biosynthesis theme fits best.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045892","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0006696","count":2}]},{"hash":"1048655760912400974","title":"Nuclear transcription and RNA processing","description":"The cluster is dominated by GO terms tied to gene expression in the nucleus, including DNA-templated transcription, spliceosomal tri-snRNP complex assembly, and regulation of RNA polymerase II activity. Additional terms touch on nuclear transport of proteins, supporting a cohesive theme of nuclear gene expression and RNA processing. A few peripheral terms (oxidative stress, ER protein folding) are present but do not define the core function. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000244","count":2},{"id":"GO:0046826","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0034599","count":1}]},{"hash":"554686841611730788","title":"Cellular redox detoxification and xenobiotic metabolism","description":"The cluster is driven by strong signals for redox balance and detoxification: GO:0098869 cellular oxidant detoxification, GO:0045454 cell redox homeostasis, and GO:0042178 xenobiotic catabolic process. Additional metabolism-related terms (methylamine metabolic process, regulation of nitrogen utilization) and calcium signaling (regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum) suggest a broader metabolic and signaling context, with some insulin-related regulation and a few incidental terms. Overall, the proteins appear to function together in detoxification and redox maintenance, with related metabolic modulation.","confidence":"Medium","size":21,"edges":156,"triangles":723,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":10},{"id":"GO:0045454","count":8},{"id":"GO:0055114","count":6},{"id":"GO:2000255","count":5},{"id":"GO:0006808","count":5}]},{"hash":"1909011355327073608","title":"Hormone-responsive signaling and inflammation","description":"This cluster centers on cellular responses to peptide hormones (estrogen, follicle-stimulating hormone) and regulation of inflammatory cytokine production, indicating a hormone signaling group with inflammatory/regulatory roles. Some terms (e.g., cerebral cortex development, transcription) are broader, but the dominant theme is hormone-driven signaling and inflammatory response, with transcriptional regulation as a downstream tie-in. ","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042997","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0071375","count":3}]},{"hash":"1169835893864727890","title":"Developmental Growth Regulators","description":"The top GO terms point to development across multiple tissues (brain, kidney, fat, prostate) and control of cell proliferation and survival, with additional roles in ubiquitination, GTPase regulation, and lipid signaling (SREBP). This suggests these proteins act as regulators of development and growth rather than a single pathway, spanning differentiation and growth control. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0050680","count":2}]},{"hash":"525718970554436128","title":"GPCR-cAMP Signaling Network","description":"These proteins are enriched for receptor-mediated signaling and second messenger pathways, including receptor guanylyl cyclase signaling, adenylate cyclase-activating GPCR signaling, GPCR adenosine receptor signaling, and intracellular signal transduction, with downstream transcriptional regulation terms. While blue light signaling and hypoxia detection appear, the common theme is GPCR/cAMP (and related) signaling leading to transcriptional changes, supporting a cohesive signaling network role.","confidence":"High","size":21,"edges":132,"triangles":395,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007168","count":13},{"id":"GO:1904322","count":13},{"id":"GO:0070483","count":13},{"id":"GO:0071880","count":13},{"id":"GO:0006355","count":13}]},{"hash":"1912898006815019787","title":"Unknown","description":"The top GO terms span pheromone response, GTPase signaling, tRNA wobble modification, cell division and budding, presynapse assembly, Ran signaling, secretion regulation, and sensory perception, showing no single shared function for the cluster.","confidence":"","size":21,"edges":6,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":21},{"id":"GO:0043547","count":21},{"id":"GO:0002098","count":20},{"id":"GO:0051301","count":20},{"id":"GO:0007117","count":20}]},{"hash":"286879046741548597","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006620","count":1},{"id":"GO:0051083","count":1},{"id":"GO:0032790","count":1}]},{"hash":"1144114215553562899","title":"Calcium-Driven Synaptic Signaling","description":"The presence of GO terms for calcium ion import across the plasma membrane and long-term synaptic potentiation points to calcium-dependent neuronal signaling and synaptic plasticity; other terms like ubiquitination and cell growth may reflect general neuronal remodeling.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098703","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0000083","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0007205","count":2}]},{"hash":"560924326705889596","title":"Polyamine and amino acid biosynthesis with acetylation","description":"This cluster is dominated by polyamine metabolism (putrescine, spermidine, spermine) and acetylation-related processes (peptidyl-lysine N6-acetylation; putrescine/spermidine acetylation), plus an amino acid biosynthesis term (L-arginine). Several other GO terms (ectoine, mycothiol, melatonin biosynthesis, chromatin-related) appear as less coherent outliers, suggesting a core theme around small-molecule biosynthesis and acetylation with some annotation noise.","confidence":"Medium","size":21,"edges":8,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019491","count":5},{"id":"GO:0006348","count":5},{"id":"GO:0046208","count":4},{"id":"GO:0018003","count":4},{"id":"GO:0010125","count":4}]},{"hash":"1216054598314553695","title":"ER Stress Response and RNA Splicing Regulation","description":"The top GO terms cluster around RNA processing and spliceosome-mediated splicing (negative/alternative splicing via spliceosome, mRNA splicing) together with ER proteostasis signals (protein folding in ER and translation initiation upregulation during ER stress). While a few terms touch on cytoskeletal or cardiac assembly, the strongest signal is ER-associated gene expression control and RNA processing, suggesting a theme of how cells manage protein quality and transcript processing under stress. Overall, this cluster centers on ER stress\u2013related translation/splicing regulation and RNA processing rather than a single structural function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0055003","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0048025","count":2},{"id":"GO:0031047","count":2}]},{"hash":"2075676104470202336","title":"Cardiovascular and Visual Signal Transduction","description":"This cluster shows a mix of visual system terms (visual perception, regulation of opsin signaling) and cardiac terms (heart development, cardiac muscle contraction) alongside general intracellular signaling and regulatory processes (intracellular signal transduction, GTPase regulation, ubiquitination). The combination suggests proteins involved in signaling in both eye and heart tissues, rather than a single, cohesive pathway, so a broad label emphasizing cross-tissue signaling is most appropriate.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0022400","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0043547","count":2}]},{"hash":"636063672426861558","title":"Developmental Neural Signaling and Morphogenesis","description":"The cluster shows strong enrichment for DNA-templated transcription and neural/developmental GO terms (axon fasciculation, cranial skeleton morphogenesis, Wnt signaling), suggesting a group of proteins involved in embryonic development and neural connectivity. Additional terms related to trafficking and broader regulation are present, but the central theme aligns with developmental signaling and neural morphogenesis.","confidence":"Medium","size":21,"edges":158,"triangles":695,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":21},{"id":"GO:0046826","count":21},{"id":"GO:0097155","count":20},{"id":"GO:0006935","count":20},{"id":"GO:0090153","count":20}]},{"hash":"1938767037620483649","title":"Diverse small-molecule metabolism","description":"This cluster contains GO terms across biosynthesis (antibiotic, biotin, cobalamin) and catabolic/degradative processes (chlorophyll, stilbene, monoacylglycerol), plus detoxification and RNA-related modifications. The common theme is metabolism of various small molecules, spanning both synthesis and breakdown, with some indication of broader metabolic regulation. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0006351","count":4}]},{"hash":"851213654410599812","title":"Neural Development and Transcriptional Regulation","description":"This cluster is dominated by GO terms for neural and broader developmental processes (multicellular organism development, forebrain development, nervous system development, skeletal muscle development) and transcription-related activity (DNA-templated transcription). While there are additional terms related to ER-stress-induced apoptosis, immune signaling, and imprinting regulation, the primary signal points to neural development governed by transcriptional control.","confidence":"Medium","size":21,"edges":70,"triangles":110,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0030900","count":7},{"id":"GO:0070059","count":7},{"id":"GO:0007118","count":7},{"id":"GO:0006351","count":7}]},{"hash":"1567790292753782485","title":"Light-responsive circadian transcription","description":"The top GO terms center on transcriptional regulation, circadian rhythm control, and light detection, with supporting terms for mRNA processing and ncRNA-mediated gene silencing, suggesting a cohesive role in coordinating light-driven transcriptional programs and RNA metabolism. The redox response term also aligns with environmental cue signaling to transcription. ","confidence":"High","size":21,"edges":41,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0061415","count":1},{"id":"GO:0017006","count":1}]},{"hash":"962858931345201077","title":"Ribosome Biogenesis and Translation","description":"The proteins in this cluster are enriched for translation and ribosome-related processes, including general translation (GO:0006412), ribosome biogenesis (GO:0042254), ribosomal subunit biogenesis (GO:0046677), ribosome assembly, and rRNA processing, with mitochondrial translation also represented. This points to a cohesive group involved in ribosome production and protein synthesis, spanning both cytosolic and mitochondrial ribosomes. A few terms about responses to translation inhibitors (antibiotics, cycloheximide) reflect stress responses but do not outweigh the primary ribosome/translation theme.","confidence":"High","size":21,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0032543","count":2}]},{"hash":"856386698394390094","title":"ERAD and Ubiquitin-Proteasome Proteostasis","description":"The top terms strongly center on ubiquitin-dependent ERAD and proteasomal degradation (ERAD pathway, SCF-dependent ubiquitylation, proteasomal protein catabolic process, unfolded protein maintenance), indicating a cluster focused on protein quality control and turnover. Some terms relate to broader regulatory processes, but the dominant theme is proteostasis via ubiquitin-proteasome and ERAD pathways.","confidence":"High","size":21,"edges":129,"triangles":335,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0031146","count":7},{"id":"GO:1902564","count":7},{"id":"GO:0000753","count":6}]},{"hash":"919538103815672066","title":"Ubiquitin-mediated proteolysis and metal stress response","description":"The cluster\u2019s top GO terms strongly point to ubiquitin-dependent protein degradation pathways (SCF-dependent ubiquitin-proteasomal catabolic process, protein polyubiquitination, ubiquitin-dependent protein catabolic process) and cellular responses to heavy metals (cadmium, arsenic, methylmercury), indicating a core theme of regulated protein turnover in response to metal-induced stress. Some links to circadian regulation and neuronal synapse processes may reflect broader stress and regulatory effects but the dominant signal is ubiquitin-mediated proteolysis coupled with metal stress response.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":9},{"id":"GO:0071276","count":8},{"id":"GO:0000209","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0046685","count":6}]},{"hash":"1819554694877659281","title":"Unknown","description":"The top terms are scattered across metabolism, development, immune and hormone signaling, light perception, and chlorophyll-related processes, with no single cohesive function tying them together. The cluster also has no edges or triangles, supporting a lack of shared function. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":3},{"id":"GO:0042220","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0006808","count":2}]},{"hash":"1004540916186666190","title":"LPS and envelope polymer biosynthesis","description":"The top GO terms cluster around biosynthesis of lipopolysaccharide components (O antigen, LPS core, ADP-L-glycero-beta-D-manno-heptose) and related envelope polymers, along with wax and lipid-associated metabolic processes (long-chain fatty-acyl-CoA, galactose) and PHB biosynthesis. This points to a cohesive theme of constructing bacterial outer-murface components and storage polymers, suggesting a focused function for the cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0017000","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0042619","count":5},{"id":"GO:0006012","count":5}]},{"hash":"1260022845498983081","title":"Ribosome Biogenesis and Co-translational Targeting","description":"Dominant GO terms cluster around ribosome large subunit assembly/export, rRNA maturation, and SRP-dependent cotranslational targeting to membranes, all pointing to ribosome biogenesis and translation processes. A few development-related terms appear less consistently and may be incidental. This label succinctly captures the core shared function of the proteins in the cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0006614","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0006397","count":2}]},{"hash":"1687272801252339253","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0051568","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0034402","count":1}]},{"hash":"1156561129236665613","title":"Calcium-dependent immune signaling and vascular responses","description":"This cluster centers on calcium-mediated signaling pathways (calcium release, dephosphorylation, NFAT regulation) in immune contexts (B cell receptor and Fc-epsilon receptor signaling) with associated vascular processes (platelet degranulation, angiogenesis), suggesting a shared Ca2+-driven signaling theme across immune and vascular functions.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0038095","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0016567","count":2}]},{"hash":"557185623686292035","title":"Muscle contraction regulation","description":"This cluster shows a strong emphasis on regulation of muscle contraction, especially cardiac/striated muscle contraction and hypertrophy, together with cytoskeletal organization such as stress fiber assembly. A subset of terms also points to neuronal signaling and pigment/opsin signaling, suggesting some functional diversity or annotation noise. The ubiquitin-dependent protein catabolic process hints at turnover mechanisms that modulate contraction-related proteins. Taken together, the dominant signal is regulation of muscle contraction and cytoskeletal dynamics.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0035024","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0043149","count":2},{"id":"GO:0022400","count":2}]},{"hash":"2030019143137186083","title":"Sphingolipid Metabolism and Signaling","description":"The dominant GO terms center on sphingolipid metabolism (sphinganine-1-phosphate, sphingosine) and regulation of sphingolipid signaling, along with associated phospholipid dephosphorylation/catabolic processes. While a couple of developmental terms (placenta development, face morphogenesis) appear, the core function hinted by multiple terms is lipid metabolism and signaling, particularly sphingolipid pathways. This makes the label representative of the cluster\u2019s primary theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":2},{"id":"GO:0042264","count":1},{"id":"GO:0060325","count":1},{"id":"GO:0097202","count":1},{"id":"GO:0098869","count":1}]},{"hash":"20332985465110566","title":"Cytoskeletal and organelle assembly with protein turnover","description":"The top GO terms cluster around assembly and organization of cellular structures (cilium assembly, mitotic spindle assembly, sarcomere organization, distal tubule morphogenesis, skeletal muscle fiber development) and protein regulation (homooligomerization, ubiquitin-dependent catabolic process, K33-linked ubiquitination). This suggests a cohesive theme of building and maintaining cellular architecture while controlling protein turnover, even though a defensive response term appears as a potential outlier. Overall, the cluster appears to reflect structural assembly and protein regulation processes rather than a single tight function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0060271","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0072156","count":1}]},{"hash":"2295507426984456482","title":"Potassium Transport and Membrane Potential Regulation","description":"The top GO terms cluster around potassium ion import/export, transmembrane transport, intracellular potassium homeostasis, and stabilization of membrane potential, pointing to coordinated regulation of potassium balance and cellular excitability. The association with startle response and skeletal muscle relaxation suggests a neuromuscular angle, where potassium dynamics influence muscle responsiveness; the testosterone response is less central. Overall, the theme is potassium-driven control of membrane potential and muscle excitability.","confidence":"High","size":20,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":5},{"id":"GO:0071805","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0030322","count":4},{"id":"GO:0030007","count":4}]},{"hash":"1578655424948110352","title":"Sterol and lipid biosynthesis","description":"The prominent GO terms point to sterol and lipid metabolism, including ergosterol biosynthesis and its regulation, unsaturated fatty acid biosynthesis, and sphingolipid metabolism, suggesting a lipid-biosynthesis module. A few terms (e.g., germline development, nitrate/nitric oxide metabolism) appear unrelated and may reflect annotation noise, but the core signal centers on sterol and fatty acid biosynthesis.","confidence":"Medium","size":20,"edges":13,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0032443","count":3},{"id":"GO:0001949","count":3}]},{"hash":"1186603925213142170","title":"Negative regulators of signaling pathways","description":"The terms show widespread inhibition of signaling: negative regulation of T cell receptor signaling, ERK/MAPK cascade, PI3K-AKT pathway, focal adhesion assembly, VEGF receptor signaling, and synaptic regulation, along with phosphatase activity and dampening of apoptotic signaling. This suggests the cluster comprises proteins that dampen diverse cellular signaling across immune, neuronal, and growth-factor contexts.","confidence":"High","size":20,"edges":182,"triangles":1010,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0050860","count":14},{"id":"GO:0070373","count":14},{"id":"GO:0000200","count":14},{"id":"GO:1903984","count":12},{"id":"GO:0035335","count":12}]},{"hash":"1457209244721455690","title":"GTPase-Regulated Vesicle Transport and Cell Division","description":"The cluster\u2019s top GO terms center on small GTPase\u2013mediated signaling and ER-to-Golgi vesicle transport, with supporting terms for mitotic spindle assembly and general cell division. This suggests a cohesive theme of GTPase-driven vesicle trafficking linked to cell cycle processes, with some neural development associations that fit within broader cellular transport and signaling roles.","confidence":"High","size":20,"edges":44,"triangles":19,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0046909","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0060999","count":4},{"id":"GO:0051301","count":4}]},{"hash":"722974498523608697","title":"ERAD and Ubiquitin Regulation","description":"The proteins cluster around ubiquitin-related processes and ER-associated degradation: GO terms for protein sumoylation, deubiquitination, and ubiquitin-dependent ERAD dominate the top terms, with supporting signals from deglycosylation and autophagy regulation. This points to a shared role in protein quality control and targeted degradation. A few terms (spindle pole body duplication, nucleotide-excision repair) likely reflect additional, multifunctional roles of some members rather than a core theme of the cluster.","confidence":"High","size":20,"edges":163,"triangles":838,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":7},{"id":"GO:0016579","count":6},{"id":"GO:0030433","count":6},{"id":"GO:1904378","count":5},{"id":"GO:1901097","count":5}]},{"hash":"1168422970752595217","title":"Vesicle Trafficking and Secretion","description":"The cluster is dominated by GO terms describing endomembrane transport (ER-Golgi cycling, endocytosis, endosome to melanosome transport) and vesicle-mediated secretion, with involvement of small GTPases and actin-driven membrane remodeling (ruffle/podosome assembly). This combination points to a cohesive theme of vesicle trafficking and exocytosis within the secretory/endomembrane system, rather than a single enzymatic or signaling activity. High","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035646","count":11},{"id":"GO:0006890","count":11},{"id":"GO:0006888","count":10},{"id":"GO:0006897","count":10},{"id":"GO:0007264","count":10}]},{"hash":"213028178264455857","title":"Neural development and synaptic vesicle trafficking","description":"Top GO terms cluster around synaptic vesicle cycling (endocytosis and exocytosis) and excitatory postsynaptic potential, indicating a focus on neuronal signaling. Additional terms point to neural development processes (neuroblast proliferation, Wnt signaling) and intracellular trafficking (Golgi localization, mitochondria distribution) with links to cellular energy and organization essential for synaptic function. Taken together, the proteins likely participate in neural development and regulation of synaptic vesicle trafficking and signaling.","confidence":"High","size":20,"edges":21,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1900242","count":7},{"id":"GO:0048312","count":7},{"id":"GO:2000300","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0060079","count":7}]},{"hash":"924825658157642225","title":"Diverse Small-Molecule Metabolism","description":"This cluster is enriched for multiple, broad metabolic processes across different small-molecule pathways, including retinoid metabolism, carbohydrate (fructose, ethanol) metabolism, amino acid (proline) biosynthesis, polyamine (putrescine) and GABA catabolism, and antibiotic biosynthesis. The common theme is general metabolic activity on diverse small molecules, justifying a label of diverse metabolism.","confidence":"High","size":20,"edges":179,"triangles":961,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0042574","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0006068","count":4}]},{"hash":"608480014802589223","title":"Ribosome Biogenesis and Translation","description":"This cluster is strongly biased toward translation-related processes: translation itself, ribosome biogenesis, initiation/termination/elongation of translation, and even selenocysteine incorporation. These terms point to core components of the protein synthesis machinery (ribosomal proteins and translation factors) and their assembly, with mRNA decay appearing as a related regulatory layer. Overall, the dominant theme is translation and ribosome biogenesis, making the label representative and specific.","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0042254","count":7},{"id":"GO:0046677","count":7},{"id":"GO:0006415","count":6},{"id":"GO:0006413","count":6}]},{"hash":"320025214176587694","title":"Isoprenoid/terpenoid biosynthesis enzymes","description":"The cluster is dominated by GO terms for isoprenoid and terpenoid biosynthesis (geranyl, farnesyl, and geranylgeranyl diphosphate biosynthesis; monoterpene and cholesterol biosynthesis; quinone biosynthesis), suggesting a core theme of prenylation and lipid biosynthetic enzymes. A couple of terms relate to protein interactions or transport, and brain development appears incidental, but the terpenoid pathway signals the main functional focus.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051290","count":4},{"id":"GO:0033384","count":4},{"id":"GO:0033386","count":4},{"id":"GO:0015031","count":4},{"id":"GO:0045337","count":4}]},{"hash":"640385157418689403","title":"Membrane Transporters and Secretion","description":"The top GO terms are dominated by membrane transport activities (molybdate, taurine, thiamine, methionine, and amino acid transport; xenobiotic and doxorubicin export) and by protein secretion via the Type I secretion system, indicating a cohesive theme around transport across membranes and secretion. Some terms like very long-chain fatty acid catabolic process and MHC class I antigen presentation are less central, but the strongest signal is transport/export and secretion.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015689","count":4},{"id":"GO:0015734","count":4},{"id":"GO:0046618","count":4},{"id":"GO:0042760","count":4},{"id":"GO:0030253","count":4}]},{"hash":"891986889177031227","title":"Unknown","description":"The top GO terms are a heterogeneous mix spanning ribosome biogenesis, proteasomal degradation, histone demethylation, catabolic processes, and various developmental events (oocyte maturation, meiosis spindle assembly, neural tube closure, brain ventricle development). With only a single edge and no clear functional cohesion, there is no single representative function linking these proteins.","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0031146","count":1},{"id":"GO:0070544","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0007057","count":1}]},{"hash":"1499927450697509709","title":"DNA replication licensing and chromatin regulation","description":"These proteins show enrichment for GO terms tied to DNA replication (pre-replicative complex assembly, DNA replication initiation, DNA replication) and chromatin regulation/heterochromatin formation, with ubiquitin-mediated proteolysis as a regulatory layer. The combination suggests a cluster of factors involved in licensing and timing of replication within a chromatin context, rather than a single signaling pathway.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0046856","count":2},{"id":"GO:0031938","count":1},{"id":"GO:0046331","count":1}]},{"hash":"1907273769014292373","title":"Cardiac and placental development regulation","description":"The top GO terms point to tissue-specific development (heart and placenta) and adipogenesis (fat cell differentiation), suggesting a developmental/regulatory theme across cardiac, placental, and adipose lineages. Additional terms like negative regulation of cardiac hypertrophy and glucose metabolismfit with growth and metabolic regulation during development, while DNA-templated transcription indicates transcriptional control. Overall, a cohesive developmental/regulatory cluster with a focus on cardiac and placental biology, plus adipogenesis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0042220","count":2},{"id":"GO:0001890","count":2}]},{"hash":"1879376236661346908","title":"Autophagy and Vesicle Trafficking","description":"The top GO terms point to autophagy-related processes (autophagosome assembly, autophagosome membrane docking) and endosome-to-lysosome transport, plus a cellular response to glucose starvation, which collectively indicate a vesicle trafficking/autophagy-focused cluster. Some terms about Golgi maintenance and centrosome cycle may reflect broader trafficking and cell-cycle context, while an outlier term about morphogenesis is likely noise. Overall, the core theme aligns with autophagy and vesicle transport under nutrient stress.","confidence":"Medium","size":20,"edges":19,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0000045","count":1},{"id":"GO:0042149","count":1},{"id":"GO:0016240","count":1},{"id":"GO:0008333","count":1},{"id":"GO:0048803","count":1}]},{"hash":"1556738158288079037","title":"Innate antiviral signaling and interferon production","description":"This cluster is defined by GO terms related to innate immune responses against viruses, including TLR and NOD signaling, interferon production, and dendritic cell cytokine regulation, along with ubiquitin-proteasome\u2013mediated protein turnover that modulates signaling. The terms cohere around antiviral innate signaling and cytokine responses, especially interferons and IL-18.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":7},{"id":"GO:0051607","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0002755","count":7},{"id":"GO:0070431","count":6}]},{"hash":"526210462867605963","title":"Cholesterol transport and lipoprotein remodeling","description":"The dominant terms center on cholesterol management and lipoprotein remodeling (HDL and VLDL remodeling, reverse cholesterol transport, cholesterol homeostasis, lipid storage). This points to a functional cluster of proteins involved in lipid trafficking and lipoprotein particle remodeling rather than other processes, despite a few outlier terms.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0043691","count":2},{"id":"GO:0034375","count":2},{"id":"GO:0019915","count":2},{"id":"GO:0034372","count":2}]},{"hash":"963591959214698885","title":"Protein and polyamine acetylation","description":"This cluster is dominated by GO terms related to acetylation, including peptidyl-lysine N6-acetylation, N-terminal peptidyl-serine acetylation, and acetylation of polyamines (spermine, spermidine, putrescine). The presence of related biosynthetic processes (melatonin, mycothiol, arginine) suggests broader acetyltransferase- and acetyl-CoA\u2013dependent metabolism. A few terms on chromatin-related processes may reflect acetylation\u2019s role in chromatin regulation. Overall, the common theme is acetylation-driven modification pathways, especially of proteins and polyamines. ","confidence":"High","size":20,"edges":29,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":15},{"id":"GO:0017198","count":15},{"id":"GO:0046208","count":14},{"id":"GO:0010125","count":14},{"id":"GO:0071962","count":14}]},{"hash":"2109488516902112252","title":"Cardiac development and cardiomyocyte signaling","description":"These proteins show a clear focus on heart development and cardiomyocyte function, with multiple terms related to left ventricular and outflow tract morphogenesis, atrial action potential regulation, and Purkinje-to-ventricular signaling, plus calcium transporter activity relevant to cardiac excitation-contraction. While a few terms touch on non-cardiac tissues (skin, bone maturation), the dominant signal is cardiac development and cardiomyocyte signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0098910","count":2},{"id":"GO:0071313","count":2},{"id":"GO:0086029","count":2},{"id":"GO:0043931","count":2}]},{"hash":"310642117365246684","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010586","count":3},{"id":"GO:1903265","count":3},{"id":"GO:1902187","count":3},{"id":"GO:0061158","count":3},{"id":"GO:2000637","count":3}]},{"hash":"755898014267345642","title":"Ribosome Biogenesis","description":"The dominant terms are maturation of 5.8S rRNA and LSU rRNA, indicating ribosome biogenesis and rRNA processing; other terms appear sporadic and less coherent with this theme, so ribosome-related function is the main signal for this cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0032933","count":1},{"id":"GO:0051016","count":1}]},{"hash":"1779243182251298243","title":"Multisystem Development and Morphogenesis","description":"The Top Terms cluster around developmental processes across multiple tissues, including heart/atrium/pericardium morphogenesis, midbrain morphogenesis, spermatogenesis, and vitellogenesis, with additional signaling regulation terms. This suggests a broad theme of organismal development and tissue morphogenesis rather than a single, specific pathway, even though some immune-development terms appear. Therefore, a label capturing cross-tissue development and morphogenesis is appropriate.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007283","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0003344","count":2}]},{"hash":"1654707764848510103","title":"Cardiac muscle contraction regulation","description":"Among the top GO terms, several explicitly relate to regulation of cardiac muscle contraction, including positive regulation of cardiac muscle contraction, negative regulation of the force of heart contraction, and negative regulation of cardiac muscle hypertrophy, with secondary heart field specification also heart-related. While there are outliers (opsin signaling, mismatch repair, centromeric cohesion), the shared theme across multiple terms points to regulation of cardiac muscle function as the core of this cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022400","count":1},{"id":"GO:0070602","count":1},{"id":"GO:0045988","count":1},{"id":"GO:0010614","count":1},{"id":"GO:0060452","count":1}]},{"hash":"1356764860508442202","title":"PNS Myelination and NFAT Signaling","description":"This cluster is strongest in terms related to peripheral nervous system development, Schwann cell development, and myelination, along with regulation of the calcineurin-NFAT signaling cascade. These points suggest a thematic grouping around calcium-dependent signaling and PNS maturation, with a few secondary terms touching chromatin regulation, dendrite morphogenesis, and muscle-related responses that are less central to the core theme. Overall, the link to Schwann cell\u2013driven myelination and NFAT signaling best captures the dominant signal in the set.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051343","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0033173","count":2},{"id":"GO:0035562","count":2},{"id":"GO:0050774","count":2}]},{"hash":"1048838020968328017","title":"Calcium signaling and transcription regulation","description":"The strongest signals in the terms are calcium transport and homeostasis (plasma membrane import/export, mitochondrial calcium transport) together with regulation of DNA-templated transcription, suggesting a core theme of calcium-dependent signaling linking ion homeostasis to gene expression. Additional terms imply broader calcium-related roles in muscle contraction and other processes, with ubiquitination and virus defense appearing as regulatory context rather than core function. Overall, calcium signaling appears central, with transcription regulation as a closely related axis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0098703","count":1},{"id":"GO:1990034","count":1}]},{"hash":"1055567248476695838","title":"Tyrosine phosphatase signaling regulation","description":"This cluster is dominated by GO terms about negative regulation and modulation of signaling pathways that involve tyrosine phosphorylation, including negative regulation of VEGF receptor signaling, regulation of protein tyrosine kinase activity, and protein dephosphorylation. These points suggest a common theme of controlling cellular signaling via tyrosine phosphatases, with a few peripheral terms related to development and granule maturation that may reflect broader regulatory roles. ","confidence":"Medium","size":19,"edges":10,"triangles":10,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030948","count":6},{"id":"GO:0006470","count":5},{"id":"GO:0000742","count":4},{"id":"GO:0000278","count":4},{"id":"GO:1900165","count":4}]},{"hash":"1024205669846803709","title":"Neurodevelopment and cell cycle regulation","description":"The cluster combines strong signals for neural development processes (dendrite morphogenesis, fasciculation of sensory neuron axons, chemotaxis) with prominent DNA replication and centrosome cycle terms, suggesting these proteins coordinate neural differentiation with cell cycle control during development.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":13},{"id":"GO:0007098","count":13},{"id":"GO:0048701","count":12},{"id":"GO:0006260","count":12},{"id":"GO:0048813","count":8}]},{"hash":"2122923838757513043","title":"Myogenesis and heart development","description":"The top GO terms point strongly to muscle-related development (myoblast fusion, response to muscle activity) and heart development, with several terms tied to organismal development and signaling (e.g., G2/M transition, protein kinase activity). While a few outliers exist (e.g., Schwann cell development, ABA signaling), the dominant theme across the cluster is muscle formation and cardiogenesis, justifying a label focused on myogenesis and heart development.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0014044","count":4},{"id":"GO:0000086","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0071902","count":4}]},{"hash":"2274476830438173640","title":"tRNA Modification and Translation Cluster","description":"The strongest GO terms center on tRNA threonylcarbamoyladenosine modification and translation, indicating a core RNA biology and protein-synthesis function; additional hints of mitochondrial translation/assembly support a translation-focused theme, while the other metabolic terms (LPS/o-antigen and sugar metabolism) may reflect peripheral or multi-functional roles rather than defining the cluster.","confidence":"High","size":19,"edges":95,"triangles":170,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0002949","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0034551","count":1},{"id":"GO:0070131","count":1},{"id":"GO:0009243","count":1}]},{"hash":"1080814077786399365","title":"Developmental signaling and morphogenesis","description":"This cluster is enriched for terms tied to developmental signaling (negative regulation of canonical Wnt signaling; positive regulation of Smoothened signaling) and morphogenesis (digestive tract morphogenesis; commissural neuron axon guidance; substrate adhesion-dependent cell spreading), suggesting a cohesive role in coordinating tissue development and neural guidance. A few terms like ribosome biogenesis and endocytosis are general cellular processes that support these developmental activities, so the label emphasizes the core developmental theme rather than every individual process.","confidence":"Medium","size":19,"edges":40,"triangles":16,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035414","count":2},{"id":"GO:0048546","count":2},{"id":"GO:0071679","count":2},{"id":"GO:0034446","count":2},{"id":"GO:0045880","count":2}]},{"hash":"2003283545162587990","title":"Cytokinesis and Microtubule Dynamics","description":"The cluster is dominated by GO terms related to cell division, cell cycle, FtsZ-dependent cytokinesis, cell septum assembly, mitotic spindle pole body duplication, mitotic and cytokinesis, and microtubule nucleation, indicating proteins involved in the cell-division machinery and cytoskeletal organization. A couple of outliers (neuron migration and interleukin-4 response) do not define the main function of the group.","confidence":"High","size":19,"edges":98,"triangles":265,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":13},{"id":"GO:0007049","count":12},{"id":"GO:0043093","count":11},{"id":"GO:0090529","count":11},{"id":"GO:1903087","count":11}]},{"hash":"1278689201428147927","title":"Mitochondrial Transport and Metabolic Regulation","description":"This cluster is dominated by GO terms describing transport across mitochondrial membranes (ATP, ornithine, NAD, thiosulfate) and regulation of mitochondrial membrane permeability, alongside related processes like apoptotic mitochondrial changes, necroptosis regulation, fatty acid response, insulin signaling, and liver regeneration. The common thread is mitochondrial metabolism and control of cell fate, suggesting a cohesive theme around mitochondrial transport/metabolic regulation and associated signaling.","confidence":"High","size":19,"edges":16,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":11},{"id":"GO:0032869","count":11},{"id":"GO:1990544","count":11},{"id":"GO:0000066","count":11},{"id":"GO:0035352","count":11}]},{"hash":"980186494392247384","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":119,"triangles":331,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:0071038","count":8},{"id":"GO:0071035","count":8},{"id":"GO:0000467","count":8}]},{"hash":"738447449728200741","title":"Mitosis and vesicle trafficking","description":"The top GO terms cluster around mitotic processes (cell division, DNA replication, CENP-A chromatin assembly, microtubule severing) as a core theme, with substantial representation of vesicle-transport activities (ER-Golgi and inter-Golgi), and autophagosome maturation, suggesting a cohesive role in both chromosome segregation and intracellular trafficking.","confidence":"High","size":19,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":15},{"id":"GO:0006888","count":13},{"id":"GO:0061641","count":13},{"id":"GO:0030433","count":13},{"id":"GO:0051013","count":13}]},{"hash":"176744034347781156","title":"DNA replication and repair cluster","description":"This cluster centers on DNA maintenance activities: DNA replication, cell cycle progression, and DNA damage responses (including the SOS response and homologous recombination repair). The presence of terms for DNA replication, cell cycle, homologous recombination repair, and SOS response suggests a cohesive group of proteins involved in DNA processing and damage signaling, with a possible aspect of protein quality control under stress. Some terms about foreign DNA clearance and bacterial-type replication further support a DNA-centric repair/maintenance theme in a prokaryotic context.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":1},{"id":"GO:0009432","count":1},{"id":"GO:0044355","count":1},{"id":"GO:0044787","count":1}]},{"hash":"2059382993769057449","title":"Translation and Replication Machinery","description":"The strongest signals are translation-related functions (cytoplasmic translation and elongation, and mitochondrial translation), suggesting a core set of ribosomal/translation components. Additional signals for DNA replication, viral genome replication, RNA-templated transcription, ER protein folding, and redox homeostasis point to a broader theme of protein synthesis coupled with nucleic acid metabolism and protein processing. Overall, the cluster appears to group translation machinery with related replication and folding/maintenance processes.","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2}]},{"hash":"968249199666527801","title":"Cell Cycle and Chromosome Condensation","description":"This cluster is dominated by GO terms tied to cell cycle control (G1/S and G2/M transitions, cell division) and chromosome dynamics (meiosis pairing, chromosome condensation via histone H3-S10 phosphorylation), suggesting a core function in mitotic progression and chromatin regulation. Some terms about transcription regulation and plant-specific processes appear as peripheral annotations, likely reflecting broader or pleiotropic roles of the proteins.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000082","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0044828","count":5},{"id":"GO:0097421","count":5},{"id":"GO:0000086","count":5}]},{"hash":"1145918613449421101","title":"Yeast Pheromone Signaling and Budding","description":"The GO terms show strong enrichment for pheromone response and regulation of GTPase activity, plus cell division and budding-related terms, which together point to a yeast-like mating signaling module coordinating growth/division. Some terms appear unrelated (visual perception, presynapse assembly), but the dominant signal is pheromone-driven signaling linked to budding; thus a yeast-centric interpretation is most plausible.","confidence":"Medium","size":19,"edges":7,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":18},{"id":"GO:0043547","count":18},{"id":"GO:0002098","count":17},{"id":"GO:0051301","count":17},{"id":"GO:0007117","count":17}]},{"hash":"813696897578952272","title":"Membrane Transporters and Xenobiotic Handling","description":"The cluster is dominated by GO terms for membrane transport and export/detoxification of xenobiotics (molybdate, taurine, thiamine, methionine, doxorubicin, xenobiotic export) plus fatty acid catabolism, suggesting a common theme around transport and detoxification. Some terms (nucleotide-excision repair, MHC I antigen processing, Type I secretion) appear as outliers, but the transport/detox theme is strongest.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":4},{"id":"GO:0015689","count":3},{"id":"GO:0015734","count":3},{"id":"GO:0046618","count":3},{"id":"GO:0042760","count":3}]},{"hash":"1079443641919728190","title":"Unknown","description":"The top GO terms are highly diverse, including chemical/ xenobiotic response, signaling cascades, metabolism, Schwann cell development, and cell-cycle/DNA repair processes. There isn\u2019t a single coherent biological function that ties these terms together, and several entries are obsolete, so a specific representative label cannot be confidently assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0051343","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0009742","count":2}]},{"hash":"1321253444987198696","title":"Unknown","description":"There are 0 edges and 0 triangles, and the top GO terms span multiple unrelated processes (histone methylation, muscle differentiation, bile-duct development, autophagy regulation, sporulation membrane formation, seed dormancy, phosphatidylinositol dephosphorylation, immune cell chemotaxis, dephosphorylation, myelin assembly). Because no single shared function or pathway ties the proteins together, a concise, representative label cannot be assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051571","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0035622","count":2},{"id":"GO:1902902","count":1},{"id":"GO:0032120","count":1}]},{"hash":"672475349134659306","title":"Plant chloroplast RNA processing and energy metabolism","description":"This cluster centers on chloroplast mRNA processing and mitochondrial/energy-related processes (ubiquinone biosynthesis and electron transport), with an additional plant-development signal (meristem) and proteostasis regulation hints, suggesting a plant organelle-focused functional theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045861","count":2},{"id":"GO:0007588","count":2},{"id":"GO:0043086","count":1},{"id":"GO:0010239","count":1},{"id":"GO:0080163","count":1}]},{"hash":"106130991808570496","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010586","count":3},{"id":"GO:1903265","count":3},{"id":"GO:1902187","count":3},{"id":"GO:0061158","count":3},{"id":"GO:2000637","count":3}]},{"hash":"223240440549247548","title":"Neural development and transcriptional regulation","description":"This cluster shows repeated GO terms tied to neural and organismal development (forebrain development, neural tube closure, multicellular organism development) and DNA-templated transcription, suggesting a group of proteins involved in developmental gene regulation, particularly for neural development. Other terms (stress responses, cadmium response, defense) appear but are less central to the core theme. Therefore, a neural development-focused label with transcriptional regulation best captures the shared function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001403","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0006349","count":5}]},{"hash":"637590031387864303","title":"Oligodendrocyte Differentiation and Glutamatergic Synaptic Regulation","description":"The cluster\u2019s GO terms are dominated by oligodendrocyte differentiation and myelination in the peripheral nervous system, as well as modulation of glutamatergic signaling (AMPA receptor activity, NMDA receptor clustering, and glutamatergic synaptic transmission). These points suggest a common theme of myelin development and excitatory synaptic regulation in the nervous system. Some terms related to lipid signaling and Rho-mediated cytoskeletal changes support the structural and signaling requirements of myelination, while a few cell division terms appear less central to this theme. Overall, the label reflects the primary neural/oligodendrocyte function represented in the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0048714","count":3},{"id":"GO:0050919","count":3},{"id":"GO:0038027","count":3}]},{"hash":"1026130288099606577","title":"Signaling and Trafficking Network","description":"The proteins are enriched for several signaling pathways (Wnt activation, Roundabout/Robo signaling, NF-\u03baB regulation) and related membrane trafficking processes (endocytic recycling, phospholipid homeostasis). This suggests a cohesive role in cell communication and membrane dynamics, with additional tissue-specific or downstream functions such as keratinization and heart contraction that can reflect context-dependent signaling networks.","confidence":"Medium","size":18,"edges":62,"triangles":83,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055091","count":18},{"id":"GO:0090263","count":18},{"id":"GO:0031424","count":18},{"id":"GO:0043124","count":18},{"id":"GO:0035385","count":18}]},{"hash":"809374718592505230","title":"Neural progenitor development and protein synthesis","description":"The cluster shows strong representation of translation and ribosome assembly, indicating a shared role in protein synthesis. It also includes neural development signals such as forebrain radial glial differentiation and scaffolding, suggesting involvement in neural progenitor formation and maturation. Some terms are broader or less directly linked (e.g., RNA silencing, immune signaling), but the dominant themes point to neural progenitor biology coupled with core translational processes.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010738","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0021943","count":2},{"id":"GO:0051301","count":2}]},{"hash":"537734598950922518","title":"Skin development and developmental signaling","description":"These proteins show enriched GO terms for multicellular organism development and skin development, suggesting a role in epidermal formation and broader developmental processes. The presence of positive regulation of serine/threonine kinase activity and autophosphorylation points to signaling cascades (kinase activity) that coordinate growth and differentiation. Additional terms such as mRNA transport, hypoxia response, and positive regulation of cell proliferation and mitotic cell cycle hint at involvement in proliferative and stress-responsive cellular programs during development. Overall, the cluster appears to capture developmental signaling linked to skin formation and tissue growth.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0043588","count":5},{"id":"GO:0031954","count":4},{"id":"GO:0071902","count":4},{"id":"GO:0051028","count":4}]},{"hash":"174394317552792701","title":"Diverse regulatory processes","description":"The top GO terms are dominated by general regulatory roles (positive/negative regulation, localization, etc.) across different processes, rather than a single pathway. Terms include regulation of GTPase activity, mitotic cell cycle, negative regulation of epithelial proliferation, triglyceride biosynthesis regulation, NF-kappaB activity, suppression of viral release, peptide amidation, and microtubule localization. This suggests proteins in the cluster participate in a variety of regulatory functions spanning cell signaling, growth control, and cellular organization, rather than a cohesive, specific pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0050680","count":2},{"id":"GO:0010867","count":2}]},{"hash":"150884729377494973","title":"Chromatin regulation and transcription control","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, plus heterochromatin maintenance, nucleosome density regulation, and histone deacetylation, indicating a focus on chromatin state governing gene expression. Some metabolism-related terms appear, but the core theme centers on chromatin-mediated transcription regulation and chromatin remodeling processes.","confidence":"High","size":18,"edges":148,"triangles":738,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0006355","count":5},{"id":"GO:0006344","count":4},{"id":"GO:0060303","count":4},{"id":"GO:0034983","count":4}]},{"hash":"1516921464453194015","title":"Interferon-driven innate immunity and ER stress","description":"The cluster is dominated by type I interferon response and innate immune terms (cellular response to type I interferon, innate immune response, defense against virus) alongside unfolded protein response in the ER and ubiquitin-dependent protein turnover (K11-linked ubiquitination). These themes point to antiviral signaling coupled with ER stress/quality-control mechanisms, even though cell division terms are present, the immune/ER-stress axis is most representative.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071357","count":9},{"id":"GO:0006986","count":8},{"id":"GO:0007091","count":8},{"id":"GO:1903071","count":8},{"id":"GO:0090526","count":8}]},{"hash":"1387228938978640815","title":"Skeletal muscle sarcomere organization and actin dynamics","description":"Top terms point to sarcomere organization and skeletal muscle fiber development, with strong signals for actin cytoskeleton remodeling (actin cortical patch localization/assembly). While a few terms relate to vesicle trafficking or meiosis, the dominant pattern emphasizes muscle fiber structure and actin-driven sarcomere assembly, justifying a muscle-focused label.","confidence":"Medium","size":18,"edges":137,"triangles":599,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":5},{"id":"GO:0030100","count":4},{"id":"GO:0051592","count":4},{"id":"GO:0000011","count":4},{"id":"GO:0045214","count":4}]},{"hash":"1257299217942838308","title":"Unknown","description":"The terms span diverse biology across immune, development, metabolism, behavior, and plant processes, with no clear shared function or pathway; the zero edges also suggest no cohesive interaction pattern. Therefore no coherent theme can be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043542","count":1},{"id":"GO:0031295","count":1},{"id":"GO:0060244","count":1},{"id":"GO:0035641","count":1},{"id":"GO:0007155","count":1}]},{"hash":"167418038464939994","title":"Core Metabolism and DNA Replication","description":"The Top Terms include several biosynthetic processes (pyruvate, serine, threonine, fatty acids, cobalamin, coenzyme M) indicating broad central metabolism and building blocks for cell growth. Additional terms cover DNA-templated transcription, DNA replication, and cell division, pointing to core growth-related processes. Together, the cluster seems to group enzymes and factors involved in primary metabolism that support DNA synthesis and cell proliferation.","confidence":"Medium","size":18,"edges":135,"triangles":580,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042866","count":4},{"id":"GO:0006565","count":4},{"id":"GO:0019518","count":4},{"id":"GO:0006633","count":4},{"id":"GO:0009236","count":4}]},{"hash":"2247908161756447150","title":"Regulation of Vesicle Trafficking","description":"This cluster centers on regulatory processes associated with vesicle movement and membrane-related signaling. The top GO terms include retrograde vesicle transport from Golgi to ER, regulation of synaptic transmission, and regulation of sphingolipid biosynthesis (which affects membrane dynamics and vesicle formation), suggesting a cohesive theme around controlling vesicle trafficking and related signaling. Some terms (granuloma formation, neutrophil degranulation, mating projection growth) are more peripheral but still reflect vesicle-related or immune signaling contexts. Confidence: Medium.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010796","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0048169","count":2},{"id":"GO:0002432","count":2}]},{"hash":"1596052170046874593","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0001403","count":3},{"id":"GO:0007275","count":3}]},{"hash":"481933822183313022","title":"Neural development and protein synthesis","description":"The Top Terms show a strong emphasis on translation-related processes (translation, ribosome biogenesis, translational termination) indicating proteins involved in protein synthesis. Additionally, neural development components (nervous system development, formation of radial glial scaffolds, bipolar cell growth, epithelial polarity) suggest the cluster is tied to neural development contexts. The converging theme is proteins engaged in core translation machinery that function in neural development and cell growth, so the label reflects both aspects without being overly broad.","confidence":"Medium","size":18,"edges":33,"triangles":22,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006415","count":2}]},{"hash":"1407372112840031992","title":"Developmental Signaling and Membrane Trafficking","description":"These terms cluster around signaling pathways (Wnt, ROBO, NF-kappaB) and membrane-related processes (phospholipid homeostasis, endocytic recycling) that drive development and tissue organization, with supporting themes in axon guidance and broader tissue functions like keratinization and heart contraction. The common thread is signaling coupled to membrane dynamics that shape cellular behavior in development and tissue maintenance.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055091","count":18},{"id":"GO:0090263","count":18},{"id":"GO:0031424","count":18},{"id":"GO:0043124","count":18},{"id":"GO:0035385","count":18}]},{"hash":"1665631007514370140","title":"Viral entry and RNA cap methylation proteins","description":"This cluster is characterized by GO terms tied to viral infection processes (virion attachment to host cell, viral RNA genome replication) and RNA cap biology (7-methylguanosine capping, cap1/cap2 and guanine-N7 methylation), suggesting proteins involved in the viral life cycle and RNA processing. The presence of phosphatidylinositol dephosphorylation hints at membrane-related steps, aligning with viral entry, while autophagy-related host interactions point to virus-host interplay. Therefore, a label focusing on viral entry and RNA cap methylation best captures the shared function.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":2},{"id":"GO:0019062","count":1},{"id":"GO:0097310","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0000466","count":1}]},{"hash":"1657892150936928170","title":"Developmental chromatin regulation","description":"This cluster\u2019s core signals point to chromatin-level control of gene expression during development: nucleosome mobilization, histone exchange, and histone acetylation indicate chromatin remodeling; transcription initiation ties to gene regulation; and terms like segment specification and regulation of vegetative-to-reproductive transition suggest developmental timing. Some terms (Wnt signaling, balance) are less direct but can relate to developmental regulatory networks, making the overall theme developmentally linked chromatin regulation. ","confidence":"Medium","size":18,"edges":17,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2000096","count":1},{"id":"GO:0016246","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0043486","count":1}]},{"hash":"1743280600382461682","title":"Ribosome biogenesis and translation","description":"The top GO terms are heavily centered on translation and ribosome biogenesis, including translation, ribosomal large subunit assembly, ribosomal large subunit biogenesis, preribosome assembly, cytoplasmic translation, and tRNA modification. This pattern strongly suggests the cluster represents proteins involved in ribosome production and protein synthesis, with some auxiliary signals like cell cycle-related terms likely reflecting broader cellular coordination rather than central function. Confidence: High.","confidence":"","size":18,"edges":93,"triangles":200,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0046677","count":5},{"id":"GO:0000027","count":3},{"id":"GO:0006400","count":3},{"id":"GO:0007049","count":3}]},{"hash":"321109985169624736","title":"Xenobiotic Detoxification and Glutathione Metabolism","description":"The top GO terms cluster around detoxification and xenobiotic processing, including cellular oxidant detoxification, xenobiotic and toxin catabolic processes, and glutathione metabolism, which together point to a glutathione-dependent detox pathway. Some auxiliary terms (auxin signaling, nitrogen regulation, and odor perception) appear as broader or off-target annotations but do not override the central detox theme. This cluster appears representative of proteins involved in processing and neutralizing xenobiotics and maintaining redox balance.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":17},{"id":"GO:2000255","count":14},{"id":"GO:0042178","count":14},{"id":"GO:0006808","count":14},{"id":"GO:0071285","count":14}]},{"hash":"1175489303654197000","title":"RNA Modification and Cofactor Biosynthesis","description":"This cluster is dominated by GO terms for RNA base methylation and tRNA methylation (rRNA base methylation, tRNA methylation, tRNA queuosine biosynthesis) alongside multiple cofactor biosynthesis processes (molybdopterin cofactor biosynthesis, biotin biosynthesis, protein lipoylation). Together these suggest a functional theme around RNA modification and essential metabolic cofactor production. Some terms like DNA replication and cell budding point to broader growth processes, but the strongest cohesive signal is RNA modification coupled with cofactor biosynthesis.","confidence":"Medium","size":18,"edges":29,"triangles":11,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007114","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0019475","count":2},{"id":"GO:0009102","count":2}]},{"hash":"6837744700767481","title":"ECM Remodeling and Lung Branching Morphogenesis","description":"The top terms converge on extracellular matrix remodeling (collagen catabolic process, basement membrane disassembly, bone resorption) and developmental lung morphogenesis (epithelial tube branching, lung morphogenesis). Hormonal and peptide signaling terms (thyroid hormone response, neuropeptide/bradykinin catabolic) suggest modulation of these remodeling processes. While there is a single immune term (T cell cytotoxicity), the dominant theme is ECM remodeling linked to organogenesis and branching.","confidence":"High","size":18,"edges":126,"triangles":485,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":16},{"id":"GO:0097067","count":16},{"id":"GO:0010813","count":16},{"id":"GO:0010815","count":16},{"id":"GO:0001913","count":16}]},{"hash":"1094476936619141495","title":"Unknown","description":"The terms cover a broad, heterogeneous set of processes including telomere maintenance and capping, Wnt signaling, microtubule localization, regulation of CDK activity, innate immune signaling (NF-kappaB), defense against Gram-positive bacteria, amino acid starvation response, and mRNA processing. There isn\u2019t a single, clear biological theme tying these GO terms together, suggesting the cluster spans multiple unrelated functions rather than a cohesive pathway. Confidence: None","confidence":"","size":18,"edges":37,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0090263","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0045087","count":2}]},{"hash":"2266813509661863260","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0080156","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0090617","count":2}]},{"hash":"1116193441380209842","title":"Spliceosome components","description":"The cluster shows strong representation of spliceosome-related GO terms (GO:0000393 and GO:0000398) indicating involvement in mRNA splicing via the spliceosome. While other terms are present (e.g., SRP-dependent targeting, mitochondrial distribution, plasmid maintenance), they are fewer and likely reflect annotation noise or multi-function proteins. Overall, the dominant signal points to splicing machinery as the representative function of this cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000393","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0048311","count":1}]},{"hash":"1660683367441636961","title":"Ubiquitin-Dependent Proteolysis","description":"The Top Terms are strongly centered on ubiquitination-related processes: ubiquitin-dependent protein catabolic process, ERAD, K63-linked ubiquitination, autoubiquitination, and general protein ubiquitination, indicating the proteins cluster around ubiquitin-mediated proteolysis. Some immune-related terms appear (innate immune response, TNF signaling), suggesting links to ubiquitin-regulated immune signaling, but the core signal is ubiquitin-driven protein turnover.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0016567","count":1}]},{"hash":"691045058064107685","title":"Nuclear DNA Repair and RNA Processing","description":"The top GO terms point to a core function in genome maintenance and RNA quality control within the nucleus, including DNA repair, DNA-templated transcription, histone mRNA and snRNA catabolic processes, and nuclear mRNA surveillance. Additional terms for DNA strand displacement, replication-related processes, and even plastid DNA replication and siRNA-directed DNA methylation fit into a broader theme of nucleic acid metabolism and genome integrity, with some plant-specific organellar links. This combination suggests a cohesive cluster of proteins involved in DNA/RNA metabolism and maintenance in the nucleus (and related organelle interactions).","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071044","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903221","count":1},{"id":"GO:0071037","count":1}]},{"hash":"1193399900265137275","title":"Unknown","description":"The top GO terms are highly diverse, including metal ion response, angiogenesis/heart development, chromatin silencing, defense response, DNA damage signaling, replication, and various metabolic and biosynthetic processes. There is no single clear function tying the proteins together, and the lack of edges suggests a non-cohesive cluster, so a unified label cannot be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046686","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0030466","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0006977","count":2}]},{"hash":"1719340674495480733","title":"GTPase-Regulated GPCR Signaling","description":"This cluster is dominated by GO terms for G protein-coupled receptor signaling and positive regulation of GTPase activity, including G protein heterotrimerization, suggesting components of heterotrimeric G protein signaling pathways. A few terms pertain to development or plant gravity sensing, which may reflect broader annotations or dataset noise, but the core signal is GPCR-GTPase signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007213","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0010255","count":2},{"id":"GO:0070208","count":2}]},{"hash":"596849569259038708","title":"Immune signaling and stress-response pathways","description":"The cluster includes terms for immune signaling (T cell receptor signaling, Fc-epsilon receptor signaling) and inflammatory regulation, along with stress/defense responses (cadmium ion response, viral process, plant hypersensitive response, hypoxia-related transcription). While spanning multiple kingdoms, the common thread is signaling networks governing immunity and stress responses, with deubiquitination as a regulatory layer.","confidence":"Medium","size":17,"edges":54,"triangles":122,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":8},{"id":"GO:0046686","count":8},{"id":"GO:0050852","count":7},{"id":"GO:0060071","count":7},{"id":"GO:0002862","count":7}]},{"hash":"1743015322994000302","title":"Ciliary and microtubule transport","description":"Most GO terms point to transport along microtubules, especially in cilia/flagella contexts (intraciliary retrograde/anterograde transport, inner dynein arm assembly, cilium movement, flagellated sperm motility) and minus-end-directed vesicle transport, plus spindle localization. This indicates a cluster of proteins involved in microtubule-based transport with a ciliary/flagellar emphasis, though a couple terms appear unrelated noise (stress granule assembly, lateral ventricle development). ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990048","count":1},{"id":"GO:0008218","count":1},{"id":"GO:0035721","count":1},{"id":"GO:0036159","count":1},{"id":"GO:0003341","count":1}]},{"hash":"1468408683161270615","title":"Developmental Regulation and Growth Control","description":"These proteins are enriched for regulatory processes spanning development, growth, and signaling (e.g., regulation of cell cycle, transcription/chromatin remodeling, anisotropic cell growth, organ and brain development, heart-rate regulation via conduction, oocyte localization, and Wnt signaling modulation). While the terms cover diverse tissues, the shared theme is regulation of development and growth rather than a specific biochemical activity, justifying a label centered on developmental regulation and growth control.","confidence":"Medium","size":17,"edges":122,"triangles":507,"max_degree":16,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007050","count":12},{"id":"GO:0048096","count":11},{"id":"GO:0051211","count":11},{"id":"GO:0021550","count":11},{"id":"GO:0048496","count":11}]},{"hash":"1920377801706047041","title":"Mitochondrial energy metabolism and redox balance","description":"This cluster centers on mitochondrial processes: the electron transport chain, TCA cycle, NADH to ubiquinone flow, and mitochondrial protein import and folding, plus redox detoxification and redox homeostasis. A few terms also touch on mitochondrial folate metabolism, all pointing to coordinated mitochondrial energy production and oxidative balance.","confidence":"High","size":17,"edges":129,"triangles":585,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0046653","count":2},{"id":"GO:0022900","count":2},{"id":"GO:0006099","count":2}]},{"hash":"2135642956442829050","title":"Carbon-source-regulated transcription","description":"The top GO terms cluster around RNA polymerase II\u2013mediated transcription regulation, especially in the context of nonfermentable carbon sources, with both positive and negative regulation represented. Additional terms link transcriptional control to cellular respiration and various metabolic processes (e.g., leucine biosynthesis) and even aflatoxin biosynthesis, suggesting a core theme of transcriptional regulation tied to nutrient status and metabolism.","confidence":"High","size":17,"edges":51,"triangles":79,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0035948","count":6},{"id":"GO:0061415","count":5},{"id":"GO:0043457","count":5},{"id":"GO:0045122","count":5}]},{"hash":"1604041344976186480","title":"Diverse signaling regulators","description":"The top GO terms point to regulation of signaling pathways across diverse contexts\u2014positive regulation of GTPase activity, calcineurin-NFAT signaling, glucocorticoid response, and neural/glial development\u2014suggesting these proteins act as broad regulators of signaling rather than a single, cohesive pathway. This breadth justifies a label centered on signaling regulation rather than a specific pathway.","confidence":"Medium","size":17,"edges":14,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0060040","count":8},{"id":"GO:0051343","count":8},{"id":"GO:0014044","count":8},{"id":"GO:0070886","count":8}]},{"hash":"942064350949729096","title":"Golgi- and Synaptic Vesicle Trafficking","description":"The top GO terms point to membrane trafficking through the Golgi and SNARE-mediated exocytosis, including ER-to-Golgi transport, intra-Golgi transport, Golgi ribbon formation, SNARE complex assembly, and neurotransmitter receptor insertion at the postsynaptic membrane, all of which indicate a coherent theme of vesicle fusion and trafficking in neurons and related cells; a single immune-related term appears as a minor outlier.","confidence":"High","size":17,"edges":111,"triangles":374,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":7},{"id":"GO:0060291","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0090161","count":7},{"id":"GO:0035493","count":7}]},{"hash":"1083237907119646433","title":"Plant Oxylipin and Jasmonic Acid Biosynthesis","description":"These terms converge on a plant lipid-signaling module: oxylipin and jasmonic acid (JA) biosynthesis, stress and toxin responses, and fatty acid metabolism closely tied to JA signaling. The inclusion of stamen development and ozone response further supports a plant-specific defense and developmental regulation theme tied to JA/oxylipins.","confidence":"High","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0010193","count":2},{"id":"GO:0033543","count":2},{"id":"GO:0031408","count":2},{"id":"GO:0048443","count":2}]},{"hash":"203406314846030493","title":"Ubiquitin-Proteasome Pathway","description":"The top GO terms center on ubiquitin-dependent protein catabolic processes, including SCF-dependent proteasomal degradation and polyubiquitination, with related ERAD activity. This points to a cluster of proteins involved in tagging and degrading substrates via the proteasome, i.e., ubiquitin-proteasome\u2013mediated proteolysis. Additional terms touching innate immune signaling and antiviral defense align with ubiquitin\u2019s role in immune responses, supporting a cohesive functional theme around proteostasis and degradation in stress/defense contexts.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0071276","count":5},{"id":"GO:0031146","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0000209","count":4}]},{"hash":"579564505182220625","title":"Mitosis control and ubiquitin-mediated proteolysis","description":"Top terms indicate strong enrichment for mitotic cell cycle processes (mitotic cell cycle, cell division, APC-dependent catabolic process) and ubiquitin-dependent protein degradation (ubiquitin-dependent ERAD pathway, ubiquitin-dependent protein catabolic process). This points to a cohesive cluster of proteins involved in mitotic regulation and proteolysis, with some ancillary RNA processing/ER stress-related terms likely secondary. Confidence reflects a solid but not exclusive link between these functions. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0071276","count":4},{"id":"GO:2001162","count":4},{"id":"GO:0061087","count":4},{"id":"GO:0000278","count":4}]},{"hash":"362028902506005906","title":"Metal Ion Stress and Cell Division","description":"Top GO terms show cellular responses to cadmium and lead ions alongside mitotic cell cycle and cell division, with supporting signals from stress/immune pathways and proteostasis (ubiquitination, protein folding/isomerization). This suggests a theme of metal-induced stress impacting cell-cycle regulation and protein homeostasis, justifying a label that captures metal ion stress linked to division and quality control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1532582418338594963","title":"Unknown","description":"The GO terms span very diverse biological contexts (pigmentation, formaldehyde metabolism, muscle development regulation, plant cytokinin signaling, glucocorticoid signaling, telomerase assembly, root growth, neuroblast polarity, centrosome localization, and host-symbiont activity). There is no clear shared function or pathway among these 17 proteins, and the network has no edges or connected components, suggesting a heterogeneous collection rather than a cohesive cluster. Therefore, no single explanatory label can be assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":1},{"id":"GO:0019647","count":1},{"id":"GO:0048642","count":1},{"id":"GO:0080037","count":1},{"id":"GO:0042921","count":1}]},{"hash":"1118850860541394256","title":"Endoplasmic reticulum organization and ER stress response","description":"The top terms converge on ER structure and function (ER tubular network organization, ER inheritance) and ER-associated processes (protein transport into membrane rafts, ER-dependent peroxisome organization) plus ER stress response, suggesting a cohesive theme around ER morphogenesis and proteostasis. Some terms (ABA response, taste perception) appear as odd outliers, likely annotation noise, but do not negate the core ER-focused signal.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009737","count":1},{"id":"GO:0050913","count":1},{"id":"GO:0071786","count":1},{"id":"GO:0050916","count":1}]},{"hash":"2103950690547474778","title":"DNA replication and telomere maintenance","description":"This cluster is dominated by GO terms related to DNA replication, DNA repair, recombination, and telomere maintenance, including telomere lengthening and protein localization to telomeres, with supporting mitotic checkpoint signals. Although translation and tRNA aminoacylation terms appear, the core signal points to genome maintenance and telomere biology, suggesting a cohesive theme around DNA metabolism and telomere dynamics.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0010833","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0070200","count":3}]},{"hash":"683236530788565150","title":"DNA repair and cellular quality control","description":"This cluster is dominated by DNA damage response terms (error-free translesion synthesis, DNA replication, UV-damage excision repair), suggesting a core role in genome maintenance. It also includes autophagy-related processes (autophagosome maturation, intralumenal vesicle formation) and vesicle trafficking, plus mitochondrial complex assembly, pointing to broader cellular quality-control and organelle maintenance. The combination indicates a general theme of maintaining cellular integrity through repair, autophagy, and organelle assembly, though the set is somewhat heterogeneous; hence the label DNA repair and cellular quality control is representative but with moderate confidence.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070914","count":2},{"id":"GO:0097352","count":1},{"id":"GO:0048219","count":1}]},{"hash":"243779006526058325","title":"Unknown","description":"The top terms cover a broad mix of processes including protein folding (peptidyl-prolyl isomerization, chaperone-mediated folding), stress responses (response to hydrogen peroxide, lead ion), metabolism (regulation of gluconeogenesis), and cell cycle (metaphase/anaphase transition), with no single unifying function; thus no coherent cluster theme can be inferred. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000324","count":1},{"id":"GO:1903646","count":1},{"id":"GO:0000413","count":1},{"id":"GO:0010288","count":1},{"id":"GO:0007091","count":1}]},{"hash":"1841920282692412265","title":"Cardiac and skeletal muscle development","description":"Based on GO terms, the cluster is enriched for heart development, myoblast fusion, and angiogenesis, pointing to muscle and cardiac tissue formation. Terms like multicellular organism development and Schwann cell development reflect broader developmental programs, while mitotic cell cycle and G2/M transition suggest proliferation accompanying tissue growth. A couple of terms (abscisic acid-activated signaling pathway, long-term synaptic potentiation) appear less directly connected and may reflect annotation noise. Overall, the dominant signal aligns with cardiac and skeletal muscle development.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0014044","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0060291","count":3}]},{"hash":"1181556905953517429","title":"Proteasome-Mediated Protein Degradation","description":"Dominated by ubiquitin-dependent proteolysis and proteasome-related processes (ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal degradation, proteasome assembly, and positive regulation of proteasomal degradation). Also includes ERAD and endosome localization, aligning with protein quality control and turnover. Other terms touch on neuronal signaling and DNA damage recognition, but the main signal is ubiquitin\u2013proteasome\u2013linked proteolysis.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0090394","count":3},{"id":"GO:0071287","count":3},{"id":"GO:0036010","count":2}]},{"hash":"1620297216989877309","title":"Embryonic organogenesis and neural development","description":"This cluster centers on developmental processes across multiple tissues: heart and skeletal muscle development, cranial skeleton morphogenesis, forebrain development, and retinal/visual development. The mix suggests a broad morphogenesis theme, with signaling-related terms (peptidyl-threonine phosphorylation, cellular response to prostaglandin E) indicating regulatory pathways involved in development. Overall, the proteins likely participate in embryonic organogenesis and neural/eye development rather than a single, narrow function.","confidence":"High","size":16,"edges":16,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007519","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0048701","count":3},{"id":"GO:0007275","count":3}]},{"hash":"157156857306843542","title":"Lymphocyte metabolism and transcription","description":"This cluster combines immune-related activity (cellular response to interleukin-4 and lymphocyte proliferation) with metabolic processes (carbohydrate metabolism, gluconeogenesis regulation, GMP biosynthesis, and sulfur amino acid pathways like transsulfuration and homocysteine catabolism). The mix suggests metabolic regulation in immune cells, particularly lymphocytes, alongside transcriptional activity.","confidence":"Medium","size":16,"edges":117,"triangles":520,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0071353","count":7},{"id":"GO:0019346","count":7},{"id":"GO:0045722","count":7},{"id":"GO:0005975","count":7}]},{"hash":"1675510231680338522","title":"Neuronal development and vesicle trafficking","description":"The top GO terms point strongly to nervous system and dendritic spine development, combined with ER-to-Golgi vesicle transport and protein localization, suggesting these proteins function in neuronal maturation and intracellular trafficking. Additional signals like glucose-mediated signaling and regulation of GTPase activity support a role in neuronal signaling and cytoskeletal dynamics. Some terms (kidney development, generic cell division) are broader and less specific, but do not outweigh the central neuronal/trafficking theme. ","confidence":"Medium","size":16,"edges":41,"triangles":48,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0046909","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0060999","count":6},{"id":"GO:0010255","count":6}]},{"hash":"557499951858948034","title":"Synaptic Vesicle Regulation and Dopaminergic Signaling","description":"The top GO terms cluster around presynaptic vesicle exocytosis and endocytosis, excitatory postsynaptic potential, and dopaminergic signaling, all pointing to neuronal synaptic function. While a few terms (bone ossification, kidney size) are less related, the dominant theme is synaptic vesicle cycling and synaptic signaling regulation, occasionally extending to Wnt-related modulation of synapses.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0043931","count":5},{"id":"GO:1900242","count":5},{"id":"GO:0060079","count":5}]},{"hash":"1957720047613208628","title":"Meiosis, spindle assembly, and cell cycle regulation","description":"This cluster centers on oocyte maturation and spindle assembly in female meiosis I, with microtubule polymerization and ubiquitin-proteasome\u2013dependent protein catabolism indicating tight regulation of the cell cycle. Some development terms (neural tube initiation and ventricle development) may reflect broader roles of these proteins in embryogenesis, but the core signal is meiosis/spindle/cell-cycle\u2013related. Confidence: Medium","confidence":"","size":16,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":1},{"id":"GO:0070544","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0007057","count":1},{"id":"GO:0021993","count":1}]},{"hash":"1391506044374379722","title":"Sphingolipid and Phospholipid Metabolism","description":"The top GO terms cluster around sphingolipid pathways (sphingosine and sphinganine-1-phosphate metabolic processes) and related phospholipid processes (phospholipid catabolic/dephosphorylation and phosphatidylglycerol biosynthesis), with a noted but peripheral link to sphingolipid signaling regulation. This suggests the proteins are grouped by lipid metabolism and sphingolipid signaling roles, rather than a single non-lipid function. ","confidence":"Medium","size":16,"edges":20,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":1},{"id":"GO:0046839","count":1},{"id":"GO:1902068","count":1},{"id":"GO:0009395","count":1},{"id":"GO:0006668","count":1}]},{"hash":"554473821674865449","title":"Spermatogenesis and meiotic cytokinesis","description":"This cluster is dominated by GO terms related to meiosis cytokinesis (meiosis I/II, male meiosis), acrosome assembly, and spermatid nuclear elongation, pointing to male germ cell development and spermiogenesis. The presence of actomyosin contractile ring contraction reinforces the spermatogenic/meiosis focus, with translation-related terms likely reflecting general cellular machinery rather than a core theme. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007111","count":2},{"id":"GO:0007110","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0008283","count":2}]},{"hash":"756869555223087236","title":"ER stress\u2013linked translation and folding","description":"These proteins converge on ER-associated protein production and quality control: translation, ER-based protein folding, stress-induced regulation of translation initiation, and targeting/transport to membranes, with some unrelated terms (axonemal assembly, hormonal response) likely reflecting annotation noise.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0034975","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0051259","count":1},{"id":"GO:0071374","count":1}]},{"hash":"1174978817075356772","title":"Ubiquitin-Proteasome Regulation and Innate Immunity","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolism (including SCF and ERAD pathways, autoubiquitination, and specific ubiquitin linkages) with supporting signals of innate immune response and stress-related signaling, indicating a theme around ubiquitin-mediated protein turnover and related immune signaling.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0031146","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0051865","count":4},{"id":"GO:1903378","count":4}]},{"hash":"1534191756481806397","title":"Rho GTPase Signaling and Cytoskeleton Dynamics","description":"The cluster is dominated by GO terms for small GTPase signaling (GO:0007264), Rho-mediated pathways (GO:0060268), and actin cytoskeleton organization (GO:0030036), plus regulation of GTPase activity (GO:0043547). This points to a cohesive module centered on GTPase-driven cytoskeletal remodeling and related signaling, with additional terms like GPCR cholinergic signaling and vascular permeability reflecting downstream or context-specific aspects of these pathways. While mitochondrial fission and heart development terms appear as outliers, they can be related through shared GTPase roles, keeping the core theme intact.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007264","count":3},{"id":"GO:0000266","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007213","count":2}]},{"hash":"565682625791986610","title":"Xenobiotic-response signaling cluster","description":"This cluster shows enrichment for cellular response to xenobiotic stimulus, response to cocaine, and positive regulation of kinase activity, pointing to a module of external-stimulus signaling and phosphorylation control. The presence of terms related to cell cycle and placental development, plus obsolete GO terms, suggests some annotation noise and broader regulatory roles rather than a single cohesive pathway. Overall, the common theme is signaling responses to external compounds and related regulatory processes.","confidence":"Medium","size":16,"edges":41,"triangles":18,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0033160","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0071902","count":3},{"id":"GO:0032516","count":3},{"id":"GO:0030433","count":2}]},{"hash":"1879834486978422632","title":"Stress-Responsive Signaling and Proteostasis","description":"The cluster combines signaling and stress-related processes (heat response, response to mechanical stimulus, regulation of kinase activity), mitochondrial dynamics (fission), chromatin-related localization, lipid metabolism, viral processes, Wnt signaling, and ubiquitin-dependent protein degradation. This pattern suggests a cohesive theme of cellular stress signaling intertwined with protein homeostasis and turnover.","confidence":"Medium","size":16,"edges":16,"triangles":2,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0090141","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0055114","count":2}]},{"hash":"170875616269243562","title":"Nuclear RNA Processing and Transcription","description":"The top GO terms are dominated by nuclear RNA metabolism and transcription activities\u2014mRNA splicing via spliceosome, deadenylation-dependent decay, exonucleolytic RNA hydrolysis, RNA catabolic processes, and DNA-templated transcription\u2014suggesting a cohesive cluster of proteins involved in processing and expressing RNA in the nucleus. Some terms also hint at stress response and metabolic processes, but the core theme centers on RNA processing and transcriptional regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015967","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0036245","count":1},{"id":"GO:0090503","count":1}]},{"hash":"156209826489487737","title":"Transcription Regulation and Chromatin Remodeling","description":"This cluster is enriched for GO terms about DNA-templated transcription, its regulation, and chromatin remodeling, suggesting a core role in controlling gene expression; the xenobiotic response and plant hormone-related terms may reflect broader regulatory contexts or multifunctional proteins.","confidence":"Medium","size":15,"edges":35,"triangles":27,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0043046","count":3},{"id":"GO:0019383","count":3},{"id":"GO:0045654","count":3},{"id":"GO:0042493","count":3}]},{"hash":"1884072012267840142","title":"Ribosome Biogenesis & RNA Processing","description":"The cluster is strongly enriched for rRNA maturation (SSU/5.8S/LSU), ribosomal large subunit biogenesis, and RNA processing steps (mRNA splicing and transcription initiation), indicating a cohesive module centered on RNA metabolism and ribosome assembly. Some terms like DNA replication and UV protection are present but less representative of the main function. ","confidence":"High","size":15,"edges":37,"triangles":38,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0009650","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000462","count":3}]},{"hash":"2054484091002411933","title":"Neuronal synaptic vesicle exocytosis regulation","description":"This cluster centers on neuronal processes, with GO terms emphasizing brain development, regulation of synaptic vesicle exocytosis, and GABAergic synaptic transmission. Additional terms point to vesicle trafficking along the secretory pathway (ER to Golgi) and membrane biology (sphingolipid biosynthesis), suggesting a cohesive module involved in synaptic vesicle formation and release, modulated by membrane composition and gene expression control in neurons.","confidence":"High","size":15,"edges":81,"triangles":217,"max_degree":14,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:0010796","count":6},{"id":"GO:0031384","count":6},{"id":"GO:2000300","count":6},{"id":"GO:0006888","count":4}]},{"hash":"2110593771350659180","title":"ER Stress and Lipid Metabolism","description":"This cluster is anchored by ER-related terms (ER organization, ER overload response, ERAD) and lipid pathways (phospholipid and sphingolipid metabolism/signaling), suggesting proteins involved in ER homeostasis and lipid signaling. A few outliers (pseudohyphal growth, osteoblast differentiation) exist but do not dominate the annotation, so the core theme is ER stress response coupled with lipid processing.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":2},{"id":"GO:0007029","count":1},{"id":"GO:0001649","count":1},{"id":"GO:0006983","count":1},{"id":"GO:0030433","count":1}]},{"hash":"856268259292689283","title":"Proteostasis and Stress Signaling","description":"The cluster is enriched for programs involved in maintaining protein homeostasis (deubiquitination, protein stabilization, negative regulation of amyloid fibril formation) and responding to cellular stress (stress-activated MAPK cascade, UV-A response, heat response). The inclusion of transport-related terms (anterograde axonal protein transport, negative regulation of intracellular transport) suggests coordination between protein quality control and cargo trafficking, spanning tissues such as neurons and lens, consistent with a proteostasis/stress-response network.","confidence":"High","size":15,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":6},{"id":"GO:0007568","count":5},{"id":"GO:0032387","count":5},{"id":"GO:0050821","count":5},{"id":"GO:1905907","count":5}]},{"hash":"322042659095202365","title":"Unknown","description":"The terms span nucleic acid metabolism and cell-cycle regulation (DNA recombination, DNA biosynthetic process, RNA hydrolysis, transcription regulation) but also include unrelated processes such as corneocyte development, renal water transport, glycogen regulation, and phosphatidylinositol dephosphorylation, with several obsolete terms. The absence of edges and this diversity imply no cohesive functional theme for the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0071897","count":2},{"id":"GO:0007568","count":2},{"id":"GO:1900087","count":2}]},{"hash":"1268896219936574172","title":"Cell division and vesicle trafficking","description":"These proteins are enriched for mitotic/cell cycle functions (cell division, mitotic cell cycle) and ciliogenesis, with additional signals for RAN/GTPase regulation and vesicle-related processes (presynapse assembly, secretion). The mix suggests a cluster of factors coordinating cell proliferation with intracellular transport and trafficking, including cytoskeletal dynamics that underlie division and vesicle trafficking. Overall, the theme centers on cell division together with trafficking/secretion pathways.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0060271","count":8},{"id":"GO:0043547","count":8},{"id":"GO:0002098","count":7}]},{"hash":"404354599754520783","title":"Developmental Signaling and Cell Fate Regulation","description":"The top GO terms point to modulation of key developmental signaling pathways (Wnt, Hippo, TGF-beta) and processes tied to cell differentiation and fate (keratinocytes, adipocytes), plus apoptosis and transcriptional control, suggesting a coherent theme of regulating growth, differentiation, and tissue development through signaling networks.","confidence":"High","size":15,"edges":39,"triangles":44,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030512","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0090263","count":6},{"id":"GO:0060044","count":6},{"id":"GO:0006915","count":6}]},{"hash":"1453698984987379997","title":"Mitochondrial metabolism and genome maintenance","description":"This cluster features GO terms centered on mitochondrial functions (protein import into the mitochondrial matrix, regulation of mitochondrial membrane permeability) and genome maintenance (DNA repair and DNA recombination), with folic acid biosynthesis suggesting a link to mitochondrial one-carbon metabolism. The mix implies a mitochondria-focused balance between metabolic processes and genome integrity, with a few peripheral terms (e.g., cell cycle regulation) that are less defining.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046656","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0010867","count":1}]},{"hash":"513302245467304402","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043420","count":1},{"id":"GO:0034516","count":1},{"id":"GO:0019265","count":1},{"id":"GO:0034354","count":1},{"id":"GO:0019805","count":1}]},{"hash":"550206849306534375","title":"Terpenoid and xenobiotic oxidative metabolism","description":"The GO terms show enrichment in terpenoid-related oxidation (ent-kaurene oxidation to kaurenoic acid; camphor catabolic process) and broader xenobiotic metabolism (isoquinoline alkaloid and carbazole catabolic processes, lipid hydroxylation), suggesting enzymes involved in oxidative modification of organic compounds. Some non-specific terms appear, but the dominant signal is oxidative metabolism of terpenoids and related xenobiotics.","confidence":"Medium","size":15,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":11},{"id":"GO:0019383","count":10},{"id":"GO:0010760","count":10},{"id":"GO:0010241","count":10},{"id":"GO:0002933","count":10}]},{"hash":"1661221821895012209","title":"Vision-related neural signaling and locomotion","description":"The proteins are mainly linked to neural functions: light detection in visual perception, membrane hyperpolarization, and regulation of synaptic plasticity, plus adult locomotory behavior. These point to a cohesive theme of sensory processing and neuron-driven movement. Some other terms (proteolysis, granuloma formation, TNF regulation, sphingolipid biosynthesis) appear less central, suggesting annotation breadth or pleiotropy rather than a single core function. Overall, the dominant signal supports a neural signaling and visual perception theme.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900122","count":2},{"id":"GO:0031914","count":2},{"id":"GO:0060081","count":2},{"id":"GO:0008344","count":2},{"id":"GO:2001268","count":2}]},{"hash":"2076122178455124074","title":"DNA repair and genome maintenance","description":"The top terms point to DNA recombination and base-excision repair, plus endonucleolytic RNA processing, which together suggest a core function in genome maintenance and DNA damage response. Some other terms (corneocyte development, renal water transport, aging) appear in the set, possibly reflecting broader roles or annotation noise, but the dominant signal aligns with DNA repair and related cell-cycle processes.","confidence":"Medium","size":15,"edges":94,"triangles":325,"max_degree":14,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":7},{"id":"GO:0006284","count":7},{"id":"GO:0007568","count":6},{"id":"GO:0042493","count":6},{"id":"GO:0090502","count":5}]},{"hash":"1856415565346861425","title":"Unknown","description":"The GO terms for this cluster are highly diverse, spanning xenobiotic response, stem cell proliferation, sodium ion transport, reproduction (ovulation), and various metabolic and RNA processing processes (acetyl-CoA metabolism, thiamine biosynthesis, carbon fixation, methanogenesis, and spliceosome-mediated splicing). There isn\u2019t a single cohesive biological process or functional theme that ties all members together, suggesting the proteins participate in multiple, unrelated pathways. Because of this heterogeneity, a concise, representative label is not well-supported.","confidence":"","size":15,"edges":96,"triangles":347,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:2000648","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0001542","count":2},{"id":"GO:0006084","count":1}]},{"hash":"465121797283365771","title":"Cell stress response and cytoskeleton transport","description":"GO terms point to stress signaling (MAPK cascade, heat response, UV-A response) and active cytoskeletal transport (anterograde axonal transport, microtubule dynamics). Additional terms on proteostasis (protein stabilization, amyloid regulation) and lens development fit within a broader stress-maintenance framework. Together, this suggests a cluster centered on cellular stress responses linked to cytoskeletal transport and protein homeostasis rather than a single narrow function.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":1},{"id":"GO:0032387","count":1},{"id":"GO:0050821","count":1},{"id":"GO:1905907","count":1},{"id":"GO:0099641","count":1}]},{"hash":"388524129193987770","title":"ER-Golgi Secretory Pathway in Oogenesis and Development","description":"This cluster centers on proteins involved in ER-to-Golgi transport and Golgi organization (COPI coating, Golgi ribbon, ER lumen retention) and secretion-related processes like Wnt secretion, along with maternal/developmental roles (axis specification, placenta development, egg-laying). The common thread is the secretory pathway coordinating development via signaling and trafficking in oogenesis/maternal contexts, with a minor outlier term about aggression that does not override the core theme.","confidence":"Medium","size":15,"edges":81,"triangles":205,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0002121","count":2},{"id":"GO:0007311","count":2},{"id":"GO:0006888","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0001893","count":2}]},{"hash":"1116442184373772500","title":"ESCRT-Dependent Vesicle Formation and Trafficking","description":"The top GO terms cluster around ESCRT-mediated membrane remodeling, including MVB formation and sorting to the vacuole/lysosome, intralumenal vesicle formation, and viral budding via ESCRT, plus related processes like nuclear envelope reassembly and virus life cycle. This points to a cohesive theme of ESCRT-driven vesicle trafficking and endosomal sorting, with tubulin involvement and autophagy-related regulation as ancillary connections. ","confidence":"High","size":15,"edges":37,"triangles":41,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0043328","count":2},{"id":"GO:0031468","count":2},{"id":"GO:0039702","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2053992186190904760","title":"Ubiquitin-Dependent Proteolysis & ERAD","description":"The cluster is dominated by GO terms tied to ubiquitin-mediated protein degradation, including ubiquitin-dependent proteolysis, SCF-dependent proteasomal degradation, and the ER-associated degradation (ERAD) pathway, with specific references to K48-linked ubiquitination and autoubiquitination. This strongly points to a proteostasis/ubiquitin-proteasome system core. Some cell-cycle and DNA-damage terms are present, consistent with regulated proteolysis during replication and repair, while a cadmium-response term suggests stress-linked proteostasis changes. Overall, the most coherent theme is ubiquitin-dependent protein degradation and ERAD pathways.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0071276","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0031146","count":4}]},{"hash":"1216662849522933578","title":"Redox Detoxification and Oxidative Stress","description":"Explanation: The cluster is enriched for GO terms related to redox biology and detoxification: cellular oxidant detoxification, oxidation-reduction processes, and hydrogen peroxide\u2013related pathways, plus positive regulation of nitric oxide biosynthesis and oxidative-stress\u2013driven programmed cell death. While there are a few outliers (nitrate metabolism, sodium transport, acetylation, and hormone response), the dominant theme ties to redox balance and detox mechanisms.","confidence":"Medium","size":15,"edges":24,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0043602","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0045429","count":1}]},{"hash":"1145649651434342682","title":"Actin remodeling for migration and podosome assembly","description":"The top GO terms emphasize actin filament bundle assembly, podosome formation, cell migration, and related membrane remodeling processes, along with epithelial polarity. Together these point to a coherent theme of actin-driven cytoskeletal reorganization enabling cell movement and adhesion, with podosome assembly as a key feature; ancillary terms like bone development or brood size regulation may be pleiotropic or non-specific. Confidence in this theme is Moderate, given the strongest cues are actin/membrane\u2013driven motility processes. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0060348","count":3},{"id":"GO:0060378","count":3}]},{"hash":"1829896026321191251","title":"Cardiac and vascular development","description":"Based on the Top Terms, several entries point to heart and blood vessel formation, including coronary vasculature development, aorta development, ventricular septum development, and left/right symmetry determination, which together suggest a cardiovascular development focus. Other terms reflect general cellular processes (intracellular transport, receptor internalization) and immune/inflammatory signaling (granuloma formation, TNF regulation) that may accompany development or be general features of these proteins, but they do not redefine the main theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0033298","count":1},{"id":"GO:0060976","count":1},{"id":"GO:0035904","count":1},{"id":"GO:0099590","count":1}]},{"hash":"2191117132430956690","title":"Physical and chemical stimulus response","description":"The cluster shows multiple GO terms related to sensing or reacting to stimuli (thermoception, response to cold, cellular response to salicylic acid stimulus, response to muscle stretch), suggesting a general role in environmental and physical cue responses. Some terms are obsolete or less coherent with others, but the core theme is stimulus-response rather than a single pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0000083","count":2},{"id":"GO:0002268","count":2},{"id":"GO:0090501","count":2}]},{"hash":"2025729649430128956","title":"Proteostasis during mitosis","description":"This cluster is dominated by terms linking proteostasis and cell division: cell division and metaphase/anaphase transition point to mitosis, while unfolded protein response, chaperone activity, and peptidyl-prolyl isomerization suggest a focus on protein folding quality control during cell-cycle progression. Some terms are peripheral or obsolete, but the core theme ties proteostasis machinery to mitotic regulation. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:2000324","count":5},{"id":"GO:1903646","count":5},{"id":"GO:0000413","count":5},{"id":"GO:0006986","count":5}]},{"hash":"1836885899515858078","title":"Sensory Neuron Development and Ion Transport","description":"Based on the top GO terms, the cluster is strongly linked to sensory neuron development (fasciculation of sensory neuron axon, sensory perception of pain) and neuronal signaling via ion transport across the plasma membrane, with broader developmental terms appearing as ancillary context. This combination points to a neural development/signaling theme rather than a non-neural process.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0019233","count":4},{"id":"GO:0001893","count":3},{"id":"GO:0097623","count":3},{"id":"GO:0098719","count":3}]},{"hash":"864139998250823538","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0000398","count":12},{"id":"GO:0000393","count":11},{"id":"GO:0045944","count":11}]},{"hash":"1576067284264794816","title":"Unknown","description":"The GO terms span DNA replication/recombination, responses to xenobiotics and desiccation, calcium transport, otolith mineralization, and osmolyte biosynthesis, with no single unifying function linking the proteins. Because there are no interactions (edges) and the terms are heterogeneous, a coherent cluster label cannot be inferred.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0042220","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0006261","count":2},{"id":"GO:0090502","count":2}]},{"hash":"1673184650375794543","title":"Endosomal trafficking and vacuolar transport","description":"The top GO terms cluster around endosomal trafficking routes\u2014early endosome to late endosome, endosome to lysosome, and endosome to Golgi\u2014plus the Cvt pathway targeting to the vacuole and GTPase activity regulation, all pointing to vesicle transport through endosomal/vacuolar compartments. Some terms like mitotic cycle or transcription appear peripheral. This supports labeling the cluster as endosomal/vacuolar trafficking.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0060348","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0008333","count":2}]},{"hash":"820869005617630693","title":"Neuronal membrane trafficking and lipid biosynthesis","description":"The top GO terms emphasize brain development, GABAergic synaptic regulation, vesicle fusion, and ER membrane organization, all pointing to neuronal membrane trafficking and signaling, supported by phospholipid biosynthesis. While immune-related terms appear (granuloma formation, TNF regulation, neutrophil degranulation), the central pattern centers on neural development and membrane dynamics, including vesicle trafficking and lipid biosynthesis. This suggests a cohesive theme around neuronal membrane trafficking and ER/lipid processes.","confidence":"Medium","size":14,"edges":18,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0002432","count":1},{"id":"GO:1904468","count":1},{"id":"GO:0090153","count":1},{"id":"GO:0010793","count":1}]},{"hash":"1368107525099671952","title":"Unknown","description":"The proteins show a scattered mix of GO terms (oligomerization, TORC1 signaling regulation, thermoception/cold response, various developmental processes, pain, heart/spinal development, and chemokine production) with no shared pathway or cohesive function, and there are no edges connecting them. This lacks a unifying theme to name a specific cluster function.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:1904263","count":2},{"id":"GO:0050955","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1494294491425801132","title":"Retroviral replication and proviral latency","description":"Based on GO terms such as viral entry into the host nucleus, RNA-templated DNA synthesis (reverse transcription), DNA replication and integration, and establishment of integrated proviral latency, the cluster appears to center on the retroviral life cycle, including entry, genome replication, integration, and latency, with host RNAi involvement.","confidence":"High","size":14,"edges":84,"triangles":293,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0075732","count":6},{"id":"GO:1903704","count":6},{"id":"GO:0006278","count":6},{"id":"GO:0006310","count":6}]},{"hash":"1143473476436722609","title":"Unknown","description":"The GO terms are a disparate mix including thermoception, cold response, salicylic acid response, and various differentiation processes, plus several obsolete terms and transcription-related annotations. With no clear, unifying function or pathway and a sparse network (no triangles, few edges), there isn\u2019t a coherent theme to name this cluster beyond Unknown.","confidence":"","size":14,"edges":17,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":1},{"id":"GO:0035994","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0002268","count":1},{"id":"GO:0090501","count":1}]},{"hash":"1325471721158716190","title":"Ubiquitin-proteasome proteostasis and ERAD","description":"This cluster's top GO terms cluster around ubiquitin-dependent protein catabolic processes, including SCF-mediated degradation and polyubiquitination, as well as ER-associated degradation (ERAD). These reflect proteostasis maintenance through the ubiquitin-proteasome system. Additional terms indicate cadmium stress response and related signaling (glucose signaling, GTPase regulation, ribosome biogenesis) that can tie into cellular homeostasis and protein turnover. Taken together, the dominant theme is protein quality control via ubiquitin-proteasome pathways, with ancillary stress- and signaling-related processes.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0010255","count":3},{"id":"GO:0070208","count":3}]},{"hash":"972240764616172851","title":"Developmental transcriptional regulation and stress responses","description":"The terms cluster around DNA-templated transcription and development (forebrain and multicellular organism development), with concurrent hints of growth (ribosome biogenesis, mitotic cell cycle) and various stress responses (ER stress, cadmium, bacterial defense). This suggests a coherent theme of gene regulation during development coupled with cellular stress management.","confidence":"Medium","size":14,"edges":46,"triangles":84,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0001403","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0006349","count":4}]},{"hash":"1821429412619284972","title":"Steroid Hormone Biosynthesis and Mitochondrial Metabolism","description":"This cluster shows enrichment for androgen and testosterone biosynthesis and C21-steroid hormone metabolism, suggesting steroidogenic activity. It also includes GO terms for pyruvate import into mitochondria and acetyl-CoA biosynthesis from pyruvate, pointing to mitochondrial energy metabolism that supports biosynthetic pathways such as steroid production. Some terms appear obsolete or less related (e.g., methotrexate response, melanin biosynthesis), so the main cohesive theme is steroid hormone biosynthesis coupled with mitochondrial metabolism.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0061370","count":2},{"id":"GO:1902361","count":2},{"id":"GO:0035774","count":2}]},{"hash":"1168255232828395490","title":"Intracellular transport and signaling","description":"Enriched terms show clear emphasis on intracellular transport (ER-Golgi and late endosome-lysosome trafficking) together with multiple signaling pathways (Wnt, ROBO, NF-kappaB, interferon). The combination suggests a cluster of proteins coordinating vesicle traffic with signaling processes relevant to development and immune responses.","confidence":"Medium","size":14,"edges":21,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0035264","count":4},{"id":"GO:0055091","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0006878","count":3}]},{"hash":"1371639345710157912","title":"Ubiquitin-Dependent ERAD Proteolysis","description":"The cluster is dominated by GO terms for ubiquitin-dependent ERAD and ubiquitin-mediated protein catabolic processes, with negative regulation of ERAD also present. This points to a cohesive theme of proteostasis via ER-associated degradation, handling misfolded proteins and their degradation. Additional terms related to immune signaling or cell cycle appear less central, but do not override the main ERAD-centric signal.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0042098","count":2},{"id":"GO:0001782","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0031468","count":1}]},{"hash":"230363312731767393","title":"Amino acid and vitamin biosynthesis","description":"The cluster is dominated by biosynthetic GO terms for vitamins and amino acids (biotin biosynthesis, protoporphyrinogen IX biosynthesis, beta-alanine and lysine biosynthesis) and related catabolic processes, suggesting a core metabolic theme. Notch signaling and cellular insulin response appear as less-connected outliers rather than central functions.","confidence":"Medium","size":14,"edges":24,"triangles":8,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009102","count":8},{"id":"GO:0006782","count":8},{"id":"GO:0019878","count":8},{"id":"GO:0019551","count":6},{"id":"GO:0042853","count":5}]},{"hash":"2301880089552032422","title":"Estrogen-responsive transcription and nuclear export regulation","description":"This cluster centers on GO terms for DNA-templated transcription, estrogen response, and regulation of protein export from the nucleus, along with linked signaling (cAMP/cGMP) and developmental processes, plus proteasomal regulation. Together they suggest proteins involved in hormone-modulated transcriptional control with dynamic nuclear-cytoplasmic transport and protein turnover, rather than a single pathway. ","confidence":"Medium","size":14,"edges":23,"triangles":11,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0032436","count":2},{"id":"GO:0043627","count":2},{"id":"GO:0046827","count":2}]},{"hash":"2173182192644710809","title":"RNA Modification Enzymes","description":"The top GO terms are dominated by RNA modification activities: tRNA wobble uridine modification, tRNA methylation, and 7-methylguanosine mRNA capping, plus N-terminal peptidyl-alanine trimethylation, pointing to enzymes that modify RNA or protein termini. Additional terms about xenobiotic/cAMP signaling and redox homeostasis suggest broader cellular stress responses, but the core signal is RNA modification machinery.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042220","count":4},{"id":"GO:0002098","count":4},{"id":"GO:0030488","count":4},{"id":"GO:0035690","count":4},{"id":"GO:0007568","count":4}]},{"hash":"822921640724611730","title":"Nuclear RNA processing and DNA replication","description":"This cluster centers on nuclear functions: DNA-templated transcription, maturation of SSU-rRNA, RNA guanine-N7 methylation, Okazaki fragment processing in replication, and DNA damage checkpoint signaling. While a couple of terms (e.g., actin capping, fertilization) seem less related and may be noise, the dominant GO terms point to RNA processing and DNA replication/repair in the nucleus, justifying a label focused on those themes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0032933","count":1},{"id":"GO:0051016","count":1}]},{"hash":"1543018044105101901","title":"Neural development and axon guidance","description":"These terms cluster around neural development: axon growth/regeneration, axon fasciculation, and Wnt signaling, plus embryonic cranial morphogenesis; together they suggest neural development and axon guidance as the primary theme, with some supporting roles in signaling and cellular processing. ","confidence":"Medium","size":14,"edges":27,"triangles":17,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006939","count":4},{"id":"GO:0048680","count":4},{"id":"GO:0097155","count":3},{"id":"GO:0006935","count":3},{"id":"GO:0090153","count":3}]},{"hash":"1947029450645463066","title":"Intracellular lipid transport and insulin signaling","description":"This cluster centers on vesicle-mediated lipid trafficking between ER, Golgi, and post-Golgi compartments (sterol/ceramide/glycerolipid transport), coupled with lipid biosynthesis and regulation of triglyceride storage, plus a connection to insulin signaling pathways. The GO terms point to both transport and metabolism of lipids (sterols, ceramides, triglycerides) and regulation of insulin receptor signaling, suggesting a cohesive theme of intracellular lipid handling with metabolic regulation. Despite no direct interaction edges, the terms collectively describe a lipid-transport/metabolic regulatory program. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042147","count":2},{"id":"GO:0015918","count":1},{"id":"GO:0006892","count":1},{"id":"GO:0010891","count":1},{"id":"GO:2001275","count":1}]},{"hash":"478123807627059392","title":"Synaptic adhesion and plasticity signaling","description":"These proteins show strong representation of synaptic signaling and plasticity terms, including integrin-mediated signaling and substrate adhesion, glutamatergic transmission regulation, AMPA receptor activity, NMDA receptor clustering, and dendritic spine maintenance/long-term potentiation. This points to a role in synaptic adhesion, receptor trafficking, and activity-dependent spine remodeling.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":3},{"id":"GO:0034446","count":3},{"id":"GO:0097062","count":2},{"id":"GO:0051044","count":2},{"id":"GO:0051968","count":2}]},{"hash":"1431344192398139901","title":"Steroid and alkaloid metabolism","description":"Top GO terms indicate a core theme of small-molecule metabolism, including androgen metabolism, testosterone biosynthesis, terpenoid/alkaloid oxidation and lipid hydroxylation. While there are outlier terms related to immune regulation and cell cycle, the dominant signals support a metabolism-focused cluster.","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":3},{"id":"GO:0061370","count":3},{"id":"GO:0019383","count":2},{"id":"GO:0010760","count":2},{"id":"GO:0010241","count":2}]},{"hash":"16730025143555981","title":"Mitochondrial respiration and protein turnover","description":"This cluster shows strong enrichment for mitochondrial electron transport and aerobic respiration (e.g., mitochondrial electron transport, ubiquinol to cytochrome c, proton transmembrane transport) along with protein catabolic processes and ubiquitin recycling. This suggests a core theme of energy production combined with proteostasis, i.e., energy metabolism and protein turnover. Some terms like viral process or pheromone maturation appear as potential noise rather than core functions.","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0010815","count":7},{"id":"GO:0009060","count":7},{"id":"GO:0051289","count":7},{"id":"GO:0006122","count":6},{"id":"GO:0044257","count":6}]},{"hash":"670978438033741113","title":"Unknown","description":"The top GO terms cover very different biological processes (protein transport, mitochondrial inner membrane insertion, unfolded protein response, wing/eye development, NK cell regulation, ER-associated retrograde proteolysis, EGFR ligand maturation, spermatid differentiation, xenobiotic catabolism), each only once. There is no unifying function or pathway linking the proteins, and the network has no edges or cohesive modules to suggest a shared role. Therefore, a meaningful, specific label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":1},{"id":"GO:0032979","count":1},{"id":"GO:0034620","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0032815","count":1}]},{"hash":"2283449563740820349","title":"DNA Replication and Repair","description":"This cluster is driven by core DNA maintenance functions, with GO terms for DNA replication and DNA repair appearing twice each, suggesting proteins involved in genome maintenance. The other terms are sporadic or inconsistent across species (e.g., plant brassinosteroid signaling, Schwann cell development), likely representing annotation noise rather than a coherent alternate theme. Overall, the dominant, high-frequency DNA maintenance terms support labeling this cluster as DNA Replication and Repair.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0046079","count":1},{"id":"GO:0051343","count":1},{"id":"GO:0042220","count":1}]},{"hash":"1215764784904209945","title":"Cilium assembly and cell cycle regulation","description":"The cluster centers on ciliogenesis and centrosome-related processes, as shown by terms for intraciliary transport, regulation of cilium assembly, and centrosome localization, aligned with mitotic cell cycle terms (cell division, cell cycle, spindle assembly checkpoint). The presence of left-right symmetry determination further supports a ciliary role in developmental patterning, while ER-to-Golgi transport and autophagosome maturation may reflect broader membrane trafficking and cellular housekeeping linked to these core processes. Confidence: Medium","confidence":"","size":13,"edges":19,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0035735","count":1}]},{"hash":"1980123662547161884","title":"Ubiquitin-Proteasome Turnover","description":"The top terms show several ubiquitin-related processes (K11- and K63-linked deubiquitination) and deneddylation, plus proteasome storage granule assembly, which together point to regulation of protein turnover and ubiquitin-like modifications. A few other terms (spliceosome dynamics, peroxisome fission, viral translation initiation) are less clearly connected, but the dominant theme appears to be protein modification and degradation control. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0000393","count":1},{"id":"GO:0070537","count":1},{"id":"GO:0048140","count":1},{"id":"GO:0000338","count":1}]},{"hash":"708312477367580151","title":"ER stress and innate immune response","description":"This cluster prominently features GO terms tied to endoplasmic reticulum stress responses (ER stress, translation initiation in ER stress, ERAD-related processes) and related mitochondrial inner membrane protein insertion, along with innate immune activities (innate immune response, negative regulation of antiviral defense). Although a few terms are obsolete or less specific, the recurring theme is cellular stress management at the ER/mitochondria with immune signaling; thus the label reflects the dominant function represented among these proteins.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0090526","count":3},{"id":"GO:0033132","count":2},{"id":"GO:0030433","count":2}]},{"hash":"452578118251870779","title":"Neural development and axon guidance signaling","description":"The top GO terms point strongly to neural development and guidance processes (substantia nigra development, axon guidance) and related signaling pathways (Wnt, Roundabout/ROBO) with associated trafficking (endocytic recycling). While there are outliers related to immune signaling and keratinization, the dominant theme across terms centers on neuronal development and guidance, supported by signaling and trafficking activities.","confidence":"Medium","size":13,"edges":32,"triangles":31,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":12},{"id":"GO:0008283","count":11},{"id":"GO:0055091","count":9},{"id":"GO:0090263","count":9},{"id":"GO:0031424","count":9}]},{"hash":"1656563415382049666","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":3},{"id":"GO:0090200","count":1},{"id":"GO:1903638","count":1},{"id":"GO:0071560","count":1},{"id":"GO:1903645","count":1}]},{"hash":"779421997102947576","title":"Cardiac Muscle Contraction and Heart Development","description":"Several top GO terms directly relate to heart biology: regulation of cardiac muscle contraction, negative regulation of the force of heart contraction by chemical signal, negative regulation of cardiac muscle hypertrophy, and positive regulation of cardiac muscle contraction, plus secondary heart field specification, which points to heart development. A few terms (opsin signaling, mismatch repair, chromatid cohesion) are less related, suggesting this cluster combines primarily cardiac function signals with some unrelated annotations. Overall, the dominant theme is cardiac muscle regulation and development, supporting this label.","confidence":"Medium","size":13,"edges":14,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0022400","count":1},{"id":"GO:0070602","count":1},{"id":"GO:0045988","count":1},{"id":"GO:0010614","count":1},{"id":"GO:0060452","count":1}]},{"hash":"2084142513018018708","title":"Adaptive immune cell differentiation and signaling","description":"The terms cluster around adaptive immunity, with NK T cell differentiation, B cell affinity maturation, IL-7 response, IL-4 production, and hemopoiesis, suggesting involvement in lymphoid development and cytokine signaling; other terms reflect transcriptional regulation and general signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0001865","count":2}]},{"hash":"1563183430127727979","title":"Integrin-Mediated Adhesion Signaling","description":"The top GO terms cluster around cell adhesion, integrin-mediated signaling, and interactions with the extracellular matrix (e.g., cell-matrix adhesion, substrate adhesion-dependent spreading, heterotypic cell-cell adhesion, platelet aggregation). Additional terms point to development-related processes like mesodermal differentiation and osteoblast proliferation, which often involve adhesion and signaling pathways. A few terms about lipid transport are less central, but do not override the adhesion-focused theme.","confidence":"High","size":13,"edges":32,"triangles":25,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:0032369","count":2},{"id":"GO:0048333","count":2},{"id":"GO:0045715","count":2},{"id":"GO:0034446","count":2}]},{"hash":"1772106068391710402","title":"Translation Initiation and TORC1 Signaling","description":"GO terms cluster around translation initiation (formation of translation preinitiation complex, translation reinitiation) and mRNA stabilization, with TORC1 signaling and multicellular growth pointing to nutrient-responsive growth control. A few terms (spinal cord development, bacterial biosynthesis) seem unrelated noise, but the dominant theme is translation regulation and TORC1-driven growth.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1039216789772225947","title":"ER Protein Folding and UPR Signaling","description":"This cluster is dominated by ER-associated protein folding terms (ER chaperones, unfolded protein response) and translation regulation in response to ER stress, with notes on redox homeostasis and hydrogen peroxide signaling. Together these indicate an ER stress response module, likely in plants given the cytokinin signaling term, linking chaperone activity, UPR, and redox regulation.","confidence":"High","size":13,"edges":19,"triangles":3,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034975","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0070389","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0036494","count":5}]},{"hash":"1278356735676826253","title":"Nucleocytoplasmic transport and ribosome export","description":"The top GO terms cluster around nuclear import/export processes: ribosomal subunit export from the nucleus, mRNA transport, and NLS-bearing protein import into the nucleus, plus an indication of Ran GTPase\u2013related regulation (GO:0043547). These point to nucleocytoplasmic trafficking, particularly of ribosomal components and RNAs. Additional terms on protein import, proteasome assembly, and protein turnover during cell division hint at coordination between transport, ribosome biogenesis, and cell-cycle\u2013related proteostasis. Overall, the proteins seem tied to shuttling cargo between nucleus and cytoplasm, with a focus on ribosome-related export and associated regulation. ","confidence":"High","size":13,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000055","count":3},{"id":"GO:0071230","count":3},{"id":"GO:0000056","count":3},{"id":"GO:0051301","count":3}]},{"hash":"969335724135246164","title":"Cardiac signaling and contraction regulation","description":"This cluster is driven by GO terms pointing to intracellular signal transduction and, importantly, regulation of cardiac muscle contraction and hypertrophy, implying a group of proteins involved in heart signaling and contraction control. Presence of tachykinin receptor signaling and opsin-mediated signaling suggests broader GPCR-based signaling themes, while a few terms (e.g., centromeric cohesion, forebrain neuron fate) are less central and may reflect broader annotation. Overall, the dominant theme is cardiac muscle signaling and contraction regulation.","confidence":"Medium","size":13,"edges":9,"triangles":0,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035556","count":7},{"id":"GO:0022400","count":5},{"id":"GO:0070602","count":5},{"id":"GO:0045988","count":5},{"id":"GO:0010614","count":5}]},{"hash":"1515981159958821233","title":"Cyclic nucleotide signaling and transcription regulation","description":"This cluster shows several GO terms tied to cyclic nucleotide signaling: cellular response to cAMP, forskolin, and receptor guanylyl cyclase signaling. The presence of DNA-templated transcription terms suggests a downstream transcriptional response linked to these signaling events. Some terms like T cell homeostasis and epithelial morphogenesis are broader annotations that may reflect annotations to pleiotropic proteins. Overall, the common theme appears to be signaling through cyclic nucleotides with accompanying transcriptional regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1902303","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0043029","count":2},{"id":"GO:1903244","count":2}]},{"hash":"1023596179719022330","title":"Drosophila oogenesis and imaginal disc development","description":"The terms point to developmental processes in Drosophila, especially oogenesis (fusome organization, oocyte nucleus migration, eggshell patterning) and imaginal disc growth, with additional notes on cortical microtubule organization and centrosome separation, and a hint of neural development (mushroom body). This suggests a broader, insect-development theme rather than a single pathway, so the label reflects a coherent but broad developmental cluster. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016319","count":1},{"id":"GO:0035957","count":1},{"id":"GO:0045572","count":1},{"id":"GO:0030723","count":1},{"id":"GO:0030381","count":1}]},{"hash":"1749484971765961976","title":"Unknown","description":"The listed GO terms cover transcription, pheromone signaling, germline development, olfactory organization, calcium-mediated muscle regulation, and mitophagy, with no single dominant function linking all proteins. Because there is no cohesive theme or pathway across the cluster, an Unknown label with no confident biological interpretation is appropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0046020","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0030708","count":1},{"id":"GO:0021629","count":1}]},{"hash":"567105594736457149","title":"Central metabolism and redox homeostasis","description":"This cluster is enriched for glycolysis, gluconeogenesis, and amino-acid catabolic processes (leucine, lysine), along with redox-related functions (superoxide removal, redox homeostasis) and malonyl-CoA biosynthesis, suggesting a group of proteins involved in core carbon metabolism and cellular redox balance, with some housekeeping roles indicated by translation and ion transport signals.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0019430","count":2},{"id":"GO:0045454","count":2}]},{"hash":"57590120862780730","title":"Innate Immune Signaling and Inflammation","description":"The cluster shows strong signals for innate immune responses, including dsRNA and LPS-related signaling, defense against bacteria, and interferon-beta production, indicating a core theme of innate immune activation. Some terms suggest neural-immune interactions (dopamine-related cellular response and synapse regulation), but the dominant pattern is innate immune signaling and inflammatory responses.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0061368","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0043330","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0031663","count":2}]},{"hash":"1929886718231131473","title":"Cytoskeletal Dynamics and Organelle Trafficking","description":"This cluster centers on cytoskeletal regulation (actin nucleation) and intracellular transport processes (mitochondrial distribution/inheritance, endocytic recycling, vesicle trafficking), with related signaling contexts (ephrin signaling, GABAergic transmission, heart contraction). The common theme is cytoskeleton-driven trafficking and associated signaling events.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045010","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1903526","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0048013","count":2}]},{"hash":"895805976551466541","title":"Unknown","description":"The GO terms span oxidative stress, inflammatory response, DNA damage repair, cytoskeleton remodeling, cell migration, RNA modification, and metabolism/development. There is no single clear function tying all terms together, making a reliable, cohesive label inappropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0006954","count":2},{"id":"GO:0006284","count":2}]},{"hash":"1324030431411919025","title":"Unknown","description":"The GO terms span DNA replication, ER-to-Golgi transport, signaling pathways, developmental processes, and even obsolete annotations across species, with no clear unifying function for the cluster.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0051343","count":1},{"id":"GO:0042220","count":1},{"id":"GO:0014044","count":1}]},{"hash":"1775758420857006402","title":"Lipid Biosynthesis and Remodeling","description":"The prominent lipid-related GO terms (CDP-diacylglycerol biosynthesis, phosphatidylcholine remodeling, triglyceride biosynthesis, and negative regulation of PC biosynthesis) suggest a lipid metabolism theme for this cluster, while other single-term annotations point to diverse areas such as immune signaling and development, which may be incidental.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016024","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0021587","count":1},{"id":"GO:0070236","count":1},{"id":"GO:0036151","count":1}]},{"hash":"1813620571194066162","title":"Innate antiviral defense","description":"Top GO terms show recurring innate immune response and defense against virus, suggesting the core function is antiviral innate immunity; other singular terms (apoptosis-related mitochondrial changes, vesicle trafficking, ion channel regulation, and muscle-related processes) appear peripheral, possibly due to multifunctional proteins or annotation noise, but do not define a cohesive alternative theme. Therefore, the label reflects the strongest shared function among the cluster\u2019s terms.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0070072","count":1},{"id":"GO:0043653","count":1},{"id":"GO:1903423","count":1}]},{"hash":"1297734919171524763","title":"DNA Damage Response and Meiotic Checkpoint","description":"The prominent GO terms point to genome integrity maintenance, with multiple entries for meiotic recombination (reciprocal meiotic recombination, meiotic recombination checkpoint signaling) and DNA damage signaling (DNA damage checkpoint signaling, cellular response to ionizing radiation). This suggests a cohesive function in DNA damage response and meiotic regulation, despite a few unrelated annotations that may reflect noise or broad roles of some proteins.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007131","count":1},{"id":"GO:0071479","count":1},{"id":"GO:0000077","count":1},{"id":"GO:0021762","count":1},{"id":"GO:0090305","count":1}]},{"hash":"1980202117955418391","title":"Ribosome Biogenesis and Protein Turnover","description":"The dominant terms point to ribosome biogenesis (including rRNA processing) and ubiquitin-proteasome\u2013dependent protein degradation, suggesting a shared theme of ribosome assembly coupled with proteostasis. While there are some unrelated developmental and trafficking terms, the core cluster appears centered on nucleolar ribosome production and ubiquitin-mediated protein quality control, potentially under stress (cadmium). Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0007369","count":3},{"id":"GO:0007338","count":3},{"id":"GO:0006888","count":3}]},{"hash":"774838994744611096","title":"ER-Golgi to plasma membrane trafficking","description":"The top GO terms are dominated by vesicle transport from the ER to the Golgi and from the Golgi to the plasma membrane, indicating a core role in the secretory pathway and membrane trafficking. Additional terms touch on cytoskeletal (tubulin complex assembly) and polarity establishment, supporting coordinated trafficking with cell polarity. Some development-related terms (kidney, bipolar cell growth) may reflect tissue-specific contexts, but the shared theme across the cluster is ER\u2013Golgi\u2013plasma membrane trafficking. ","confidence":"High","size":12,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051519","count":1},{"id":"GO:0021943","count":1},{"id":"GO:0051301","count":1}]},{"hash":"2034850548900144522","title":"Microtubule dynamics in cell division and neuron maintenance","description":"The cluster shows strong enrichment for spindle assembly and microtubule-related processes (meiotic spindle orientation, microtubule-kinetochore attachment, centrosome separation, cytokinesis) together with terms on neuron projection maintenance and cerebellar Purkinje cell layer organization, indicating a shared theme of microtubule-based cytoskeletal regulation in both dividing cells and neurons.","confidence":"High","size":12,"edges":30,"triangles":28,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051296","count":9},{"id":"GO:0099607","count":9},{"id":"GO:0000911","count":9},{"id":"GO:0036334","count":9},{"id":"GO:0032886","count":9}]},{"hash":"1282647714453418870","title":"Cell cycle control and chromatin remodeling","description":"The top GO terms cluster around G1 DNA damage response, Okazaki fragment processing in mitosis, and histone modification (acetylation/deacetylation), pointing to nuclear processes that regulate replication and chromatin state. Some terms (SREBP signaling, ER-Golgi transport, tissue-specific growth) are peripheral, suggesting the cluster mainly reflects cell cycle and chromatin regulation with a few outliers.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032933","count":7},{"id":"GO:0060770","count":7},{"id":"GO:0072432","count":7},{"id":"GO:1903461","count":7},{"id":"GO:0043984","count":7}]},{"hash":"751790552528592657","title":"Calcium signaling and synaptic plasticity","description":"The dominant GO terms cluster around calcium signaling and synaptic function: regulation of voltage-gated calcium channels, cellular response to calcium, long-term potentiation, and neurotransmitter secretion. This points to calcium-dependent neuronal signaling and synaptic plasticity as the shared theme; other terms like VEGF signaling, ABA signaling, and mitotic cell cycle may reflect broader cross-talk but do not redefine the core function of the cluster.","confidence":"High","size":12,"edges":54,"triangles":128,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":10},{"id":"GO:0036324","count":6},{"id":"GO:1901387","count":6},{"id":"GO:0060291","count":6},{"id":"GO:0009738","count":6}]},{"hash":"2119310062318093688","title":"Spindle orientation and microtubule dynamics","description":"This cluster is enriched for mitotic spindle orientation, kinetochore attachments, centrosome separation, and regulation of microtubule-based processes, indicating a common theme of cytoskeletal control in cell division and structural organization. Additional terms relating to development and neural architecture align with microtubule-dependent morphogenesis across tissues.","confidence":"High","size":12,"edges":41,"triangles":68,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051296","count":10},{"id":"GO:0099607","count":10},{"id":"GO:0000911","count":10},{"id":"GO:0036334","count":10},{"id":"GO:0032886","count":10}]},{"hash":"736355620087171295","title":"Terpenoid, alkaloid, and steroid metabolism","description":"This cluster centers on GO terms for camphor catabolic, kaurene oxidation, isoquinoline alkaloid metabolism, carbazole catabolic, and cortisol biosynthetic processes, all pointing to oxidation-linked metabolism of terpenoids, alkaloids, and steroids. Additional terms like lipid hydroxylation and metal ion\u2013responsive cellular processes suggest broad enzymatic oxidation and detoxification roles, making a cohesive label around diverse xenobiotic and steroid metabolism. Confidence: Medium","confidence":"Medium","size":12,"edges":19,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":3},{"id":"GO:0010760","count":3},{"id":"GO:0010241","count":3},{"id":"GO:0002933","count":3},{"id":"GO:1900087","count":3}]},{"hash":"12918672868141979","title":"Preribosome assembly and rRNA maturation","description":"The top GO terms are dominated by LSU rRNA maturation from tricistronic transcripts, assembly of the large subunit preribosome, and ITS1 processing, which together define ribosome biogenesis and preribosome maturation. Other terms related to transcription and DNA processes appear less central to the cluster\u2019s core function. This supports labeling the cluster as involved in ribosome biogenesis, specifically large subunit assembly and rRNA processing.","confidence":"High","size":12,"edges":12,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0018144","count":2}]},{"hash":"2143647028644258509","title":"ER stress response and ERAD/ubiquitin signaling","description":"This cluster\u2019s top GO terms heavily emphasize endoplasmic reticulum (ER) stress\u2013driven processes: intrinsic apoptotic signaling in response to ER stress, ER-associated degradation (ERAD) via ubiquitination, ER-to-Golgi vesicle transport, and unfolded protein\u2013related maintenance. Additional terms for protein phosphorylation and interferon signaling support a broader regulatory context around ER quality control and downstream signaling. Together, these suggest a cohesive theme of ER stress response and protein quality control pathways.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1762094842107442894","title":"Organelle Protein Import and Ubiquitin-Dependent Degradation","description":"The top GO terms center on importing proteins into mitochondria and chloroplasts, inserting proteins into the mitochondrial inner membrane, and ubiquitin-dependent catabolic processes including ubiquitin recycling and vacuole/MVB-mediated degradation. This points to a cohesive theme of protein targeting to organelles and coordinated turnover via ubiquitin-proteasome and related pathways, with a few outliers like response to food that are less central.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0045037","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0032094","count":2},{"id":"GO:0045039","count":2}]},{"hash":"1925502309438378777","title":"Cell-cycle control and stress-immune signaling","description":"This cluster centers on cell-cycle regulation (cell division, mitotic control) and includes stress- and immune-related terms (innate immune response, UV-A response, ER-stress\u2013related translation), with supporting RNA processing/chromatin terms (snoRNP assembly, histone modification). The mix suggests a module where cell-cycle processes intersect with cellular stress responses and antiviral signaling, rather than a single, narrow function.","confidence":"Medium","size":12,"edges":28,"triangles":15,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0071492","count":3},{"id":"GO:0045070","count":3},{"id":"GO:0036494","count":3},{"id":"GO:0050689","count":3}]},{"hash":"1866074893357695634","title":"Developmental signaling and morphogenesis","description":"The top GO terms cluster around development and morphogenesis, including embryonic cranial skeleton morphogenesis, multicellular organism development, and Wnt signaling, along with neural development cues like axon fasciculation and chemotaxis. While lipid metabolism and Golgi transport terms appear, the dominant signal points to signaling pathways that guide development and tissue patterning.","confidence":"Medium","size":12,"edges":34,"triangles":51,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0097155","count":12},{"id":"GO:0006935","count":12},{"id":"GO:0090153","count":12},{"id":"GO:0071374","count":12},{"id":"GO:0042997","count":12}]},{"hash":"794442019173733554","title":"Vitamin K biosynthesis and energy metabolism","description":"The cluster centers on biosynthetic processes for phylloquinone (vitamin K1) and menaquinone (vitamin K2), indicating vitamin K pathways. It also includes multiple catabolic and energy-related processes (fatty acid beta-oxidation, valine and phenylacetate catabolism, ketone body biosynthesis, and response to starvation), suggesting a broader metabolic/energy-generation theme. A few GO terms about development appear to be incidental. Taken together, the proteins seem tied to vitamin K biosynthesis coupled with energy metabolism, justifying the label.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0006635","count":9},{"id":"GO:0006574","count":8},{"id":"GO:0010124","count":8},{"id":"GO:0042372","count":8}]},{"hash":"212206238426755740","title":"ER Stress, Protein Folding, and Oxidative Stress Response","description":"Top terms show ER stress response and ER protein folding, plus oxidative stress response and detoxification, suggesting a module focused on managing misfolded proteins in the ER and protecting against oxidative damage; a few transcription-related terms imply regulation of gene expression under stress, reinforcing a cohesive stress-response cluster despite no network edges.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034976","count":2},{"id":"GO:0046826","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0006351","count":1}]},{"hash":"104263722291088114","title":"RNA processing and translation regulation","description":"This cluster is dominated by translation (GO:0006412) and several RNA-processing terms (RNA splicing, intron splicing, rRNA maturation, RNA folding), suggesting a cohesive role in RNA metabolism and protein synthesis control. A few signaling-related terms are present but less represented, indicating the main theme is RNA processing and translation.","confidence":"Medium","size":12,"edges":18,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0033120","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0000372","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1172029588407115728","title":"Cell Division and RNA Surveillance","description":"The top GO terms show strong representation for mitotic cell cycle and cell division, indicating a proliferative role. At the same time, terms related to RNA quality control and ribosome turnover (non-stop decay, nonfunctional rRNA decay, RNA surveillance, ribosome disassembly) suggest involvement in translation-associated quality control and RNA metabolism, with additional hints of nutrient response and cilium assembly. Overall, this cluster appears to coordinate cell proliferation with RNA and ribosome quality control processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0070481","count":2},{"id":"GO:0070651","count":2},{"id":"GO:0008283","count":2}]},{"hash":"2305788275029298750","title":"Nuclear transcription and stress-response proteins","description":"This cluster features GO terms tied to nuclear roles (DNA-templated transcription, nuclear pore localization) and cellular stress responses (response to xenobiotic stimulus, cellular response to hydrogen peroxide), with a couple transport terms (molybdate, taurine) that don\u2019t strongly redefine the theme. The strongest common thread is nuclear involvement in gene expression alongside general stress signaling, suggesting proteins that participate in transcription regulation and stress responses rather than a single unified pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0031081","count":2},{"id":"GO:0007568","count":2}]},{"hash":"158004259641915296","title":"Neural development and axon guidance","description":"The cluster shows strong representation of neural and developmental processes, including fasciculation of sensory neuron axons (GO:0097155) and regulation of Wnt signaling (GO:0090263), along with embryonic cranial skeleton morphogenesis (GO:0048701) and multicellular organism development (GO:0007275). These terms point to proteins involved in neural development and axon guidance as a cohesive theme. Additional terms touching lipid biosynthesis regulation and Golgi-to-plasma membrane transport suggest supporting roles in membrane dynamics and protein processing, but do not override the central neural development signal. Confidence: Medium","confidence":"","size":12,"edges":18,"triangles":5,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0097155","count":12},{"id":"GO:0006935","count":12},{"id":"GO:0090153","count":12},{"id":"GO:0071374","count":12},{"id":"GO:0042997","count":12}]},{"hash":"802024543958666741","title":"Unknown","description":"The terms span immune/inflammatory processes (granuloma formation, TNF regulation, neutrophil degranulation) as well as membrane trafficking and autophagy (ER membrane organization, vesicle fusion, ribophagy) and lipid metabolism (sphingolipid and phosphatidylethanolamine biosynthesis). With only single-term annotations and no dominant shared function, there is no clear, cohesive theme to assign a more specific label.","confidence":"","size":12,"edges":11,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002432","count":1},{"id":"GO:1904468","count":1},{"id":"GO:0090153","count":1},{"id":"GO:0010793","count":1},{"id":"GO:0032228","count":1}]},{"hash":"482952743290332640","title":"GPCR Signaling Components","description":"This cluster is dominated by terms for intracellular signal transduction and regulation of G protein-coupled receptor signaling, including GPCR pathway regulation and G-protein cycles. The presence of diverse developmental and signaling contexts likely reflects broad GPCR-mediated signaling roles across processes and organisms.","confidence":"Medium","size":12,"edges":22,"triangles":12,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":1},{"id":"GO:0071870","count":1},{"id":"GO:0000750","count":1},{"id":"GO:0072513","count":1},{"id":"GO:0048527","count":1}]},{"hash":"390418316996366481","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":2},{"id":"GO:0010019","count":2},{"id":"GO:1900865","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0090617","count":2}]},{"hash":"71530184071413532","title":"Unknown","description":"The top GO terms cover a wide range of functions\u2014from gut epithelium maintenance and hearing to L-arabinose metabolism, coagulation, locomotion, BMP signaling regulation, junction assembly, angiogenesis, and otolith tethering\u2014without a unifying biological theme. While BMP pathway regulation and junction-associated terms hint at developmental or tissue organization roles, the diverse set prevents a single cohesive label. Therefore, Unknown with None confidence. ","confidence":"","size":12,"edges":32,"triangles":56,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030277","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0046373","count":3},{"id":"GO:0042381","count":3},{"id":"GO:0008344","count":3}]},{"hash":"2054013908666756997","title":"RNA Splicing and mRNA Processing Regulation","description":"The dominant GO terms point to spliceosome-mediated RNA processing (cis and alternative splicing) and related post-transcriptional controls such as poly(A) tail regulation and ncRNA-mediated gene silencing, indicating a cluster focused on RNA processing and splicing regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048873","count":2},{"id":"GO:1902499","count":2},{"id":"GO:0048025","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0000380","count":1}]},{"hash":"2215306280220034633","title":"ESCRT/MVB Vesicle Trafficking and Degradation","description":"The top GO terms cluster around ESCRT-mediated trafficking, including MVB sorting, intralumenal vesicle formation, and MVB-lysosome fusion, along with ubiquitin-dependent degradation; related terms like nuclear membrane reassembly and viral budding also rely on ESCRT. This points to a cohesive function in endosomal sorting and lysosomal degradation, with some broader ESCRT-associated roles.","confidence":"High","size":11,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043328","count":4},{"id":"GO:0031468","count":4},{"id":"GO:0039702","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0070676","count":4}]},{"hash":"882248930748869729","title":"Neuronal signaling and development","description":"The cluster includes terms centered on neuronal signaling and development, such as glutamate receptor signaling, forebrain neuron development, vesicle fusion, cellular response to electrical stimulus, and sensory perception of taste, indicating a shared function in neuronal communication and maturation. A few terms (cell cycle, pseudohyphal growth, gibberellin signaling) seem less related and may reflect noise or broader functional associations, but the neuronal-related terms provide a coherent theme.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0007124","count":1},{"id":"GO:0007215","count":1},{"id":"GO:1904322","count":1},{"id":"GO:0050916","count":1}]},{"hash":"1050147578620663196","title":"Nucleolar transcription and ribosome export","description":"The strongest signals are ribosomal large subunit export from the nucleus and positive regulation of nucleolar rRNA transcription by RNA Pol I, together with chromatin-associated processes such as establishment of protein localization to chromatin and histone modification regulation. While a couple of terms hint at cytoskeletal assembly, the core theme centers on nucleolar function, ribosome biogenesis, and chromatin regulation, suggesting a cluster tied to nuclear/chromosome-associated ribosome production rather than cytoskeletal structures.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0051764","count":2},{"id":"GO:1902896","count":2},{"id":"GO:2000617","count":1},{"id":"GO:0070286","count":1}]},{"hash":"1981789705830635482","title":"Synaptic organization and receptor trafficking","description":"Most GO terms cluster around neuronal synapses: regulation of NMDA receptor activity, dendritic spine maintenance, and postsynaptic density organization, together with receptor-mediated endocytosis and Golgi-to-plasma membrane transport that supports synaptic receptor trafficking. Although there are a couple of outliers (sarcomere organization, defense response to fungus), the predominant theme is synaptic structure and function and associated trafficking processes.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904783","count":1},{"id":"GO:1902951","count":1},{"id":"GO:0050832","count":1},{"id":"GO:1905875","count":1},{"id":"GO:0043001","count":1}]},{"hash":"1176220303116700104","title":"Carbon-source dependent transcription regulation","description":"The top GO terms point to DNA-templated transcription and regulation of transcription from RNA polymerase II in response to nonfermentable carbon sources, along with links to cellular respiration and gluconeogenesis. This pattern suggests a cluster of proteins involved in transcriptional control that adjusts metabolic gene expression according to carbon source, tying transcription to respiration and metabolic flux.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0061415","count":5},{"id":"GO:0043457","count":5},{"id":"GO:0035948","count":5},{"id":"GO:0045122","count":5}]},{"hash":"1308920630395457879","title":"Nucleolar transcription and ribosome biogenesis","description":"The cluster\u2019s top GO terms cluster around transcription initiation by RNA polymerases I, II, and III, including tRNA transcription and nucleolar rRNA transcription, along with ribosome biogenesis. This points to a coherent theme of nucleolar transcription activity driving ribosome assembly, with one outlier term likely noise. Confidence: High","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001023","count":1},{"id":"GO:0060213","count":1},{"id":"GO:0045948","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0010590","count":1}]},{"hash":"1410612690683857848","title":"Synaptic signaling and vesicle exocytosis regulation","description":"The top GO terms are dominated by neuronal synaptic functions\u2014regulation of synaptic vesicle exocytosis and long-term potentiation\u2014supported by phosphatidylinositol signaling and protein processing. While a few terms reference other contexts (plant ABA signaling, myoblast fusion), the strongest and most cohesive signal is synaptic communication and vesicle trafficking, justifying a label centered on neuronal signaling and vesicle exocytosis regulation.","confidence":"Medium","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":4},{"id":"GO:0010796","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0036324","count":3},{"id":"GO:0060291","count":3}]},{"hash":"656478658625441146","title":"Cofactor biosynthesis and DNA repair","description":"This cluster is driven by two prominent biosynthetic terms: molybdopterin cofactor biosynthesis and menaquinone biosynthesis, suggesting involvement in cofactors essential for metabolism. The presence of DNA repair terms (interstrand cross-link repair and recombinational repair) also supports a link to genome maintenance. While other terms like translation and iron homeostasis appear, the combination of cofactor biosynthesis with repair processes provides a cohesive, albeit broad, functional theme.","confidence":"Medium","size":11,"edges":40,"triangles":67,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0046632","count":1},{"id":"GO:0000733","count":1}]},{"hash":"1151082177223400414","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035975","count":1},{"id":"GO:0019546","count":1},{"id":"GO:0009088","count":1},{"id":"GO:0009090","count":1},{"id":"GO:0044210","count":1}]},{"hash":"2020710555879286605","title":"Unknown","description":"The top GO terms are a scattered mix across biosynthetic processes (some plant-specific), transcription, various metabolic processes, and even a proprioception term, with no clear, unifying function. Obsolete terms and diverse contexts suggest these proteins do not share a coherent pathway or cellular role, so a meaningful, specific label cannot be inferred.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009718","count":1},{"id":"GO:0009242","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006541","count":1}]},{"hash":"766054501671149324","title":"Polyamine and Protein Acetylation","description":"The cluster shows a recurring emphasis on acetylation-related processes: peptidyl-lysine N6-acetylation, and acetylation of putrescine and spermidine, along with spermine catabolic activity. This suggests a cohesive theme around acetylation regulation intertwined with polyamine metabolism. The presence of other unrelated terms (e.g., mycothiol biosynthesis, melatonin and arginine biosynthesis, chromatin-related processes) indicates broader metabolic and regulatory roles, so the connection is plausible but not exclusive. ","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0046208","count":10},{"id":"GO:0018003","count":10},{"id":"GO:0010125","count":10},{"id":"GO:0071962","count":10},{"id":"GO:0032920","count":10}]},{"hash":"959290100630988765","title":"Ubiquitin-Proteasome Degradation","description":"These proteins are enriched for ubiquitin-dependent proteolysis and related processes (ubiquitination, SCF-dependent proteasomal degradation, glycoprotein catabolism). This points to a cohesive theme around the ubiquitin-proteasome system governing protein turnover. Some development- or obsolete-term annotations appear incidental and not representative of the core function.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0000209","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0030433","count":3}]},{"hash":"1551793475991321515","title":"Phospholipid Biosynthesis and Lipid Mediator Production","description":"Dominant GO terms are about biosynthesis of phospholipids (phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine) and related lipid signaling (platelet activating factor), with some regulatory signals related to phospholipid pathways. Minor terms touch on cell-cycle and hematopoiesis but do not define the cluster, so the core theme is phospholipid biosynthesis and lipid signaling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010512","count":2},{"id":"GO:1905711","count":2},{"id":"GO:0006655","count":2},{"id":"GO:0006659","count":2},{"id":"GO:0070317","count":2}]},{"hash":"1945291832186627884","title":"Amino acid and small-molecule transport cluster","description":"Most terms point to transport processes: amino acid transmembrane transport (e.g., methionine, general amino acids), various nutrient transports (thiamine, molybdate), xenobiotic/export of compounds, and even a secretion system term tied to export. While there are outliers (antigen processing, long-chain fatty acid catabolism), the dominant theme is transport/export of nutrients and small molecules, justifying this label.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015689","count":1},{"id":"GO:0015734","count":1},{"id":"GO:0046618","count":1},{"id":"GO:0042760","count":1},{"id":"GO:0030253","count":1}]},{"hash":"2280482320234665907","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":2},{"id":"GO:1902187","count":2},{"id":"GO:0061158","count":2},{"id":"GO:2000637","count":2},{"id":"GO:0018032","count":2}]},{"hash":"1193779219694170428","title":"Transcriptional regulators of metabolism and cold response","description":"The cluster is dominated by GO terms for DNA-templated transcription and regulation of transcription, with accompanying terms related to metabolic regulation and stress (cold response, respiration, gluconeogenesis, leucine biosynthesis). This pattern suggests proteins that act as transcription factors or regulators coordinating gene expression in response to environmental and nutritional cues, linking metabolism and stress responses; while some terms are obsolete and one term points to secondary metabolism (aflatoxin biosynthesis), the core theme remains transcriptional control of metabolism under stress.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0009409","count":3},{"id":"GO:0061415","count":3},{"id":"GO:0043457","count":3}]},{"hash":"140341705347503522","title":"Dephosphorylation and kinase regulation in mitosis","description":"The cluster is dominated by GO terms related to dephosphorylation of tyrosine and threonine residues and negative regulation of kinase activity, including JNK, together with cell cycle and mitotic spindle-kinetochore interactions. This points to a cohesive theme of phosphatase-driven signaling that governs mitotic progression, with a few ancillary processes likely representing noise or broader cellular roles.","confidence":"High","size":10,"edges":23,"triangles":19,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":6},{"id":"GO:0007049","count":5},{"id":"GO:0046959","count":4},{"id":"GO:0035970","count":4},{"id":"GO:0060266","count":4}]},{"hash":"1547244023419325914","title":"Vesicle trafficking and secretion","description":"Top GO terms indicate exosomal secretion and general protein secretion, with Rab protein signal transduction pointing to vesicle trafficking as a core function. Although other terms touch on development or immunity, the strongest signal centers on secretory vesicle pathways and cargo transport, supporting a label around vesicle trafficking/secretion for this cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990182","count":2},{"id":"GO:0015628","count":1},{"id":"GO:0048169","count":1},{"id":"GO:0060753","count":1},{"id":"GO:0042832","count":1}]},{"hash":"791913371247678543","title":"Ribosome biogenesis and cell-cycle signaling","description":"These proteins show strong enrichment for rRNA maturation steps (LSU and 5.8S rRNA processing) and RNA methylation, core to ribosome assembly, along with mitotic cell cycle and cell division terms. The presence of TORC1 signaling supports growth coordination with ribosome production. Other terms like mRNA transport, GTPase regulation, and cilium assembly may reflect broader cell-cycle\u2013related regulation, but the dominant theme is ribosome biogenesis linked to cell-growth and division control.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0070262","count":3}]},{"hash":"1047122553343810931","title":"RNA splicing and mRNA processing regulation","description":"The cluster\u2019s top GO terms cluster around spliceosome-mediated mRNA processing (alternative and standard splicing), regulation of mRNA stability and polyadenylation, plus ncRNA-mediated gene silencing and translation initiation. This pattern points to a cohesive group focused on post-transcriptional RNA processing and regulation of gene expression at the RNA level, including stress-responsive mRNA stability.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":7},{"id":"GO:1901407","count":7},{"id":"GO:0048025","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0000380","count":6}]},{"hash":"347781456580478665","title":"Unknown","description":"The terms are broad and divergent: mitochondrial inner membrane protein insertion alongside obsolete mitochondrial targeting terms, plus immune and neuronal signaling terms (mast cell degranulation, inflammatory response, NMDA receptor regulation, T cell differentiation). There isn\u2019t a single cohesive function or pathway that links these terms, so a concise, representative label cannot be confidently assigned.","confidence":"","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0045039","count":1},{"id":"GO:2000310","count":1},{"id":"GO:1901888","count":1}]},{"hash":"642760229916746301","title":"Spliceosome Assembly and RNA Processing","description":"This cluster is dominated by GO terms for spliceosome assembly, snRNP assembly, and mRNA splicing via the spliceosome, along with SSU-rRNA maturation and nuclear import, pointing to a core role in RNA processing and RNA maturation. Some ABA/water deprivation and cell-cycle related terms may reflect broader stress-responsive regulation or developmental context, but the strongest signal is RNA processing/splicing.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":8},{"id":"GO:0051170","count":8},{"id":"GO:0000245","count":8},{"id":"GO:0008334","count":8},{"id":"GO:0000387","count":8}]},{"hash":"1125021665207207920","title":"Nuclear RNA processing and transcription-coupled repair","description":"The top terms show clear signals for ribosomal RNA maturation ( LSU/5.8S rRNA processing ), together with transcription-related activities (RNA polymerase II promoter initiation and promoter clearance) and transcription-coupled nucleotide-excision repair, plus a few chromatin and proteasome-related processes. This pattern suggests a nuclear module that links RNA processing with transcription and genome maintenance rather than a single isolated pathway. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0006367","count":2},{"id":"GO:0006260","count":2}]},{"hash":"979467429903428446","title":"RNA and protein methylation","description":"The cluster is dominated by GO terms related to methylation, including peptidyl-lysine dimethylation, N-terminal peptidyl-glycine methylation, and rRNA methylation, pointing to RNA and protein modification processes. While there are a few unrelated terms (xenobiotic response, Schwann cell development, plant signaling), the strongest shared function among several terms is methylation activity, supporting a label around RNA and protein methylation. ","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0031167","count":2}]},{"hash":"25103139563864184","title":"Dendritic spine morphogenesis and Wnt signaling","description":"This cluster centers on neuronal dendrite development, spine morphogenesis, and actin-driven protrusion assembly (filopodium/lamellipodium), with supportive links to hippocampus development and canonical Wnt signaling. Golgi-to-plasma membrane transport suggests synaptic trafficking, tying the functions to neuronal synapse formation and maturation. Overall, the terms point to neuronal spine development and Wnt-regulated morphogenesis.","confidence":"High","size":10,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0060999","count":3},{"id":"GO:0061001","count":3}]},{"hash":"530907760442375652","title":"Unknown","description":"The top GO terms span neuronal plasticity, immune and skin processes, transcriptional regulation, neuronal migration, Rab signaling, lipid homeostasis, and nucleolar localization, showing no single shared function or pathway linking the proteins. Therefore, a coherent cluster label cannot be assigned beyond Unknown, with no confidence.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048169","count":1},{"id":"GO:0060753","count":1},{"id":"GO:0042832","count":1},{"id":"GO:0097278","count":1},{"id":"GO:0003334","count":1}]},{"hash":"1372719678676638119","title":"Bacterial Aromatic Compound Degradation","description":"The terms center on catabolic and detoxification pathways for aromatic compounds (stilbene, beta-ketoadipate, 1,2-dichloroethane, 3-phenylpropionate) and a general response to toxic substances, with a few biosynthetic terms as minor context. This suggests proteins involved in breaking down aromatics and handling xenobiotic stress rather than a single, narrow pathway.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046272","count":1},{"id":"GO:0042952","count":1},{"id":"GO:0019260","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0009234","count":1}]},{"hash":"841073928825077865","title":"Sarcomere organization and actin cytoskeleton dynamics","description":"This cluster is dominated by GO terms for skeletal muscle fiber development, sarcomere organization, and actin-related processes (actin cortical patch localization/assembly), suggesting a shared role in sarcomere assembly and actin-driven cytoskeleton remodeling. Additional signals like regulation of endocytosis and calcium response fit with actin-mediated trafficking and signaling, though some terms (brain development, meiosis) are less coherent with muscle function.","confidence":"Medium","size":9,"edges":30,"triangles":50,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048741","count":8},{"id":"GO:0021762","count":8},{"id":"GO:0030100","count":4},{"id":"GO:0051592","count":4},{"id":"GO:0000011","count":4}]},{"hash":"1817896791015370329","title":"Actin Cytoskeleton Remodeling and Endomembrane Trafficking","description":"The top GO terms point to actin dynamics via Arp2/3 nucleation, regulation of endocytosis, and vesicle/vacuole interactions, all aligning with cytoskeletal remodeling and membrane trafficking. Additional terms about sarcomere organization and calcium response support a role for actin-based structural dynamics, while histone-related terms appear as outliers. Overall, the cluster seems centered on actin-driven cytoskeleton processes and related trafficking.","confidence":"Medium","size":9,"edges":19,"triangles":18,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034314","count":4},{"id":"GO:0043981","count":4},{"id":"GO:0043982","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0030100","count":3}]},{"hash":"1652101678369205516","title":"Proteostasis and stress signaling regulation","description":"This cluster is dominated by protein quality control and degradation pathways (proteasome- and ubiquitin-dependent catabolism) and autophagy regulation (ERAD involvement, autophagosome maturation), suggesting a central role in maintaining protein homeostasis under stress. The presence of transcriptional regulation and signaling terms (RNA Pol II\u2013driven transcription, TNF signaling) indicates broader regulatory connections, but the proteostasis theme appears strongest.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000753","count":9},{"id":"GO:0045759","count":9},{"id":"GO:0045944","count":9},{"id":"GO:1903265","count":9},{"id":"GO:1901799","count":9}]},{"hash":"24744343157265920","title":"Ribophagy and ubiquitin-mediated proteolysis","description":"The cluster is dominated by proteostasis-related terms: ribophagy, ubiquitin recycling, and SCF-dependent proteasomal degradation, suggesting a core theme of protein turnover. The presence of Arp2/3-mediated actin nucleation and positive regulation of GTPase activity suggests linked cytoskeletal regulation, and cell polarity maintenance aligns with spatial protein turnover. Some terms like RNA import and IL-6 regulation are more peripheral but may reflect broader regulatory roles in this protein set.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034517","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0010992","count":2},{"id":"GO:2000601","count":2}]},{"hash":"1252875198686243262","title":"Apoptosis and Intracellular Signaling","description":"The terms point to stress- and signal-transduction-related processes, including apoptosis initiation (mitochondrial outer membrane permeabilization; extrinsic death receptor signaling), intracellular signaling cascades (cAMP/cGMP biosynthesis and forskolin response; general intracellular signal transduction), and related trafficking/localization (lysosome localization; synaptic vesicle transport). While diverse, the unifying theme is cellular signaling linked to cell fate decisions and stress responses, justifying a label centered on apoptosis and signaling.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0097345","count":1},{"id":"GO:0032418","count":1},{"id":"GO:0008625","count":1},{"id":"GO:0048490","count":1},{"id":"GO:0007168","count":1}]},{"hash":"503282509364037926","title":"Intracellular protein trafficking (ER-Golgi-PM)","description":"The top GO terms cluster around vesicle-mediated transport along the secretory pathway (ER to Golgi, Golgi to plasma membrane, and retrograde Golgi-to-ER), plus general protein transport; a few terms are less related (keratinization, copper/homeostasis, Wnt signaling). Overall, this cluster likely represents secretory/vesicular trafficking proteins.","confidence":"High","size":9,"edges":10,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043001","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0090316","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0031424","count":4}]},{"hash":"1295868489489185546","title":"Meiotic DNA Replication and Chromatin Regulation","description":"The cluster centers on DNA replication machinery (MCM complex, replication initiation, strand elongation) and meiosis-related processes (late recombination nodules, female gamete generation), with a notable emphasis on chromatin regulation via heterochromatin formation (mating-type cassette silencing, subtelomeric heterochromatin). This suggests a coordinated program of replication and chromatin remodeling during gametogenesis, including oogenesis-related amplification events. ","confidence":"High","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007307","count":6},{"id":"GO:0048478","count":6},{"id":"GO:0042140","count":6},{"id":"GO:0072689","count":6},{"id":"GO:1902975","count":6}]},{"hash":"2014534242025764244","title":"Pexophagy and Phagophore Targeting","description":"This cluster is dominated by GO terms tied to autophagy, especially peroxisome autophagy (pexophagy), targeting to the phagophore assembly site, and the Cvt pathway, indicating a shared role in autophagosome formation and selective degradation of organelles. While a few terms relate to lipid signaling (lipoxygenase pathway, leukotriene production) and other signaling processes (retinoic acid, calcium), the strongest and most coherent theme is autophagy-related vesicle formation and organelle turnover, centered on peroxisomes. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030242","count":1},{"id":"GO:0034497","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0002540","count":1},{"id":"GO:0019372","count":1}]},{"hash":"759303172500616874","title":"Lipid metabolism and quinone biosynthesis","description":"The top GO terms are dominated by lipid-related processes: lipid homeostasis, regulation of ubiquinone (coenzyme Q) biosynthetic process, regulation of tocopherol cyclase activity, and regulation of sphingolipid biosynthesis, suggesting a core theme around lipid and cofactor membrane biosynthesis. Some terms (potassium ion transport, cerebellar Purkinje cell layer morphogenesis, axon fasciculation, chemotaxis, parathyroid hormone response) appear sporadic or unrelated, likely represent annotation noise or multi-function proteins. Overall, the cluster appears best described by lipid metabolism and quinone/cofactor biosynthesis.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":2},{"id":"GO:0010795","count":1},{"id":"GO:0055088","count":1},{"id":"GO:1902171","count":1},{"id":"GO:1901006","count":1}]},{"hash":"1224126378063163625","title":"Angiogenesis-Linked Cell Adhesion and Migration","description":"This cluster centers on adhesion and migration-related processes (substrate adhesion-dependent spreading, fibroblast migration, integrin signaling, PDGF response) and includes angiogenesis-related activities (sprouting angiogenesis and tube development) with anoikis resistance, suggesting a cohesive theme of cells coordinating adhesion, signaling, and movement during blood vessel formation.","confidence":"High","size":9,"edges":6,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034446","count":4},{"id":"GO:0010763","count":3},{"id":"GO:0036120","count":3},{"id":"GO:0002042","count":3},{"id":"GO:2000811","count":3}]},{"hash":"1568729978578733881","title":"Ubiquitin-Dependent Proteolysis in Mitosis","description":"The top GO terms point to ubiquitin-mediated protein degradation (polyubiquitination, K11-linked ubiquitination, ERAD pathway) and cell-cycle regulation (mitotic cell cycle, APC/C-dependent catabolic process, anaphase-promoting complex activity). This combination strongly suggests proteins in this cluster primarily govern proteolysis via ubiquitin signaling during mitosis, with a few peripheral terms (cadmium response, transcription) not altering this core theme. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0070208","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070979","count":3}]},{"hash":"72532428693625036","title":"Oxidative Stress Response and Glutathione Metabolism","description":"This cluster centers on redox balance and detoxification, with proteins involved in glutathione metabolism, protein glutathionylation, cellular redox homeostasis, and oxidant detoxification, plus responses to ethanol and metal ions and links to energy metabolism (TCA cycle).","confidence":"Medium","size":9,"edges":13,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016575","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0010731","count":2}]},{"hash":"293282033220398191","title":"Developmental signaling and cell migration","description":"These terms cluster around developmental processes and cytoskeletal dynamics: mesoderm formation and neural development (dendritic spine morphogenesis, neural tube patterning), along with cell motility and signal-regulated cytoskeletal remodeling (cell migration, GTPase activity, podosome assembly). DNA replication appears present but not central to the dominant theme. Together they suggest a functional group of proteins involved in coordinating developmentally programmed cell movement and morphogenesis.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0016477","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071374","count":2}]},{"hash":"2042923977341585980","title":"Unknown","description":"The top terms span vesicle transport (ER-Golgi), dephosphorylation, plant hormone signaling, neural development, calcium signaling, and metabolic processes, with no single, cohesive function tying the proteins together.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0016311","count":2},{"id":"GO:0051343","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0014044","count":2}]},{"hash":"691130535700221841","title":"Cell growth and GTPase signaling","description":"GO terms center on positive regulation of GTPase activity, cell division, DNA replication checkpoints, and actin cytoskeleton dynamics, with additional signaling in metabolism (glucose signaling and SREBP). Together these suggest a coherent theme of growth, proliferation, and GTPase-driven signaling with developmental and DNA maintenance links.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:1903461","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0010255","count":3},{"id":"GO:0070208","count":3}]},{"hash":"2062284819515108030","title":"Ribosome biogenesis and rRNA processing","description":"This cluster is driven by rRNA maturation terms (SSU rRNA processing from a tricistronic transcript; ITS1 cleavage) and RNAP I transcription termination, pointing to ribosome production. Additional terms (RNA Pol II promoter clearance, RNA-protein cross-linking, chromatin-related DNA methylation and nucleosome positioning) seem ancillary, but collectively the data suggest coordination of ribosome biogenesis with transcription and chromatin context.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000462","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0090394","count":5},{"id":"GO:0001111","count":4},{"id":"GO:0018144","count":4}]},{"hash":"600222028716109290","title":"Unknown","description":"The top GO terms span several unrelated areas, including chromatin modification (histone acetylation/deacetylation), DNA replication (Okazaki fragment processing), nutrient and growth signaling (response to nutrient, SREBP signaling, invasive growth with glucose limitation), vesicle transport (ER-Golgi), and even fertilization, indicating no single cohesive function ties these 9 proteins together. Therefore, no clear theme can be assigned. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0032933","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0072432","count":1},{"id":"GO:1903461","count":1}]},{"hash":"2152570995692877781","title":"Developmental signaling and differentiation","description":"This cluster centers on development and differentiation-related processes, with neural signaling (neurotrophin TRK receptor signaling), forebrain and skeletal/muscle development, and myotube differentiation, along with transcriptional regulation. Though there are a couple of outliers related to stress and immune responses, the dominant theme is developmental signaling and differentiation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048011","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0070059","count":2}]},{"hash":"2224118369780992308","title":"Chromatin-regulated neural development","description":"This cluster shows a clear tilt toward neural development terms (cerebellar cortex development, dendrite development) and chromatin-associated regulation (protein localization to chromatin, transcription regulation by RNA Pol II, histone modification references). Some outliers like liver regeneration and IgA isotype switching may reflect broader developmental roles or annotation noise, but the dominant signal supports chromatin-mediated transcription in neural development.","confidence":"Medium","size":9,"edges":8,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":1},{"id":"GO:0045944","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0021695","count":1},{"id":"GO:1900006","count":1}]},{"hash":"2291799863249772798","title":"Neddylation and ubiquitin-mediated DNA damage response","description":"The cluster\u2019s top GO terms point to protein neddylation, ubiquitin-protein transferase activity, and K27-linked ubiquitination, alongside error-free postreplication DNA repair, translesion synthesis, and DNA damage checkpoint signaling. This suggests a cohesive set of proteins coordinating ubiquitin-like modifications (NEDD8) and ubiquitin pathways to regulate DNA replication and damage tolerance/repair. Some terms such as viral processes or Fc-epsilon receptor signaling may be ancillary or broader annotations, but the core theme is ubiquitin/neddylation-driven DNA damage response.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0045116","count":9},{"id":"GO:0042275","count":9},{"id":"GO:0031571","count":9},{"id":"GO:0051092","count":9},{"id":"GO:0016032","count":9}]},{"hash":"1831309378579203442","title":"Unknown","description":"The top GO terms span diverse, unrelated processes (RNA modification, proteasome assembly, metabolism, plant hormone signaling, animal development, and drug response) with no clear shared function or pathway linking the proteins, so there is no cohesive theme to label; thus Unknown with no confidence.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":1},{"id":"GO:0010950","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0051343","count":1}]},{"hash":"67711286052633048","title":"Telomere Maintenance and Chromatin Regulation","description":"This cluster centers on telomere biology and chromatin control, with terms like telomere maintenance via lengthening, subtelomeric heterochromatin formation, and protection from NHEJ at telomeres, alongside chromatin-related processes (establishment of protein localization to chromatin, regulation of chromatin silencing) and DNA damage response (HR repair regulation). These together suggest a cohesive theme around telomere-associated chromatin regulation and telomere-maintenance pathways.","confidence":"High","size":9,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0031936","count":1},{"id":"GO:0071169","count":1},{"id":"GO:0051092","count":1},{"id":"GO:0032205","count":1},{"id":"GO:0010833","count":1}]},{"hash":"2066754360422406435","title":"Mitochondrial respiration and translation","description":"The GO terms show mitochondrial energy metabolism (mitochondrial electron transport, proton translocation, aerobic respiration, complex III assembly) together with tRNA aminoacylation and translation terms. This points to proteins involved in both mitochondrial respiration and the mitochondrial translation apparatus (e.g., mt tRNA synthetases), suggesting a cohesive mitochondrial functional cluster rather than a general cytosolic process.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0034551","count":2}]},{"hash":"1237076093402827272","title":"Aromatic compound degradation and detox","description":"This cluster centers on catabolic pathways for aromatic and xenobiotic substrates (stilbene, beta-ketoadipate, glucuronoside, 1,2-dichloroethane) and detox-related processes (epoxygenase P450 pathway; response to toxic substance). Together, these GO terms support a cohesive theme of aromatic compound degradation and detoxification, typical of microbes that metabolize environmental pollutants.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046272","count":4},{"id":"GO:0046839","count":4},{"id":"GO:0097755","count":4},{"id":"GO:0042952","count":3},{"id":"GO:0042619","count":3}]},{"hash":"1339723344150237898","title":"Glycolysis and sugar metabolism","description":"The Top Terms cluster around central carbohydrate metabolism: glycolytic process, gluconeogenesis, fructose metabolism, fructose-2,6-bisphosphate regulation, carbohydrate phosphorylation, and pentose-phosphate shunt regulation. This suggests proteins in this cluster predominantly participate in energy-yielding sugar pathways rather than other cellular processes. A couple of terms (intestinal epithelial cell development and regulation of DNA damage response) appear peripheral or incidental but do not override the core glycolytic/sugar metabolism theme.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0043456","count":1},{"id":"GO:0006000","count":1}]},{"hash":"1021625572016554063","title":"Unknown","description":"The top GO terms span muscle development and sarcomere organization, post-translational modification (poly-ADP-ribosylation, ubiquitination), cell cycle/DNA damage signaling, and unrelated plant/kidney pathways, with no coherent common function or interaction pattern linking the proteins. There are no edges, and the terms do not converge on a single biology, so a specific label cannot be confidently assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0007095","count":2},{"id":"GO:0072156","count":1},{"id":"GO:0009742","count":1}]},{"hash":"601317922385751434","title":"Modulation of Signaling Pathways","description":"The proteins span several GO terms centered on regulating signaling cascades (insulin receptor signaling, BMP secretion, Rac signaling, phosphatidylinositol dephosphorylation) and related immune/developmental processes, suggesting a cohesive theme of signaling modulation, despite a couple of outliers related to development or metabolism.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051497","count":2},{"id":"GO:0007480","count":1},{"id":"GO:0090334","count":1},{"id":"GO:0043114","count":1},{"id":"GO:0032760","count":1}]},{"hash":"892215370633535747","title":"Secretory Transport and Development Signaling","description":"The top GO terms strongly point to components of the secretory pathway (ER-Golgi transport and Golgi-to-plasma membrane transport), suggesting a cluster enriched for proteins involved in trafficking between organelles. At the same time, there are clear developmental signals (liver and forebrain neuron development, digit morphogenesis) and signaling pathway terms (adrenergic receptor signaling, gibberellin signaling) that imply regulatory roles in development. The combination indicates proteins linked to secretory trafficking with developmental or signaling functions, though some terms may reflect broader or cross-species annotations. ","confidence":"Medium","size":8,"edges":24,"triangles":38,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":8},{"id":"GO:0042733","count":8},{"id":"GO:0046909","count":8},{"id":"GO:0001889","count":8},{"id":"GO:0021884","count":8}]},{"hash":"873400011995077433","title":"Intracellular trafficking and organelle dynamics","description":"The cluster shows strong representation of vesicle and organelle transport processes (endosome-to-lysosome transport, Golgi-related transport, protein-containing complex localization) alongside organelle remodeling activities (mitochondrial fission, ER stress response) and related cellular remodeling events (cytokinesis, dendritic spine development). This pattern suggests a cohesive theme centered on intracellular transport and organelle dynamics with linked stress and remodeling responses, rather than a single narrow function.","confidence":"High","size":8,"edges":13,"triangles":7,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006878","count":7},{"id":"GO:1902824","count":7},{"id":"GO:0060999","count":7},{"id":"GO:0031584","count":7},{"id":"GO:1990386","count":7}]},{"hash":"40720350096722388","title":"Ubiquitin-Dependent Mitosis and DNA Repair","description":"Based on the prominent GO terms, the cluster centers on ubiquitin-mediated regulation of mitosis (K11-linked ubiquitination, APC-dependent catabolic process, mitotic cell cycle, spindle assembly checkpoint) and DNA repair (homologous recombination), with additional links to chromatin organization and ERAD. Although a few terms (e.g., neuron projection development) are less connected, the core theme is ubiquitin-regulated cell-cycle control and DNA damage response.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0031175","count":2},{"id":"GO:0031497","count":2}]},{"hash":"902987742665409108","title":"Cytoskeletal organization and organelle inheritance","description":"The cluster is dominated by GO terms tied to cytoskeletal dynamics (actin patch assembly, sarcomere organization), organelle inheritance (vacuole and mitochondrion inheritance), cell polarity and shape regulation, and membrane trafficking (endocytosis regulation), with calcium signaling and muscle-related development terms (skeletal muscle fiber development) also represented. This points to a cohesive theme of cytoskeletal control of intracellular organization, membrane processes, and muscle structure, rather than a single isolated pathway. ","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000011","count":8},{"id":"GO:0000147","count":8},{"id":"GO:0000001","count":8},{"id":"GO:0071963","count":8},{"id":"GO:0030100","count":7}]},{"hash":"1682948463366082867","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019350","count":3},{"id":"GO:0009611","count":2},{"id":"GO:0046444","count":2},{"id":"GO:1990966","count":2},{"id":"GO:0015937","count":2}]},{"hash":"293461730189060472","title":"Neural development and ER-stress\u2013induced apoptosis","description":"The top GO terms cluster around nervous system development (forebrain development, nervous system development) and dendrite morphogenesis, plus apoptotic signaling in response to endoplasmic reticulum stress and the ER unfolded protein response. These together point to a function in neural development with stress-induced cell death. DNA replication and repair terms appear but are less central to the dominant neural/stress theme, suggesting that the core identity centers on neural development and ER-stress\u2013mediated apoptosis.","confidence":"High","size":8,"edges":9,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0030968","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0030900","count":5}]},{"hash":"974678373935880670","title":"Meiosis and Telomere Maintenance","description":"The cluster's GO terms are largely centered on meiotic events (reciprocal recombination, male meiosis I, chiasma assembly) and on chromosome-associated processes such as DNA replication, DNA repair, and telomere maintenance via telomerase, suggesting proteins involved in meiotic chromosome dynamics and telomere upkeep. A single outlier term links to neuronal synaptic plasticity, which appears to be noise relative to the dominant meiotic/telomeric theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031914","count":2},{"id":"GO:0007131","count":1},{"id":"GO:0007141","count":1},{"id":"GO:0051026","count":1},{"id":"GO:0006279","count":1}]},{"hash":"911749910436562028","title":"Nuclear transcription and RNA processing proteins","description":"This cluster's top GO terms cluster around RNA synthesis and processing: RNA Pol II promoter clearance, RNA Pol I transcription termination, rRNA processing, and transcription-coupled DNA repair. Together these suggest a shared role in nuclear gene expression and ribosome biogenesis, with some signals toward DNA repair and development; the synaptic regulation term appears peripheral. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090394","count":4},{"id":"GO:0001111","count":3},{"id":"GO:0018144","count":3},{"id":"GO:0016584","count":3},{"id":"GO:0006363","count":3}]},{"hash":"1257399128474627289","title":"Triglyceride catabolism and glycerolipid remodeling","description":"The cluster is dominated by lipid catabolic terms: triglyceride catabolic process, triglyceride mobilization, triglyceride acyl-chain remodeling, and phospholipid (phosphatidylcholine/phosphatidylethanolamine) catabolic processes, indicating a theme of glycerolipid turnover and lipid remodeling. A few terms related to signaling (PKA regulation) or neuronal plasticity appear sparsely, but the lipid metabolism terms overwhelmingly define the cluster.","confidence":"High","size":8,"edges":9,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2000480","count":5},{"id":"GO:0034638","count":5},{"id":"GO:0010898","count":5},{"id":"GO:0036153","count":5},{"id":"GO:0006642","count":5}]},{"hash":"2055357377918952934","title":"Neural differentiation and ECM signaling","description":"This cluster is driven by neural development terms (retinal bipolar neuron differentiation; Schwann cell development) and extracellular matrix organization, with supporting signals in calcium/NFAT pathways and kinase activity regulation. The combination suggests a role in nervous system differentiation coupled to ECM dynamics.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0051343","count":1},{"id":"GO:0060040","count":1},{"id":"GO:0014044","count":1}]},{"hash":"2075249527023307849","title":"ER Stress and Protein Folding","description":"Most prominent GO terms center on the cellular response to unfolded proteins and ER-associated processes, including unfolded protein response and post-translational protein targeting to membranes, suggesting the cluster reflects ER protein handling and trafficking under stress. Some terms (iron-sulfur cluster assembly, karyogamy, fungal cell wall biosynthesis) are less directly related and may represent background or multifunctional proteins. Overall, the theme is ER-associated protein folding and quality control, with related stress response signaling.","confidence":"Medium","size":8,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006880","count":1},{"id":"GO:0034620","count":1},{"id":"GO:0000902","count":1},{"id":"GO:1900035","count":1},{"id":"GO:1903382","count":1}]},{"hash":"1875953474242226889","title":"RNA processing and transcription regulation","description":"These proteins cluster around RNA processing (especially spliceosome-mediated splicing) and transcription control (Pol II promoter clearance and termination), with additional hints of ncRNA-mediated regulation and RNA-protein interactions. This suggests a coherent module of RNA processing and transcription regulation.","confidence":"Medium","size":8,"edges":13,"triangles":8,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0006369","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0045292","count":3}]},{"hash":"1788037471584410032","title":"Secretory vesicle exocytosis","description":"The terms cluster around degranulation and vesicle trafficking across immune and neuronal contexts (NK/neutrophil degranulation, synaptic vesicle exocytosis, Golgi to plasma membrane transport, and related membrane fusion events), indicating a shared function in secretory vesicle exocytosis and secretion.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043320","count":1},{"id":"GO:0048280","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0043312","count":1},{"id":"GO:0016240","count":1}]},{"hash":"1174314051386402830","title":"Neuronal actin remodeling and spine morphogenesis","description":"This cluster is dominated by terms tied to actin cytoskeleton dynamics (actin cortical patch localization/assembly, podosome and ruffle assembly) and neuronal morphology (neuron projection morphogenesis, regulation of dendritic spine maintenance). While a couple terms relate to ribosome biogenesis or the mitotic cell cycle, the prevailing signal points to actin-driven remodeling and protrusive processes relevant to neuronal shape and spine structure.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0043984","count":2},{"id":"GO:1902951","count":2},{"id":"GO:0044379","count":2},{"id":"GO:0000147","count":2}]},{"hash":"1694442079966256598","title":"Xenobiotic and nutrient transmembrane transport","description":"This cluster is dominated by GO terms for transporting a range of small molecules across membranes, including xenobiotics, vitamins, taurine, molybdate, thiamine, and related exports, along with a secretion system-related transport. The doxorubicin transport and xenobiotic export terms reinforce the idea of membrane transport of xenobiotics and nutrients; an immune-related term is present but peripheral. ","confidence":"Medium","size":8,"edges":10,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":8},{"id":"GO:0035461","count":8},{"id":"GO:0015689","count":6},{"id":"GO:0015734","count":6},{"id":"GO:0046618","count":6}]},{"hash":"1067434298340820351","title":"RNA Processing and Transcriptional Regulation","description":"The cluster contains terms related to RNA processing (spliceosome assembly and mRNA splicing, rRNA maturation), epigenetic programming and transcriptional control (epigenetic gene expression, histone methylation, transcription from RNA Pol II), and signaling that can influence gene expression (Ras signaling, various context-dependent transcriptional regulation). This suggests a cohesive theme centered on how gene expression is regulated at RNA and chromatin levels, with ancillary signaling inputs.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0045585","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0000481","count":1},{"id":"GO:0010588","count":1}]},{"hash":"630601162543083511","title":"APC/C-Driven Mitotic Regulation","description":"These proteins strongly point to ubiquitin-mediated control of mitosis: K11-linked ubiquitination, APC/C-dependent catabolic processes, spindle assembly, and mitotic cell cycle. While innate immune and antiviral terms appear in the list, the dominant theme is APC/C-regulated proteolysis during cell division, with some annotation noise from ubiquitin-related pathways and chromatin modification. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071276","count":2}]},{"hash":"59826208027773195","title":"Nuclear transcription and cell cycle regulation","description":"The top GO terms point to processes centered on gene expression control within the nucleus (DNA-templated transcription, nuclear export of proteins) and cell cycle progression (G1/S transition) with both pro- and anti-proliferative signals (positive regulation of apoptosis, negative regulation of Wnt signaling, negative regulation of cell population proliferation). A cohesive theme is regulation of transcriptional programs that govern cell cycle entry and proliferation, with some links to signaling pathways and cell migration. Confidence in this label is Medium.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":3},{"id":"GO:0046827","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0007118","count":2}]},{"hash":"670728385757652171","title":"Bacterial metabolism and metabolite biosynthesis","description":"The top GO terms cluster around microbial metabolic activities: pyruvate fermentation to acetate, menaquinone and siderophore biosynthesis, various fatty-acid catabolic/metabolic processes, malonate catabolism, bile acid metabolism, and bioluminescence. These are characteristic of bacterial primary and secondary metabolism and metabolite production. Some plant-specific terms appear as outliers, but they do not define the core theme of the cluster. Overall, the dominant signal points to bacterial metabolism and metabolite biosynthesis.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019654","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0019290","count":3},{"id":"GO:0036112","count":3},{"id":"GO:0000038","count":3}]},{"hash":"1411613177983367470","title":"Amino acid metabolism and vitamin biosynthesis","description":"This cluster centers on amino acid catabolic processes (alanine, valine, threonine) and related amino acid-derived pathways, along with biosynthesis of vitamins and cofactors (pyridoxine, retinol) and related metabolite production (tyrosine, oxaloacetate, porphyrinogen IX). The common theme is metabolic functions tied to amino acid turnover and vitamin/cofactor biosynthesis, with a secondary signal for immune response to lipopolysaccharide that does not define the primary function. ","confidence":"Medium","size":8,"edges":7,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042853","count":4},{"id":"GO:0019518","count":4},{"id":"GO:0006571","count":3},{"id":"GO:0006107","count":3}]},{"hash":"849564267105131419","title":"Sphingolipid and phospholipid metabolism","description":"The top GO terms cluster around lipid metabolism, especially sphingolipids (sphingosine and sphinganine metabolic processes) and phospholipids (phospholipid dephosphorylation, catabolic and biosynthetic processes). There is also an indication of regulation of sphingolipid-mediated signaling, suggesting a signaling facet. A single term for glucose-6-phosphate transport is present but less central. Overall, the proteins appear to form a lipid biosynthesis/turnover module with possible signaling roles.","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":1},{"id":"GO:0046839","count":1},{"id":"GO:1902068","count":1},{"id":"GO:0009395","count":1},{"id":"GO:0006668","count":1}]},{"hash":"2025637817099165843","title":"Nucleotide and Vitamin Biosynthesis Metabolism","description":"Several GO terms cluster around nucleotide/nucleoside metabolism (deoxycytidine catabolic process, cytidine deamination, cytosine metabolic process, UMP salvage, uridine biosynthetic process) and vitamin biosynthesis (thiamine and riboflavin biosynthesis). The co-occurrence suggests these proteins participate in broader metabolic functions linking nucleoside turnover with cofactor/vitamin biosynthesis rather than a single isolated pathway.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0006217","count":2},{"id":"GO:0009972","count":2}]},{"hash":"759828419800984541","title":"Transcription Regulation and Chromatin Dynamics","description":"This cluster centers on transcriptional control and chromatin-related processes, with GO terms for RNA polymerase II and I elongation, transcription-coupled DNA repair regulation, and histone modification (e.g., ubiquitination), plus a few differentiation-related terms. The common theme is gene expression regulation via transcriptional elongation and chromatin remodeling rather than a single specific pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032515","count":1},{"id":"GO:0032516","count":1},{"id":"GO:0007094","count":1},{"id":"GO:2001209","count":1},{"id":"GO:0001711","count":1}]},{"hash":"1935638039270566185","title":"Unknown","description":"The top terms are highly diverse (aging, cell cycle regulation, renal water transport, glycogen synthase regulation, corneocyte development, phosphatidylinositol dephosphorylation, xenobiotic response, cAMP signaling) and include obsolete terms, with no shared pathway or clear functional theme; plus no observed edges, making it impossible to derive a coherent label. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:1900087","count":2},{"id":"GO:2001153","count":2},{"id":"GO:2000466","count":2},{"id":"GO:1903507","count":2}]},{"hash":"1387416717020970585","title":"Mitochondrial and organelle dynamics with synaptic signaling","description":"The cluster centers on mitochondrial fission and peroxisome dynamics (fission and fragmentation) with ancillary links to broader signaling processes such as synaptic vesicle recycling, postsynaptic receptor internalization, and calcium channel regulation, plus muscle-related signaling. This suggests a common theme of organelle dynamics closely tied to cellular signaling in neural and muscular contexts, making a label around \"mitochondrial and organelle dynamics with synaptic signaling\" appropriate.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":2},{"id":"GO:0090149","count":2},{"id":"GO:0043653","count":1},{"id":"GO:1903423","count":1},{"id":"GO:1901387","count":1}]},{"hash":"1598104246742892264","title":"RNA Pol II/III Transcription Initiation","description":"The cluster is dominated by GO terms related to transcription initiation and promoter interactions for RNA polymerase II and III, including start-site selection, promoter initiation, and preinitiation complex assembly, indicating these proteins are part of transcription initiation machinery across Pol II and III.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001174","count":1},{"id":"GO:0006351","count":1},{"id":"GO:1904798","count":1},{"id":"GO:0050434","count":1},{"id":"GO:0006367","count":1}]},{"hash":"101373238230053171","title":"Neuronal development and transcription regulation","description":"The cluster includes GO terms centered on DNA-templated transcription and regulation of gene expression, with specific neuronal development signals such as embryonic olfactory bulb interneuron precursor migration and regulation of long-term synaptic plasticity. While there are a few terms tied to keratinocyte development and immune defense, the dominant theme across the terms points to neuronal development and transcriptional control. Confidence: Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0048169","count":1},{"id":"GO:0060753","count":1},{"id":"GO:0042832","count":1}]},{"hash":"62833248642848357","title":"Lipid and amino acid metabolism","description":"This cluster shows enrichment in lipid- and amino acid-related catabolic processes, including cholesterol metabolism, ketone body catabolism, propionyl-CoA biosynthesis, and L-isoleucine catabolism, along with lipid transport and mitochondrial regulation of apoptosis. The combination suggests a broader energy-metabolism cluster centered on lipid and amino acid turnover, with mitochondrial involvement; a few terms (like aromatic compound catabolism) are less cohesive but do not override the main theme.","confidence":"Medium","size":7,"edges":8,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019619","count":4},{"id":"GO:1901373","count":4},{"id":"GO:1902109","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0001889","count":4}]},{"hash":"1557271467116633382","title":"Neural and craniofacial development with Wnt signaling","description":"This cluster is enriched for neural and craniofacial developmental terms\u2014cerebellar cortex development, embryonic cranial skeleton morphogenesis, and axon fasciculation\u2014often regulated by Wnt signaling. The presence of multicellular development and other related terms supports a core neurodevelopmental/craniofacial theme, despite some miscellaneous associations.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021695","count":3},{"id":"GO:0097155","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0090153","count":2},{"id":"GO:0071374","count":2}]},{"hash":"890634771378210072","title":"Vesicle trafficking and endocytosis","description":"The top GO terms cluster around endocytosis, Golgi-to-ER transport, and Golgi vesicle budding, with contributions from late endosome to lysosome transport and membrane lipid/homeostasis, pointing to a core role in vesicle trafficking and membrane dynamics; peripheral terms likely reflect annotation noise or broader cellular contexts.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0048194","count":2},{"id":"GO:0055091","count":1},{"id":"GO:0090263","count":1}]},{"hash":"779040169863936683","title":"Calcium/NFAT signaling regulation","description":"This cluster is dominated by GO terms related to calcium signaling and the calcineurin-NFAT pathway (e.g., regulation of Ca2+ release from the sarcoplasmic reticulum and calcineurin-NFAT signaling cascades). Some terms reference neural and glial development (retinal bipolar neuron differentiation, Schwann cell development), which can be influenced by calcium/NFAT signaling, while others touch broader, intersecting responses (glucocorticoid response). The common thread appears to be calcium-dependent transcriptional signaling via NFAT, justifying this label, though several terms are peripheral or obsolete, making the connection moderate in strength.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051343","count":2},{"id":"GO:0060040","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0070886","count":2},{"id":"GO:2000256","count":2}]},{"hash":"1140577944079827621","title":"Neural adhesion and myelination signaling","description":"The proteins cluster around neural-specific functions: integrin-mediated signaling, cell-matrix and cell-cell adhesion, ganglioside metabolism, and CNS myelin formation, plus regulation of axon growth. This points to a module coordinating adhesion and signaling required for neural development and myelination, with some related neuronal migration/regeneration inhibition signals, rather than unrelated processes.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":"wound healing","top_go_terms":[{"id":"GO:0007229","count":4},{"id":"GO:0007161","count":4},{"id":"GO:0034113","count":4},{"id":"GO:0061097","count":3},{"id":"GO:0001573","count":3}]},{"hash":"1534711574465513423","title":"Ribosome Biogenesis and RNA Processing","description":"Predominant signals are ribosome biogenesis and ribosomal subunit export/processing (ribosome biogenesis, ribosomal small subunit biogenesis, rRNA processing/ITS2 cleavage, tRNA modification). The inclusion of cell cycle and cell division terms suggests a broader growth-related context, but the core cluster centers on assembly and maturation of the translation machinery.","confidence":"High","size":7,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0090529","count":1}]},{"hash":"704147902994284845","title":"Neural and Craniofacial Development","description":"Based on the predominance of terms related to neural axon fasciculation, cranial skeleton morphogenesis, Wnt signaling, and overall multicellular development, this cluster appears to represent developmental processes focused on nervous system and facial skeletal structures; peripheral terms about protein transport/processing are present but not defining. ","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":7},{"id":"GO:0097155","count":6},{"id":"GO:0006935","count":6},{"id":"GO:0090153","count":6},{"id":"GO:0071374","count":6}]},{"hash":"768090574778518305","title":"DNA transcription and chromatin modification","description":"This cluster centers on nuclear processes: DNA-templated transcription and multiple histone modifications (H3K4/K79 methylation and H4K16 acetylation) suggesting regulation of chromatin state, plus Okazaki fragment processing and DNA damage checkpoint signaling pointing to DNA replication/repair coordination. The overall theme points to gene expression control tied to chromatin regulation, with a few outlier terms that seem less related.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0051568","count":4},{"id":"GO:0034729","count":4},{"id":"GO:0032933","count":3},{"id":"GO:0060770","count":3}]},{"hash":"686162510637985541","title":"Peptidoglycan turnover and amino sugar metabolism","description":"The top GO terms cluster around carbohydrate and amino sugar metabolism and a specific muropeptide turnover pathway (including 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process), which points to bacterial cell wall remodeling and recycling. A few terms (poly(A)+ mRNA export from nucleus; positive regulation of ATP-dependent activity/helicase activity) seem unrelated to cell wall metabolism, suggesting either annotation noise or multi-domain proteins. Overall, the dominant signal favors a cell wall\u2013related metabolic theme, hence this name. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006040","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0009254","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0097175","count":1}]},{"hash":"2033391434180573629","title":"Unknown","description":"The top GO terms span DNA replication, intracellular trafficking, DNA damage tolerance, cytoskeleton remodeling, peroxisomal import, and energy metabolism, with no single coherent function linking all proteins, making a specific, intuitive label difficult to justify.","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006888","count":6},{"id":"GO:0070987","count":6},{"id":"GO:0031117","count":6},{"id":"GO:0016562","count":6}]},{"hash":"688843221326642054","title":"Ribosome Biogenesis and RNA Methylation","description":"The cluster is enriched for ribosome biogenesis and RNA modification processes (rRNA and tRNA methylation), as well as spliceosomal complex assembly, which together point to a group of proteins involved in RNA processing and ribosome assembly. The presence of various RNA modification terms suggests a common theme around maturation of ribonucleic acids and ribosome construction, with a few unrelated terms likely representing incidental annotations. ","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000245","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0070476","count":2},{"id":"GO:0043985","count":2}]},{"hash":"953371397573879912","title":"Unknown","description":"The Top Terms cover a wide range of processes: collagen catabolic, chromatin organization, transcription regulation, RNA processing, translation, protein maturation/stabilization, proteolysis, ribosomal RNA maturation, Pol III transcription, and even glomerular filtration. This breadth shows no single cohesive theme linking the cluster proteins, suggesting heterogeneous functions or annotation noise. Therefore, an Unknown label is most appropriate.","confidence":"","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":2},{"id":"GO:0034724","count":2},{"id":"GO:0034396","count":2},{"id":"GO:0035551","count":2},{"id":"GO:0000462","count":1}]},{"hash":"329876058385637379","title":"Ribosome biogenesis and translation","description":"The top GO terms center on ribosome assembly/disassembly, translation and termination, and mRNA decay, pointing to core protein synthesis machinery and its regulation. Additional terms about cell division and Golgi retention appear as related growth/process contexts, with viral genome replication representing a possible interaction context rather than a distinct functional module. Overall, the cluster seems anchored in ribosome biogenesis and translation-related processes.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0045053","count":2},{"id":"GO:0032790","count":2}]},{"hash":"1273566020900458423","title":"Xenobiotic and nutrient membrane transport","description":"The cluster is dominated by GO terms describing transmembrane transport of xenobiotics, vitamins, and minerals (e.g., xenobiotic transport/export, vitamin and thiamine transport, molybdate, taurine), plus related secretion activity (Type I secretion system). This points to a shared function of moving diverse substrates across membranes and exporting compounds, rather than a single specific substrate. The MHC class I antigen presentation term appears to be an outlier and not central to the main theme.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":6},{"id":"GO:0035461","count":6},{"id":"GO:0015689","count":5},{"id":"GO:0015734","count":5},{"id":"GO:0046618","count":5}]},{"hash":"850635943512745888","title":"Central carbon metabolism and energy homeostasis","description":"These proteins are enriched for core metabolic processes: glycolysis, the TCA cycle, gluconeogenesis, amino acid and nucleotide metabolism, and lipid biosynthesis, with an additional link to cAMP-mediated signaling. This suggests a coherent role in central carbon metabolism and energy regulation rather than a single isolated pathway.","confidence":"High","size":7,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0006103","count":4},{"id":"GO:0006096","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0006552","count":2}]},{"hash":"201673312887590513","title":"Mitochondrial respiration and proton transport","description":"The top GO terms cluster around energy production via aerobic respiration and electron transport, including proton transmembrane transport and the mitochondrial electron transport step from ubiquinol to cytochrome c. These indicate components of oxidative phosphorylation. A few outlier terms (antibiotic/nylon catabolism, ubiquitin recycling) seem incidental noise, but do not outweigh the core energy metabolism signal. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0046677","count":1},{"id":"GO:0019876","count":1},{"id":"GO:0033252","count":1}]},{"hash":"389493037144843320","title":"Golgi\u2013ER Trafficking & Small GTPase Signaling","description":"This cluster is dominated by terms about Golgi localization, ER-to-Golgi vesicle transport, and endosomal transport to the postsynaptic membrane, all pointing to vesicle trafficking within the secretory pathway. The presence of small GTPase\u2013mediated signaling further supports a trafficking/regulatory theme. Some developmental terms (liver/brain development) likely reflect broader roles of these processes in development, but the core signal remains Golgi/ER transport and vesicle trafficking.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051683","count":3},{"id":"GO:0098887","count":3},{"id":"GO:0097498","count":3},{"id":"GO:0090334","count":3},{"id":"GO:0090051","count":3}]},{"hash":"41070033879380436","title":"Membrane Transporters (ions and sugars)","description":"This cluster centers on transmembrane transport activities across multiple substrates\u2014phosphate, sodium and potassium ions, various sugars like galactose and arabinose, sialic acid, nitrate assimilation, and neurotransmitter loading\u2014indicating a general role as membrane transporter proteins with diverse specificities.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":4},{"id":"GO:0071805","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0015739","count":3}]},{"hash":"27160107305790433","title":"Bacterial metabolism and envelope biosynthesis","description":"These proteins appear enriched for bacterial biosynthetic processes, including amino acid synthesis (glutamate, tyrosine, lysine), cofactor biosynthesis (cobalamin), and cell envelope components (enterobacterial common antigen), with some transport activity, suggesting a theme of metabolism and envelope assembly in bacteria.","confidence":"High","size":7,"edges":13,"triangles":8,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019551","count":4},{"id":"GO:0019518","count":4},{"id":"GO:0009246","count":3},{"id":"GO:0019550","count":3},{"id":"GO:0032869","count":3}]},{"hash":"271321923703119528","title":"Retinoid Metabolism and Regulation","description":"The top GO terms are retinol and retinal metabolic processes (each 7) and a regulatory term for retinoic acid biosynthesis, indicating a cohesive retinoid metabolism theme despite some noise from unrelated terms.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":7},{"id":"GO:0042574","count":7},{"id":"GO:1901653","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0072061","count":4}]},{"hash":"1733569610437456268","title":"Unknown","description":"There is no clear common function: one term relates to mRNA splice site recognition and the other to negative regulation of striated muscle development; each appears only once among the proteins, yielding no coherent theme. A reliable label is not apparent from the available GO terms.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":1},{"id":"GO:0045843","count":1}]},{"hash":"2214584057485481205","title":"Cytokinin-Regulated Plant Growth and Development","description":"The cluster is enriched with GO terms centered on cytokinin-activated signaling and growth regulation, including cytokinin signaling, regulation of seed growth, and positive regulation of vegetative development, along with positive regulation of secondary cell wall biogenesis, suggesting a cohesive module where cytokinin signaling drives plant growth and developmental processes; a few telomere-related terms appear incidental rather than defining the core function.","confidence":"High","size":7,"edges":7,"triangles":1,"max_degree":4,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":7},{"id":"GO:1903086","count":6},{"id":"GO:1901348","count":6},{"id":"GO:0031848","count":6},{"id":"GO:0080113","count":6}]},{"hash":"1806310072456531529","title":"Unknown","description":"The top GO terms cover thermoception, cold response, muscle stretch response, salicylic acid response, and various differentiation processes, with several obsolete annotations; there is no clear, shared function linking these proteins into a single cohesive theme, so the cluster cannot be confidently labeled with a specific biology term.","confidence":"","size":7,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":4},{"id":"GO:0035994","count":4},{"id":"GO:0000083","count":4},{"id":"GO:0002268","count":4},{"id":"GO:0090501","count":4}]},{"hash":"280045619612610707","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning thermoception, cold response, differentiation of various cell types, transcriptional regulation, and other diverse processes, with several obsolete terms. There is no clear, single functional theme uniting these proteins, so a concise, unified label isn\u2019t justifiable.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050955","count":1},{"id":"GO:0035994","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0002268","count":1},{"id":"GO:0090501","count":1}]},{"hash":"263725863795525255","title":"Neural/glial development and Wnt-calcium signaling","description":"The top GO terms converge on development of neural and glial lineages (astrocyte activation, Schwann cell development, retinal bipolar neuron differentiation) and calcium/Wnt signaling (Wnt calcium modulating pathway, calcineurin-NFAT signaling). This suggests proteins in this cluster are involved in neural/glial differentiation with calcium-dependent signaling mechanisms. Some terms indicate broader organ morphogenesis, but the dominant theme is neural/glial development tied to calcium signaling.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0007223","count":2},{"id":"GO:0048143","count":2},{"id":"GO:0003151","count":2},{"id":"GO:0051343","count":1}]},{"hash":"2165944719299026921","title":"Axon Guidance and Synaptic Development","description":"The cluster is dominated by neuronal connectivity terms: axon guidance, Roundabout signaling, and positive regulation of dendritic spine development, along with endocytic recycling, suggesting a group of proteins involved in neurite pathfinding and synapse formation, supported by membrane trafficking and phospholipid homeostasis context. A few terms (keratinization, heart contraction) may reflect broader functional overlaps or annotation noise but do not override the neuronal focus. ","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055091","count":4},{"id":"GO:0031424","count":4},{"id":"GO:0043124","count":4},{"id":"GO:0035385","count":4},{"id":"GO:0032729","count":4}]},{"hash":"1257752592677785141","title":"DNA replication and genome maintenance","description":"This cluster is dominated by GO terms tied to DNA recombination, telomere maintenance, mitochondrial DNA repair, and DNA strand elongation during mitotic replication, as well as replication fork reversal, indicating a core theme of genome integrity and DNA replication/repair. A few outlier terms (positive regulation of Wnt signaling, negative regulation of T cell differentiation, imaginal disc morphogenesis) are less connected to this core and may reflect pleiotropy or dataset noise, but do not override the main signal.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0006471","count":2},{"id":"GO:0071932","count":1},{"id":"GO:0090263","count":1},{"id":"GO:0045581","count":1}]},{"hash":"1038957465839860901","title":"Spindle orientation and microtubule regulation","description":"This cluster is dominated by GO terms about mitotic spindle orientation, microtubule-kinetochore attachments, centrosome separation, and regulation of microtubule-based processes, pointing to a core function in microtubule dynamics during cell division. While there are additional terms related to development and neuronal maintenance, the strongest signal centers on spindle/microtubule regulation, justifying a label focused on these processes.","confidence":"High","size":6,"edges":11,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051296","count":6},{"id":"GO:0099607","count":6},{"id":"GO:0000911","count":6},{"id":"GO:0036334","count":6},{"id":"GO:0032886","count":6}]},{"hash":"999473544313058571","title":"Transcription Regulation by Metabolic Cues","description":"The terms cluster around transcriptional processes (DNA-templated transcription and RNA Pol II\u2013mediated regulation) and metabolic context (regulation of respiration, amino acid biosynthesis, and carbon-source\u2013dependent regulation), suggesting a cohesive theme of transcriptional control in response to metabolic state. Some terms are older/obscure, but the overall pattern supports this label.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051262","count":2},{"id":"GO:0007612","count":2},{"id":"GO:0061415","count":2},{"id":"GO:0043457","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1501845416942319557","title":"DNA replication and double-strand break repair","description":"Based on the GO terms, the proteins cluster around DNA replication and various double-strand break (DSB) repair processes, including meiotic recombination and nonhomologous end joining. While some terms appear unrelated or obsolete (potential noise), the core signal is clearly genome maintenance through replication and repair pathways.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:1990918","count":4},{"id":"GO:0051343","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0014044","count":3}]},{"hash":"1994483430927531307","title":"Mitotic Division and ER-Golgi Vesicle Trafficking","description":"This cluster shows strong signals for cell cycle and mitotic processes (cell division, mitotic cell cycle, mitotic spindle assembly) alongside vesicle trafficking steps (ER-to-Golgi transport, COPII-coated vesicle budding), indicating members involved in both division machinery and secretory pathway dynamics. While there is a brain development term present, the dominant themes are mitosis and vesicle transport, with ribosome biogenesis and GTPase activity supporting broader cellular machinery.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0090114","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1037519123558210365","title":"Unknown","description":"The GO terms span lipid signaling, DNA replication/repair, chromatin modification, vesicle transport, fertilization, and growth responses, with no single dominant function tying all proteins together.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0072432","count":1},{"id":"GO:1903461","count":1},{"id":"GO:0043984","count":1}]},{"hash":"1783075462801741068","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010586","count":1},{"id":"GO:1903265","count":1},{"id":"GO:1902187","count":1},{"id":"GO:0061158","count":1},{"id":"GO:2000637","count":1}]},{"hash":"737207267329285008","title":"G-protein signaling in development","description":"The top GO terms point to G-protein signaling (protein heterotrimerization and GTPase activity) with broader involvement in MAPK signaling and cell cycle processes, plus developmental themes (brain, skeletal system, hair follicle placode). A vesicle transport term and glucose signaling further suggest signaling/trafficking roles tied to growth and development. Overall, these proteins appear linked to G-protein\u2013mediated signaling affecting development and cell division. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071701","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0060789","count":2}]},{"hash":"1483500487773189150","title":"Unknown","description":"GO terms are scattered across metabolism, DNA replication/repair, cytoskeleton, development, fertilization, and include obsolete annotations; there is no cohesive shared function or pathway linking the six proteins, so a specific label cannot be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0019740","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0032933","count":1},{"id":"GO:0051016","count":1}]},{"hash":"2250052762411093684","title":"GPCR-mediated cAMP/cGMP Signaling","description":"These proteins cluster around GPCR-linked signaling pathways that regulate cyclic nucleotide second messengers, including cGMP biosynthesis (receptor guanylyl cyclase, cGMP biosynthetic process) and cAMP production (adenylate cyclase-activating pathways, forskolin response, adenosine receptor signaling). Intracellular signal transduction ties these processes together, suggesting a shared function in GPCR-driven second messenger cascades. Some terms like hypoxia detection and transcription regulation appear peripherally but do not define the core theme. Confidence: High","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007168","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0035556","count":1},{"id":"GO:0030828","count":1},{"id":"GO:0006171","count":1}]},{"hash":"1862544587307453843","title":"Ribosome biogenesis and translation","description":"The top GO terms are centered on translation and rRNA maturation (maturation of 5.8S and LSU rRNA), cytoplasmic translation, and RNA capping/methylation steps, which together point to roles in ribosome assembly and mRNA processing for protein synthesis. Some viral-related terms appear but do not define the main function of the cluster.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0019062","count":1}]},{"hash":"869687876242450343","title":"Ribosome biogenesis and translation","description":"The terms cluster around ribosome assembly and function, including ribosome biogenesis, maturation of SSU-rRNA, subunit export from the nucleus, and core translation steps such as initiation and termination, indicating these proteins are linked to ribosome production and protein synthesis.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0001732","count":1}]},{"hash":"404522875437419990","title":"Unknown","description":"The terms span innate immunity, DNA damage recognition, post-translational modification (neddylation, sumoylation), transcriptional regulation, snoRNP assembly, and metabolic regulation, with no clear shared function linking all proteins. Therefore no cohesive label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0045116","count":2},{"id":"GO:0000715","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0000122","count":2}]},{"hash":"195705911997104195","title":"Mitochondrial Translation and Electron Transport","description":"This cluster is enriched for translation and mitochondrial respiration terms (mitochondrial respiratory chain complex II assembly and NADH to ubiquinone electron transport), plus rRNA maturation, suggesting a link between mitochondrial protein synthesis and oxidative phosphorylation. The additional regulatory terms (transcription, cell cycle, and apoptosis/necroptosis regulation) likely reflect mitochondria's broader roles in signaling and cell fate. Overall, the proteins appear to coordinate mitochondrial gene expression with respiratory function and related signaling.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0034553","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0031564","count":1}]},{"hash":"296866798325123412","title":"Ribosome Biogenesis and RNA Methylation","description":"This cluster centers on ribosome biogenesis and assembly, with multiple terms for cytosolic ribosome assembly and LSU rRNA maturation, complemented by RNA modification steps (rRNA and tRNA methylation, mRNA capping). The combination points to a cohesive role in building ribosomes and ensuring RNA quality for translation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070131","count":2},{"id":"GO:0042256","count":2},{"id":"GO:0002127","count":2},{"id":"GO:0070475","count":2},{"id":"GO:0006355","count":2}]},{"hash":"2180906108472821048","title":"Embryonic neural and craniofacial development","description":"The cluster is dominated by GO terms related to early neural and craniofacial formation, including neural tube development, forebrain development, and face development, with additional embryonic morphogenesis terms (forelimb morphogenesis). Metabolic processes are a minor component, not defining the cluster.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019545","count":6},{"id":"GO:0021915","count":6},{"id":"GO:0019413","count":6},{"id":"GO:0030900","count":6},{"id":"GO:0006537","count":6}]},{"hash":"2209250805229673529","title":"Ribosome maturation and translation regulation","description":"The GO terms are centered on translation (GO:0006412), regulation of translation (GO:0006417), and maturation of SSU-rRNA (GO:0000462), indicating a focus on ribosome biogenesis and protein synthesis. Obsolete acetylation terms appear as noise but do not change the main theme. Overall, the cluster seems to represent ribosome assembly/translation processes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0033119","count":1}]},{"hash":"50573696598855843","title":"ER-Golgi Vesicle Transport and Protein Localization","description":"This cluster is best described by terms centering around intracellular trafficking between the ER and Golgi, targeting to vacuoles, and endosome/vacuole transport pathways, as well as protein retention/localization in the ER lumen. While a few terms touch on signaling and development, the strongest shared function across members is vesicle-mediated transport and protein localization within the secretory and endosomal systems.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0006890","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0071340","count":1}]},{"hash":"2206585673137357593","title":"DNA replication and chromosome maintenance","description":"The major GO terms point to DNA replication, chromosome separation, DNA topology, and telomere maintenance, indicating a core genome maintenance module for the cluster. A few RNA-processing terms appear but do not override the dominant DNA-related functions.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009307","count":2},{"id":"GO:0043007","count":2},{"id":"GO:0051304","count":2},{"id":"GO:1902969","count":2},{"id":"GO:0006265","count":2}]},{"hash":"169832926415342588","title":"Unknown","description":"The terms span metabolism (thiamine biosynthesis, glycerol-3-phosphate catabolism), RNA processing and chromatin modification (spliceosome, tRNA wobble modification, histone methylation/deacetylation), and even brain development, with no single shared function linking all proteins, so no well-defined cluster label can be assigned.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009229","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0046168","count":1},{"id":"GO:0051572","count":1}]},{"hash":"2018424296955052361","title":"Actin Cytoskeleton and Microvilli Organization","description":"These GO terms center on actin-based structures and their organization, including cell polarity and shape maintenance, sarcomere-related and cortex/microvilli features (microvillus length, terminal web), and related transport processes. The intestinal glucose absorption term reinforces the epithelial microvilli context. Together, the cluster points to actin cytoskeleton organization and microvilli/polarity control as the shared theme.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071963","count":3},{"id":"GO:0045214","count":2},{"id":"GO:0051666","count":2},{"id":"GO:0001951","count":2},{"id":"GO:0032532","count":2}]},{"hash":"1840627242147616324","title":"Intracellular trafficking and organelle dynamics","description":"The top GO terms center on vesicle transport and organelle dynamics (endosome\u2013lysosome transport, Golgi/vesicle transport, protein localization to complexes, mitochondrial fission) and related stress responses (ER stress). While some terms (copper homeostasis, dendritic spine development) are less directly about trafficking, the dominant pattern points to intracellular transport and organelle remodeling as the core function of this cluster.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006878","count":3},{"id":"GO:1902824","count":3},{"id":"GO:0060999","count":3},{"id":"GO:0031584","count":3},{"id":"GO:1990386","count":3}]},{"hash":"732848587831005962","title":"Vesicle trafficking and autophagy","description":"The top GO terms center on membrane trafficking and autophagy, including autophagosome maturation, inter-Golgi vesicle transport, intralumenal vesicle formation, and SNARE complex disassembly, which together point to vesicle trafficking and autophagic processes as the cluster\u2019s core theme. Some other terms (e.g., cell division, mitochondrial complex III assembly, blastocyst development, dephosphorylation) seem less specific to this theme, suggesting additional context but not overriding the main signal.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0097352","count":1},{"id":"GO:0048219","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0070676","count":1}]},{"hash":"1513331575223035552","title":"Membrane lipid and sterol biosynthesis","description":"The top GO terms cluster around lipid and sterol metabolism (mannosyl-inositol phosphorylceramide metabolic process, ergosterol biosynthetic process, and unsaturated fatty acid biosynthetic process), suggesting membrane lipid production and sterol biosynthesis as a unifying theme. Some terms (myelin maintenance, sebaceous gland differentiation, nitrate assimilation, nitric oxide biosynthesis) are less connected to lipid metabolism and may reflect broader, less specific annotations.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":5},{"id":"GO:0032286","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0001949","count":5},{"id":"GO:0000001","count":5}]},{"hash":"479454846060624646","title":"DNA Damage Response and Mitosis Checkpoints","description":"This cluster centers on cell cycle control and DNA repair, with multiple terms about mitotic checkpoint signaling, spindle-kinetochore attachment, and nonhomologous end joining, indicating a cohesive theme around DDR during mitosis. Some terms are unrelated or obsolete, but the dominant pattern supports a DDR/mitosis function. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051343","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0014044","count":5},{"id":"GO:0009742","count":5},{"id":"GO:0061587","count":5}]},{"hash":"879334109289697997","title":"Ubiquitination and Related PTMs","description":"The top GO terms are ubiquitination, neddylation, and sumoylation, all post-translational modifications of proteins, suggesting the cluster centers on proteins involved in ubiquitin-like modification systems. Other terms are heterogeneous and less informative, but the repeated enrichment for ubiquitin-related processes supports a cohesive theme. Given the small size and lack of network structure, the label focuses on the shared modification functions of these proteins.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0045116","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0051343","count":1},{"id":"GO:0042220","count":1}]},{"hash":"2234635494776269501","title":"Membrane Transport and Lipid Homeostasis","description":"The top GO terms cluster around membrane transport (sodium ion, carbohydrate, and transmembrane transport) and lipid-related processes (lipid homeostasis, ubiquinone/tocopherol regulation), suggesting a membrane-associated, lipid-metabolism connection. However, the presence of unrelated terms (brain morphogenesis, histone methylation, translesion synthesis) and several obsolete terms indicate weak cohesion, so the label is tentative.","confidence":"Low","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":1},{"id":"GO:0008643","count":1},{"id":"GO:0055085","count":1},{"id":"GO:0010795","count":1},{"id":"GO:0055088","count":1}]},{"hash":"1120800558166426094","title":"Unknown","description":"The GO terms across the 5 proteins are highly diverse, covering lipid signaling (SREBP), actin dynamics, epithelial proliferation in prostate development, DNA damage response, DNA replication, histone modification (obsolete), fertilization, ER-Golgi transport, and glucose-responsive invasive growth. There is no clear shared pathway or function tying them together, and the graph has no edges, suggesting independent or unrelated roles. Therefore this cluster is best labeled Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":1},{"id":"GO:0051016","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0072432","count":1},{"id":"GO:1903461","count":1}]},{"hash":"1393224206531404212","title":"Fungal stress response and apoptosis regulation","description":"The top GO terms point to cellular stress responses (e.g., response to antibiotic, unfolded protein response, ER stress\u2013related apoptotic signaling, hydrogen peroxide) and regulation of these pathways, with a few fungal-specific processes (beta-glucan biosynthesis, karyogamy) that hint at a fungal context. The shared theme is how cells respond to stress and modulate apoptosis, rather than a single, narrow function, so a label emphasizing stress response and cell fate regulation is appropriate. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0006880","count":1},{"id":"GO:0034620","count":1},{"id":"GO:0000902","count":1},{"id":"GO:1900035","count":1}]},{"hash":"2055160162478911615","title":"Unknown","description":"The terms include immune signaling, protein degradation, cell adhesion, extracellular matrix metabolism, plant development, and neuronal growth, spanning multiple species with no unifying function; the cluster appears functionally heterogeneous.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":1},{"id":"GO:0007229","count":1},{"id":"GO:0030212","count":1},{"id":"GO:0002291","count":1},{"id":"GO:0048455","count":1}]},{"hash":"1673783993326836406","title":"Amino acid biosynthesis and related metabolism","description":"The terms cluster around biosynthetic processes for amino acids (including aromatic amino acids and cysteine-related pathways), transsulfuration, and related metabolic biosynthesis (plus a few non-specific or obsolete terms like PHB and coenzyme M biosynthesis). This points to a general theme of amino acid and related metabolic biosynthesis, rather than a single highly specific pathway. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0019295","count":1},{"id":"GO:0019346","count":1},{"id":"GO:0042866","count":1}]},{"hash":"853558062467364647","title":"Unknown","description":"The top terms cover lipid homeostasis, keratinization, NF-kappaB regulation, ROBO signaling, interferon production, axon guidance, endocytic recycling, heart contraction, ribosomal export, and dendritic spine development. This diverse mix does not point to a single coherent function or pathway, spanning skin, neural development, immune signaling, and muscle processes, so a unifying label isn\u2019t evident.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055091","count":3},{"id":"GO:0031424","count":3},{"id":"GO:0043124","count":3},{"id":"GO:0035385","count":3},{"id":"GO:0032729","count":3}]},{"hash":"809224383227215768","title":"Phytochrome signaling and jasmonate pathways","description":"The GO terms strongly point to plant-specific signaling: red and far-red light responses and phototransduction indicate phytochrome-mediated light signaling, while jasmonic acid mediation signals a jasmonate pathway involved in plant defense and development. The presence of flower development regulation and cell cycle/chromatin regulation terms fits plant developmental control. Together, these terms suggest a cluster centered on light-regulated plant development and hormone signaling, rather than a general animal or microbial process.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035563","count":1},{"id":"GO:0009911","count":1},{"id":"GO:0048147","count":1},{"id":"GO:0009867","count":1},{"id":"GO:0071158","count":1}]},{"hash":"796783870741171480","title":"ER Proteostasis and Quality Control","description":"Based on the strong emphasis on endoplasmic reticulum\u2013related protein folding, ER stress\u2013responsive translation, protein targeting and transport, and ubiquitin-proteasome\u2013mediated quality control, the cluster appears to represent ER-associated proteostasis mechanisms that ensure proper folding and clearance of misfolded proteins. Some terms are peripheral noise, but the core signal centers on ER quality control.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0051259","count":1},{"id":"GO:0071374","count":1},{"id":"GO:1905259","count":1}]},{"hash":"1023182315179569849","title":"Cell cycle control and DNA damage response","description":"This cluster is driven by GO terms indicating tight regulation of cyclin-dependent kinase activity and DNA damage\u2013responsive cell cycle arrest (CDK regulation, p53-mediated pathway), plus related nuclear processes (nuclear export, kinetochore localization) and cell death. While there are some development-related terms (brain regions, keratinocyte differentiation), the dominant theme is cell cycle control and DNA damage signaling. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0021766","count":2}]},{"hash":"1461382140456580625","title":"Unknown","description":"The terms span DNA replication, metabolism, spermatogenesis, protein homeostasis, unfolded protein response, and stress signaling with no single dominant function, indicating a heterogeneous cluster without a clear shared theme.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0045732","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0006595","count":1},{"id":"GO:0090316","count":1}]},{"hash":"2272810266079835586","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000028","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0009451","count":1},{"id":"GO:0070129","count":1}]},{"hash":"1233480137538233739","title":"Spliceosome-Mediated mRNA Splicing and Stress Response","description":"These proteins are enriched for processes tied to mRNA splicing via the spliceosome (including regulation and alternative splicing) and stress-related mRNA regulation, such as localization to cytoplasmic stress granules and mRNA stability in stress. A few terms touch on transcription termination, but the dominant signal is post-transcriptional RNA processing and splicing. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0010610","count":3},{"id":"GO:1903608","count":2}]},{"hash":"2280712702064237834","title":"GPCR-driven cGMP and cAMP signaling","description":"This cluster is dominated by GO terms for receptor guanylyl cyclase signaling and GPCR pathways, with multiple links to cGMP and cAMP biosynthesis, various GPCR-mediated signaling routes (adenylate cyclase-activating adrenergic/adenosine receptor pathways), and forskolin responses, all pointing to a coherent GPCR-driven second-messenger signaling module that can influence transcriptional regulation.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007168","count":3},{"id":"GO:0070483","count":3},{"id":"GO:0035556","count":3},{"id":"GO:0030828","count":3},{"id":"GO:0006171","count":3}]},{"hash":"1926147433554036433","title":"Sterol and lipid biosynthesis","description":"This cluster is dominated by GO terms for sterol and lipid metabolism, including ergosterol and cholesterol biosynthesis, fatty acid biosynthesis, and ether lipid metabolism, as well as sterol-related oxidation steps. Additional terms related to lipid-rich biological contexts (myelin maintenance and sebaceous gland differentiation) reinforce a lipid/sterol-centric theme. A couple of terms (glutamate biosynthesis, B cell chemotaxis) are less directly connected but do not override the main lipid signal. Overall, the label captures the core functional theme of the cluster.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0097054","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0080065","count":2},{"id":"GO:0006696","count":2},{"id":"GO:0032286","count":2}]},{"hash":"2160480478344364600","title":"Ribosome biogenesis and translation","description":"The Top Terms are dominated by ribosome-related processes (ribosome biogenesis, ribosomal subunit biogenesis/export, and tRNA modification), with a few terms tied to cell growth/division (cell cycle, cell division, septum). This suggests the cluster centers on ribosome assembly and translation-related functions, with some ancillary links to growth-related processes. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0090529","count":1}]},{"hash":"1255392353538876153","title":"Unknown","description":"The GO terms span cell cycle regulation, development (third ventricle and oocyte maturation), circadian rhythm, neural processes (synapse assembly and neuronal apoptotic signaling), cytoskeleton (microtubule polymerization), and various stress/metabolic responses (arsenic exposure, glycoprotein catabolic process). The broad and disparate functions do not converge on a single coherent theme, so no specific, representative label can be assigned.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0031571","count":1},{"id":"GO:0001556","count":1},{"id":"GO:0042752","count":1}]},{"hash":"700068174536893700","title":"Regulated translation initiation and GTPase signaling","description":"Based on the top GO terms, the cluster shows enrichment for regulation of translational initiation (cytoplasmic and general) and positive regulation of GTPase activity, suggesting proteins involved in controlling protein synthesis and GTPase-mediated signaling. Methylation is also represented, which can influence translation, while other terms like responses to NO or ethylene and oligodendrocyte development are less cohesive with the main theme. Overall, the dominant signal points to translational control with signaling modulation, making this a reasonable high-level label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":2},{"id":"GO:0071732","count":1},{"id":"GO:0019284","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0006446","count":1}]},{"hash":"250333953820672334","title":"ER stress response and protein quality control","description":"This cluster\u2019s GO terms cluster around endoplasmic reticulum proteostasis: protein folding in the ER, ER stress\u2013driven regulation of translation, misfolded protein transport, and nuclear ubiquitin-proteasome\u2013mediated quality control, pointing to ER-associated folding/degradation pathways. Some terms (mesoderm formation, parathyroid hormone response) are less directly connected, but the dominant signals support an ER folding/quality-control theme.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0051259","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0006452","count":1}]},{"hash":"1248672324963830838","title":"MAPK signaling and redox regulation","description":"Based on terms showing ERK5 and p38MAPK cascades, the cluster aligns with MAPK signaling. Additional redox-related terms (hydrogen peroxide metabolism, respiratory burst) and inflammatory/endothelial context suggest a broader MAPK-driven, redox-regulated inflammatory signaling role. Confidence is moderate given the diversity of terms but a coherent MAPK-redox theme is evident.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000667","count":1},{"id":"GO:1900745","count":1},{"id":"GO:0045668","count":1},{"id":"GO:0060263","count":1},{"id":"GO:0045217","count":1}]},{"hash":"334807699054433715","title":"Nitrogen Metabolism and Symbiont Host Interaction","description":"The cluster's strongest coherent theme is nitrogen metabolism, with terms for nitrogen fixation, cellular response to nitrogen starvation, and ammonia assimilation. The presence of additional terms related to host interaction and regulation suggests some annotation noise, but nitrogen metabolism is the most representative function across the set.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009399","count":2},{"id":"GO:0006995","count":1},{"id":"GO:0019676","count":1},{"id":"GO:0050679","count":1},{"id":"GO:0009405","count":1}]},{"hash":"2295030161316646282","title":"Spindle Orientation and Microtubule Regulation","description":"The top GO terms cluster around spindle assembly and microtubule dynamics\u2014establishment of spindle orientation, kinetochore-microtubule attachment, centrosome separation, and general regulation of microtubule-based processes\u2014pointing to a cohesive role in organizing the spindle and supporting cell division. A few terms related to tissue development and neuron morphology may reflect broader cytoskeletal functions in growth and differentiation, but the dominant signal is spindle/microtubule control.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051296","count":4},{"id":"GO:0099607","count":4},{"id":"GO:0000911","count":4},{"id":"GO:0036334","count":4},{"id":"GO:0032886","count":4}]},{"hash":"1106673561960063895","title":"Lipid and Energy Metabolism","description":"GO terms point to metabolic and lipid-related processes, including cholesterol and propionyl-CoA metabolism, ketone body catabolism, isoleucine catabolism, lipid transport, and poly-hydroxybutyrate biosynthesis, with an additional mitochondrial regulation link. The common thread is metabolic energy management and lipid processing rather than a single, cohesive pathway.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019619","count":2},{"id":"GO:1901373","count":2},{"id":"GO:1902109","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0001889","count":2}]},{"hash":"450339089831529856","title":"RNA and protein methylation","description":"The cluster\u2019s top GO terms are dominated by methylation-related processes: tRNA wobble uridine modification, tRNA methylation, 7-methylguanosine mRNA capping, and various forms of peptidyl- and arginine methylation, suggesting a shared function in methylation-based modifications. While other terms like cofactor biosynthesis and xenobiotic responses appear, they are less central to this cluster\u2019s apparent theme.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0018012","count":1},{"id":"GO:0006744","count":1}]},{"hash":"22783325486067870","title":"Unknown","description":"The top GO terms are highly diverse and span lipid signaling, prostate development, DNA damage response, DNA replication, chromatin modification, fertilization, vesicle transport, glucose-responsive invasive growth, and cell cycle transitions. With no edges and a tiny, mixed set of proteins, there is no coherent shared function to name this cluster confidently.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":2},{"id":"GO:0060770","count":2},{"id":"GO:0072432","count":2},{"id":"GO:1903461","count":2},{"id":"GO:0043984","count":2}]},{"hash":"1865196679150395884","title":"Neuronal morphogenesis and signaling regulation","description":"The GO terms cluster around neuronal development and signaling\u2014dendrite morphogenesis, axonogenesis regulation, Wnt and JNK signaling, calcium-dependent exocytosis, and focal adhesion dynamics\u2014suggesting a theme of how signaling pathways control neuronal morphology and synaptic-related processes. Some mitosis-related terms may reflect shared cytoskeletal components, but the strongest signal points to neuronal development and signaling regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007100","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0043304","count":2}]},{"hash":"1068420794623774571","title":"Interneuron development and dendrite morphogenesis","description":"Most of the top GO terms cluster around neuronal development, especially interneuron generation, migration, and dendrite morphogenesis (dendrite morphogenesis, dendritic spine development, GABAergic interneuron development, olfactory bulb and cortical interneuron migration). Additional terms reflect cell polarity and actin remodeling (ruffle assembly), as well as vesicle docking/exocytosis. Altogether, these suggest a cohesive role in shaping interneuron dendrites during development, with supporting trafficking processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006904","count":3},{"id":"GO:0007107","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0071963","count":3},{"id":"GO:0060999","count":3}]},{"hash":"987187976455925623","title":"RNA splicing and post-transcriptional regulation","description":"This cluster centers on post-transcriptional RNA processing, especially splicing control via the spliceosome (including positive/negative regulation and alternative splicing), plus mRNA stability and polyadenylation regulation. There is an outlier term related to IRES-dependent translation, but the dominant signal is spliceosome-mediated RNA processing and ncRNA-mediated silencing, indicating a cohesive post-transcriptional regulatory theme.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0048025","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0045292","count":2}]},{"hash":"385419728980592831","title":"Genome maintenance and stress response","description":"The cluster centers on DNA metabolism, with GO terms for DNA recombination and DNA replication, and includes regulation of mRNA stability plus multiple stress-related responses (xenobiotic, cold, salicylic acid, thermoception, muscle stretch). This combination suggests proteins involved in genome maintenance that also modulate gene expression under stress, including meiotic recombination signals that align with genome dynamics.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0050955","count":1}]},{"hash":"2228964076010506580","title":"Spliceosome-Driven mRNA Processing","description":"The GO terms converge on RNA maturation, especially spliceosome-mediated splicing (including alternative splicing) and regulation of polyadenylation, tail shortening, and mRNA stability. This suggests the proteins function together in post-transcriptional mRNA processing and splicing regulation, with supportive signals like ncRNA-mediated silencing. Overall, a coherent theme of mRNA processing/splicing regulation emerges.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048025","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0060211","count":2}]},{"hash":"1138490491706779624","title":"Proteostasis and Autophagy Regulation","description":"The GO terms center on protein quality control and turnover, including sumoylation, ER-associated degradation (ERAD) of unfolded proteins, and modulation of proteasomal activity. They also highlight autophagy-related processes, such as mitophagy and autophagosome maturation regulation, plus vesicle formation and protein processing. Taken together, the cluster seems to reflect coordinated proteostasis through both proteasomal degradation and selective autophagy pathways (mitophagy), with a hint of broader cellular remodeling. Some terms (like cell morphogenesis in conjugation) are less central, but do not override the dominant proteostasis/autophagy theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0000753","count":3},{"id":"GO:1903265","count":3},{"id":"GO:1904378","count":3},{"id":"GO:1901799","count":3}]},{"hash":"724561136708678209","title":"Vesicle trafficking and membrane remodeling","description":"The top GO terms point to membrane-related processes: endosome transport, intralumenal vesicle formation, phosphatidylinositol signaling, and microvillus assembly, all tied to membrane dynamics and trafficking. Mitotic cytokinesis also involves coordinated membrane remodeling, supporting a unifying theme of vesicle trafficking and surface remodeling. A few terms (bone development, brood size, histamine secretion) appear peripheral, likely reflecting broader signaling roles across contexts rather than core cluster function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000281","count":2},{"id":"GO:0060348","count":1},{"id":"GO:0070676","count":1},{"id":"GO:1903595","count":1},{"id":"GO:0048015","count":1}]},{"hash":"1026183010675000312","title":"Th2 cytokine signaling in heart development","description":"This cluster centers on IL-4/IL-13\u2013related immune signaling and T-helper 2 differentiation, with multiple heart development terms such as endocardial cushion development, atrial septum morphogenesis, and cardiac tissue regeneration. The combination suggests a link between Th2 cytokine pathways and cardiac morphogenesis/regeneration processes. Confidence: Medium","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000667","count":2},{"id":"GO:0061026","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0045064","count":2},{"id":"GO:0032703","count":2}]},{"hash":"681429400992790877","title":"RNA transcription and rRNA processing","description":"Most terms point to transcription and RNA maturation (RNA polymerase II promoter clearance, RNA polymerase I transcription termination, ribosomal RNA processing such as ITS1 cleavage, and transcription-coupled DNA repair). A couple of development-related terms may reflect broader gene roles or annotation noise, but the dominant theme is RNA biosynthesis and processing.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001111","count":1},{"id":"GO:0018144","count":1},{"id":"GO:0016584","count":1},{"id":"GO:0006363","count":1},{"id":"GO:0000464","count":1}]},{"hash":"703198344829759269","title":"Autophagy and Vesicle Trafficking","description":"The top GO terms cluster around autophagosome maturation, vesicle transport between Golgi cisternae, intralumenal vesicle formation, and SNARE complex disassembly, pointing to proteins involved in intracellular membrane trafficking and autophagy pathways. Some terms (cell division, centriole elongation) may reflect multifunctional proteins, but the dominant pattern is vesicle formation/trafficking with autophagy involvement.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0097352","count":2},{"id":"GO:0048219","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0034551","count":2}]},{"hash":"403976866001887377","title":"Nuclear transcription and DNA replication","description":"Top terms cluster around core nuclear processes: DNA-templated transcription, DNA replication, and meiotic cell cycle, with a note on positive regulation of protein export from the nucleus. These central terms suggest a theme of nuclear gene expression and cell-cycle regulation, with a few peripheral annotations from signaling and metabolism. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0097338","count":1}]},{"hash":"559316980616355999","title":"Unknown","description":"The terms span multiple distinct biological themes (cell cycle regulation, RNA silencing, telomere maintenance, cardiac and Sertoli cell development, neural migration, histone mRNA turnover, and dopamine signaling) with no single cohesive function or tissue context. The lack of edges also suggests no shared pathway, so a specific, representative label isn\u2019t warranted.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045842","count":2},{"id":"GO:0031047","count":1},{"id":"GO:0032208","count":1},{"id":"GO:2000727","count":1},{"id":"GO:1903125","count":1}]},{"hash":"1409698884062037408","title":"Nuclear transcription and chromatin regulation","description":"This cluster centers on nuclear processes that control gene expression and DNA/chromatin dynamics: transcription elongation and regulation by RNA Pol II, chromatin organization, and related cell-cycle events such as DNA replication, chromosome condensation, and mitotic regulation. The inclusion of circadian gene expression and embryonic cleavage further suggests regulation of gene expression in developmental and timing contexts, all within the nucleus.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006357","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0007097","count":1},{"id":"GO:0006333","count":1},{"id":"GO:0032922","count":1}]},{"hash":"867603063057279211","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070481","count":1},{"id":"GO:0034475","count":1},{"id":"GO:0016973","count":1},{"id":"GO:0071034","count":1},{"id":"GO:0071042","count":1}]},{"hash":"696554149495209501","title":"Unknown","description":"The top GO terms span widely different processes (chromatin organization, transcription regulation, ribosomal assembly, RNA modification, DNA replication, protein maturation, vesicle trafficking, collagen catabolism), and there is no clear shared function or pathway linking them. With no coherent theme and no edges among proteins, a single informative label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034724","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0035551","count":1},{"id":"GO:0070475","count":1}]},{"hash":"1346633335305677553","title":"Unknown","description":"The top GO terms are diverse, spanning chromatin remodeling and mitotic processes, various developmental and organ-identity related terms, heart-rate regulation, ciliary transport, and even viral processes. There isn\u2019t a single clear function or pathway that ties these terms together, so the cluster does not map to a coherent biological theme.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0030466","count":3},{"id":"GO:0048096","count":3},{"id":"GO:0051211","count":3},{"id":"GO:0021550","count":3},{"id":"GO:0048496","count":3}]},{"hash":"1390294976233608222","title":"Proteostasis: ERAD, Proteasome, Autophagy","description":"This cluster shows strong representation of ubiquitin-proteasome and autophagy-related processes (ERAD pathway, proteasome-mediated degradation, autophagosome assembly), which together reflect cellular protein quality control and turnover. The other terms are less cohesive but may reflect peripheral connections to stress responses or cell cycle-related processes. Overall, the clearest shared theme is proteostasis through degradation pathways.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0031468","count":1},{"id":"GO:0000045","count":1},{"id":"GO:0008219","count":1},{"id":"GO:0031134","count":1}]},{"hash":"1831766821756981141","title":"DNA Damage Response and Ubiquitination","description":"This cluster centers on protein modification by ubiquitin and ubiquitin-like modifiers (neddylation/ubiquitination) and on DNA damage response and repair pathways, including error-free postreplication repair and mitotic G1 DNA damage checkpoint signaling. The co-occurrence of terms for neddylation, ubiquitin-protein transferase activity, K27-linked ubiquitination, and translesion synthesis, together with DNA repair and checkpoint processes, supports a cohesive theme of DNA damage sensing/repair regulated by ubiquitin-like modifications. Some terms such as viral process or Fc-epsilon receptor signaling appear ancillary or noisy relative to the core function. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0045116","count":4},{"id":"GO:0042275","count":4},{"id":"GO:0031571","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0016032","count":4}]},{"hash":"158480521166889644","title":"DNA Damage Response and Ubiquitination","description":"The set is dominated by ubiquitination and neddylation-related terms (protein neddylation; K27-linked ubiquitination; positive regulation of ubiquitin-protein transferase activity) and key DNA damage response processes (error-free postreplication DNA repair; mitotic G1 DNA damage checkpoint signaling; error-free translesion synthesis). These connect to protein modification and checkpoint/repair pathways, making a coherent theme around DNA damage response coordinated by ubiquitin-like modifications. Some terms like viral process and Fc-epsilon receptor signaling appear tangential, but do not override the central theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0045116","count":4},{"id":"GO:0042275","count":4},{"id":"GO:0031571","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0016032","count":4}]},{"hash":"1204708996559932519","title":"Secretory vesicle trafficking","description":"These four proteins cluster around vesicle trafficking and secretion functions, with GO terms including neutrophil/NK cell degranulation, Golgi-to-plasma membrane transport, vesicle fusion with Golgi, and synaptic vesicle exocytosis, indicating a shared role in secretory vesicle dynamics and exocytosis.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043320","count":1},{"id":"GO:0050775","count":1},{"id":"GO:0048280","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0043312","count":1}]},{"hash":"400133679019168569","title":"Unknown","description":"The two GO terms point to unrelated processes (phagosome-associated activity vs. nuclear import regulation during the spindle checkpoint), and there are no network connections among the proteins to reveal a common function. Because of the lack of a coherent theme, the cluster is best labeled Unknown with no confidence.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044655","count":1},{"id":"GO:1901925","count":1}]},{"hash":"1278546755032414055","title":"DNA Damage Repair and Genome Maintenance","description":"The dominant GO terms point to nucleotide-excision repair, error-free postreplication repair, translesion synthesis, and DNA damage checkpoint signaling, with neddylation and ubiquitin-protein transferase activity linking to repair regulation. Despite a few noisy or obsolete terms, the core function represented is genome integrity maintenance through DNA repair pathways.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":2},{"id":"GO:0045116","count":1},{"id":"GO:0042275","count":1},{"id":"GO:0031571","count":1},{"id":"GO:0051092","count":1}]},{"hash":"1573657375284262797","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0000453","count":2},{"id":"GO:0017183","count":1},{"id":"GO:0050843","count":1},{"id":"GO:0055114","count":1}]},{"hash":"542031160016889454","title":"Bacterial LPS core and sugar nucleotide biosynthesis","description":"The GO terms are dominated by LPS-related processes (O antigen biosynthesis, LPS core region biosynthesis) and sugar nucleotide biosynthesis (UDP-D-xylose, GDP-mannose, rhamnose, galactose, galacturonate, etc.), pointing to production of outer membrane polysaccharides and their precursors in bacteria. This combination suggests a cohesive role in cell envelope biosynthesis rather than a single metabolic pathway.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009243","count":2},{"id":"GO:0033320","count":2},{"id":"GO:0006012","count":2},{"id":"GO:0009244","count":2},{"id":"GO:0019673","count":2}]},{"hash":"1984518154659556518","title":"Cell fate specification and differentiation","description":"The top GO terms center on developmental decisions across tissues, including wing cell fate specification, cone cell fate commitment, spermatid differentiation, and EGFR ligand maturation, indicating a theme of cell fate specification and differentiation. Some terms about unfolded protein response and ER-to-cytosol proteolysis reflect the protein processing needed to support signaling and maturation in these developmental contexts, suggesting a cohesive though broad developmental differentiation theme rather than a single straightforward pathway.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034620","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0032815","count":1},{"id":"GO:1904211","count":1},{"id":"GO:0042676","count":1}]},{"hash":"1831720748647745349","title":"Glutamatergic receptor recycling","description":"The included GO terms point to endosomal trafficking and recycling of receptors, particularly in glutamatergic synapses (GO:0001881 receptor recycling; GO:0035249 synaptic transmission, glutamatergic). The regulation of endosome size (GO:0051036) and Rho signaling (GO:0035023) support a role in trafficking and cytoskeleton dynamics at synapses. While there are some general terms like transcription and RNA export, the standout themes are neuronal receptor recycling and glutamatergic synaptic function, suggesting this cluster represents components involved in recycling glutamatergic receptors at the synapse.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051036","count":1},{"id":"GO:0034968","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0060316","count":1},{"id":"GO:0006355","count":1}]},{"hash":"260509408064910882","title":"Cajal body RNA localization and telomerase RNA","description":"The most coherent signal in the terms is RNA localization to Cajal bodies, including scaRNA localization and telomerase RNA localization to Cajal bodies, suggesting a shared function in RNA trafficking within nuclear bodies and telomerase RNA handling. Some terms like response to cocaine or TNF production appear unrelated and may reflect incidental annotations or noise. Overall, the strongest theme is Cajal body\u2013associated RNA localization and telomerase RNA, justifying this label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0050821","count":3},{"id":"GO:1904874","count":3},{"id":"GO:0090666","count":3}]},{"hash":"2104022796809279391","title":"Neural vesicle trafficking and membrane biosynthesis","description":"This cluster centers on intracellular transport and membrane-related processes, including intracellular protein transport, ER membrane organization, and lipid biosynthesis (phosphatidylethanolamine and sphingolipid regulation), with supporting signals of brain development and synaptic transmission. While there are some immune-related terms present, the dominant theme appears to be neuronal trafficking and membrane biogenesis relevant to brain development and synaptic function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0002432","count":1},{"id":"GO:1904468","count":1},{"id":"GO:0090153","count":1}]},{"hash":"1883028330358186354","title":"Immune signaling and Wnt pathway cross-talk","description":"Top GO terms show immune receptor signaling (T cell receptor, Fc-epsilon receptor) and regulation of inflammatory responses, plus Wnt pathway activity (planar cell polarity and canonical Wnt signaling). This pattern suggests proteins involved in immune signaling with some cross-talk to Wnt pathways, rather than a single narrowly defined process. Confidence reflects moderate certainty given the mix of terms spanning immune signaling and Wnt regulation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":2},{"id":"GO:0060071","count":2},{"id":"GO:0002862","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0061418","count":2}]},{"hash":"653937623655435378","title":"Actin cytoskeleton organization and sarcomere assembly","description":"The cluster is dominated by GO terms related to actin dynamics (actin filament polymerization; actin cortical patch assembly/localization) and muscle architecture (sarcomere organization; skeletal muscle fiber development), with supporting signals from calcium response and endocytosis regulation that tie into actin remodeling. Some terms such as meiotic chromosome movement and vacuole inheritance may reflect broader cytoskeletal roles or annotation noise, but the core theme points to actin cytoskeleton organization and sarcomere/muscle structure formation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030100","count":3},{"id":"GO:0051592","count":3},{"id":"GO:0000011","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0016344","count":3}]},{"hash":"1849278167034660317","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The top GO terms show a cohesive theme around meiosis and oocyte maturation, including spindle assembly in female meiosis I, microtubule polymerization, and ubiquitin-proteasome\u2013related protein turnover, indicating involvement in meiotic progression and spindle dynamics in oocytes. While a few terms touch on broader development, the dominant signal is meiotic/oocyte-specific processes, supporting this label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":1},{"id":"GO:0070544","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0007057","count":1},{"id":"GO:0021993","count":1}]},{"hash":"809552723389701158","title":"Autophagy-Linked Vesicle Trafficking","description":"This cluster is driven by GO terms tied to autophagy and vesicle transport, including autophagosome maturation, intralumenal vesicle formation, SNARE complex disassembly, and inter-Golgi vesicle transport, which together suggest a shared function in autophagy-related vesicle trafficking. Some terms related to cell division and ubiquitin regulation appear as secondary associations, but the dominant theme is vesicle trafficking linked to autophagy.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0097352","count":3},{"id":"GO:0048219","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0070676","count":3},{"id":"GO:0034551","count":3}]},{"hash":"853522164071366392","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (neural plasticity regulation, mast cell chemotaxis, defense against protozoa, transcription regulation, complement-mediated cytotoxicity, keratinocyte development, embryonic interneuron migration, Rab signaling, phospholipid homeostasis). There is no clear, single functional theme or pathway linking these proteins, and the terms do not point to a cohesive module, so a specific, representative label cannot be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048169","count":3},{"id":"GO:0060753","count":3},{"id":"GO:0042832","count":3},{"id":"GO:0000083","count":3},{"id":"GO:0097278","count":3}]},{"hash":"989535862871027354","title":"SR Ca2+ Release Regulation","description":"Based on the GO terms, the cluster centers on regulation of calcium release from the sarcoplasmic reticulum, particularly through ryanodine-sensitive channels, indicating a shared calcium signaling function. The presence of additional terms related to redox homeostasis may reflect ancillary cellular stress responses, but the dominant theme is SR Ca2+ release regulation. The small cluster size with linked calcium-regulatory terms supports a coherent functional module around calcium signaling.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010880","count":2},{"id":"GO:0042994","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0060315","count":2},{"id":"GO:2000255","count":2}]},{"hash":"1231271527722726774","title":"Unknown","description":"The GO terms span lipid signaling (SREBP pathway), cell cycle and DNA replication processes (G1 checkpoint signaling, Okazaki fragment processing), chromatin modification (histone acetylation/deacetylation), vesicle transport (ER to Golgi), and various growth or fertilization-related processes. This diverse mix does not point to a single cohesive function or pathway, so no intuitive, specific label can be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032933","count":3},{"id":"GO:0060770","count":3},{"id":"GO:0072432","count":3},{"id":"GO:1903461","count":3},{"id":"GO:0043984","count":3}]},{"hash":"1309518210594033629","title":"Unknown","description":"The listed GO terms are highly heterogeneous (associative learning, chiasma assembly, RNA polymerase activities, nucleosome positioning, rRNA processing, DNA repair, renal development) and there are no edges or interactions among the proteins in the cluster. Several terms are obsolete, suggesting annotation noise rather than a unified function. There isn\u2019t a clear, shared theme to tie these proteins together, so Unknown with no confidence is the appropriate label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008306","count":2},{"id":"GO:0051026","count":2},{"id":"GO:0001111","count":1},{"id":"GO:0018144","count":1},{"id":"GO:0016584","count":1}]},{"hash":"2263787637467393071","title":"Actin Cytoskeleton Dynamics and Endocytosis","description":"The Top Terms are dominated by actin-related processes (actin cortical patch localization/assembly, actin filament polymerization) and regulation of endocytosis, with additional cytoskeletal-associated terms (vacuole inheritance, sarcomere organization). This points to a common theme of actin cytoskeleton remodeling linked to membrane trafficking, rather than a single tissue- or organelle-specific function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030100","count":3},{"id":"GO:0051592","count":3},{"id":"GO:0000011","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0016344","count":3}]},{"hash":"1859341933554769729","title":"RNA pseudouridylation and ribosome biogenesis","description":"The cluster is dominated by GO terms for pseudouridine synthesis on rRNA and tRNA, plus rRNA processing and ribosomal large subunit biogenesis, indicating a focus on RNA modification and ribosome assembly.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000455","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0015684","count":1}]},{"hash":"583169408051140398","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000393","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0018144","count":2},{"id":"GO:0000480","count":2}]},{"hash":"1685226809182896918","title":"Cajal body RNA localization and telomerase regulation","description":"The dominant GO terms point to RNA localization to Cajal bodies (scaRNA and telomerase RNA) and regulation of telomerase activity, suggesting a nuclear RNA-processing/telomerase assembly role centered on Cajal bodies. Other terms (e.g., response to cocaine, cell division) are less cohesive with this core theme, so the label emphasizes the RNA-processing/telomerase context within Cajal bodies.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0050821","count":3},{"id":"GO:1904874","count":3},{"id":"GO:0090666","count":3}]},{"hash":"2092341893291005890","title":"Meiosis and DNA repair","description":"The terms point to meiotic recombination processes (homologous chromosome pairing at meiosis, meiotic joint molecule formation, t-circle formation) and DNA repair/damage responses (interstrand cross-link repair, response to X-ray, response to toxic substance). Some development-related terms (spermatid development, blastocyst growth) fit with germ cell development and early embryogenesis, reinforcing a meiotic/gametogenesis context. Together, the strongest common theme is meiosis-associated recombination and DNA repair.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001832","count":1},{"id":"GO:0000732","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0007129","count":1},{"id":"GO:0000709","count":1}]},{"hash":"1030237332098069295","title":"Proteostasis and Stress Signaling","description":"These proteins cluster around maintaining protein homeostasis (protein stabilization, negative regulation of amyloid fibril formation) while engaging stress response pathways (stress-activated MAPK cascade, regulation of cellular response to heat) and cytoskeletal/trafficking dynamics (anterograde axonal transport, microtubule polymerization/depolymerization). The shared theme is proteostasis under cellular stress, integrated with transport and microtubule regulation, rather than a single developmental or tissue-specific function.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":1},{"id":"GO:0032387","count":1},{"id":"GO:0050821","count":1},{"id":"GO:1905907","count":1},{"id":"GO:0099641","count":1}]},{"hash":"1892006442992168173","title":"Redox-Responsive Developmental Regulation","description":"The top GO terms point to redox state sensing and oxidative/reductive processes, with notes on responses to redox state and antioxidants, alongside regulation of transcription and developmental events (heart morphogenesis and trabecula formation) and neuronal signaling. This suggests a theme where cellular redox status influences gene regulation and developmental pathways, rather than a single narrowly defined function. Confidence: Medium.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0051301","count":1},{"id":"GO:0061077","count":1},{"id":"GO:0000412","count":1}]},{"hash":"1270735054122404082","title":"Lipid biosynthesis and fatty acid metabolism","description":"GO terms cluster around lipid production and modification (fatty acids, sphingolipids, sterols, phylloquinone), with a few unrelated terms; overall indicates a lipid metabolism theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031427","count":1},{"id":"GO:0042438","count":1},{"id":"GO:0008207","count":1},{"id":"GO:0042619","count":1},{"id":"GO:0042208","count":1}]},{"hash":"1333736238632501100","title":"Signaling and Proteostasis Regulators","description":"The top GO terms indicate involvement in regulating signaling pathways (TLR3, TNF), transcription, and proteostasis processes (proteasomal degradation, ERAD maintenance), plus some metabolic regulation terms. This pattern suggests a set of proteins that broadly regulate signaling and protein quality control, rather than a single, cohesive pathway, justifying a label focused on signaling and proteostasis regulation.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034140","count":2},{"id":"GO:0000753","count":1},{"id":"GO:0045759","count":1},{"id":"GO:0045944","count":1},{"id":"GO:1903265","count":1}]},{"hash":"947465242482001283","title":"Ubiquitin-Proteasome\u2013Mediated Proteolysis","description":"These proteins are enriched for ubiquitination and proteasome-dependent degradation (SCF and APC/C pathways) and neddylation, with cell division terms reinforcing a role in ubiquitin-mediated proteolysis during the cell cycle.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045116","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0031146","count":3}]},{"hash":"562011826516354354","title":"Unknown","description":"The three proteins carry unrelated GO terms (mitochondrial respiratory chain complex II assembly; pollen sperm cell differentiation; translation) and have no connecting edges, so there is no clear shared function uniting them.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0006412","count":1}]},{"hash":"2087095432207889121","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0000393","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0035640","count":1}]},{"hash":"629312601144314518","title":"Ribosome biogenesis and RNA processing","description":"The predominant terms are translation and ribosome biogenesis, plus snoRNP assembly, snRNA pseudouridine synthesis, and nonsense-mediated decay, pointing to RNA maturation and ribosome production as the cluster\u2019s core; a few signaling terms are present but not defining. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0048025","count":1},{"id":"GO:0000185","count":1},{"id":"GO:0046330","count":1}]},{"hash":"1747822689093879805","title":"Translation machinery and ribosome biogenesis","description":"The top GO terms point to core components of protein synthesis and RNA processing: cytoplasmic and general translation, tRNA aminoacylation, ribosome biogenesis, and rRNA pseudouridylation. These collectively define the translation apparatus and ribosome assembly/modification pathways, with some regulatory terms (e.g., negative regulation of translational initiation) reflecting control of translation fidelity. Despite the presence of one transcription term, the dominant theme is translation machinery and RNA modification.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0045947","count":1},{"id":"GO:1990145","count":1},{"id":"GO:0006437","count":1}]},{"hash":"1743565574080302552","title":"Cell cycle and signaling regulation","description":"The top terms show strong enrichment for cell cycle (GO:0007049) and negative regulation of ERK1/ERK2 cascades (GO:0070373), pointing to control of cell division via signaling pathways. Additional terms related to ubiquitin-protein transferase activity, ribophagy, and Wnt signaling suggest involvement in proteostasis and growth signaling linked to proliferation. Overall, the cluster appears to reflect proteins coordinating cell-cycle progression with signaling and protein turnover.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0070373","count":2},{"id":"GO:0045732","count":1},{"id":"GO:0010793","count":1},{"id":"GO:0090263","count":1}]},{"hash":"137656259431742880","title":"Unknown","description":"The GO terms are scattered across nucleolus organization, temperature/thermal responses, muscle stretch, salicylic acid response, and various differentiation/regulation terms, with several obsolete terms as well. There is no clear, shared function or pathway tying the proteins together, so a coherent label cannot be inferred.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007000","count":1},{"id":"GO:0050955","count":1},{"id":"GO:0035994","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0002268","count":1}]},{"hash":"1657418572478087585","title":"Neural development and embryonic morphogenesis","description":"This cluster is driven by neural development and embryogenesis terms\u2014fasciculation of sensory neuron axons, embryonic cranial skeleton morphogenesis, and multicellular organism development (with Wnt signaling)\u2014indicating a cohesive theme of neural morphogenesis and developmental signaling.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0097155","count":3},{"id":"GO:0006935","count":3},{"id":"GO:0090153","count":3},{"id":"GO:0071374","count":3},{"id":"GO:0042997","count":3}]},{"hash":"2208363315542207124","title":"Immune Signaling and ECM Remodeling","description":"The proteins appear to participate in immune signaling pathways (TLR3 signaling, IL-2 production, T cell polarity) along with processes of cell adhesion and extracellular matrix remodeling (cadherin-mediated adhesion, ECM disassembly). Some terms (SREBP signaling, inner mitochondrial membrane organization) are more general or metabolic, but the strongest signals cluster around immune activation coupled with changes in cell\u2013cell and matrix interactions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":2},{"id":"GO:2000049","count":2},{"id":"GO:0052547","count":2},{"id":"GO:0007007","count":2},{"id":"GO:0022617","count":2}]},{"hash":"1803542411096949319","title":"ECM catabolic regulation","description":"The top GO terms include negative regulation of elastin and collagen catabolic processes, pointing to inhibition of extracellular matrix breakdown. While other terms (endothelial chemotaxis, bone mineralization, circadian rhythm, xenobiotic response, and sperm binding) are more varied and less cohesive, the shared signal across the cluster is regulation of ECM catabolism. I label this cluster ECM catabolic regulation to reflect the strongest, specific theme, with the caveat that the small size and mixed terms may reflect multifunctional proteins. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060311","count":1},{"id":"GO:2001027","count":1},{"id":"GO:0042747","count":1},{"id":"GO:0010711","count":1},{"id":"GO:0009743","count":1}]},{"hash":"1581901862229521519","title":"Photoreceptor cell organization and morphogenesis","description":"The top GO terms are strongly photoreceptor-focused (photoreceptor outer segment organization and photoreceptor morphogenesis), suggesting a cohesive retina-related role for this cluster. While other terms touch on cell cycle and neural development, the clearest signal is photoreceptor development and organization, indicating proteins likely function together in photoreceptor structure and maturation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035845","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000278","count":2}]},{"hash":"908221252561177310","title":"Oxidative stress and innate immune responses","description":"The proteins in this cluster appear enriched for oxidative stress response (cellular response to hydrogen peroxide) and innate antiviral defense terms (innate immune response, defense response to virus), suggesting a focus on stress-induced immune regulation. There is also a hint of ER-stress\u2013related translation regulation, but several other terms (cell division, leptin signaling, glucocorticoid signaling, histone modification, blood pressure regulation) seem peripheral, implying broader regulatory roles rather than a single cohesive pathway. Overall, the strongest shared themes are stress response and antiviral/immune signaling, though the connection is not tight across all members.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0050689","count":2},{"id":"GO:0045087","count":2}]},{"hash":"693619176971746067","title":"Terpenoid and aromatic compound metabolism","description":"The GO terms are dominated by catabolic and oxidative processes across diverse organic substrates: camphor catabolism, kaurene oxidation, isoquinoline alkaloid metabolism, carbazole catabolism, and lipid hydroxylation. This suggests a functional cluster of enzymes involved in oxidative metabolism and processing of terpenoids, aromatics, and related lipids, i.e., xenobiotic/secondary metabolite metabolism. A few terms about ion responses or cell-cycle regulation are present but don\u2019t define the core theme.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019383","count":1},{"id":"GO:0010760","count":1},{"id":"GO:0010241","count":1},{"id":"GO:0002933","count":1},{"id":"GO:1900087","count":1}]},{"hash":"1277005562680907887","title":"Ubiquitin-Dependent Protein Degradation","description":"The top terms are dominated by ubiquitination and proteasomal degradation (polyubiquitination, monoubiquitination, proteasomal ubiquitin-dependent protein catabolic process), pointing to a proteostasis-focused cluster. Vesicle trafficking and general homeostasis terms appear less strongly, but do not override the ubiquitin/proteasome theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070050","count":1},{"id":"GO:0055069","count":1},{"id":"GO:1903265","count":1},{"id":"GO:0099074","count":1},{"id":"GO:1902530","count":1}]},{"hash":"615982610126837069","title":"Innate immune signaling and ubiquitination","description":"The terms converge on innate immune defense against viruses, regulation of TLR/TNF signaling, and ubiquitin-related processes (monoubiquitination and polyubiquitination), suggesting a module of antiviral immune signaling coupled with protein ubiquitination.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":1},{"id":"GO:1901253","count":1},{"id":"GO:0048535","count":1},{"id":"GO:2000620","count":1},{"id":"GO:0045087","count":1}]},{"hash":"1979147256144184817","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning phosphoinositide signaling, aging, cell cycle regulation, renal water transport, glycogen synthase regulation, transcription, skin development, hemolysis, xenobiotic response, and cAMP signaling. With only three proteins and a single edge, there is no clear, cohesive function that unites these terms into a single, interpretable cluster label. ","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":2},{"id":"GO:0007568","count":1},{"id":"GO:1900087","count":1},{"id":"GO:2001153","count":1},{"id":"GO:2000466","count":1}]},{"hash":"1774599998555733312","title":"Neuronal-Immune Signaling and Development","description":"The terms include regulation of long-term neuronal synaptic plasticity and interneuron precursor migration, plus Rab protein signal transduction, which point to signaling/trafficking roles in neurons. Immune-related terms (defense against protozoan, complement-dependent cytotoxicity, mast cell chemotaxis) suggest broader signaling in immune contexts, while keratinocyte development and transcription regulation indicate tissue-wide regulatory roles. Overall, there is no single cohesive pathway, but a theme of signaling/trafficking proteins functioning across neural, immune, and epidermal development contexts.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048169","count":1},{"id":"GO:0060753","count":1},{"id":"GO:0042832","count":1},{"id":"GO:0000083","count":1},{"id":"GO:0006516","count":1}]},{"hash":"1419310080487833606","title":"Splicing and mRNA processing regulation","description":"The terms are dominated by spliceosome-mediated splicing, alternative splicing, and regulation of polyadenylation, with additional signals for mRNA stability and related post-transcriptional control. This points to a cohesive cluster centered on RNA processing and post-transcriptional regulation, despite a few outliers related to translation and RNA silencing.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048025","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0060211","count":1}]},{"hash":"2137950530667606856","title":"Unknown","description":"The top GO terms are diverse and largely unconnected (DNA damage tolerance, signal transduction, VEGF signaling, vesicle docking, equilibrioception, vacuole inheritance, neuroblast division), with several obsolete terms, and no edges or coherent shared pathway linking the proteins. There isn\u2019t a clear common function to label the cluster, so the appropriate designation is Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006301","count":1},{"id":"GO:0035556","count":1},{"id":"GO:2001022","count":1},{"id":"GO:1900748","count":1},{"id":"GO:1902405","count":1}]},{"hash":"2092162705676729502","title":"RNA Processing RNPs and Telomerase Assembly","description":"The GO terms cluster around snoRNP assembly and RNA modification (box H/ACA snoRNPs, snoRNA-guided pseudouridylation, ribosome biogenesis) as well as telomerase RNA regulation and holoenzyme assembly, suggesting involvement in RNA-processing RNP biogenesis including snoRNPs and telomerase complexes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904874","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000454","count":1},{"id":"GO:0000493","count":1}]},{"hash":"1377877770832539367","title":"Peptide hormone processing and secretion","description":"These proteins show GO terms related to maturation and release of signaling peptides and hormones (insulin processing, renin secretion, nerve growth factor production, peptide pheromone maturation). While an outlier term about sporulation appears, the dominant terms point to peptide/protein processing and secretion roles, suggesting a cohesive theme around peptide hormone maturation and release.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032805","count":1},{"id":"GO:0001920","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0032902","count":1},{"id":"GO:0007323","count":1}]},{"hash":"1299520824975428415","title":"Unknown","description":"The GO terms are scattered across diverse metabolic and regulatory processes (amino acid and lipid metabolism, insulin response, fruit ripening) with several obsolete annotations, giving no single coherent function for the three proteins. Therefore, no reliable cluster label can be assigned. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019550","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0015908","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0009835","count":1}]},{"hash":"1503389018271207387","title":"Unknown","description":"No GO terms or common function are evident for this trio; with only 3 proteins and sparse connectivity, there isn\u2019t a clear theme to label. Therefore Unknown with None confidence.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"720815221540833482","title":"Gluconeogenesis and Carbohydrate Metabolism","description":"GO terms point to gluconeogenesis and broader carbohydrate metabolism (glycerol and fructose/sucrose pathways) and glucose starvation response, suggesting a metabolic cluster focused on sugar handling and energy balance; the other terms (dephosphorylation, Ras signaling, xenobiotic response) may reflect broader regulatory context rather than core function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019563","count":1},{"id":"GO:0006111","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0042149","count":1}]},{"hash":"209156383614083096","title":"Zinc Ion Transport and Homeostasis","description":"The GO terms cluster around zinc handling: import across membranes, detoxification, intracellular homeostasis, and response to zinc starvation, indicating a shared role in zinc transport and cellular zinc balance. Some terms (e.g., limb development) appear incidental, but the dominant zinc-related terms support grouping these proteins as zinc transport/homeostasis factors.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":1},{"id":"GO:0006830","count":1},{"id":"GO:0010312","count":1},{"id":"GO:0044749","count":1},{"id":"GO:0006882","count":1}]},{"hash":"577803182139938840","title":"Unknown","description":"The three proteins show a highly diverse set of GO terms spanning lipid receptor catabolism, receptor recycling, sporulation, nerve growth factor production, pheromone maturation, protein processing, insulin processing, and hormone secretion. This broad mix suggests no single shared function or pathway binding the cluster, and there are no interactions evident (edges/triangles are zero). Therefore, a specific functional label cannot be reliably assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032805","count":1},{"id":"GO:0001920","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0032902","count":1},{"id":"GO:0007323","count":1}]}]