[{"hash":"1409336085894185263","title":"Ribosome Biogenesis and RNA Processing Core","description":"This cluster centers on fundamental cellular machinery: ribosome biogenesis, DNA replication, and RNA processing (splicing and polyadenylation), with additional hints of cytoskeletal and cell division components (tubulin assembly, division septum). Together these terms point to core gene-expression and genome-maintenance processes rather than a single specialized function.","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000917","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000381","count":2}]},{"hash":"1705566452121678588","title":"Membrane transporters for ions and metabolites","description":"The GO terms are dominated by transmembrane transport activities for diverse substrates (nitrate, nitrite, potassium, sodium, phosphate, arabinose, fucose, vitamins) and a vesicular neurotransmitter loading step, pointing to a cluster of proteins functioning primarily as membrane transporters moving ions and small molecules across membranes.","confidence":"High","size":29,"edges":36,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":5},{"id":"GO:0015707","count":4},{"id":"GO:1900754","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0098700","count":4}]},{"hash":"767143575029040917","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0000447","count":4},{"id":"GO:0000472","count":4}]},{"hash":"1774000574902025764","title":"Notch signaling and transcriptional regulation","description":"This cluster centers on Notch signaling and transcriptional control, with GO terms for the Notch pathway, DNA-templated transcription, and RNA polymerase II\u2013mediated transcription. The presence of estradiol response suggests hormone-related regulation, while the metabolic process terms (kynurenine, alanine catabolic, porphyrin biosynthesis) imply broader links between signaling, transcription, and metabolism. Together these terms point to a function in signaling-driven gene expression with ancillary metabolic connections.","confidence":"Medium","size":29,"edges":78,"triangles":226,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0071392","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0097053","count":3}]},{"hash":"1987271272726287289","title":"RNA processing and ribosome biogenesis","description":"The top GO terms are dominated by mRNA processing steps (splicing via spliceosome, polyadenylation, pre-mRNA cleavage, RNA methylation) and ribosomal large subunit biogenesis, pointing to RNA maturation and ribosome assembly as the core theme of this cluster. Some DNA repair and growth terms appear but are less central to the cluster\u2019s primary signal, which is RNA metabolism and ribosome biogenesis.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0098789","count":2},{"id":"GO:0036265","count":2}]},{"hash":"1426893134498259623","title":"Metabolic Regulation of RNA Pol II Transcription","description":"Most terms cluster around regulation of transcription by RNA polymerase II under various metabolic cues (oleic acid, carbon sources, sterol biosynthesis, respiration, amino acid biosynthesis). The proteins likely coordinate gene expression in response to metabolic state rather than performing a direct enzymatic function, suggesting a transcriptional regulatory role in metabolism, particularly in a fungal context.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061429","count":2},{"id":"GO:0061415","count":2},{"id":"GO:0035961","count":2},{"id":"GO:2001196","count":2},{"id":"GO:0043457","count":2}]},{"hash":"947808231131105846","title":"RNA processing and transcription regulation","description":"The listed GO terms cluster around RNA metabolism and gene expression control\u2014mRNA splicing, translation initiation, and transcription/elongation\u2014along with DNA-templated transcription and DNA repair, suggesting a nuclear RNA-processing/transcription theme, though a few trafficking terms appear peripheral.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007032","count":2},{"id":"GO:0032418","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1435061162325305007","title":"Golgi-Associated Vesicle Trafficking","description":"The top GO terms are dominated by vesicle transport events centered on the Golgi and ER (ER-to-Golgi, Golgi-to-ER, intra-Golgi, and endosome-to-Golgi), as well as Golgi ribbon formation, indicating a core function in Golgi-associated trafficking and organization. A couple of terms (nucleotide-excision repair, mitochondrial complex IV assembly) appear as minor, non-representative hits, but the prevailing signal points to Golgi-related vesicle transport. ","confidence":"High","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0090161","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0048280","count":2}]},{"hash":"295831027004765597","title":"Bacterial LPS and PHB biosynthesis","description":"The top GO terms point to lipopolysaccharide biosynthesis and O-antigen biosynthesis, both key steps in bacterial envelope construction, along with poly-hydroxybutyrate biosynthesis, a common bacterial storage polymer pathway. These cohesive themes suggest the cluster concentrates on bacterial biosynthetic processes, especially envelope components and storage polymers. Some terms (e.g., ER transport, P granule organization) appear less related or cross-species artifacts, but the strongest signal is bacterial biosynthesis. ","confidence":"Medium","size":28,"edges":9,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006541","count":3}]},{"hash":"1419887225170251588","title":"Mitochondrial Translation and Respiration","description":"The top GO terms cluster around mitochondrial protein synthesis (mitochondrial translation and initiation) and energy production (electron transport chain components and ATP synthase assembly), indicating a mitochondria-centered group involved in mitochondrial translation and respiration rather than nuclear-encoded cytosolic translation or other pathways. Although there is a separate term for brain development, the prevailing signal is mitochondrial function. ","confidence":"High","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0019740","count":2},{"id":"GO:0006121","count":2}]},{"hash":"1562241432064631639","title":"Unknown","description":"The top GO terms cover heart development, T cell signaling, neuronal plasticity and spine morphogenesis, transcription, apoptosis, and cytoskeletal organization, with no single dominant theme tying these proteins together. This broad and diverse set suggests a heterogeneous cluster rather than a specific, coherent function.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0051666","count":3},{"id":"GO:0055072","count":2},{"id":"GO:0038083","count":2},{"id":"GO:0050852","count":2}]},{"hash":"2295878200576577516","title":"Transcription and DNA Replication Core","description":"Top GO terms indicate a core emphasis on DNA-templated transcription and DNA replication/replication initiation, with translation as a supporting process and a minor signal-regulation theme. This suggests the proteins cluster around fundamental nuclear processes governing gene expression and genome duplication, despite a few peripheral terms related to development or immune signaling. Overall, a coherent label is the core transcription/replication machinery, with some incidental signaling notes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0032147","count":2},{"id":"GO:0001824","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0055059","count":1}]},{"hash":"1717574217081438030","title":"Membrane Ion and Metabolite Transporters","description":"The Top Terms are dominated by membrane transport processes (potassium, sodium, phosphate, nitrite, vitamin transport, and neurotransmitter loading into vesicles), suggesting a core theme of transporter proteins moving ions and small metabolites across membranes. While a couple of terms touch on transcription and cytoskeleton, these are less represented, so the cluster is best described as transporters with related trafficking/metabolic roles.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030866","count":2},{"id":"GO:0015707","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0071805","count":2}]},{"hash":"1849092479209797174","title":"Neural development and maturation","description":"This cluster is enriched for neural development terms, including cerebral cortex development, neuron maturation, and pituitary gland development, suggesting a core theme of brain development and neuronal maturation. Additional terms related to signaling (cellular response to cAMP), immune/ xenobiotic responses (response to xenobiotic stimulus, response to lipopolysaccharide), as well as RNA processing (alternative mRNA splicing) and metabolism (guanine, thiamine biosynthetic processes) indicate broader regulatory and metabolic contexts accompanying neural differentiation. Overall, the dominant neural development signals support the label, with some heterogeneity from ancillary processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":10},{"id":"GO:0042493","count":9},{"id":"GO:0009228","count":9},{"id":"GO:0045793","count":9},{"id":"GO:0032496","count":8}]},{"hash":"2066540456189624697","title":"Chromatin regulation and zinc homeostasis","description":"The proteins in this cluster show GO terms tied to transcriptional regulation and chromatin modification (negative regulation of DNA-templated transcription, histone acetylation/exchange) along with DNA repair, and also terms related to zinc and metal ion transport and response (zinc ion import, response to zinc starvation, cadmium transport). This points to a nuclear, chromatin-regulatory program that is linked to zinc homeostasis, possibly involving zinc-dependent chromatin modifiers or DNA repair factors. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045892","count":1},{"id":"GO:0043967","count":1},{"id":"GO:0042993","count":1},{"id":"GO:0043968","count":1},{"id":"GO:0043486","count":1}]},{"hash":"949573486066810831","title":"Unknown","description":"The Top Terms are highly diverse (follicle cell adhesion, glycosylation, cytokine regulation, NF-kappaB, retina development, brassinosteroid biosynthesis, hyaluronan biosynthesis, etc.) and include obsolete GO entries, with no clear shared function or pathway linking the 28 proteins. The lack of edges and a unifying theme suggests no coherent cluster function can be inferred from these terms.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007299","count":2},{"id":"GO:0006488","count":2},{"id":"GO:0032715","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0060041","count":2}]},{"hash":"1055996394846023843","title":"Unknown","description":"The top terms are highly heterogeneous, including glycolytic metabolism, DNA replication, ER-to-Golgi transport, cellulose catabolic processes, and various stress or xenobiotic responses, with several obsolete terms. This lack of a single cohesive function or pathway makes it infeasible to assign a specific, representative label for the cluster. Confidence in a meaningful label is therefore None.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0030324","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0006096","count":3}]},{"hash":"1647259550405455657","title":"Neuronal development and ubiquitin-mediated proteolysis","description":"Top terms mix neural development (initiation of neural tube closure, third ventricle development) with ubiquitin-dependent protein catabolic processes and cytoskeletal dynamics (microtubule polymerization), plus glycoprotein turnover and stress-related signals. This suggests a cohesive theme of neurodevelopmental regulation coupled to proteostasis and cytoskeletal remodeling, with additional stress-response context (oxidative stress, metal exposure). Confidence in this label is Medium.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:1903378","count":6},{"id":"GO:0008285","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0021678","count":6}]},{"hash":"677698568532412634","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":3},{"id":"GO:0006397","count":2},{"id":"GO:0006367","count":2},{"id":"GO:0051123","count":2},{"id":"GO:0000472","count":2}]},{"hash":"349833616862893747","title":"Mitotic and meiotic spindle assembly and chromosome pairing","description":"Most terms describe microtubule dynamics and spindle-kinetochore interactions (positive regulation of microtubule polymerization; attachment of spindle microtubules to kinetochore; sister chromatid biorientation; centrosome localization) and meiotic chromosome events (telomere tethering to nuclear envelope; homologous chromosome pairing). This points to a unified function in spindle assembly and chromosome pairing during mitosis and meiosis. Some outlier terms (nuclear envelope organization; nuclear matrix anchoring; spliceosome generation; osteoblast differentiation) appear less connected, but do not overwhelm the core signal.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031116","count":2},{"id":"GO:1990758","count":2},{"id":"GO:0051987","count":2},{"id":"GO:0000350","count":2},{"id":"GO:0006998","count":1}]},{"hash":"1792787120728076598","title":"Transcription Regulation and Biosynthesis","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, alongside several biosynthetic processes (antibiotic, biotin, lysine, pyrimidine). The co-occurrence suggests genes/proteins that link transcriptional control to biosynthetic pathway activity, possibly regulatory factors that tune biosynthesis in response to nutrients or signals.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0061429","count":4},{"id":"GO:0061415","count":4}]},{"hash":"1696784690966563910","title":"Unknown","description":"The top GO terms cover a broad mix: DNA replication, DNA-templated transcription, mitochondrial inheritance, regulation of aerobic respiration, potassium ion transport, chemotaxis, and dendrite morphogenesis, with some obsolete terms present. There isn\u2019t a single, cohesive function that unites these terms, so a specific, representative label isn\u2019t justifiable.","confidence":"","size":27,"edges":7,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0035335","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0000001","count":2},{"id":"GO:1903715","count":2}]},{"hash":"926282147865253274","title":"Immune and neuronal receptor signaling network","description":"The cluster centers on membrane receptor\u2013mediated signaling pathways, including ephrin receptor signaling, T cell receptor signaling, and Wnt signaling, with downstream regulation of GTPase activity and calcium-dependent exocytosis. The presence of apoptotic processes, DNA-templated transcription, and Golgi localization suggests signaling is connected to trafficking and gene expression, spanning immune and neural contexts. This combination supports labeling as an immune/neural receptor signaling network rather than a single, narrowly defined pathway.","confidence":"Medium","size":27,"edges":19,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048013","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0090263","count":4}]},{"hash":"1128172560094513374","title":"Nuclear transcription and RNA processing","description":"This cluster centers on nuclear gene expression processes: chromatin remodeling and RNA Pol II elongation are central to transcription, while mRNA splicing, regulation of Pol II activity, and rRNA maturation/export reflect RNA processing and ribosome biogenesis activities in the nucleus. The mix suggests a cohesive theme around transcriptional regulation and RNA maturation within the nuclear compartment, with a possible link to ribosome assembly and DNA replication initiation. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0000398","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0000055","count":1}]},{"hash":"1242193132969333109","title":"Neural development and cytoskeleton regulation","description":"The GO terms emphasize neural development (cerebral cortex development, negative regulation of axonogenesis) along with cytoskeletal remodeling (regulation of focal adhesion assembly, actin cytoskeleton-related processes) and translation/proliferation signals, plus a metabolic stress response (amino acid starvation). This combination points to a coherent role in neural development with cytoskeletal dynamics and growth signaling, rather than a broad, non-specific set. ","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0034198","count":3},{"id":"GO:0045793","count":3},{"id":"GO:0043552","count":3}]},{"hash":"1460816920468446070","title":"Mitochondrial respiration and redox balance","description":"The top GO terms point strongly to mitochondrial energy metabolism, including mitochondrial electron transport (NADH to ubiquinone; cytochrome c to oxygen) and complex I assembly, as well as redox homeostasis and superoxide removal. While translation and transcription terms appear, they may reflect mitochondrial gene expression; the dominant theme is oxidative phosphorylation and ROS detoxification. Collectively, these proteins likely function together in mitochondrial respiration and oxidative stress management.","confidence":"High","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0043046","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045654","count":2}]},{"hash":"1855529727832712769","title":"RNA and protein methyltransferases","description":"This cluster is dominated by GO terms related to methylation: RNA guanine-N7 methylation and N-terminal peptidyl-alanine trimethylation, suggesting a set of enzymes that transfer methyl groups to RNA and protein substrates. While there are other diverse terms (biosynthetic and various stress/immune responses), the recurring methylation theme best captures the core shared function of the proteins.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":7},{"id":"GO:0036265","count":6},{"id":"GO:0042220","count":6},{"id":"GO:0035902","count":6}]},{"hash":"765205471814383013","title":"Unknown","description":"This cluster mixes viral-life-cycle processes (viral release from host cell, virion assembly) with a variety of unrelated host-cell functions (cell cycle/division, mitochondrial protein import, proteasome assembly, chaperone-mediated assembly, nucleologenesis, tRNA methylation), showing no single cohesive function to name.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0045041","count":2},{"id":"GO:0051131","count":2}]},{"hash":"1404895557374798384","title":"Carbon-source\u2013driven transcription in yeast","description":"The top terms center on regulation of RNA polymerase II transcription in response to different carbon sources (oleic acid, nonfermentable carbon sources, starvation) and include related metabolic processes (ergosterol, amino acid, nucleotide biosynthesis, and respiration). This suggests a fungal transcriptional program that links carbon availability to metabolic regulation, justifying a label around carbon-source\u2013driven transcription and metabolism.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901717","count":2},{"id":"GO:0061429","count":2},{"id":"GO:0061415","count":2},{"id":"GO:0035961","count":2},{"id":"GO:2001196","count":2}]},{"hash":"368720950247921961","title":"Unknown","description":"The cluster shows heterogeneous GO terms, with carbohydrate catabolic processes (cellulose/xylan) alongside nucleotide catabolism, transcription, DNA repair, and p53-mediated apoptosis, giving no single cohesive theme to name it beyond Unknown. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0045493","count":2},{"id":"GO:0006694","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006154","count":1}]},{"hash":"713070254965082137","title":"Transcription and Signaling Regulators","description":"The GO terms point to regulatory roles in transcription (DNA-templated transcription) and a broad spectrum of signaling-related processes (ERK cascade, LPS signaling, interferon-beta production, apoptosis, synapse assembly), with ubiquitination suggesting modulation of transcription factors and signaling proteins. The absence of edges/triangles implies these are diverse regulators rather than a single cohesive complex, aligning with a label focused on regulatory functions in transcription and signaling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0016567","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0007601","count":2}]},{"hash":"1315097718747814993","title":"Cytoskeleton signaling via small GTPases","description":"Top GO terms point to actin cytoskeleton organization and small GTPase-mediated signal transduction, suggesting a core role in regulating cytoskeletal dynamics and signaling. While other terms imply broader regulatory roles (neutrophil degranulation, IGF signaling, nutrient response), the shared motif centers on cytoskeleton-related signaling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0032094","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0007264","count":2}]},{"hash":"605852375164119589","title":"Unknown","description":"The GO terms span ER protein folding, sterol biosynthesis, ncRNA-mediated gene silencing, transcriptional regulation, viral processes, autophagosome assembly, and peroxisome protein import\u2014i.e., a broad mix of unrelated cellular processes. There is no clear single function linking these proteins, so a coherent, specific label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1267204265757923068","title":"Yeast cell polarity and budding","description":"The dominant GO terms point to mating projection formation, regulation of budding site selection, and GTPase-mediated polarity control, all core to cell polarization and morphogenesis in yeast. Microtubule dynamics further support a role in directing growth sites, while some other terms (DNA repair, apoptotic process) may reflect broader cellular stress signals rather than the primary function of this cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007026","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0070911","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0007039","count":2}]},{"hash":"1042163968831254006","title":"Radial glial development and synaptic plasticity","description":"The terms cluster around neural development, especially radial glia differentiation and scaffold formation in the forebrain, including substantia nigra development and learning, plus signaling pathways tied to synaptic plasticity (ephrin and Rap signaling, adrenergic receptor signaling, and cAMP-related responses such as forskolin). This combination points to a theme of developing neural tissue with connectivity and plasticity.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021861","count":2},{"id":"GO:0032486","count":2},{"id":"GO:0071880","count":2},{"id":"GO:1904322","count":2},{"id":"GO:0051835","count":2}]},{"hash":"632705790180454916","title":"Membrane Transport of Ions and Small Molecules","description":"GO terms are dominated by diverse transmembrane transport activities, including xenobiotics, nitrite, ions (K+, Na+), vitamins, phosphate, and small metabolites. A couple of terms reflect unrelated processes, but the core theme is transport across membranes.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0043622","count":2},{"id":"GO:0015707","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0071805","count":2}]},{"hash":"339228916897197667","title":"Growth, defense, and chromatin maintenance","description":"Proteins in this cluster show enrichment for translation (protein synthesis), plant defense signaling (response to salicylic acid), and growth-related processes (cell wall organization, vegetative growth regulation), along with genome maintenance signals (DNA repair and subtelomeric heterochromatin formation). Although some terms pertain to obscure or nonspecific biosynthetic processes, the core theme ties to growth, defense responses, and chromatin regulation, suggesting roles in coordinating development with genome integrity.","confidence":"Medium","size":26,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0009751","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0019878","count":2}]},{"hash":"977665752672360910","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0071805","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1286152994359968361","title":"Ribosome and Translation Machinery","description":"Top GO terms cluster around translation and ribosome biogenesis, including initiation, elongation, termination, large subunit assembly, ribosome disassembly, and mitochondrial translation, with a minor link to antibiotic response. This combination strongly suggests a set of proteins involved in protein synthesis machinery and ribosome assembly.","confidence":"High","size":26,"edges":324,"triangles":2576,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":23},{"id":"GO:0006415","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0000027","count":5},{"id":"GO:0046677","count":5}]},{"hash":"1120545734268265092","title":"Metabolic-Responsive Transcription Regulation","description":"This cluster is dominated by GO terms about DNA-templated transcription and regulation of transcription from RNA polymerase II promoter, influenced by metabolic signals (cAMP, oleic acid, carbon source) and metabolic processes. While some terms touch on specific catabolic or regeneration contexts, the unifying theme is transcriptional control in response to metabolic and environmental cues, suggesting proteins that modulate transcription in metabolic contexts.","confidence":"High","size":26,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0019383","count":4},{"id":"GO:0097421","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0061429","count":3}]},{"hash":"1223427005330950275","title":"Endomembrane trafficking and autophagy","description":"Based on the top GO terms, several entries point to the secretory/endomembrane pathway (ER to Golgi transport), vesicle dynamics regulated by GTPases, and catabolic turnover in the vacuole, together with autophagy. While some terms are flagged as obsolete, the recurring themes of membrane trafficking and intracellular degradation best unify these proteins, justifying a label like Endomembrane trafficking and autophagy.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051479","count":1},{"id":"GO:0016358","count":1},{"id":"GO:0045212","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1770428074040361137","title":"Nutrient sensing and growth signaling","description":"This cluster centers on TORC1 signaling and nutrient response, with links to cell proliferation and post-translational regulation, suggesting a loose grouping around growth control and metabolic sensing. Although several terms are labeled obsolete, the recurring themes point to growth signaling in response to nutrients.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0051568","count":4},{"id":"GO:0050679","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0055114","count":3}]},{"hash":"1799505290079540384","title":"Unknown","description":"The terms span diverse processes (retina development, lipid metabolism, xenobiotic response, ion transport, growth regulation) plus several obsolete GO terms, and there are no edges connecting proteins. This points to no single cohesive function for the cluster, so a Unknown label is appropriate.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060041","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0042136","count":4},{"id":"GO:0030245","count":4},{"id":"GO:0006695","count":4}]},{"hash":"1803784116284648769","title":"Mitotic spindle and actin cytoskeleton dynamics","description":"The top GO terms center on mitosis (establishment of spindle orientation, mitotic cell cycle, cell division) and actin cytoskeleton remodeling (Arp2/3 complex\u2013mediated nucleation), with developmental themes (multicellular organism development, skin development). This suggests a cohesive cluster of proteins involved in cell division and cytoskeletal dynamics within a developmental context, even though there are no observed interactions in the network. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000132","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3}]},{"hash":"2251661445758044957","title":"Unknown","description":"This cluster shows a mix of lipid biosynthesis, bone remodeling signaling, neural transmission regulation, transcription, pigmentation development, platelet granule organization, and vesicle trafficking with no dominant common function or connections, making a cohesive theme unlikely.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":1},{"id":"GO:0045670","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0032229","count":1}]},{"hash":"607346824679759648","title":"Fungal pseudohyphal growth and chromatin remodeling","description":"This cluster is best labeled by the prominent signals for morphological change and chromatin dynamics: chromatin remodeling and pseudohyphal growth are top terms, suggesting a fungal stress response involving a switch to filamentous growth accompanied by chromatin remodeling and transcriptional regulation. While there are outlier terms (angiogenesis, uterine gland development) and some obsolete annotations, the shared theme centers on growth form changes in yeast-like organisms linked to changes in transcription and chromatin state. Overall, the cluster seems to reflect fungal growth adaptation with underlying chromatin regulation.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0007124","count":2},{"id":"GO:0045945","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0038028","count":2}]},{"hash":"1505167470420230978","title":"Ribosome biogenesis and translation during cell cycle","description":"The Top Terms are dominated by ribosome biogenesis and cytoplasmic translation, with supporting signals for cell cycle and transcription, suggesting a cluster of proteins involved in producing ribosomes and facilitating protein synthesis in proliferating cells. This makes \"Ribosome biogenesis and translation during cell cycle\" a concise, representative label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0019877","count":2},{"id":"GO:0009089","count":2},{"id":"GO:0006351","count":2}]},{"hash":"858303228225381959","title":"Actin-based protrusions and cell motility","description":"The cluster centers on actin cytoskeleton remodeling: assembly of filopodia, podosomes, and ruffles, along with processes that govern cell polarity, adhesion, spreading, and movement, and supported by related signaling such as Wnt and synaptic plasticity. Peripheral terms like cellular response to xenobiotic stimulus and ribosomal export are noted but do not redefine the main theme.","confidence":"High","size":25,"edges":75,"triangles":69,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000056","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0097178","count":4},{"id":"GO:0071963","count":4},{"id":"GO:0035690","count":4}]},{"hash":"363209453207511799","title":"Ubiquitin-regulated ER-Golgi trafficking","description":"The top GO terms cluster around ubiquitin-related regulation (positive regulation of ubiquitin ligase activity; ubiquitin-dependent ERAD pathway) and vesicle transport between the Golgi and the ER, which together suggest a focus on protein quality control and intracellular trafficking. While there are some terms related to brain development, splicing, and cell-cycle regulation, the strongest, most consistent signals point to ubiquitin-mediated regulation of ER-Golgi trafficking. Confidence: Medium","confidence":"","size":25,"edges":3,"triangles":1,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0045143","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0070317","count":4}]},{"hash":"810413546607278055","title":"Unknown","description":"The top GO terms span transcription regulation, chemotaxis, plant hormone signaling, metabolism, and development (e.g., DNA-templated transcription, regulation of transcription, chemotaxis, ethylene signaling, placenta development), with no single cohesive function connecting all 25 proteins. Therefore a specific, representative label cannot be confidently assigned.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006935","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0010105","count":2}]},{"hash":"820554685339354187","title":"Vitamin biosynthesis and fatty-acid metabolism","description":"Enriched for thiamine and menaquinone biosynthesis and medium-chain fatty-acid metabolism, including thiamine diphosphate biosynthesis and fatty-acyl-CoA transport; antibiotic-related terms are present but secondary.","confidence":"Medium","size":25,"edges":10,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009228","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0036112","count":4},{"id":"GO:0042208","count":4}]},{"hash":"2305350841656171721","title":"Mitochondrial respiration and redox homeostasis","description":"This cluster is dominated by mitochondrial energy metabolism and redox-related terms, notably NADH-to-ubiquinone electron transport, redox homeostasis, and oxidative-stress response, suggesting a cohesive theme of mitochondrial respiration and cellular redox balance. The presence of translation and DNA-templated transcription terms may reflect general cellular housekeeping processes co-annotated with mitochondria-associated genes.","confidence":"High","size":25,"edges":276,"triangles":1930,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0006412","count":2}]},{"hash":"1685724249646848266","title":"Unknown","description":"The terms are mixed across neural-related processes (myelination, cocaine response) and xenobiotic response with unrelated areas like lipid A biosynthesis and miRNA processing. There is no single coherent function tying these proteins together, so a clear, representative label cannot be formed.","confidence":"","size":25,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0022011","count":3},{"id":"GO:0042220","count":3},{"id":"GO:2001241","count":3},{"id":"GO:0051262","count":3}]},{"hash":"2247297703536827452","title":"Neuronal GPCR Signaling and Trafficking","description":"Top GO terms point to dopamine signaling and GPCR desensitization, as well as neural processes (visual perception, axon extension) and membrane trafficking (endosome-to-Golgi, recycling endosome transport). This pattern suggests a cluster of proteins involved in neuronal GPCR signaling with accompanying intracellular trafficking; ancillary terms like cholesterol biosynthesis and protein tetramerization may reflect membrane biology and assembly needs. Overall, the dominant theme is neuronal signaling intertwined with endosomal trafficking.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0051262","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0045773","count":2},{"id":"GO:0071955","count":2}]},{"hash":"1135021743548237444","title":"Diverse membrane transporters for ions and nutrients","description":"This cluster is enriched for transmembrane transport GO terms across multiple substrates (nitrite/nitrate, phosphate, potassium, arabinose, vitamin transport, etc.), plus related metabolic context (nitrate assimilation, fucose metabolism). The common theme is transport of ions and small molecules across membranes, suggesting the proteins largely function as various membrane transporters rather than a single pathway. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0015707","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0042891","count":2}]},{"hash":"1657549964486417341","title":"Bacterial cell wall and capsule biosynthesis","description":"The GO terms are dominated by peptidoglycan biosynthesis, cell wall organization, capsule polysaccharide biosynthesis, and cell division, indicating proteins involved in building and remodeling the bacterial cell envelope and coordinating cytokinesis.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0009252","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2112041601695640583","title":"Actin-Driven Filopodium Formation and Synaptic Vesicle Trafficking","description":"The cluster centers on actin cytoskeleton dynamics (filopodium assembly, actin cortex patches) and membrane trafficking processes (vesicle budding/endocytosis, plasma membrane tubulation) with associated Rho GTPase signaling. This suggests a cohesive role in actin-driven membrane remodeling relevant to filopodia and synaptic vesicle trafficking.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051489","count":2},{"id":"GO:0046847","count":2},{"id":"GO:1901998","count":2},{"id":"GO:0016185","count":2},{"id":"GO:0090630","count":2}]},{"hash":"1553661934742957472","title":"Nutrient-Responsive Transcription Regulation","description":"The Top Terms are dominated by DNA-templated transcription and positive regulation of transcription from RNA polymerase II promoters in response to metabolic cues (nonfermentable carbon source, oleic acid) and metabolic stress (hypoxia, glyoxylate cycle references). There are also related terms for protein turnover (proteasome assembly, endopeptidase activity), consistent with transcriptional programs that coordinate gene expression and proteostasis under nutrient conditions. Together they suggest a cluster of proteins involved in regulating transcription in response to nutrients and metabolic state.","confidence":"High","size":24,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1900399","count":2},{"id":"GO:2001158","count":2},{"id":"GO:0061414","count":2},{"id":"GO:0035959","count":2}]},{"hash":"503997468305738","title":"DNA replication and cell-cycle regulation under stress","description":"The cluster is dominated by terms related to DNA replication, viral genome replication, and cell division, pointing to a core function in genome duplication and progression through the cell cycle. Additional terms about stress responses (stress granule disassembly, SCF complex disassembly in cadmium stress) and transcription elongation suggest a broader link to cellular stress adaptation and gene expression control, though these are less central. Overall, the proteins appear to converge on replication and division with auxiliary stress-response regulation.","confidence":"Medium","size":24,"edges":20,"triangles":14,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0035617","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0051301","count":4}]},{"hash":"165510120442977315","title":"Chromatin Regulation and Transcription","description":"The cluster is mainly enriched for chromatin-associated processes (histone modification, transcription regulation, chromatin localization) with a secondary signal for ribosome biogenesis, suggesting a nuclear chromatin/transcription-focused module rather than a purely cytoplasmic pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0072583","count":1}]},{"hash":"2208258689364640552","title":"Unknown","description":"The top GO terms cover a wide, unrelated set of processes\u2014including fungal lipid metabolism (mannosyl-inositol phosphorylceramide and ergosterol), general lipid biosynthesis, CNS myelin maintenance, nitrate assimilation, sebaceous gland differentiation, mitochondrial inheritance, nitric oxide production, face morphogenesis, and hypoxia response\u2014without a single coherent biological theme. Because no clear common function ties these proteins together, I cannot assign a meaningful label.","confidence":"","size":24,"edges":22,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0042128","count":1}]},{"hash":"772929545367955967","title":"Methylation and Biosynthesis Enzymes in Microbes","description":"The cluster\u2019s top GO terms converge on methylation activities (RNA and protein N7-methylation) and various biosynthetic processes (antibiotic, biotin, cobalamin), suggesting a group of enzymes involved in methylation alongside diverse biosynthetic pathways common in microbes. A few terms about immune responses may be annotation noise and not representative of the core function. Overall, a cohesive theme around methylation plus biosynthesis fits best, though with some heterogeneity.","confidence":"Medium","size":24,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0018012","count":4},{"id":"GO:0070555","count":4}]},{"hash":"1737632312643096659","title":"Neurodevelopment and synaptic organization","description":"The cluster is enriched for neural development and synapse-related processes: floor plate development, somitogenesis, and amacrine cell differentiation point to early neural patterning and neuron specification, while postsynaptic density protein 95 clustering suggests synapse formation. Transcription by RNA polymerase II indicates active gene-expression programs underlying these developmental events, with xenobiotic and drug-response terms possibly reflecting regulatory responsiveness during development. Overall, a cohesive theme around neural development and synaptic organization best fits the shared GO signals.","confidence":"Medium","size":24,"edges":270,"triangles":1896,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":6},{"id":"GO:0060426","count":5},{"id":"GO:0001756","count":5},{"id":"GO:0048712","count":5},{"id":"GO:0006366","count":5}]},{"hash":"1982033382017321959","title":"Unknown","description":"The GO terms show a mix of Notch signaling and several unrelated metabolic processes (alanine, pyruvate, kynurenine catabolism, insulin response); there isn\u2019t a single coherent function that links most proteins in this cluster, so a concise, representative label cannot be assigned.","confidence":"","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":11},{"id":"GO:0097053","count":11},{"id":"GO:0042853","count":11},{"id":"GO:0042866","count":9},{"id":"GO:0033512","count":9}]},{"hash":"1458383155446023988","title":"Ubiquitin-Dependent Chromatin and Immune Regulation","description":"The cluster is dominated by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, various ubiquitination types) and histone modification terms (H4-K16 acetylation, H4-K20 methylation, H2A K63 ubiquitination, histone catabolic process), with additional enrichment for innate immune response and TNF signaling. This suggests a shared theme of ubiquitin-mediated control of chromatin state and related signaling, justifying the name.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0030433","count":3},{"id":"GO:2000620","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0009048","count":3}]},{"hash":"1748085825502080746","title":"Membrane trafficking and receptor maturation","description":"The top GO terms cluster around retrograde transport between the Golgi and ER, membrane protein processing linked to that transport, and maturation of EGFR ligands, which together point to membrane trafficking and receptor maturation pathways. Although a few terms touch on signaling and developmental outcomes, the core pattern is membrane trafficking and receptor processing.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904211","count":2},{"id":"GO:0051533","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0032815","count":1}]},{"hash":"503575923393706936","title":"Protein Synthesis and Energy Metabolism","description":"This cluster is driven by translation and cell growth signals (translation, leading strand elongation, cell division) and is reinforced by energy-related terms (oxidative phosphorylation, aerobic respiration) plus proteostasis/ER quality-control cues (response to misfolded protein, ERAD). Together these point to a cohesive module that links protein production with cellular energy supply and protein quality control, justifying the label. Note that several terms are obsolete in the dataset but the core theme remains translation-proliferation coupled with energy metabolism.","confidence":"Medium","size":24,"edges":51,"triangles":18,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0071218","count":2},{"id":"GO:0000733","count":2},{"id":"GO:0006272","count":2}]},{"hash":"606224745155421456","title":"Hair Follicle Development via Wnt Signaling","description":"The cluster shows enrichment for canonical Wnt signaling (GO:0060070) and hair follicle placode formation (GO:0060789), which together point to a role in hair follicle morphogenesis. Supporting terms related to cell proliferation and lamellipodium assembly suggest epithelial remodeling and movement during development, while ER-Golgi transport and metabolic responses are more general cellular processes. Overall, the dominant theme is Wnt-driven hair follicle development.","confidence":"Medium","size":24,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0034198","count":2},{"id":"GO:1990314","count":2},{"id":"GO:0060070","count":2},{"id":"GO:0060789","count":2}]},{"hash":"198356132727613694","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominantly related to ubiquitin-mediated proteolysis (ubiquitin-dependent catabolic process, autoubiquitination) and ER-associated degradation, with another term linking to peroxisomal matrix protein import via ubiquitination cycling. While some terms touch on cell division or microtubule dynamics, the strongest signal centers on ubiquitin tagging for proteasomal turnover and related trafficking, suggesting a proteostasis-focused cluster. Therefore, the label captures the main common theme among the proteins.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0016558","count":3}]},{"hash":"404685431754143279","title":"Neurodevelopment and transcription regulation","description":"The presence of brain-development terms such as substantia nigra development and cerebral cortex development, along with DNA-templated transcription, points to proteins involved in brain development and regulation of gene expression. Other terms about multicellular development and histone methylation are supportive but less specific; mitochondria-related assembly terms may reflect neuronal energy needs but do not define the core function.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0021762","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0033617","count":2}]},{"hash":"1525930543042553224","title":"N-terminal acetylation and modification cluster","description":"The top GO terms are dominated by various N-terminal acetylation and related N-terminal modifications (serine, methionine, glutamic acid) along with propionylation, indicating a core theme of N-terminal post-translational modification. Additional terms touch on N-acetylglucosamine metabolism and polyamine (putrescine, spermine) catabolism, suggesting some linked amino-acid metabolism processes. A few unrelated terms appear but do not obscure the prevailing signal of N-terminal modification activity across the cluster.","confidence":"High","size":24,"edges":263,"triangles":1767,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0017198","count":21},{"id":"GO:0006348","count":20},{"id":"GO:0006526","count":19},{"id":"GO:0017196","count":19},{"id":"GO:0009447","count":19}]},{"hash":"799783878924441629","title":"Membrane Transporters","description":"The terms show widespread transmembrane transport roles (sodium/potassium ion transport, nitrite and sugar transport, vitamin and metabolite transport) and vesicular loading, suggesting a cluster of membrane transport proteins.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0015707","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0098700","count":3}]},{"hash":"2283588074078666265","title":"Nutrient-Responsive RNA Pol II Transcription Regulation","description":"The dominant GO terms cluster around DNA-templated transcription and regulation of transcription from RNA polymerase II promoter, with multiple entries tied to nutrient and metabolic cues (oleic acid, carbon source, respiration, amino acid and nucleotide biosynthesis). This suggests the proteins function collectively as transcriptional regulators responding to metabolic states rather than a single metabolic enzyme pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035948","count":4},{"id":"GO:0061429","count":3},{"id":"GO:0061415","count":3},{"id":"GO:0035961","count":3}]},{"hash":"492586449247148655","title":"Cell Cycle and Apoptosis Regulation","description":"This cluster centers on cell cycle, mitosis, and cell division terms (e.g., mitotic cell cycle, cell division) with supporting protein ubiquitination, a key regulatory mechanism of proliferation and apoptosis. The presence of apoptotic terms for specific tissues (myeloid/hepatocyte) and mentions of cohesion regulation further support a theme of balancing cell proliferation with programmed cell death. Some terms like epithelial polarity or dendrite development appear less directly connected but may reflect broader regulatory roles of these proteins. Confidence: Medium","confidence":"","size":23,"edges":28,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0033028","count":2}]},{"hash":"307259608169198909","title":"Proteostasis: Ubiquitin-Dependent Degradation and Trafficking","description":"The GO terms cluster around ubiquitin-mediated protein turnover and associated trafficking: ubiquitin-dependent proteolysis, deubiquitination (including K63-linked), and protein transport to the vacuole via the multivesicular body pathway, all of which are core components of proteostasis. Regulation of translational initiation also fits into maintaining protein homeostasis. A few terms on peroxisome fission or morphogenesis appear peripheral, but the dominant signal is proteostasis through ubiquitin pathways and degradation. ","confidence":"Medium","size":23,"edges":12,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0043524","count":1},{"id":"GO:0010950","count":1},{"id":"GO:0016559","count":1},{"id":"GO:0070452","count":1},{"id":"GO:0043328","count":1}]},{"hash":"2104587917844029967","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002088","count":2},{"id":"GO:0010659","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0000472","count":2}]},{"hash":"981293942336394243","title":"Actin-driven migration and endocytosis regulation","description":"The top GO terms point to actin cytoskeleton dynamics and membrane trafficking\u2014lamellipodium morphogenesis, phagocytosis, endocytosis, and GTPase activity regulation\u2014indicating a shared function in cytoskeletal remodeling and vesicle trafficking that underpins cell movement and immune cell responsiveness. Some terms (like skeletal development) are less central but may reflect broader developmental regulation, yet the dominant theme remains cytoskeleton-driven migration and endocytosis.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034260","count":3},{"id":"GO:1904888","count":2},{"id":"GO:2000394","count":2},{"id":"GO:0042997","count":2},{"id":"GO:0006909","count":2}]},{"hash":"26726747706428863","title":"Ribosome biogenesis and RNA transcription machinery","description":"The top terms cluster strongly around ribosome biogenesis and ribosomal subunit biogenesis, with associated nucleolar rRNA transcription and translational initiation terms. Additional transcription-related terms across RNA polymerases I\u2013III suggest coordination between ribosome assembly and transcription/translation processes. This combination supports a label focusing on ribosome biogenesis with linked transcriptional activity.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0042790","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0006367","count":1}]},{"hash":"958189403518379556","title":"Nuclear transcription and chromatin regulation","description":"This cluster is defined by GO terms tied to DNA-templated transcription and transcription initiation, RNA polymerase II preinitiation complex assembly, and histone acetylation, along with rDNA heterochromatin formation. These points indicate a focus on nuclear gene expression control and chromatin state. While ribosome biogenesis terms appear, they likely reflect broader nucleolar context rather than a primary ribosome-production role for the cluster. Overall, the theme centers on transcription regulation and chromatin architecture.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043966","count":3},{"id":"GO:0006352","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035948","count":3},{"id":"GO:0042254","count":2}]},{"hash":"2281828405117917898","title":"Chromatin remodeling and cell cycle regulation","description":"The cluster is dominated by GO terms tied to chromatin dynamics (rDNA heterochromatin formation, DNA replication-dependent chromatin assembly, transcription initiation-coupled chromatin remodeling) and cell-cycle control (centrosome cycle, regulation of cell cycle), with additional links to chromatin-related processes such as chromatin assembly and autophagy regulation. Though a few terms touch on development or immunity, the core theme centers on chromatin state management and progression through the cell cycle.","confidence":"High","size":23,"edges":17,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0001525","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0006335","count":2}]},{"hash":"473238289759492502","title":"Membrane amino acid and ion transporters","description":"The cluster\u2019s terms center on transmembrane transport of small molecules: multiple amino acids (lysine, methionine, arginine, D-alanine) and ions (potassium), plus related polyamine transport and a connection to nitric oxide production via arginine metabolism. This points to a coherent theme of membrane transport activity for amino acids and related metabolites, rather than a single enzyme or pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0097639","count":2},{"id":"GO:0015812","count":2},{"id":"GO:0044690","count":2},{"id":"GO:1902269","count":2}]},{"hash":"1427114458976853823","title":"Amino acid and neurotransmitter transporters","description":"The cluster is dominated by membrane transport terms for amino acids (lysine, methionine, arginine) and the neurotransmitter GABA, along with polyamine transport. While there are adjacent terms related to nucleocytoplasmic transport and DNA metabolism, the strongest and most coherent signal is membrane transport of amino acids and related small molecules, suggesting these proteins function primarily as transporters or transporter-associated regulators.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006283","count":3},{"id":"GO:0000056","count":3},{"id":"GO:0097639","count":2},{"id":"GO:0015812","count":2}]},{"hash":"1631076169230805557","title":"RNAP II Transcription Regulation by Metabolic Cues","description":"The top terms are dominated by DNA-templated transcription and regulation of transcription from RNA polymerase II promoters, including responses to metabolic signals such as oleic acid and nonfermentable carbon sources. Additional terms point to metabolic and stress-related regulation (cadmium response, regulation of cellular respiration, lysine biosynthesis) and some transport/localization processes that can accompany regulatory programs. This suggests a coherent theme of transcriptional control modulated by metabolic cues, with secondary links to metabolism and trafficking.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035372","count":2},{"id":"GO:0045056","count":2},{"id":"GO:0031571","count":2},{"id":"GO:0071276","count":2}]},{"hash":"955044584213691802","title":"Developmental morphogenesis and signaling","description":"The cluster centers on tissue development and morphogenesis (cerebral cortex development, face development, skeletal muscle tissue development, cell morphogenesis) with associated transcriptional regulation (DNA-templated transcription) and signaling pathways (insulin receptor signaling, B cell receptor signaling). The mix of development-related GO terms suggests a broad developmental/differentiation theme rather than a single pathway, so the label focuses on morphogenesis with signaling. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0021987","count":5},{"id":"GO:0045793","count":4},{"id":"GO:0007095","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000902","count":4}]},{"hash":"1410743411105830566","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0055114","count":3}]},{"hash":"524916023336036908","title":"Amino acid and chlorophyll/quinone biosynthesis","description":"Most top GO terms point to biosynthetic processes: several amino acid pathways (lysine via diaminopimelate, arginine, isoleucine) along with chlorophyll biosynthesis and phylloquinone/menaquinone biosynthesis. A minor proteolysis term is present, but the dominant theme is metabolic assembly of essential molecules, suggesting this cluster groups proteins involved in amino acid and pigment/quinone biosynthesis pathways.","confidence":"Medium","size":23,"edges":13,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009097","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0006508","count":2}]},{"hash":"1957939782621549499","title":"Neuronal differentiation and telomere regulation","description":"The protein set shows GO terms tied to neural development (striatal medium spiny neuron differentiation; CNS projection neuron axonogenesis) along with terms related to telomere maintenance via telomerase, suggesting a module centered on neural differentiation with connections to telomere biology, despite some peripheral cell-cycle terms.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1904908","count":1},{"id":"GO:2001108","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0045617","count":1}]},{"hash":"1799512005727451777","title":"Developmental signaling and growth control","description":"The top GO terms point to broad developmental processes (forebrain, skeletal, multicellular development) and differentiation (keratinocytes) along with growth-regulating pathways (hippo signaling). Some terms also reflect general stress responses (ER-stress\u2013related apoptosis, DNA repair). The cluster seems to span development and growth-control rather than a single cohesive pathway, so a label emphasizing developmental signaling and growth control fits best.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0001501","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006351","count":2}]},{"hash":"398747939305578126","title":"Electron transport chain and energy production","description":"The top GO terms cluster around photosynthesis, respiratory and mitochondrial electron transport, and proton transmembrane transport, indicating a core energy metabolism module. While there are some auxiliary terms related to transcription and protein processing, the dominant signal is electron transport and energy generation in chloroplast/mitochondrial contexts.","confidence":"High","size":23,"edges":250,"triangles":1709,"max_degree":22,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0022904","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0006122","count":3},{"id":"GO:0051291","count":2}]},{"hash":"726690739631688306","title":"RNA Pol III Transcription Machinery","description":"Most GO terms point to transcription by RNA polymerase III and preinitiation complex assembly (including 5S rRNA transcription by Pol III), suggesting these proteins form the RNA Pol III transcription machinery; the few unrelated terms appear incidental noise.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001041","count":1},{"id":"GO:0000999","count":1},{"id":"GO:0001009","count":1},{"id":"GO:0001021","count":1},{"id":"GO:0042791","count":1}]},{"hash":"787738403985976409","title":"Membrane Transporters","description":"The cluster shows a clear tilt toward membrane-associated transport processes: phospholipid translocation, various transmembrane transport activities (taurine, long-chain fatty acids into peroxisomes, teichoic acid transport, oligopeptide export from mitochondrion), and drug transport (daunorubicin). A few terms relate to mitochondrial or nuclear functions (cytochrome complex assembly, nucleotide-excision repair), but the dominant signal is transport across membranes, suggesting these proteins function largely as transporters or in membrane-associated transport pathways. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045332","count":3},{"id":"GO:0043215","count":2},{"id":"GO:0030153","count":2},{"id":"GO:0017004","count":2},{"id":"GO:0015734","count":2}]},{"hash":"775309222365385576","title":"Methylation Enzymes and Gene Expression","description":"The cluster is dominated by GO terms for peptidyl-lysine methylation (mono- and dimethylation), N-terminal methylation, and DNA-templated transcription, with translation also present. This pattern points to enzymes that add methyl groups to proteins involved in gene expression, including transcription-related regulation. The carbohydrate metabolism terms may reflect broader cellular roles but do not define the cluster as strongly as the methylation- and transcription-related terms.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0018026","count":2},{"id":"GO:0019262","count":2}]},{"hash":"820444119054428621","title":"Amino Acid Transport Across Plasma Membrane","description":"The top GO terms are dominated by amino acid transport across the plasma membrane (lysine, methionine import; arginine catabolic process) and related transport of GABA and polyamines, suggesting a core function as amino acid transporters. Additional terms reference inflammatory signaling (nitric oxide production) and TGF-beta\u2013mediated responses, which may reflect context-dependent regulation rather than a separate module. Overall, the cluster appears best described by amino acid transport and related transmembrane movement, with secondary signaling links. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0097639","count":1},{"id":"GO:0015812","count":1},{"id":"GO:0044690","count":1}]},{"hash":"912009069073357145","title":"Bacterial cell growth and division","description":"The top GO terms cluster around cell cycle, cell growth, cell division, cell wall organization, and peptidoglycan biosynthesis/turnover, indicating a shared function in bacterial growth and envelope biogenesis; a few terms (G-quadruplex DNA formation, positive regulation of GTPase activity) are less central but can relate to regulatory aspects of division.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0009252","count":2}]},{"hash":"90095751047829503","title":"Unknown","description":"The GO terms here mix porphyrin/heme/chlorophyll biosynthesis with general cellular processes like endocytosis and GTPase regulation, plus fungal cell wall organization, showing no single cohesive function across all 23 proteins. This heterogeneous set doesn\u2019t support a specific shared role beyond broad eukaryotic metabolism, so Unknown with None confidence is appropriate.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006730","count":2},{"id":"GO:0031505","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0015995","count":1}]},{"hash":"1747220158414614203","title":"Amino acid and one-carbon metabolism","description":"The prominent GO terms cluster around amino acid metabolism (L-methionine cycle, L-valine biosynthesis) and one-carbon metabolic processes, suggesting a metabolic module focused on amino acid and one-carbon chemistry. Additional terms for transcription, trafficking, circadian rhythm, and immune response are present but appear peripheral to the main metabolic theme, likely reflecting pleiotropy in these proteins.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001887","count":2},{"id":"GO:0071268","count":2}]},{"hash":"1253002853014048054","title":"Fungal cell wall biosynthesis and mating","description":"The strongest fungal-specific signals are the fungal-type cell wall beta-glucan biosynthetic process and karyogamy (nuclear fusion in fungal mating), supported by related cell morphogenesis terms, suggesting a theme centered on fungal cell wall construction and mating processes. Other terms (DNA replication, SRP-dependent targeting, iron-sulfur cluster assembly) are more general, but do not outweigh the fungal-focused signals.","confidence":"Medium","size":22,"edges":25,"triangles":5,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006880","count":4},{"id":"GO:0006616","count":4},{"id":"GO:0090084","count":4},{"id":"GO:0000902","count":4}]},{"hash":"1732135939507183146","title":"Spliceosome-mediated mRNA splicing and regulation","description":"This cluster is dominated by GO terms tied to mRNA splicing via the spliceosome, including positive regulation of splicing, standard splicing, and alternative splicing, with additional signals of post-transcriptional regulation such as RNA silencing and stress-responsive mRNA stability. Some translation-related terms may reflect coupling between splicing factors and translation, but the core theme is spliceosome-driven mRNA processing and its regulation.","confidence":"High","size":22,"edges":219,"triangles":1322,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":15},{"id":"GO:0031047","count":15},{"id":"GO:0006378","count":10},{"id":"GO:0000398","count":10},{"id":"GO:0045292","count":9}]},{"hash":"830209811866001110","title":"RNA Processing and Ribosome Biogenesis Network","description":"This cluster appears to center on RNA metabolism and ribosome biogenesis. The top GO terms include mRNA polyadenylation and pre-mRNA processing, transcription termination, and ribosome biogenesis/mitochondrial ribosome assembly, pointing to core gene-expression and protein-synthesis machinery. Additional terms related to Golgi-to-plasma membrane transport and exosomal secretion suggest a link to protein trafficking and secretion that may coordinate production with export. Overall, the common theme ties transcription/RNA processing with ribosome assembly and cellular trafficking.","confidence":"Medium","size":22,"edges":75,"triangles":62,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0090394","count":2},{"id":"GO:0071287","count":2},{"id":"GO:1903542","count":2},{"id":"GO:0098789","count":2}]},{"hash":"586625695550148889","title":"Mitochondrial Transport and Energy Metabolism","description":"The cluster is dominated by GO terms related to transport of ions and metabolites across the mitochondrial membranes (alpha-ketoglutarate, NAD, magnesium, pyrimidine nucleotides) and mitochondrial-associated energy regulation and thermogenesis, with supporting signals such as insulin response and amino acid starvation. This converges on a mitochondria-centric transport/metabolic role, justifying the label.","confidence":"High","size":22,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000002","count":9},{"id":"GO:0035435","count":8},{"id":"GO:0034198","count":8},{"id":"GO:0006828","count":7},{"id":"GO:0015742","count":7}]},{"hash":"581473089435182171","title":"Cell wall remodeling (chitin and peptidoglycan)","description":"The top GO terms point to cell wall biology: chitin catabolic process and cellular response to chitin, alongside peptidoglycan biosynthesis/catabolism and cell wall organization. This indicates the cluster is enriched for genes involved in building, modifying, or breaking down cell walls, spanning chitin-containing organisms and bacteria, with sporulation-related terms reflecting wall changes during spore formation. A regulatory term on nitrosylation is less central to the core theme but may reflect broader cellular regulation.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071323","count":2},{"id":"GO:0030435","count":2},{"id":"GO:1902083","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0009252","count":2}]},{"hash":"1898714184117381149","title":"Ubiquitin-Proteasome Proteolysis and ERAD","description":"The top GO terms point to ubiquitin-dependent protein degradation pathways: SCF-dependent proteasomal ubiquitin-dependent catabolic process, ubiquitin-dependent ERAD, and protein polyubiquitination, which together define the ubiquitin-proteasome proteolysis axis. Additional terms about glycoprotein catabolic processes and cell-cycle related microtubule functions suggest related proteostasis and cell-cycle remodeling, but the central theme is proteasome-mediated degradation via ubiquitination. Confidence: High","confidence":"","size":22,"edges":12,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0021678","count":3},{"id":"GO:0070544","count":3}]},{"hash":"2069716053984428897","title":"Nutrient-Responsive Transcription Regulation","description":"The cluster is dominated by GO terms for DNA-templated transcription and regulation of transcription from RNA polymerase II, especially in the context of nutrient signals such as oleic acid and carbon source availability. Many terms also touch on linked biosynthetic and metabolic processes (ergosterol, amino acid, pyrimidine, and respiration regulation), suggesting a coordinated transcriptional response that ties gene expression to metabolic state.","confidence":"High","size":22,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0018013","count":6},{"id":"GO:0061429","count":6},{"id":"GO:0061415","count":6},{"id":"GO:0035961","count":6}]},{"hash":"420267764734400934","title":"Mitotic Cell Cycle Regulation","description":"The top GO terms cluster tightly around mitosis: G1/S and G2/M transitions, spindle pole separation, chromosome condensation, re-entry into mitosis, and DNA-templated transcription during the cell cycle. While a couple terms touch on broader signaling, the dominant signal is proteins involved in mitotic progression and its regulation.","confidence":"High","size":22,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:2000775","count":2},{"id":"GO:0010696","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1045957678838110176","title":"Unknown","description":"The GO terms span pigmentation and melanin biosynthesis (melanin biosynthetic process, melanosome organization, pigmentation) as well as neural development (neuroblast proliferation, ventricular zone neuroblast division) and even bacterial teichoic acid biosynthesis, with no clear shared function across proteins. The cluster also has no edges, indicating a lack of cohesive functional link. Therefore, there isn\u2019t a single interpretable theme to label this cluster beyond Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019350","count":2},{"id":"GO:1904541","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0048023","count":2},{"id":"GO:0002052","count":2}]},{"hash":"1756696650113345240","title":"Unknown","description":"The GO terms include antibiotic biosynthesis and response, alongside several unrelated metabolic processes (retinoic acid, melanin, phylloquinone, fatty acid elongation, sphinganine metabolism) with only sparse connectivity (max degree 1, 3 edges). There is no clear shared function tying all proteins together, so a generic Unknown label with no confidence is appropriate.","confidence":"","size":22,"edges":3,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0046677","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0030497","count":4},{"id":"GO:0042376","count":4}]},{"hash":"557854601945288149","title":"Glycan and Cell Wall Biosynthesis","description":"The top GO terms cluster around O-linked glycosylation, UDP-glucose metabolism, and biosynthesis of cell wall polysaccharides such as teichoic acid and hyaluronan, plus cellulose-related processes. This points to a cohesive function in polysaccharide/glycan assembly and cell wall construction in bacteria, aligning with a common theme of glycan biosynthesis and cell envelope formation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018242","count":1},{"id":"GO:0030244","count":1},{"id":"GO:0006011","count":1},{"id":"GO:0019350","count":1},{"id":"GO:0030213","count":1}]},{"hash":"2074428274331144275","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000070","count":1},{"id":"GO:0007080","count":1},{"id":"GO:0051533","count":1}]},{"hash":"71410370312210975","title":"Vesicle Transport and Lysosome Targeting","description":"The GO terms point primarily to intracellular trafficking and sorting: vesicle-mediated transport, targeting to lysosome, Golgi retention, vacuolar transport, and ubiquitin-dependent multivesicular body pathways. While there are a few outlier terms related to exosome assembly and signaling pathway regulation, the dominant theme is vesicle trafficking and lysosomal/vacuolar protein targeting, suggesting a proteostasis-focused cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016192","count":1},{"id":"GO:0006622","count":1},{"id":"GO:1903551","count":1},{"id":"GO:0045743","count":1},{"id":"GO:0045752","count":1}]},{"hash":"813074945943157341","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":6},{"id":"GO:0042273","count":5},{"id":"GO:0000472","count":5},{"id":"GO:0000462","count":5}]},{"hash":"36225867065454089","title":"Heterochromatin Formation and Gene Silencing","description":"This cluster largely centers on chromatin state regulation: multiple terms describe heterochromatin maintenance, silent mating-type cassette silencing, subtelomeric heterochromatin formation, and transcription by RNA polymerase II. The predominance of silencing and heterochromatin terms suggests a module involved in establishing or maintaining repressive chromatin and gene expression control, with a minority of terms pointing to broader stress or signaling contexts. ","confidence":"Medium","size":21,"edges":141,"triangles":643,"max_degree":16,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0070059","count":6},{"id":"GO:0006344","count":6},{"id":"GO:0061186","count":6},{"id":"GO:0009737","count":6},{"id":"GO:0030466","count":6}]},{"hash":"1672633349163654586","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms related to ubiquitination and the ER-associated degradation (ERAD) pathway, including ubiquitin-dependent protein catabolic process, protein ubiquitination, and K63-linked ubiquitination, with additional related terms like actin ubiquitination and general ubiquitination. While there are a few outliers (response to vitamin D, peroxisome matrix import, host-mediated suppression of symbiont invasion), the strongest, most prevalent signals point to components of the ubiquitin-proteasome quality-control system driving the cluster. Confidence: High","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0070534","count":5},{"id":"GO:0033280","count":5},{"id":"GO:0016567","count":5}]},{"hash":"1754019678135231428","title":"Ribosome Biogenesis and Cotranslational Targeting","description":"The cluster shows enrichment for ribosome biogenesis and SRP-dependent cotranslational protein targeting to membranes, which together point to roles in making ribosomes and directing nascent polypeptides to membranes (ER). The other GO terms are heterogeneous and less cohesive, suggesting noise from diverse proteins, but the core signal supports translation-related processes. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0015734","count":2}]},{"hash":"1141747255129228966","title":"Growth and metabolic signaling regulation","description":"The terms cluster around regulation of insulin signaling and downstream PI3K/AKT pathways, along with growth-control pathways such as hippo signaling and processes tied to development and differentiation. Although many terms are regulatory, they collectively point to modulation of growth and metabolic signaling networks, justifying a concise label. Some terms are organism- or process-specific, but the overarching theme is signaling-based control of growth and metabolism.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038016","count":1},{"id":"GO:0051898","count":1},{"id":"GO:0046627","count":1},{"id":"GO:0042733","count":1},{"id":"GO:0046325","count":1}]},{"hash":"1832449665766930448","title":"Unknown","description":"The top GO terms are diverse and do not converge on a single biological function for the cluster. They include nitrate assimilation, several catabolic processes (phosphatidylserine, pectin, cellulose), lipid remodeling (acylglycerol acyl-chain remodeling), vacuolar protein processing, and signaling/defense terms (salicylic acid signaling, camalexin biosynthesis, and endocannabinoid signaling). Because there is no clear common theme tying most proteins together, this cluster cannot be assigned a specific, coherent label.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0042136","count":1},{"id":"GO:0006660","count":1},{"id":"GO:2000124","count":1},{"id":"GO:0080151","count":1}]},{"hash":"1102133427092095386","title":"Kidney tubule development and organ morphogenesis","description":"This cluster is dominated by GO terms related to metanephric tubule development (proximal/distal) and collecting duct development, pointing to kidney nephrogenesis as a core theme. Additional terms such as lymph vessel morphogenesis, mesonephric duct development, and cartilage condensation suggest a broader, but still developmental morphogenesis context. The strongest cohesive signal is kidney tubule formation, with some supporting organogenesis terms, so a label focusing on kidney development with an overall morphogenesis theme is most representative.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036303","count":2},{"id":"GO:0072237","count":2},{"id":"GO:0072287","count":2},{"id":"GO:0080028","count":1},{"id":"GO:0031659","count":1}]},{"hash":"183628048066907292","title":"Nutrient-responsive transcriptional regulation","description":"The top GO terms center on DNA-templated transcription and positive regulation of transcription from RNA polymerase II promoters, including nitrogen catabolite activation and regulation conditioned by carbon sources, with additional terms toward regulation of various catabolic/metabolic processes. This points to a cohesive theme of transcriptional control in response to nutrient and metabolic cues.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007049","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0043388","count":2},{"id":"GO:1901717","count":2}]},{"hash":"241240764433269816","title":"RNA and protein methylation enzymes","description":"GO terms highlight RNA guanine-N7 methylation and N-terminal peptidyl-alanine trimethylation, pointing to methyltransferase activities on RNA and proteins. Other terms reference biosynthetic processes (cobalamin, antibiotic biosynthesis) typical of bacterial metabolism, which often involve methylation steps. The common thread is methylation-related modification and transfer reactions across substrates and pathways, justifying the name.","confidence":"Medium","size":21,"edges":209,"triangles":1311,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006099","count":2},{"id":"GO:0018012","count":2},{"id":"GO:0070555","count":2}]},{"hash":"1202877392263380251","title":"Transmembrane Solute Transporters","description":"This cluster is dominated by GO terms for transmembrane transport of diverse solutes and ions (nitrite, nitrate, phosphate, potassium, arabinose, fucose, vitamins, xenobiotics), indicating membrane transporter proteins rather than metabolic enzymes.","confidence":"High","size":20,"edges":47,"triangles":18,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":7},{"id":"GO:0035461","count":7},{"id":"GO:0042128","count":7},{"id":"GO:0042891","count":7},{"id":"GO:0071805","count":7}]},{"hash":"1196290458779920624","title":"RNA processing and membrane transport","description":"The cluster shows enrichment for RNA processing/regulation terms (positive regulation of mRNA splicing via spliceosome; regulatory ncRNA-mediated gene silencing; obsolete mRNA polyadenylation) alongside multiple membrane transport and metabolic terms (nitrite transport; nitrate assimilation; vitamin transmembrane transport; potassium ion transport; fucose metabolic process). This pattern suggests proteins involved in both RNA-level regulation and membrane transport/metabolic functions, pointing to a multifunctional or dual-role cluster rather than a single straightforward function.","confidence":"Medium","size":20,"edges":157,"triangles":706,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0015707","count":2}]},{"hash":"212808472797867786","title":"Amino acid and cofactor biosynthesis with TCA","description":"The top GO terms cluster around biosynthetic processes for amino acids (e.g., leucine, lysine) and cofactors (thiamine, molybdopterin), plus involvement in the tricarboxylic acid cycle, suggesting a coherent theme of primary metabolism and vitamin/cofactor production. While one term (postsynaptic density clustering) is a potential outlier, the dominant signal points to metabolic biosynthesis rather than signaling or transport. Confidence in this label is Medium.","confidence":"Medium","size":20,"edges":39,"triangles":14,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042136","count":4},{"id":"GO:0051384","count":4},{"id":"GO:0019878","count":4},{"id":"GO:0009228","count":3},{"id":"GO:0009098","count":3}]},{"hash":"1880959351361539292","title":"Nutrient-regulated RNA Pol II transcription","description":"Top GO terms indicate broad regulation of DNA-templated transcription and multiple positive regulation of transcription from RNA polymerase II promoter under different metabolic cues (e.g., nonfermentable carbon source, oleic acid), plus links to pyrimidine nucleotide biosynthesis. This points to a functional cluster centered on transcriptional regulation in response to metabolic state, rather than a single signaling pathway. Confidence in this label is High.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1900399","count":3},{"id":"GO:0006351","count":3},{"id":"GO:2001158","count":3},{"id":"GO:0061414","count":3},{"id":"GO:0035959","count":3}]},{"hash":"1424263251658012949","title":"ECM Remodeling and Adhesion","description":"Based on GO terms like hyaluronan metabolic process, integrin-mediated signaling, calcium-independent cell-matrix adhesion, and metallopeptidase activity, the cluster seems centered on extracellular matrix interactions and remodeling, including adhesion signaling and matrix turnover. Some outliers (nucleotide-excision repair, stamen formation, cholesterol and fatty acid metabolism) exist, but the strongest repeated theme is ECM dynamics and cell-ECM communication.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030212","count":2},{"id":"GO:0007229","count":2},{"id":"GO:1905050","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0006289","count":2}]},{"hash":"2261788720667098007","title":"Unknown","description":"The top GO terms are highly diverse, spanning vesicle transport, vacuolar sorting, chromatin localization, antibacterial response, plasmid partitioning, and dosage compensation, with little to no cohesive functional theme. The sparse edges and lack of a common biological process suggest no single representative function for this cluster. ","confidence":"","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016192","count":1},{"id":"GO:0043328","count":1},{"id":"GO:1901998","count":1},{"id":"GO:0031954","count":1},{"id":"GO:0042766","count":1}]},{"hash":"1867266247498038260","title":"Membrane Transporters for Sugars and Nutrients","description":"This cluster is dominated by GO terms for transport across the plasma membrane of various substrates (nitrite, D-xylose, fructose, vitamins, xenobiotics) and includes osmotic stress response, indicating a cohesive set of membrane transporter proteins involved in nutrient uptake and osmotic balance. Regulatory terms are present but appear ancillary to the core transport theme.","confidence":"High","size":20,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":6},{"id":"GO:0015707","count":4},{"id":"GO:0015753","count":4},{"id":"GO:1990539","count":4},{"id":"GO:0035461","count":4}]},{"hash":"116197023764813012","title":"Amino Acid Membrane Transporters","description":"Most terms describe transport across the plasma membrane for amino acids and related small molecules (lysine, methionine, arginine, GABA, D-alanine) and polyamines. A couple of terms touch transcription regulation or nitric oxide production, but these are minor. The dominant signal is transmembrane transport of amino acids, suggesting the cluster mainly groups transporter proteins handling amino acid import.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045943","count":2},{"id":"GO:0097639","count":1},{"id":"GO:0015812","count":1},{"id":"GO:0044690","count":1},{"id":"GO:1902269","count":1}]},{"hash":"1002052386490505987","title":"Unknown","description":"The top GO terms describe a wide and diverse set of processes (redox and redox-related metabolism, transcription, viral processes, glycosylation, and disparate biosynthetic/metabolic pathways) with no clear shared function binding the proteins. The absence of edges and a cohesive enrichment pattern suggests there is no single representative function for this cluster. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0045454","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035269","count":3}]},{"hash":"2014531032677482837","title":"Chromatin modification and RNA processing regulators","description":"The top GO terms point to histone modification (even if obsolete) and RNA-related processes (RNA methylation and mRNA transport), suggesting a core role in regulating gene expression at both chromatin and post-transcriptional levels. Additional terms related to ubiquitin ligase activity, development, and immune signaling appear, but the strongest signal is for chromatin/RNA regulatory functions, justifying a label centered on these processes.","confidence":"Medium","size":20,"edges":6,"triangles":0,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043981","count":5},{"id":"GO:1904668","count":4},{"id":"GO:0002534","count":4},{"id":"GO:0010659","count":4},{"id":"GO:0051028","count":4}]},{"hash":"428439729696459635","title":"Central carbon metabolism and xenobiotic response","description":"These proteins cluster around core energy and metabolism pathways (TCA cycle, glycolysis, propylene catabolic process) and biosynthesis/oxidation-related steps (porphyrin-related biosynthesis, oxidant detoxification). There are also links to antibiotic biosynthesis and responses to antibiotics or xenobiotics. Together, this suggests a group involved in primary energy metabolism with concomitant detoxification and secondary metabolite/antibiotic-related functions, making the label \u201ccentral carbon metabolism and xenobiotic response\u201d appropriate.","confidence":"Medium","size":20,"edges":182,"triangles":1003,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0019878","count":5},{"id":"GO:0006096","count":4}]},{"hash":"327613736896861179","title":"Core Metabolism and Protein Synthesis","description":"GO terms point to central metabolism (TCA cycle) and diverse biosynthetic pathways (amino acids, biotin, sphinganine, porphyrinogen IX), plus translation, implying a broad housekeeping metabolic/protein-synthesis module.","confidence":"Medium","size":20,"edges":19,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":5},{"id":"GO:0006782","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006099","count":3}]},{"hash":"497605503638644377","title":"Small-molecule biosynthesis pathways","description":"The cluster shows a concentration of GO terms for biosynthetic processes: glycerol-3-phosphate biosynthesis/catabolism, polysaccharide and lipopolysaccharide biosynthesis, pantothenate biosynthesis, and serine biosynthesis, pointing to involvement in assembling basic metabolites and cell-wall related components. A couple of outlying terms (spliceosome conformational change, brain-derived neurotrophic factor response) are less connected and may reflect annotation noise or multifunctional proteins. Overall, the proteins appear as a metabolically cohesive module focused on small-molecule biosynthesis.","confidence":"Medium","size":20,"edges":65,"triangles":53,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0000388","count":2},{"id":"GO:1990416","count":2},{"id":"GO:0046167","count":2},{"id":"GO:0000271","count":2}]},{"hash":"1822101801849132138","title":"Centrosome and spindle assembly with RNA processing","description":"The top GO terms are dominated by centrosome cycle and spindle assembly, pointing to a centrosome/spindle apparatus-focused function in cell division. Additional terms on stress granule assembly and deadenylation-dependent mRNA decay suggest a link to RNA processing and stress response alongside mitotic processes, indicating a cluster of proteins involved in centrosomal functions with RNA metabolism dynamics.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":3},{"id":"GO:0034063","count":2},{"id":"GO:0000288","count":2},{"id":"GO:1901726","count":2},{"id":"GO:2000584","count":2}]},{"hash":"1826297898972292635","title":"Cell cycle and DNA replication","description":"The Top Terms show a strong emphasis on cell division, cell cycle progression, DNA replication-dependent chromatin assembly, and meiotic chromatid cohesion, which together point to core processes of genome duplication and division. Peripheral terms like vacuolar acidification, antibiotic response, and specific signaling regulation are present but less central, while transcription and RNA transport terms may reflect gene expression programs linked to division. Overall, the cluster appears to represent cell-cycle\u2013related machinery and chromatin dynamics.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0042518","count":2}]},{"hash":"673435773341405972","title":"Diverse metabolite biosynthesis","description":"This cluster\u2019s top GO terms center on biosynthetic processes across lipids, vitamins, hormones, pigments, and other metabolites (fatty acid elongation, retinoic acid, melanin, estrogen, glucocorticoids, phylloquinone, tetrahydrobiopterin, etc.), suggesting proteins that participate in the assembly of diverse metabolic pathways rather than a single pathway. The common theme is synthesis of a broad range of metabolites.","confidence":"High","size":20,"edges":151,"triangles":605,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030497","count":20},{"id":"GO:0042376","count":20},{"id":"GO:0002138","count":20},{"id":"GO:0042438","count":20},{"id":"GO:0006666","count":20}]},{"hash":"448830110230177495","title":"Unknown","description":"The top GO terms span very different biological areas, including spindle assembly (cell division), chloroplast thylakoid protein import, cell-cycle transcription regulation (obsolete), and innate immune signaling (NOD2 pathway), plus chromatin-related processes and neural development. Several terms are obsolete or non-specific, and there is no clear, shared function tying all 20 proteins together. Because there is no cohesive theme, the cluster is best labeled Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0045038","count":2},{"id":"GO:0000083","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2}]},{"hash":"1326832333532945612","title":"RNA Pol II Transcription Regulation","description":"The proteins in this cluster are primarily associated with the regulation of transcription from RNA polymerase II promoters (DNA-templated transcription, regulation of transcription from RNA Pol II promoter). This indicates a core theme of transcriptional control, rather than core metabolic enzymes; other metabolism-related GO terms likely reflect downstream regulatory roles or context-specific regulation (e.g., ergosterol biosynthesis, nucleotide and amino acid biosynthesis) rather than a shared catalytic function. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0061429","count":1},{"id":"GO:0061415","count":1},{"id":"GO:0035961","count":1},{"id":"GO:2001196","count":1}]},{"hash":"704149027597246553","title":"Telomere maintenance and telomerase regulation","description":"The top GO terms are dominated by telomere-related processes: maintenance via telomerase, telomere assembly, localization to telomeres, telomere capping, and regulation of DNA strand elongation. A minority term on lipid catabolic process appears as noise; overall, the set points to proteins involved in telomere maintenance and telomerase-related regulation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016042","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0032202","count":1},{"id":"GO:0071166","count":1},{"id":"GO:0051973","count":1}]},{"hash":"244685541243064103","title":"Amino acid transport across membranes","description":"The most represented terms are about importing amino acids across the plasma membrane (lysine, methionine, arginine, leucine) and transporting GABA, pointing to a transporter/ carrier role. Some terms also mention carbohydrate metabolism and nitric oxide production, but the transport theme for amino acids is strongest; overall, these proteins likely function as amino acid transporters or related membrane carriers.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0097639","count":1},{"id":"GO:0015812","count":1},{"id":"GO:0044690","count":1}]},{"hash":"2048446211876311048","title":"Chromatin modification and transcription regulation","description":"The top GO terms center on histone methylation (H3-K4, H3-K79) and RNA guanine-N7 methylation, plus DNA-templated transcription, which together point to regulation of chromatin state and gene expression. Additional terms like cell division and hypoxia response suggest broader involvement in cell-cycle and stress-responsive transcriptional control, while the vacuolar protein catabolic process is less aligned but may reflect regulation of protein turnover for these processes. Overall, the cluster seems best described by chromatin modification and transcriptional regulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007039","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0034729","count":2}]},{"hash":"1859065153005491377","title":"Unknown","description":"The GO terms across the cluster are heterogeneous, including coenzyme A biosynthesis, pantothenate catabolism, sporulation, insect gonad development, Malpighian tubule regulation, ecdysone response, and transcription regulation, with no evident shared pathway linking most proteins. With no edges clustering or a dominant functional theme, a concise, representative label cannot be derived.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015937","count":2},{"id":"GO:0015941","count":1},{"id":"GO:1901285","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0061040","count":1}]},{"hash":"669185842103000199","title":"Amino acid and porphyrin biosynthesis","description":"The dominant GO terms point to biosynthetic pathways for amino acids (shikimate/chorismate leading to aromatic amino acids; L-proline; L-alanine metabolism) and for porphyrin biosynthesis (protoporphyrinogen IX). Additional terms touch on one-carbon metabolism and phosphorylation, with only a minor hint of stress response, suggesting the cluster mainly reflects metabolic biosynthesis rather than signaling or interaction. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0085014","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0019632","count":1},{"id":"GO:0009423","count":1}]},{"hash":"1055361249660871487","title":"Membrane Nutrient and Xenobiotic Transporters","description":"Proteins in this cluster are predominantly linked to membrane transport, including nitrite, D-xylose, fructose, vitamin, and xenobiotic transmembrane transport, plus nitrate assimilation. This pattern suggests a core role in nutrient uptake and export of foreign compounds, with some ancillary terms reflecting related stress responses.","confidence":"High","size":19,"edges":118,"triangles":395,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":4},{"id":"GO:0015753","count":4},{"id":"GO:1990539","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0042908","count":4}]},{"hash":"2165302913885612453","title":"Nutrient and Ion Transmembrane Transport","description":"This cluster is dominated by transmembrane transport GO terms for multiple substrates (nitrite, nitrate, phosphate, potassium, fucose, arabinose, xenobiotics, vitamins), indicating a cohesive set of transporter proteins facilitating diverse substrate uptake/export. A metabolic term (fucose metabolic process) is present but secondary; the main signal is transport across membranes. ","confidence":"High","size":19,"edges":22,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0071805","count":3}]},{"hash":"1437475908829036340","title":"Rho Signaling and Cell Morphogenesis","description":"The cluster shows prominent GO terms for Rho protein signal transduction and cell morphogenesis, indicating roles in cytoskeletal dynamics and cell shape changes. The presence of mitotic sister chromatid biorientation also hints at cell division involvement, though several terms are obsolete or general, so the core theme is cytoskeletal regulation linked to morphogenesis via Rho signaling.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0034351","count":2},{"id":"GO:0007266","count":2},{"id":"GO:1990758","count":2}]},{"hash":"1280897856414951118","title":"Membrane dynamics and cell migration","description":"This cluster centers on membrane-associated processes: phosphatidylinositol phosphate biosynthesis, protein localization to the plasma membrane, and post-translational targeting to membranes, along with ruffle assembly and fibroblast migration, indicating roles in membrane trafficking and cytoskeletal remodeling during cell movement. Autophagosome assembly regulation also ties to membrane dynamics. Some terms (translational elongation, transcription regulation) appear more general and may be noise. Overall, the theme is cohesive around membrane dynamics and motility.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046854","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0006414","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0042070","count":1}]},{"hash":"2272097682509615632","title":"Membrane Transporters and Golgi Organization","description":"The cluster centers on membrane transport functions, with multiple transmembrane transport GO terms (protein, D-xylose, fructose, xenobiotic transport) and Golgi organization as a consistent theme. While other terms like brain development and replicative senescence appear, the strongest, most representative signal relates to transport across membranes and Golgi-related processes, suggesting a role for transporter proteins associated with Golgi function.","confidence":"Medium","size":19,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071806","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0007030","count":2},{"id":"GO:0007420","count":2}]},{"hash":"202036319873824846","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0048568","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0000472","count":4}]},{"hash":"936798950407214217","title":"Ribosome Biogenesis and Translation Initiation","description":"The top GO terms converge on ribosome biogenesis and rRNA maturation (SSU/LSU), formation of translation preinitiation complexes, and TORC1 signaling, plus supporting roles in mRNA transport, indicating a cohesive function in ribosome assembly and initiation of translation.","confidence":"High","size":19,"edges":39,"triangles":27,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000462","count":4}]},{"hash":"335131698959608421","title":"Unknown","description":"The top terms are highly diverse, ranging from oxidation-reduction and xenobiotic response to various development and cell cycle processes, with no single dominant theme. The low maximum degree and lack of a shared functional pathway suggest the proteins do not form a coherent, easily namingable cluster, so a generic Unknown label with no clear function is most appropriate.","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042493","count":2},{"id":"GO:0097421","count":2},{"id":"GO:2000678","count":2},{"id":"GO:0021762","count":2}]},{"hash":"1706973105008274418","title":"Fungal morphogenesis and cell wall biogenesis","description":"The top GO terms show a clear emphasis on fungal-type cell wall biogenesis, budding cell growth, and filamentous growth, pointing to proteins involved in fungal morphogenesis and cell wall construction. Other terms like DNA replication and immune signaling appear ancillary, but do not redefine the dominant fungal-centric theme. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043029","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0030447","count":2},{"id":"GO:0009272","count":2},{"id":"GO:0007117","count":2}]},{"hash":"1260589330832104490","title":"Golgi-to-vacuole and endosome vesicle trafficking","description":"This cluster is centered on transport between the Golgi, vacuole, and endosome, plus vesicle docking and targeting to vacuoles, indicating a cohesive vesicle trafficking/secretory pathway function. Although a few terms relate to specialized secretory roles (platelet granules, leukocyte cytotoxicity), the dominant theme is intracellular vesicle transport.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0032229","count":1},{"id":"GO:0048070","count":1},{"id":"GO:0043524","count":1}]},{"hash":"2245486221801298299","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0015707","count":1},{"id":"GO:1900754","count":1}]},{"hash":"889847907029782920","title":"Mitochondrial translation and respiration","description":"The cluster\u2019s top terms cluster around mitochondrial biology: mitochondrial translation (glycyl-tRNA aminoacylation, general translation), NADH-to-ubiquinone electron transport, and heme biosynthesis. Together these reflect a mitochondria-centric module involving protein synthesis within mitochondria and energy production, with a few outliers (e.g., embryonic development) that do not redefine the core function.","confidence":"High","size":19,"edges":135,"triangles":463,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0006120","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0006378","count":2}]},{"hash":"1127018117399755286","title":"Cytoskeletal Regulation and Adhesion Signaling","description":"The top GO terms cluster around regulation of cell shape, negative regulation of GTPase and protein kinase activities, and regulation of focal adhesion assembly, all core to cytoskeletal remodeling and cell\u2013matrix adhesion. Some terms also tie to neural development (axonogenesis, synaptic potentiation) and heart development, which can be driven by cytoskeletal and signaling changes. Together, these points support a theme of coordinated cytoskeletal dynamics and adhesion signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":3},{"id":"GO:0034260","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0043552","count":2}]},{"hash":"2154492788068707414","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071076","count":1},{"id":"GO:0033621","count":1},{"id":"GO:0048366","count":1},{"id":"GO:0031440","count":1},{"id":"GO:0071036","count":1}]},{"hash":"1771259812246120291","title":"Unknown","description":"The cluster terms mix eukaryotic cell-cycle and signaling processes (cell cycle, Wnt signaling, cell division, regulation of cell shape, mitotic cohesion) with bacterial cell-wall related processes (peptidoglycan biosynthesis, cell wall organization) and sensory/antibiotic response. There are no edges connecting the proteins, suggesting no cohesive functional module. Because the terms do not converge on a single clear function, the cluster is best described as Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0009252","count":2}]},{"hash":"431216333590304444","title":"Unknown","description":"The Top Terms span both bacterial processes (peptidoglycan biosynthesis, cell wall organization, turnover) and eukaryotic processes (regulation of non-motile cilium assembly, ER stress\u2013related translation initiation), with no clear shared function linking all members, and there are no edges among proteins to support a unified pathway. This lack of a coherent theme warrants an Unknown label.","confidence":"","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:0008360","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1705593426771229207","title":"Exosome Secretion and Immune Signaling","description":"The top GO terms point to extracellular vesicle biology, with positive regulation of exosomal secretion and regulation of extracellular exosome assembly, plus ATP export which can fuel vesicle trafficking. The inclusion of response to lipopolysaccharide and T cell homeostasis suggests an immune-related role, possibly intercellular communication via exosomes during immune responses. Although a few terms are developmental or obsolete, the strongest cohesive theme is exosome biogenesis/secretory activity linked to immune signaling.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:1904669","count":2},{"id":"GO:1903543","count":2},{"id":"GO:1903551","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0051092","count":2}]},{"hash":"1294805894633585529","title":"Mitochondrial metabolism and cristae formation","description":"This cluster includes terms tied to mitochondria: cristae formation, regulation of fatty acid oxidation, tetrapyrrole linkage (heme-related), and protein folding, all pointing to mitochondrial structure and energy metabolism. Hypoxia signaling (HIF-1alpha pathway) and broader metabolic signaling (insulin receptor, transcription regulation) can intersect with mitochondrial function, supporting a cohesive theme around mitochondrial metabolism and organization. Although some terms are more general, the strongest shared context is mitochondrial structure and metabolism.","confidence":"Medium","size":18,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046944","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0018105","count":1},{"id":"GO:0097411","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1951886899099985757","title":"Endocytic Trafficking and Autophagy","description":"This cluster is dominated by GO terms for vesicle handling\u2014endocytosis, endocytic recycling, microautophagy, and vacuole fusion\u2014pointing to trafficking and autophagic processes. While there are some neuronal development and signaling terms present (substantia nigra development, dendrite morphogenesis, Rho signaling), the clearest signal is vesicle trafficking and autophagy, justifying a focused label on endocytosis/autophagy.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0016237","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0042144","count":2}]},{"hash":"1227586499844201488","title":"Transcription, splicing, and ubiquitination","description":"Top GO terms include mRNA splicing via spliceosome (GO:0000398), DNA-templated transcription (GO:0006351), and protein polyubiquitination/ERAD (GO:0000209, GO:0030433), indicating a cluster centered on gene expression regulation and protein quality control. Additional terms touching on viral life cycle and proviral latency suggest possible host-viral interaction contexts, but the core signal is transcription and RNA processing linked to ubiquitin-mediated protein fate.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035948","count":2}]},{"hash":"1690444203044446143","title":"Ion Transport and Vacuolar Acidification","description":"Based on the GO terms, this cluster centers on proton-driven transport and ion translocation across membranes (proton motive force-driven ATP synthesis, proton transmembrane transport, monoatomic cation and sodium transport) and on vacuolar processes (vacuole organization, protein targeting to vacuole, vacuolar acidification). Copper ion homeostasis also appears, suggesting metal ion handling within organelles. Together, these cues point to a coherent module of membrane transporters and vacuolar function tightly linked to energy gradients. ","confidence":"Medium","size":18,"edges":140,"triangles":627,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0007033","count":2}]},{"hash":"1365956034992006164","title":"Stress and Hormone Response Signaling","description":"The top GO terms point to diverse stress and defense processes (abiotic and biotic stress responses, unfolded protein response, seed maturation, mechanical stimulus, and pigment-related defenses) across organisms, suggesting a broad, non-specific stress/hormone signaling theme rather than a single pathway.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0006990","count":2}]},{"hash":"2060369406846729066","title":"Filopodium dynamics and small GTPase signaling","description":"The prominent GO terms cluster around actin-based protrusions (filopodium assembly and its regulation), cell spreading/adhesion, and small GTPase signaling, indicating a core function in cytoskeleton remodeling and related signaling. While there are additional transport and DNA replication terms, the strongest, coherent theme is cytoskeleton dynamics tied to GTPase-mediated signaling.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0045740","count":3},{"id":"GO:0051932","count":3},{"id":"GO:0046847","count":3}]},{"hash":"1899117346069152595","title":"Nuclear DNA Replication and RNA Processing","description":"The top GO terms cluster around DNA replication, repair, and genome maintenance (DNA replication, recombination, SOS response, transcription-coupled repair, transcription) along with RNA processing and quality control (splicing, mRNA decay) and nuclear ribosome biogenesis, suggesting a cohesive group of nuclear DNA metabolism and RNA processing activities. The viral genome replication term may reflect shared host factors rather than a viral-specific function. ","confidence":"Medium","size":18,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0019079","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0006283","count":4}]},{"hash":"2052871465705626078","title":"ER-Golgi Vesicle Trafficking and GTPase Regulation","description":"The top GO terms cluster around vesicle transport between the endoplasmic reticulum and Golgi, including ER-to-Golgi and retrograde Golgi-to-ER trafficking, and the positive regulation of GTPase activity, which commonly governs vesicle budding and trafficking. This points to a coherent theme of secretory pathway transport and its regulatory machinery, with a few outlier terms likely due to annotation noise. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0016192","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1018337489019587376","title":"Bioluminescence-linked fatty acid metabolism","description":"Top GO terms cluster around fatty acid metabolism across chain lengths, biosynthesis, transport, and redox processes, with a notable bioluminescence term suggesting involvement in energy pathways that support light emission. While some terms appear more general (malonate catabolism, phenylpropanoid metabolism), the dominant pattern is lipid metabolism tied to redox activity and, in part, luminescent function.","confidence":"Medium","size":18,"edges":100,"triangles":255,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0001579","count":5},{"id":"GO:0090410","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0000038","count":5}]},{"hash":"1960686667635254340","title":"Ribosome biogenesis and translation","description":"The top terms are dominated by translation and ribosome assembly, with a note on tRNA wobble uridine modification, indicating a core role in protein synthesis machinery. While there are additional, perhaps peripheral terms (lipopolysaccharide biosynthesis, iron-sulfur cluster assembly, retinol metabolism), the strongest signal across the cluster centers on ribosome-related processes. ","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0009103","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0042572","count":2}]},{"hash":"1870957426498559979","title":"Unknown","description":"The cluster features a heterogeneous set of GO terms, including oxidation-reduction and formaldehyde catabolic processes, lipid A biosynthesis, Golgi-to-vacuole transport, and several negative regulatory processes (miRNA processing, EMT, chromosome condensation). There is no clear, single biological function tying all proteins together, so a specific high-level label cannot be assigned.","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0046294","count":2},{"id":"GO:0010323","count":2},{"id":"GO:0090503","count":2},{"id":"GO:1903799","count":1}]},{"hash":"1919679605363145008","title":"Carbohydrate and amino acid biosynthesis","description":"This cluster is dominated by metabolic biosynthesis signals: gluconeogenesis, fructose metabolism, fructose 2,6-bisphosphate metabolism, carbohydrate phosphorylation, and L-serine biosynthesis, plus cobalamin biosynthetic process. The presence of brain development and cardiac muscle apoptotic regulation terms likely reflects pleiotropy or broader signaling roles rather than a single shared function. Overall, the strongest theme is carbohydrate and amino acid biosynthesis with related cofactor biosynthesis.","confidence":"Medium","size":18,"edges":5,"triangles":1,"max_degree":3,"top_function":"autophagy","top_go_terms":[{"id":"GO:0006094","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0010666","count":3},{"id":"GO:0046835","count":3}]},{"hash":"1352129727292158578","title":"Mitochondrial Metabolism and Transport","description":"The cluster\u2019s terms predominantly describe mitochondrial transport of metabolites (alpha-ketoglutarate, NAD, pyrimidine nucleotides), ion transport (Mg2+, Mn2+), and energy-related processes such as fatty acid response and adaptive thermogenesis, plus insulin signaling, pointing to a coherent mitochondrial metabolism/energy homeostasis theme.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":4},{"id":"GO:0032869","count":3},{"id":"GO:0006828","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0035352","count":2}]},{"hash":"2253491733227095002","title":"Nuclear gene expression and developmental signaling","description":"The proteins show enrichment for nuclear processes (DNA replication, DNA-templated transcription, cohesin loading) along with signaling and developmental roles (insulin receptor signaling, growth hormone signaling, cell-matrix adhesion, axon guidance, retina vasculature development). This pattern suggests a cluster of factors coordinating gene expression with developmental signaling and morphogenesis.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0046626","count":3},{"id":"GO:0007160","count":3},{"id":"GO:0008045","count":3}]},{"hash":"2172913636518633402","title":"Amino acid metabolism and N-terminal protein modifications","description":"Top GO terms include arginine biosynthesis and polyamine catabolism (spermine, putrescine) along with multiple N-terminal acetylation/propionylation terms, pointing to a shared theme of amino acid metabolism and protein N-terminal modifications. Some outlier biosynthetic processes (melatonin, ectoine) are present but do not overwhelm the core pattern. This supports a cohesive label focusing on metabolism of amino acids and related PTMs.","confidence":"Medium","size":18,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":4},{"id":"GO:0046208","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006526","count":3},{"id":"GO:0017196","count":3}]},{"hash":"2009993214799730742","title":"Embryogenesis and Tissue Morphogenesis","description":"The top GO terms cluster around developmental processes across multiple tissues and organs\u2014left-right patterning, cartilage morphogenesis, EMT in heart development, endocrine and placental development, pancreatic cell development, and trophoblast differentiation\u2014pointing to a shared theme of embryonic development and tissue morphogenesis rather than a single molecular function. A general transcription term appears, but the dominant signal is developmental differentiation. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0003323","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0003198","count":1}]},{"hash":"398243985098944997","title":"Nuclear transcription and chromatin regulation","description":"Most top GO terms point to nuclear gene expression control (DNA-templated transcription; transcription from RNA Pol II promoter) and chromatin state (histone H3-K9 methylation, though obsolete in list). A few terms touch on the mitotic cell cycle and protein homooligomerization, which can relate to regulation of transcription complexes. Other annotations (endocytosis, neurotrophic factor production, folate metabolism) are less cohesive with the core pattern. Overall, the cluster seems enriched for transcriptional regulation and chromatin-related processes, with sparse involvement in other pathways; thus this label is a reasonable concise summary.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1570153305934844268","title":"Membrane trafficking and kidney basement membrane processes","description":"The GO terms cluster around membrane-associated activities (receptor-mediated endocytosis, GPI anchor biosynthesis, lipid catabolism in membranes) and kidney extracellular environment (glomerular filtration, basement membrane development), with immune signaling and angiogenesis regulation aligning with surface-receptor\u2013mediated processes. Overall, a coherent but broad theme of membrane-related and kidney extracellular processes. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000394","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0003094","count":1},{"id":"GO:1903165","count":1},{"id":"GO:0045765","count":1}]},{"hash":"2181668545227243083","title":"mRNA Splicing and Processing Regulation","description":"This cluster is dominated by GO terms related to spliceosome-mediated mRNA processing: cis splicing, alternative splicing, and regulation (positive/negative) of mRNA splicing, as well as regulation of mRNA poly(A) tail shortening and nuclear mRNA export. While a couple of terms touch on chloroplast mRNA modification or developmental processes, the strongest signal is mRNA splicing/processing regulation, making this label representative of the cluster\u2019s core function.","confidence":"High","size":17,"edges":79,"triangles":139,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0046832","count":1},{"id":"GO:1901407","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0071600","count":1},{"id":"GO:1900871","count":1}]},{"hash":"646844132576505729","title":"Gene expression and protein quality control","description":"The cluster shows a mix of nucleic acid metabolism and gene expression terms (DNA replication, rRNA maturation, mRNA transport, transcription regulation) together with protein quality control and trafficking processes (ERAD, post-translational targeting to membranes, chaperone/refolding, regulation of protein kinase activity, inclusion body dynamics). This suggests a functional module tying gene expression machinery to protein homeostasis and membrane-associated processing, rather than a single narrow pathway. ","confidence":"Medium","size":17,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0090084","count":2}]},{"hash":"1515614387029164643","title":"Immune Signaling and Cell Migration","description":"This cluster is enriched for GO terms linked to signal transduction and motility (positive regulation of GTPase activity, integrin-mediated signaling, PDGF receptor signaling, cell migration). There are immune-related terms (interleukin-4 production, B cell affinity maturation), suggesting a theme of immune cell activation and trafficking. A few terms pertain to RNA processing and DNA regulation, indicating some multifunctional proteins, but the dominant theme centers on signaling and movement in immune contexts.","confidence":"Medium","size":17,"edges":29,"triangles":12,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0000398","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0032298","count":2}]},{"hash":"1504393629407664179","title":"Mitotic DNA Replication and Cell Division","description":"The cluster is dominated by mitosis-related GO terms: mitotic cell cycle, cell division, and multiple steps of mitotic DNA replication (initiation, elongation, and break-induced replication). A few terms point to ER-to-Golgi transport, but the strongest signal ties to mitotic progression and DNA replication during cell division, suggesting proteins functioning in mitosis and genome duplication.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1902969","count":1},{"id":"GO:0000727","count":1}]},{"hash":"731907897574513869","title":"Mitochondrial Metabolite Transport and Energy Metabolism","description":"The top GO terms cluster around mitochondrial metabolite transport (alpha-ketoglutarate, NAD, pyrimidine nucleotides) and ion transport (manganese, magnesium), with energy-related processes (adaptive thermogenesis, insulin response) suggesting a core function in mitochondrial transport and energy regulation; the meiotic cohesion term seems incidental rather than core to the cluster.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":2},{"id":"GO:0006828","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0035352","count":1},{"id":"GO:1990616","count":1}]},{"hash":"1288016218024294684","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000717","count":2},{"id":"GO:0006296","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0071051","count":2},{"id":"GO:0071042","count":2}]},{"hash":"1415178552530553290","title":"Bacterial biosynthesis pathways","description":"Most represented terms are lipopolysaccharide biosynthetic process, O antigen biosynthetic process, and antibiotic biosynthetic process, which together point to enzymatic pathways that assemble complex microbial molecules. While several other terms (galactose catabolic process, DNA-templated transcription, development terms) appear, they may reflect broad or cross-annotation; the cluster's core signal is biosynthetic activity in microbes. Therefore, a concise label: \"Bacterial biosynthesis pathways\". ","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:1902987","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0060716","count":4},{"id":"GO:0008218","count":3}]},{"hash":"1032486460717366783","title":"DNA replication and cell cycle regulation","description":"The top GO terms cluster around nuclear DNA processes such as DNA replication, recombination, and repair, and also include regulation of the cell cycle (centrosome cycle; positive regulation of nuclear DNA replication). Developmental terms (multicellular organism development and embryonic cranial skeleton morphogenesis) suggest roles in organismal growth, while the mitochondrial inner membrane insertion term adds a possible mitochondrial context. Overall, the dominant signal is genome maintenance and cell-cycle control, so the label reflects the core function of the cluster.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0010571","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0007275","count":2}]},{"hash":"794029076245810115","title":"Protein maturation and proteolysis","description":"This cluster\u2019s GO terms cluster around proteolytic processing and maturation of proteins/peptides: membrane protein proteolysis, protein autoprocessing, and angiotensin maturation, as well as related renin-angiotensin regulation. Other terms such as xylan catabolic process, antigen presentation, and mesonephros development appear less related and likely represent annotation noise. Overall, the dominant theme is enzymatic processing and maturation of proteins/peptides.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0070305","count":1},{"id":"GO:0019886","count":1}]},{"hash":"1314052180135995844","title":"Developmental signaling and neural morphogenesis","description":"The top GO terms center on embryonic development, cranial skeleton morphogenesis, and neural extension regulation (JNK cascade, negative regulation of axon extension, multicellular development), suggesting a theme of developmental signaling and neural/craniofacial morphogenesis. Supporting terms like translation, protein targeting, and proteasomal degradation indicate accompanying cellular- homeostatic processes that enable development. Overall, the cluster seems best described by a developmental, neural morphogenesis orientation rather than a single metabolic pathway.","confidence":"Medium","size":17,"edges":81,"triangles":196,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0032436","count":3},{"id":"GO:0007254","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1600082466200586061","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":7,"triangles":0,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070987","count":3},{"id":"GO:0000733","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0070914","count":3}]},{"hash":"2090467721065653649","title":"Lipid and Vitamin Metabolism with Developmental Signals","description":"The top GO terms point to a range of lipid- and vitamin-related metabolic processes (fatty acid elongation, sphinganine metabolism, retinoic acid biosynthesis, phylloquinone and estrogen biosynthesis) alongside pigment biosynthesis (melanin) and a development-related term (lung development). This pattern suggests a cluster centered on lipid/vitamin and steroid metabolism with links to developmental regulation and transcriptional control. Overall, a cohesive theme emerges around metabolic pathways that supply signaling and structural lipids during development.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0030324","count":5},{"id":"GO:0030497","count":4},{"id":"GO:0042376","count":4},{"id":"GO:0042208","count":4}]},{"hash":"1811390583967884342","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019262","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0006090","count":2},{"id":"GO:0001889","count":2}]},{"hash":"892991027243597124","title":"Chromatin Regulation and DNA Repair","description":"The top GO terms cluster around chromatin-related processes such as establishment of protein localization to chromatin, subtelomeric heterochromatin formation, and nucleolar transcription by RNA polymerase I, plus genome maintenance functions like regulation of double-strand break repair via homologous recombination and chromatin localization. While a couple terms hint at broader stress responses, the dominant theme ties to chromatin organization, transcriptional activity in the nucleolus, and DNA repair, supporting a cohesive label. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071420","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0042790","count":1},{"id":"GO:2000620","count":1}]},{"hash":"400566703798289335","title":"Membrane Transport Proteins","description":"The top GO terms are dominated by various transmembrane transport processes (ions, nitrite, vitamins, metabolites) and vesicular neurotransmitter loading, suggesting a shared role in moving substances across membranes. Minor representation of mitotic cell cycle terms likely reflects noise rather than a core function. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0015707","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0071805","count":1}]},{"hash":"657845117264639775","title":"Synaptic Vesicle Trafficking and PI Signaling","description":"Based on the GO terms, the proteins appear linked to neuronal signaling and membrane trafficking: synaptic vesicle uncoating, receptor recycling regulation, and phosphoinositide metabolism (both catabolic and biosynthetic). Although the terms span development and locomotion, the most coherent theme centers on synaptic vesicle dynamics and phosphoinositide-driven membrane processes that modulate neuronal activity and movement. The lack of direct edge connections suggests a broad, functionally related set rather than a tightly interacting complex.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031161","count":1},{"id":"GO:0001921","count":1},{"id":"GO:0043058","count":1},{"id":"GO:0016191","count":1},{"id":"GO:0031642","count":1}]},{"hash":"2134516740614599051","title":"DNA replication and chromatid cohesion","description":"Based on the GO terms, the cluster centers on DNA replication and chromosome maintenance during mitosis (DNA replication, mitotic sister chromatid cohesion, maintenance of DNA trinucleotide repeats, regulation of DNA polymerase activity, and related chromatin-associated acetylation). A few outlier terms (fungal-type cell wall biogenesis and developmental processes) are present but do not override the core replication/maintenance theme. Therefore, the label reflects the main functional theme of the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035351","count":2},{"id":"GO:0006260","count":1},{"id":"GO:0007064","count":1},{"id":"GO:0035753","count":1},{"id":"GO:0034088","count":1}]},{"hash":"2122706650428633236","title":"Unknown","description":"The cluster contains a mix of terms tied to mammalian development and cell proliferation (liver regeneration, lactation, mammary gland epithelial cell proliferation, cell division, Wnt signaling) but also plant polysaccharide catabolic processes (cellulose/xylan catabolism) and autophagy/obsolete histone phosphorylation terms, giving no single coherent function. This heterogeneity and lack of a unifying theme suggest no clear cluster function can be defined.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":2},{"id":"GO:0007595","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0030245","count":2}]},{"hash":"40813057293704656","title":"Brain Development and Gene Regulation","description":"The cluster centers on brain development (GO:0007420) with accompanying regulatory functions such as transcription by RNA polymerase II and negative regulation of translation, plus broader growth regulation. Although some terms are obsolete or general, the presence of a neural development signal plus transcriptional/translation control supports a label focused on neurodevelopmental gene regulation. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0032715","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0006366","count":2},{"id":"GO:0007420","count":1}]},{"hash":"2105155764526952128","title":"Neurodevelopment and Cell Cycle Regulators","description":"The top GO terms emphasize neural development (forebrain development, neural tube closure) and broader skeletal development, coupled with cell-cycle regulation (G0 to G1 transition, APC-dependent catabolic process) and transcription. This points to a cluster of proteins involved in neurodevelopmental processes linked with cell-cycle control and transcriptional regulation, rather than a single, narrow pathway. Some outliers (stress responses, fungal-related terms) may reflect annotation noise or cross-species terms, but the core signal aligns with development and cell-cycle regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0032995","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0070059","count":2}]},{"hash":"650335937062365302","title":"Membrane Transporters for Ions and Sugars","description":"The top GO terms point to transmembrane transport activities for various ions (sodium, potassium, phosphate, nitrite) and small molecules (arabinose, fucose, sialic acid, 4-hydroxyphenylacetate), plus a vesicular neurotransmitter loading step. This pattern indicates a cluster enriched in membrane transporter proteins with broad substrate specificity rather than a single metabolic process. Therefore, the label 'Membrane Transporters for Ions and Sugars' best captures the shared function.","confidence":"High","size":16,"edges":12,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0035725","count":2}]},{"hash":"868829587147100878","title":"Golgi-ER trafficking and peroxisome import","description":"The GO terms point to intracellular transport and organelle import processes: proteins retained in the Golgi, ER-to-Golgi vesicle transport, and protein import into peroxisomes, including receptor recycling. While there are a couple of cell cycle terms and envelope/outer membrane assembly terms, the dominant theme across the cluster is trafficking and biogenesis of organelles (Golgi, ER, peroxisomes). ","confidence":"Medium","size":16,"edges":13,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0016562","count":2},{"id":"GO:0006888","count":2}]},{"hash":"365667318071645844","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":12,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034473","count":1},{"id":"GO:0034475","count":1},{"id":"GO:0071051","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0016120","count":1}]},{"hash":"1813849224412587168","title":"Growth regulation and development","description":"The top GO terms point to core growth and gene expression processes (translation initiation, transcription, DNA repair, cell division) alongside growth-control signaling (negative regulation of TORC1) and stress responses (ER-stressed apoptotic signaling). Developmental terms (forebrain, skeletal system, multicellular organism development) further tie these processes to organismal maturation. Overall, this cluster appears to group proteins involved in coordinating growth, stress responses, and developmental programs, hence Growth regulation and development.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0030900","count":2},{"id":"GO:0001501","count":2},{"id":"GO:1904262","count":2}]},{"hash":"644099262186167394","title":"Mitochondrial Energy Metabolism and Nucleotide Biosynthesis","description":"Key terms center on mitochondrial electron transport and various metabolic pathways (guanine and thiamine/beta-alanine biosynthesis), suggesting a metabolism/energy-production theme. A few terms (development, epigenetics) seem incidental noise, so the label focuses on mitochondria-driven metabolism and nucleotide biosynthesis.","confidence":"Medium","size":16,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":7},{"id":"GO:0045648","count":6},{"id":"GO:0045471","count":6},{"id":"GO:0043046","count":6},{"id":"GO:0009228","count":6}]},{"hash":"956547885227321635","title":"DNA Repair and Recombination","description":"Top GO terms are dominated by nucleotide-excision repair, base-excision repair, and DNA recombination, indicating core involvement in DNA repair and genome maintenance. Some other terms point to stress responses or oxidative processes, but the recurrent DNA repair signals define the cluster\u2019s primary function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0006284","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0006310","count":2}]},{"hash":"983316447156469464","title":"Fatty acid metabolism and transport","description":"The top GO terms cluster tightly around fatty acid biosynthesis, various chain-length fatty acid metabolic processes, and both import and transport of fatty acids, suggesting a coherent module of enzymes and transporters for fatty acid synthesis and cellular uptake. Other terms like bioluminescence and nonribosomal peptide biosynthesis appear peripheral or incidental, but do not define the main theme. Overall, fatty acid metabolism and transport best explains the cluster\u2019s functional profile.","confidence":"High","size":16,"edges":18,"triangles":19,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":4},{"id":"GO:0001579","count":3},{"id":"GO:0090410","count":3},{"id":"GO:0000038","count":3},{"id":"GO:0008218","count":3}]},{"hash":"1423262916651366280","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by ribosome-related processes: ribosome biogenesis (including large subunit biogenesis and preribosome assembly), maturation of rRNA, and multiple stages of translation (initiation and termination). This pattern points to a cluster of proteins involved in assembling the ribosome and in the translation machinery, rather than a single specific subfunction. ","confidence":"High","size":16,"edges":72,"triangles":163,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0001731","count":3}]},{"hash":"101561068273589640","title":"Ubiquitin-Proteasome Regulation in Cell Division","description":"Top GO terms indicate ubiquitin-dependent proteolysis (SCF, APC, ERAD), various ubiquitin linkages (K11, K6), and widespread cell-cycle processes (cell division, mitotic checkpoints, anaphase-promoting complex activity). The cluster thus represents proteins involved in tagging and degrading cell-cycle regulators via the ubiquitin-proteasome system to coordinate mitosis and DNA damage responses.","confidence":"High","size":16,"edges":31,"triangles":30,"max_degree":15,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0031146","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0000724","count":7},{"id":"GO:0031145","count":7},{"id":"GO:0051301","count":7}]},{"hash":"276677368391495210","title":"Apoptosis and Innate Immune Signaling","description":"This cluster centers on regulated cell death and immune signaling, as shown by prominent terms for apoptotic process, pyroptotic inflammatory response, and innate immune response. Additional terms for microtubule nucleation and spindle assembly point to cell-cycle involvement, while translation and rRNA maturation suggest coordinated changes in protein synthesis and ribosome biogenesis during cellular stress. Overall, the theme links apoptosis/pyroptosis with innate immunity, with ancillary links to cell division and gene expression. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0090307","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0042135","count":2},{"id":"GO:0090063","count":2}]},{"hash":"2158763486144466729","title":"ER-Golgi vesicle transport regulators","description":"The cluster is dominated by GO terms for ER\u2013Golgi and retrograde Golgi\u2013ER vesicle transport and GTPase activity regulation, pointing to a core function in vesicle trafficking between the ER and Golgi, with additional RNA methylation and translational control annotations likely reflecting broader cellular coordination.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0007584","count":3}]},{"hash":"2132525692914843375","title":"Unknown","description":"The top GO terms are very diverse, ranging from plant development (lateral root formation) to yeast nutrient-stress\u2013related morphogenesis (pseudohyphal and invasive growth), plus tRNA wobble thiolation, urmylation, translation, and even p53-related DNA damage responses. With no clear shared pathway or function and no edges connecting proteins, there isn\u2019t a coherent theme to label; thus the cluster is Unknown with None confidence.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010311","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0002143","count":1}]},{"hash":"760398813142768211","title":"Unknown","description":"The top GO terms point to several unrelated processes, including carbohydrate and nucleotide metabolism (inositol catabolic, pentose-phosphate shunt, xylose metabolism), vitamin C catabolism, and DNA repair, plus a few immune differentiation terms and obsolete annotations. There is no single cohesive function or pathway tying these terms together, suggesting diverse or noisy annotations rather than a unified cluster function.","confidence":"","size":16,"edges":16,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019310","count":2},{"id":"GO:0006098","count":2},{"id":"GO:0019854","count":2},{"id":"GO:0042732","count":2},{"id":"GO:0006281","count":2}]},{"hash":"437708621807211527","title":"Metabolic Catabolism and Detoxification","description":"This cluster centers on catabolic processes of diverse organic compounds (uracil, stilbene, 3-phenylpropionate) and detoxification-related terms (cellular oxidant detoxification, response to toxic substances), suggesting a general theme of metabolism with emphasis on breakdown of compounds and handling of toxins. Some terms are obsolete, and overall connections are broad rather than a single cohesive pathway, but the common thread is metabolic degradation and detox processes.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":5},{"id":"GO:0097755","count":5},{"id":"GO:0046839","count":5},{"id":"GO:0046272","count":5},{"id":"GO:0055114","count":5}]},{"hash":"1004419748332516874","title":"Fungal nutrient-regulated transcription and metabolism","description":"This cluster centers on transcriptional regulation from RNA polymerase II promoters in response to nutrients (oleic acid, nonfermentable carbon sources) and associated metabolic biosynthesis processes (lysine, leucine, pyrimidine) as well as regulation of cellular respiration. The presence of terms related to ergosterol biosynthesis, a fungal-specific pathway, supports a fungal context where nutrient signals drive transcriptional programs and metabolic adaptation. Overall, the proteins appear linked by a theme of nutrient-responsive transcriptional control coupled to metabolic biosynthesis.","confidence":"Medium","size":16,"edges":8,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:1901717","count":5},{"id":"GO:0061429","count":5},{"id":"GO:0061415","count":5},{"id":"GO:0035961","count":5}]},{"hash":"1160373679122221947","title":"Mammary Epithelial Proliferation and Wnt Signaling","description":"This cluster features GO terms centered on mammary gland epithelial cell proliferation and the canonical Wnt signaling pathway, indicating a shared theme of proliferative signaling in mammary epithelium. While other terms (transcription regulation, autophagy, histone phosphorylation, and metal/vitamin responses) are present, they are less cohesive with the main theme, so the core association is best captured by mammary proliferation linked to Wnt signaling.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033197","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0033601","count":2},{"id":"GO:1905866","count":2}]},{"hash":"1417066049306057939","title":"Embryonic Development and Organogenesis","description":"The top GO terms center on developmental processes across embryonic axes and organ formation, including mesoderm development, left\u2013right patterning, palate and cartilage morphogenesis, endocardial cushion EMT, and endocrine system development. This suggests the cluster reflects proteins involved in embryogenesis and tissue patterning rather than a single specific pathway.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0007498","count":1},{"id":"GO:0060021","count":1}]},{"hash":"1992033287621869813","title":"Developmental gene expression and trafficking regulators","description":"Top GO terms cluster around DNA-templated transcription and mRNA splicing (nuclear gene expression) and vesicle-mediated transport between the ER and Golgi, with additional links to development, growth signaling (TORC1), GTPase activity, ubiquitin ligase regulation, and inflammatory cytokine production. This pattern suggests a set of proteins that regulate gene expression and intracellular trafficking during development and organismal growth, potentially integrating protein turnover and signaling pathways. The lack of observed edges does not refute a shared functional theme, but the terms cover a broad, related spectrum, making this a best-effort label with moderate confidence.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0007064","count":3},{"id":"GO:0006888","count":3}]},{"hash":"323937795007359924","title":"Actin Cytoskeleton Remodeling and Lamellipodium Dynamics","description":"The cluster shows enrichment for multiple actin-related GO terms, including actin filament polymerization, capping, nucleation, and bundle organization, plus lamellipodium morphogenesis and ruffle assembly. This points to coordinated actin remodeling driving protrusive structures and membrane dynamics, consistent with actin-based cytoskeleton regulation.","confidence":"High","size":15,"edges":77,"triangles":221,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0051016","count":5},{"id":"GO:0030041","count":4},{"id":"GO:2000394","count":3},{"id":"GO:1903912","count":3},{"id":"GO:0090110","count":3}]},{"hash":"1514519228113888221","title":"Fungal cell wall remodeling and ion transport","description":"The top GO terms cluster around fungal-type cell wall organization and glucan catabolic process, plus several ion transport processes across membranes (calcium, manganese, potassium). This points to a coherent theme of cell wall remodeling coupled with membrane ion transport, likely from fungal proteins. A few terms related to neuronal signaling appear, but these are likely annotation noise and not central to the cluster\u2019s function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006076","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0006828","count":1},{"id":"GO:0098703","count":1},{"id":"GO:0048022","count":1}]},{"hash":"1002210164975329810","title":"Transcriptional Regulators of Metabolic Pathways","description":"The dominant GO terms point to DNA-templated transcription and regulation of transcription from RNA polymerase II promoter under various metabolic cues, with several entries tied to biosynthetic and respiratory regulation. This pattern suggests the proteins function primarily as transcriptional regulators coordinating metabolic processes, rather than as enzymes or structural components. The lack of edges supports a regulatory rather than physical interaction theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0035961","count":4},{"id":"GO:0061429","count":3},{"id":"GO:0061415","count":3},{"id":"GO:2001196","count":3}]},{"hash":"294034065107338690","title":"Synaptic development and plasticity","description":"The cluster is dominated by GO terms related to brain development, synapse assembly, regulation of synaptic vesicle exocytosis, long-term potentiation, and IP3 signaling, all pointing to neuronal synapse formation, maturation, and signaling. A few terms (tight junction assembly, mating projection growth) are less related, but the core pattern supports a synaptic development/plasticity theme.","confidence":"High","size":15,"edges":94,"triangles":333,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0070830","count":3},{"id":"GO:0010796","count":2},{"id":"GO:0009395","count":2},{"id":"GO:0007420","count":2},{"id":"GO:2000300","count":2}]},{"hash":"419858706910581778","title":"Developmental Morphogenesis and Growth","description":"The cluster is enriched for terms tied to development and morphogenesis, including placenta development (GO:0001890), cell morphogenesis (GO:0000902), retinal ganglion cell axon guidance (GO:0031290), and mast cell differentiation (GO:0060374), as well as chemotaxis (GO:0006935) and positive regulation of cell size (GO:0045793). While there are metabolic and replication terms (glucose metabolic process GO:0006006 and DNA replication GO:0006260), these likely reflect the proliferative state accompanying development. Together, these suggest a theme of developmental growth with morphogenetic and migratory activity. ","confidence":"Medium","size":15,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0006935","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0045793","count":3}]},{"hash":"687640454237844988","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":103,"triangles":429,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0000472","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0000463","count":5}]},{"hash":"1972476483451924694","title":"Ribosome Biogenesis and Translation","description":"Primarily enriched for translation- and ribosome-related GO terms (translation, cytoplasmic translation, ribosome biogenesis, tRNA modification) with supporting cell-cycle terms (cell division, cell cycle), indicating a cluster of proteins involved in ribosome assembly and protein synthesis driving growth and division. Some terms related to antibiotic response and LPS biosynthesis may reflect broader bacterial physiology but do not override the core theme.","confidence":"Medium","size":15,"edges":17,"triangles":7,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0055114","count":3}]},{"hash":"1758797680521566058","title":"Transmembrane nutrient and xenobiotic transporters","description":"GO terms point to transmembrane transport of nitrite, nitrate, phosphate, sugars (arabinose, fucose), potassium, vitamins, and xenobiotics, suggesting a cohesive group of membrane transport proteins with broad substrate specificity. The shared function of transporting diverse nutrients and xenobiotics across membranes justifies this label.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0071805","count":3}]},{"hash":"1822505663199797578","title":"Transcription Regulation and RNA Processing","description":"The cluster centers on transcription-related processes\u2014DNA-templated transcription, transcription elongation by RNA Pol II and I, and transcription antitermination\u2014together with RNA processing activities such as mRNA capping, RNA guanine-N7 methylation, and spliceosomal snRNP assembly. These cohesive terms suggest a group of proteins coordinating transcription with RNA maturation, with a few stress/DNA damage response terms that may be contextual rather than core. Confidence: High","confidence":"","size":15,"edges":11,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":3},{"id":"GO:0032968","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006977","count":2},{"id":"GO:0000387","count":2}]},{"hash":"1658721764319521039","title":"Hepatocyte differentiation and nitrogen metabolism","description":"Most prominent GO terms cluster around liver biology, including hepatocyte differentiation and liver development, and nitrogen-related metabolism such as the urea cycle (carbamoyl phosphate biosynthesis, ammonium ion response) and amino acid handling. Translation is a general, housekeeping process but common in actively functioning liver tissue. Taken together, the cluster appears to reflect hepatocyte identity with liver-specific metabolic functions, especially nitrogen metabolism. ","confidence":"High","size":15,"edges":100,"triangles":396,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0001889","count":3},{"id":"GO:0006526","count":2},{"id":"GO:0070365","count":2},{"id":"GO:0009636","count":2}]},{"hash":"1281757133419223505","title":"Neuronal signaling and cell junctions","description":"Based on the top GO terms, this cluster is enriched for neural communication processes (synaptic vesicle maturation; voltage-gated calcium channel complex assembly) and cell\u2013cell junctions/barrier functions (zonula adherens assembly; epithelial polarity; endothelial intestinal barrier). Although translation and metabolic terms appear, the prominent themes are neural signaling alongside junctional and barrier-related activities, suggesting a cohesive focus on signaling at synapses and at intercellular junctions. ","confidence":"Medium","size":15,"edges":63,"triangles":93,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0007035","count":2},{"id":"GO:0090162","count":1},{"id":"GO:0071625","count":1},{"id":"GO:2001205","count":1}]},{"hash":"254304858060320897","title":"Transmembrane solute transporters","description":"The GO terms are dominated by diverse transmembrane transport activities for ions (Na+, K+, phosphate), substrates like nitrite and arabinose, and other solutes such as heme and vitamins, plus a note on neurotransmitter loading into synaptic vesicles. This pattern strongly indicates a cluster of membrane transporter proteins that move solutes across membranes, rather than enzymes or signaling components. The wide substrate range suggests a broad transporter family rather than a single-substrate enzyme. Overall, the cluster appears to represent solute/ion transmembrane transporters.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035351","count":1},{"id":"GO:0015707","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0098700","count":1}]},{"hash":"1736721265982775415","title":"Diverse metabolite biosynthesis","description":"These proteins show enrichment across a variety of biosynthetic and metabolic processes\u2014from poly-hydroxybutyrate synthesis and fatty acid elongation to sphingolipid metabolism, pigment and vitamin biosynthesis (retinoic acid, phylloquinone, estrogen), and even energy production via proton motive force-driven ATP synthesis, along with transcription regulation. The unifying theme is participation in multiple biosynthetic pathways rather than a single specific function, pointing to broad metabolic biosynthesis activity rather than a discrete pathway. ","confidence":"Medium","size":15,"edges":21,"triangles":7,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042619","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0015986","count":3},{"id":"GO:0030497","count":3},{"id":"GO:0042376","count":3}]},{"hash":"2000938345228951537","title":"Metabolism and Immune Signaling","description":"The term set mixes broad biosynthetic processes (fatty acid, fructose, and pyruvate fermentation) with inflammatory/immune-related terms (response to lipopolysaccharide, prostaglandin metabolism), suggesting a cluster of proteins involved in general metabolism that interfaces with immune signaling rather than a single, cohesive pathway. Some obsolete or plant-specific terms are present, but the overall theme centers on metabolic activity linked to immune responses. ","confidence":"Medium","size":15,"edges":90,"triangles":307,"max_degree":14,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0032496","count":14},{"id":"GO:0009809","count":14},{"id":"GO:0006116","count":14},{"id":"GO:0006633","count":14},{"id":"GO:0006069","count":14}]},{"hash":"524800610910228946","title":"Embryo and Neuron Development with Cell Cycle Regulation","description":"The cluster centers on developmental processes (in utero embryonic development; neuron projection development) and cell proliferation (cell division), with additional signals for neuron survival (negative regulation of neuron apoptotic process) and genome maintenance (telomere maintenance via recombination; ubiquitination-related processes). Although there are some immune and obsolete terms present, the dominant pattern points to nuclear regulation of early development and cell fate along with genome integrity maintenance, supporting a cohesive themed label.","confidence":"Medium","size":15,"edges":47,"triangles":80,"max_degree":9,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0001701","count":7},{"id":"GO:0010976","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0006344","count":6},{"id":"GO:0006915","count":6}]},{"hash":"516906272396735514","title":"Xenobiotic stress response and metabolism","description":"This cluster centers on GO terms related to responding to xenobiotics and toxins (response to xenobiotic stimulus, response to toxic substance) and oxidative stress (positive regulation of hydrogen peroxide-mediated programmed cell death). It also includes various metabolic regulation terms (cholesterol biosynthesis, flavonoid metabolism, L-cysteine biosynthetic process, regulation of lipase activity), suggesting a broader theme of how cells adjust metabolism in stress conditions. While the links span multiple pathways, the xenobiotic/oxidative stress angle combined with metabolic regulation provides a coherent, if broad, label.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0042176","count":3},{"id":"GO:1901300","count":2},{"id":"GO:0045542","count":2},{"id":"GO:0019344","count":2}]},{"hash":"167481425670637184","title":"Retinoid and Lipid Metabolism with Detox and Stress Response","description":"The cluster shows strong enrichment for retinol and retinal metabolic processes (GO:0042572/GO:0042574) and other lipid-related biosynthesis (bile acids, sorbitol) along with detox/metabolism of xenobiotics (doxorubicin) and multiple stress-response terms (cadmium, hydrogen peroxide, prostaglandin/thyroid hormone signaling). The prominent retinoid/lipid metabolism signals\u2014and the accompanying detox and stress-response terms\u2014point to a cohesive theme of lipid- and retinoid-based metabolism with cellular stress signaling.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":12},{"id":"GO:0042574","count":12},{"id":"GO:0051897","count":10},{"id":"GO:0071799","count":10},{"id":"GO:0006061","count":10}]},{"hash":"1257486624832976108","title":"Unknown","description":"The GO terms span antimicrobial biosynthesis, responses to antibiotics and xenobiotics, various small-molecule biosyntheses (biotin, alkaloids), stress responses (hyperosmotic, amine), and distinct cellular organization processes (mitotic spindle assembly/orientation, cell polarity). This heterogeneity, along with zero edges in the cluster, suggests there is no single cohesive function tying all proteins together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0009820","count":3},{"id":"GO:0014075","count":2}]},{"hash":"203308740455956425","title":"Growth signaling and gene expression regulation","description":"This cluster shows enrichment for regulators of signaling (positive regulation of GTPase activity; positive regulation of protein serine/threonine kinase activity; autophosphorylation) alongside gene expression processes (ribosome biogenesis; mRNA transport) and growth-related events (mitotic cell cycle; positive regulation of cell proliferation). Developmental (neural tube closure) and stress (hypoxia response) terms hint at broader regulatory roles in growth and adaptation. The common theme is regulation of signaling pathways that control growth, proliferation, and gene expression during development and stress responses.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0071456","count":3}]},{"hash":"1519831301277874656","title":"Gene Expression and Ribosome Biogenesis","description":"The top terms cluster around transcription, rRNA processing, ribosome assembly, and translation, suggesting a cohesive theme of gene expression and ribosome biogenesis. Other terms (antibiotic response, protein secretion, and quinone biosynthesis) are more peripheral and could be incidental or context-dependent.","confidence":"Medium","size":15,"edges":13,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000448","count":1},{"id":"GO:0042255","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1665008462678359782","title":"Transmembrane Ion and Nutrient Transporters","description":"Top GO terms cluster around transport across membranes for ions (nitrite, potassium, sodium, phosphate) and various nutrients/sugars (arabinose, fucose, sialic acid, vitamin), plus a vesicle-related term for neurotransmitter loading. This pattern strongly suggests proteins that function as membrane transporters, covering ion transport and nutrient/sugar transport, with a related vesicular transport role.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":4},{"id":"GO:1900754","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0098700","count":4},{"id":"GO:0035725","count":4}]},{"hash":"1539214518769186980","title":"Phospholipid Biosynthesis and ER-Golgi Transport","description":"This cluster\u2019s top GO terms are dominated by phospholipid biosynthesis (phosphatidylethanolamine, phosphatidylserine, phosphatidylglycerol) and lipid mediator synthesis (platelet activating factor), plus endoplasmic reticulum to Golgi vesicle transport. Together, these terms point to a cohesive theme of lipid metabolism and vesicle trafficking, rather than a single protein function, supporting a lipid biosynthesis/transport cluster label.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050766","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0006663","count":1},{"id":"GO:0006659","count":1},{"id":"GO:0070317","count":1}]},{"hash":"889064012493819546","title":"Meiosis and Synaptonemal Complex Assembly","description":"The top GO terms are centered on meiotic processes: meiotic cell cycle, synaptonemal complex assembly, male/female meiotic nuclear division, chromosome segregation, recombination resolution, and fertilization, with a note on regulation of sumoylation. This suggests a cohesive cluster of proteins involved in meiosis and the synaptonemal complex, with regulatory ties to protein modification.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051321","count":2},{"id":"GO:0007130","count":1},{"id":"GO:0007060","count":1},{"id":"GO:0033235","count":1},{"id":"GO:0007140","count":1}]},{"hash":"460459280395812444","title":"DNA replication and centrosome cycle regulation","description":"The top GO terms are dominated by DNA replication and nuclear cell cycle processes (DNA replication, regulation of nuclear DNA replication, DNA unwinding) along with the centrosome cycle. This suggests a cluster of proteins coordinating replication with centrosome functions during cell division, with some secondary involvement in developmental signaling terms that may reflect multifunctional proteins.","confidence":"High","size":14,"edges":29,"triangles":23,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0046827","count":6},{"id":"GO:0007098","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0010571","count":5}]},{"hash":"1697865483668353191","title":"Spliceosome-Mediated Splicing Regulation and mRNA Export","description":"The terms cluster around RNA processing: mRNA splicing via the spliceosome, regulation of alternative splicing, and mRNA export, with related post-transcriptional regulation by miRNA pathways. This points to a cohesive group of splicing regulators and mRNA processing factors rather than direct transcription factors.","confidence":"High","size":14,"edges":27,"triangles":7,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045292","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0000381","count":2}]},{"hash":"931287206304776966","title":"Mitochondrial Transporters","description":"The GO terms show multiple transmembrane transport activities for ions and metabolites into and out of mitochondria (phosphate, manganese, NAD, magnesium, alpha-ketoglutarate, pyrimidine nucleotides), with related energy metabolism signals (insulin response, adaptive thermogenesis). This pattern points to a cluster of mitochondrial transporters and related metabolic regulators.","confidence":"High","size":14,"edges":33,"triangles":27,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":7},{"id":"GO:0000002","count":6},{"id":"GO:0006828","count":5},{"id":"GO:0015742","count":5},{"id":"GO:0035352","count":5}]},{"hash":"338113647510012504","title":"Bacterial LPS and cell wall polysaccharide biosynthesis","description":"The top GO terms point to lipopolysaccharide and slime layer polysaccharide biosynthesis, lipid A biosynthesis, GDP-mannose biosynthesis, and cell wall organization, indicating proteins involved in assembling bacterial outer-mear/envelope polysaccharides and related sugar-nucleotide pathways. Some regulatory terms appear but are ancillary; overall the cluster appears tied to polysaccharide production and cell envelope biosynthesis, hence the name.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0035969","count":1},{"id":"GO:0009298","count":1},{"id":"GO:1900399","count":1}]},{"hash":"1692717147317661532","title":"Fungal Cell Wall Biogenesis and Polysaccharide Catabolism","description":"The top GO terms point to fungal-type cell wall biogenesis/organization, and catabolic processes of plant polysaccharides (xylan, arabinan, L-arabinose), suggesting enzymes involved in remodeling or breaking down plant cell walls in a fungal context. The inclusion of a \u201csymbiotic process benefiting host\u201d term supports a host-associated fungal role. A few nuclear processes appear, but the dominant signal is fungal cell wall synthesis/remodeling and polysaccharide degradation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0042766","count":2},{"id":"GO:0043486","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0031505","count":2}]},{"hash":"2113865961649611003","title":"Unknown","description":"The annotated GO terms are scattered across diverse processes (phagocytosis, osmoregulation, prostaglandin biosynthesis, hepatocyte differentiation, fibroblast proliferation, hormone responses, cholesterol transport, metal ion response) with no connections between the proteins, giving no single cohesive function for the cluster. Therefore a precise, representative label cannot be inferred.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000733","count":1},{"id":"GO:0006909","count":1},{"id":"GO:0009992","count":1},{"id":"GO:0031394","count":1},{"id":"GO:0070365","count":1}]},{"hash":"507392407652971692","title":"Plant chromatin remodeling and telomere regulation","description":"The GO terms cluster around chromatin remodeling, subtelomeric heterochromatin formation, and shelterin-associated telomere maintenance, suggesting a plant-specific chromatin/telomere function, with additional signals for root growth regulation and osmotic stress response reflecting broader developmental/stress roles.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:1905615","count":1},{"id":"GO:0035390","count":1},{"id":"GO:1901347","count":1},{"id":"GO:1901430","count":1}]},{"hash":"937483861616363545","title":"Autophagy Machinery and Membrane Targeting","description":"The GO terms are strongly centered on autophagy processes: mitophagy, macroautophagy, autophagosome assembly, Cvt pathway targeting, andpiecemeal microautophagy of the nucleus, plus a note on C-terminal protein lipidation and general protein targeting to membranes. This points to a cohesive set of autophagy-related proteins functioning at membrane interfaces, with auxiliary calcium transport terms appearing ancillary. Overall, the cluster appears to be autophagy-focused with membrane trafficking aspects.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000422","count":2},{"id":"GO:0044805","count":2},{"id":"GO:0000045","count":2},{"id":"GO:0034727","count":2},{"id":"GO:0032258","count":2}]},{"hash":"1318397216285648939","title":"Adhesion and biofilm formation","description":"The top GO terms point to cell adhesion and biofilm-related processes (adhesion of symbiont infection structure to host; cell adhesion in single-species biofilm formation), suggesting a cohesive theme around adhesion and community assembly. A handful of obsolete chromatin-related terms appear but are minimal and do not define the cluster's core function, so the label focuses on adhesion/biofilm activity. ","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006337","count":1},{"id":"GO:0075001","count":1},{"id":"GO:0031939","count":1},{"id":"GO:1900471","count":1},{"id":"GO:2000217","count":1}]},{"hash":"14708685945887059","title":"Unknown","description":"The GO terms are scattered across disparate processes (DNA replication, fungal ascospore formation, lipid A biosynthesis, EMT regulation, epithelial differentiation, miRNA processing, etc.) with only a couple of terms shared by multiple proteins. There is no single cohesive function or pathway that consistently ties the cluster together, so a meaningful, specific label cannot be confidently assigned.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1903799","count":1},{"id":"GO:0009245","count":1}]},{"hash":"966025175506751018","title":"Hormone-Responsive Development","description":"The top terms point to hormone signaling and developmental processes (peptide hormone response, regulation of Wnt signaling, forebrain development, ovulation, vitamin D metabolism), with additional non-specific cellular processes (lipid catabolism, DNA replication initiation) that don\u2019t define a single function. This pattern suggests a broad theme where hormonal regulation interfaces with development, rather than a tightly focused pathway. ","confidence":"Low","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":3},{"id":"GO:0090090","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0043277","count":2},{"id":"GO:0010800","count":2}]},{"hash":"1271786172812183023","title":"Developmental differentiation across tissues","description":"This cluster is primarily linked to cell differentiation across multiple tissues, with GO terms for chondrocyte differentiation, Sertoli cell development, and skeletal muscle differentiation appearing prominently. While other terms (e.g., mitochondrial transcription, iron metabolism) are present, the strongest common theme is diverse developmental programs across cell types, rather than a single coherent pathway. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0032332","count":2},{"id":"GO:0042984","count":1},{"id":"GO:0042167","count":1},{"id":"GO:0033212","count":1}]},{"hash":"1270140649342023670","title":"Neuroimmune Development and Signaling","description":"The top GO terms point to neural development (axonogenesis, corpus callosum development, synapse assembly) alongside immune-related responses (LPS signaling, interferon-beta production, dsRNA response), suggesting a neuroimmune network role rather than a single pathway. The connection is plausible but not highly cohesive, given the sparse interactions observed. ","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071375","count":2},{"id":"GO:0051965","count":2},{"id":"GO:0031663","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0014068","count":2}]},{"hash":"2107165987447869739","title":"DNA Replication, Repair, and Cell Cycle","description":"The top GO terms cluster around genome maintenance and cell division, including DNA replication, DNA repair, DNA-templated transcription, and mitotic cell cycle. The ionizing radiation response also fits DNA damage response, reinforcing the theme. Some terms are peripheral (cocaine response, placenta development, T cell signaling), but the dominant pattern points to genome maintenance and cell cycle control.","confidence":"High","size":14,"edges":10,"triangles":2,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0071479","count":7},{"id":"GO:0006281","count":7},{"id":"GO:0042220","count":7},{"id":"GO:0001890","count":7}]},{"hash":"373200704192234605","title":"Diverse Biosynthetic Pathways","description":"This cluster is characterized by GO terms centered on biosynthesis across different contexts (antibiotic biosynthesis, PHB biosynthesis, LPS biosynthesis, L-serine biosynthesis, and related metabolic activities), with occasional related oxidation and catabolic processes. The absence of network edges suggests these proteins may be involved in a variety of separate biosynthetic routes rather than a single, cohesive pathway, so a label reflecting broad biosynthetic/metabolic involvement is most appropriate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0046272","count":4},{"id":"GO:0019373","count":4},{"id":"GO:0097755","count":4}]},{"hash":"1470826706799225433","title":"Central carbon metabolism","description":"The proteins in this cluster are tied to core energy and carbon-flux pathways, including glycolysis, the TCA cycle, gluconeogenesis, and reactions feeding substrates like pyruvate and alpha-ketoglutarate into acetyl-CoA. Amino-acid catabolism (e.g., leucine, lysine) and fatty acid biosynthesis/malonyl-CoA production further support a central metabolism theme driving energy production and biosynthesis; the presence of sodium transport is likely ancillary or contextual. ","confidence":"High","size":14,"edges":87,"triangles":320,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":10},{"id":"GO:0006552","count":6},{"id":"GO:0006096","count":6},{"id":"GO:0006103","count":5},{"id":"GO:0033512","count":5}]},{"hash":"2039074674159336564","title":"Gastrulation and Embryonic Morphogenesis","description":"The top GO terms cluster around gastrulation-related processes (cell migration, cell\u2013cell adhesion, germ band extension), basement membrane organization, and vasculature development, all indicating embryonic tissue morphogenesis. While there are some general housekeeping terms (ribosomal assembly, pre-replicative complex), they are much less represented, making the gastrulation/morphogenesis signal dominant.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090038","count":1},{"id":"GO:0042074","count":1},{"id":"GO:0070586","count":1},{"id":"GO:0010004","count":1},{"id":"GO:0007193","count":1}]},{"hash":"399992477499823611","title":"Stress responses and monoamine regulation","description":"The top GO terms mix immune/oxidative stress responses (response to lipopolysaccharide, redox homeostasis, metal ion responses, corticosterone) with neurotransmitter regulation (dopamine metabolism, serotonin secretion). This suggests a cluster of proteins involved in general stress responses that modulate monoamine signaling, rather than a single specific pathway, hence the label.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0010269","count":2},{"id":"GO:0014063","count":2},{"id":"GO:0010044","count":2}]},{"hash":"271451079700570512","title":"Oxidative stress response and detoxification","description":"The cluster is dominated by GO terms tied to handling oxidative stress and detoxification, including cellular oxidant detoxification, redox homeostasis, and glutathione metabolism, with supporting signals from toxin catabolic processes and DNA repair (nucleotide-excision repair). While there are some unrelated terms (calcium signaling and reproduction regulation), the strongest pattern points to antioxidant defenses and damage control pathways.","confidence":"High","size":14,"edges":82,"triangles":279,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":10},{"id":"GO:0045454","count":9},{"id":"GO:2000255","count":6},{"id":"GO:0006289","count":6},{"id":"GO:0006749","count":6}]},{"hash":"1758983632099699990","title":"Unknown","description":"The top terms are very diverse, spanning plant-specific chlorophyll breakdown, immune signaling, neural behavior, endothelial migration, ECM regulation, hypoxia response, and detoxification. This mix lacks a single cohesive biological theme, so there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0015996","count":2},{"id":"GO:0010716","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0001666","count":2}]},{"hash":"262084457073696380","title":"Diverse metabolite biosynthesis and catabolism","description":"The top GO terms point to a wide range of biosynthetic and catabolic processes (acetoin, phylloquinone, melanin, steroid hormones, antibiotics, etc.) and even sporulation. This suggests the cluster centers on broad metabolic production and turnover of diverse metabolites rather than a single specific pathway, hence a label focusing on diverse metabolite biosynthesis/metabolism.","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0045150","count":10},{"id":"GO:0042376","count":9},{"id":"GO:0042438","count":9},{"id":"GO:0030435","count":9}]},{"hash":"2081215759739543398","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":64,"triangles":179,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0033129","count":3},{"id":"GO:0070935","count":3},{"id":"GO:0048026","count":3}]},{"hash":"1971964867742491585","title":"Actin Cytoskeleton Remodeling and Cell Motility","description":"This cluster centers on actin cytoskeleton dynamics and associated cell movement, with terms for actin organization, contractile ring/sarcomere assembly, mesenchyme migration, and phagocytosis, plus related endocytosis regulation and gene expression.","confidence":"High","size":13,"edges":48,"triangles":88,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":5},{"id":"GO:0042766","count":3},{"id":"GO:0006909","count":3},{"id":"GO:0051666","count":3},{"id":"GO:0030240","count":3}]},{"hash":"1266763363030742946","title":"DNA Repair and Recombination","description":"The cluster is driven by GO terms related to DNA double-strand break repair pathways (SSA and NHEJ) and DNA recombination, indicating a core theme around DNA repair processes. A few other terms touch on immune cell differentiation (T and B cells) and amino acid transport, which appear as minor or incidental annotations and do not outweigh the primary signal. Overall, the dominant function appears to be DNA repair/recombination.","confidence":"Medium","size":13,"edges":33,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045002","count":1},{"id":"GO:1904378","count":1},{"id":"GO:0030217","count":1},{"id":"GO:0097680","count":1},{"id":"GO:0030183","count":1}]},{"hash":"747246076838727025","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1905815","count":1}]},{"hash":"2091984074340178998","title":"Developmental signaling and actin remodeling","description":"The Top Terms include developmental processes (outflow tract morphogenesis), multiple phosphorylation regulators (peptidyl-tyrosine and serine/threonine kinase activity), and Arp2/3-mediated actin nucleation, pointing to signaling control of cytoskeletal dynamics during development. Other terms like responses to calcium or hypoxia and mitosis suggest broader regulatory ties, but the common thread centers on kinase-driven signaling that governs actin remodeling in developmental contexts.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003151","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0031954","count":2}]},{"hash":"162475089416437650","title":"Membrane Transport of Vitamins, Lipids, and Xenobiotics","description":"The dominant GO terms point to transmembrane transport activities for vitamins, xenobiotics, thiamine, cholesterol, and phospholipids, suggesting the cluster is centered on membrane transport of diverse substrates. A couple of terms (sensory perception of sound, radiation/mercury response) are less clearly tied to transport and may reflect annotation noise or shared protein functions, but the overall pattern supports a transport-focused function.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0042760","count":1}]},{"hash":"1210117093819731987","title":"Unknown","description":"These proteins map to a wide mix of processes\u2014DNA-templated transcription, translation initiation/reinitiation and mRNA transport, ubiquitin ligase regulation, immune/inflammatory responses, and various developmental processes (neuronal/forebrain, cardiac apoptosis) and phagolysosome assembly. There is no clear single shared function or pathway tying the cluster together, so a single, cohesive label cannot be assigned with confidence.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:1904668","count":1},{"id":"GO:0002534","count":1}]},{"hash":"1057304125696467979","title":"Nucleotide Catabolism and Salvage","description":"The top GO terms cluster around catabolic and salvage pathways for nucleotides and nucleosides (uridine catabolic process, purine ribonucleoside salvage, nucleotide catabolic process, nicotinamide riboside catabolic process). There is also a spliceosomal complex assembly term tied to RNA metabolism, and a few growth-related terms that are less directly connected, which may reflect organismal context. Overall, the dominant theme is nucleotide metabolism.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030447","count":1},{"id":"GO:0009272","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0051692","count":1},{"id":"GO:0000245","count":1}]},{"hash":"975613920055112139","title":"Spliceosome-Mediated mRNA Processing and Regulation","description":"The terms are dominated by spliceosome-dependent mRNA splicing (including alternative and cis-splicing) and several post-transcriptional regulatory processes such as mRNA stability, poly(A) tail regulation, and translational initiation, with additional ncRNA-mediated gene silencing signals. This points to a cohesive function centered on RNA processing and post-transcriptional control rather than broader transcriptional regulation.","confidence":"High","size":13,"edges":17,"triangles":11,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000398","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0045292","count":2}]},{"hash":"954958015656900862","title":"Membrane transporters for vitamins, xenobiotics, lipids","description":"Top GO terms indicate multiple membrane transport activities (vitamin and xenobiotic transport, LDL remodeling) and lipid metabolism, alongside nutrient-sensing signals (TOR pathway, amino acid starvation response) and inflammatory processes (monocyte chemotaxis, inflammatory response). This suggests a cohesive theme of membrane transporters coordinating nutrient/vitamin and lipid mediator handling with inflammation, though the functional scope is diverse. Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032007","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0034440","count":1}]},{"hash":"1254664641240044904","title":"Stress-Induced Transcription Regulation","description":"The proteins in this cluster show GO terms centered on DNA-templated transcription and regulation of transcription in response to various stresses (heat, heavy metals, oxidative/toxic stress, unfolded protein response, hypoxia). This suggests a cohesive theme around transcriptional control under diverse stress conditions, rather than a single specific pathway.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0071276","count":1},{"id":"GO:1903936","count":1},{"id":"GO:2001033","count":1}]},{"hash":"2229363224240730751","title":"Endosome-to-vacuole trafficking and MVB sorting","description":"The top GO terms cluster around endomembrane trafficking: Golgi-to-endosome transport, endocytosis, late endosome-to-vacuole delivery via the multivesicular body pathway, and multivesicular body sorting, with actin involvement in endocytic processes. Together they indicate a shared function in endosomal vesicle transport and vacuolar targeting, while peripheral terms like transcription regulation and cellulose catabolism likely represent noise. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0006895","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0032511","count":1}]},{"hash":"1943618812770159162","title":"Diverse Transmembrane Transporters","description":"Top GO terms are all about transport across membranes for a variety of substrates, including metal ions, vitamins, nucleotides, NAD, and xenobiotics, with several entries tied to mitochondria. This suggests a cluster of proteins whose common theme is membrane transport rather than a single substrate or pathway.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006855","count":2}]},{"hash":"1510184074826983180","title":"Unknown","description":"The GO terms span stress response (hydrogen peroxide), chaperone-assisted assembly, transcription regulation, and various biosynthetic/metabolic processes, with no clear, single function tying them all together; due to this scattered representation, a specific, confident label isn\u2019t identifiable.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034766","count":2},{"id":"GO:0051131","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0017000","count":2}]},{"hash":"1667488021552082135","title":"Development and Tissue Organization","description":"Based on the prominent GO terms, the cluster centers on tissue development and organization (placenta development, spinal cord development, skeletal muscle tissue regeneration, and establishment of epithelial cell polarity). While other terms touch on cell-cycle regulation or sensory processes, the strongest recurring theme is developmental and tissue-forming activity, justifying this label as representative of the cluster's function. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1904908","count":1}]},{"hash":"145194706656366215","title":"Neural development and dopamine metabolism","description":"The cluster features GO terms centered on brain development and neurotransmitter metabolism, including CNS neuron development, striatum development, and dopamine metabolic process, suggesting a brain-specific theme. While there are additional metabolic terms present (purine, GMP, uracil salvage, etc.), the neural-related terms provide the most coherent functional signal for the cluster.","confidence":"Medium","size":13,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0021954","count":1},{"id":"GO:0045982","count":1},{"id":"GO:0006223","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0046651","count":1}]},{"hash":"1748927942921442567","title":"Neural Development (Brain and Retina)","description":"The cluster is dominated by neural development terms, notably retina development and brain development, indicating a nervous system-focused function. Additional terms like positive regulation of GTPase activity, apoptosis, and cell proliferation align with developmental signaling and remodeling in neural tissues, while transport terms appear ancillary. Overall, neural development best captures the main theme of this cluster.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0060041","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006915","count":2}]},{"hash":"2157695566527611131","title":"Ribosome Large Subunit Biogenesis","description":"This cluster is dominated by GO terms tied to large subunit ribosome biogenesis and rRNA processing, including LSU export, preribosome assembly, and maturation of 5.8S/LSU rRNA. While a few plant-specific terms appear (chloroplast movement, ABA homeostasis), the core signal points to ribosome assembly functions.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0045035","count":1},{"id":"GO:0009903","count":1},{"id":"GO:0031022","count":1},{"id":"GO:1902265","count":1}]},{"hash":"1901359085657174363","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":2},{"id":"GO:0008380","count":2},{"id":"GO:0071039","count":1},{"id":"GO:0000973","count":1},{"id":"GO:0071033","count":1}]},{"hash":"1666645450805136734","title":"Cell Migration and Membrane Trafficking","description":"The top GO terms cluster around cytoskeletal remodeling and membrane dynamics (lamellipodium morphogenesis, endocytosis, angiogenesis) with supporting lipid metabolism processes (phosphatidylcholine catabolism, triglyceride storage), suggesting proteins involved in cell movement and vesicle trafficking during development and immune-related contexts.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000394","count":2},{"id":"GO:1903165","count":2},{"id":"GO:0045765","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0006898","count":2}]},{"hash":"197199207792597561","title":"Methylation Enzymes (RNA/Protein)","description":"The top GO terms are dominated by methylation-related activities: N-terminal peptidyl-alanine trimethylation, peptidyl-lysine dimethylation, and RNA guanine-N7 methylation/rRNA methylation, suggesting a cluster of methyltransferases acting on RNA and proteins. Other terms in the list (immune responses, cobalamin biosynthesis, aerobic respiration) are less frequent and likely incidental. Therefore, a cohesive label is methylation enzymes serving RNA or protein substrates.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018012","count":1},{"id":"GO:0070555","count":1},{"id":"GO:0002347","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0018027","count":1}]},{"hash":"1230836431157060179","title":"RNA Processing and Transcription Termination","description":"This cluster is enriched for RNA metabolism and transcription control terms, including regulatory ncRNA-mediated gene silencing, mRNA splice site recognition, termination of RNA Pol II transcription (exosome-dependent and poly(A)-coupled), and histone mRNA catabolism. Together these suggest a cohesive RNA-processing/regulatory theme around RNA maturation, decay, and transcription termination, with a few ancillary links to cell-cycle regulation and mitochondrial autophagy.","confidence":"Medium","size":12,"edges":46,"triangles":75,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0030847","count":2},{"id":"GO:0030846","count":2},{"id":"GO:0071044","count":2}]},{"hash":"796012889479627467","title":"Membrane transport and xenobiotic metabolism","description":"This cluster\u2019s GO terms span membrane transport (amino acids and neurotransmitters) and metabolic pathways often linked to membrane-associated enzymes (epoxygenase P450) and lipid remodeling, suggesting a broad theme around membrane-associated transport and metabolism rather than a single, cohesive function. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0097755","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1405477037336369239","title":"Plant cell division and microtubule dynamics","description":"Many top terms center on microtubule organization during mitosis (centrosome separation, spindle midzone, metaphase alignment) and cytokinesis, plus regulation of microtubule-based processes, with plant-specific hints like chloroplast movement and root development. This suggests a cluster of proteins coordinating cytoskeleton dynamics during cell division and related plant organelle positioning.","confidence":"High","size":12,"edges":41,"triangles":36,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":7},{"id":"GO:0007100","count":7},{"id":"GO:0051255","count":6},{"id":"GO:0032886","count":6},{"id":"GO:0007080","count":6}]},{"hash":"644882902134235377","title":"Cell cycle regulation and transcription","description":"The top GO terms are centered on cell cycle control (G0 to G1 transition, cell division) and DNA-templated transcription, with supporting signals like TGF-beta response. A few lipid biosynthesis terms exist but do not define the cluster, so the core theme is regulation of cell growth/proliferation and transcription.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0033197","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0006351","count":2}]},{"hash":"465277554938078451","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0014075","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0006526","count":1},{"id":"GO:0070365","count":1},{"id":"GO:1903718","count":1}]},{"hash":"1005261950266328788","title":"Drosophila epithelial polarity and cytokinesis","description":"The top GO terms point to insect epithelial development, with emphasis on follicular epithelium polarity maintenance, cell adhesion, and processes of cytokinesis (actomyosin contractile ring, division septum site selection, septum digestion), plus related morphological events such as follicle cell organization and visual primordium formation. While a few terms are more general (histone mRNA catabolism, transcription regulation by glucose), the dominant theme fits Drosophila epithelial development and cytokinesis.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071044","count":2},{"id":"GO:0000432","count":1},{"id":"GO:0007299","count":1},{"id":"GO:0000918","count":1},{"id":"GO:0075015","count":1}]},{"hash":"79426273480254638","title":"Peroxisome Biogenesis and Dynamics","description":"The cluster is dominated by GO terms for peroxisome organization (ER-dependent), inheritance, fission, and protein import into the peroxisome membrane, pointing to a cohesive theme of peroxisome biogenesis and maintenance. Other terms like miRNA silencing and neuronal/gonadal development appear ancillary but do not override the strong peroxisome signal.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002677","count":2},{"id":"GO:0035865","count":2},{"id":"GO:0008585","count":2},{"id":"GO:1904948","count":2},{"id":"GO:0035195","count":2}]},{"hash":"1841087908370206210","title":"Cell cycle and translation regulation","description":"The dominant GO terms cluster around mitotic spindle assembly and cell division, along with translation initiation and preinitiation complex formation, and TORC1 signaling, indicating regulation of cell growth, proliferation, and protein synthesis. Additional terms for ubiquitin ligase activity, cytokine production, cardiac apoptosis, mRNA transport, and neuron projection development are present but less central; overall, the cluster seems to reflect coordination of cell cycle control with protein synthesis/degradation rather than a single specific pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:1904263","count":5}]},{"hash":"1726258006207905880","title":"Neuronal development and synaptic signaling","description":"This cluster is dominated by GO terms tied to nervous system development and synaptic function (axonogenesis, Schwann cell development, long-term potentiation, excitatory postsynaptic potential, visual perception), suggesting a cohesive group of proteins involved in neural wiring and synaptic plasticity, with additional signals related to broader sensory/motor development.","confidence":"High","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":10},{"id":"GO:0007601","count":10},{"id":"GO:0007520","count":10},{"id":"GO:0009738","count":10},{"id":"GO:0060079","count":10}]},{"hash":"1963329546606478108","title":"Neural development and cell polarity","description":"The top GO terms cluster around brain development and neural progenitor biology (substantia nigra development, forebrain radial glial cell differentiation, negative regulation of neuron apoptotic process) and cell polarity (establishment or maintenance of apical/basal cell polarity). Additional terms touch on neuronal energy/trafficking (regulation of mitochondrial depolarization; endosome to melanosome transport), with a few terms about migration that may reflect broader cellular motility. Taken together, the strongest theme is neural development with emphasis on progenitor differentiation and polarity.","confidence":"Medium","size":12,"edges":19,"triangles":3,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":5},{"id":"GO:0043524","count":4},{"id":"GO:0051900","count":4},{"id":"GO:0035088","count":4},{"id":"GO:0021861","count":4}]},{"hash":"1399946568115515621","title":"Unknown","description":"GO terms span antibiotic metabolism, DNA repair, chromatin regulation, translation initiation, nuclear RNA tethering, and developmental processes, with no clear unifying function or connectivity. This dispersion suggests no cohesive cluster function to name beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019876","count":1},{"id":"GO:0030655","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0033252","count":1},{"id":"GO:0006283","count":1}]},{"hash":"1782838445964070153","title":"Chromosome condensation and segregation in cell division","description":"Most terms point to chromosome condensation and segregation during cell division (mitosis/meiosis), such as mitotic chromosome condensation, mitotic sister chromatid separation, and meiotic chromosome condensation/segregation. A few terms relate to plant development and tRNA clustering that are less connected, but the dominant theme is chromosome dynamics in cell division.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007076","count":1},{"id":"GO:0051306","count":1},{"id":"GO:0070058","count":1},{"id":"GO:0048567","count":1},{"id":"GO:0051301","count":1}]},{"hash":"1841286969988169596","title":"DNA replication and cell cycle","description":"This cluster is driven by GO terms for DNA replication, replication initiation, pre-replicative complex assembly, and G1/S transition, with additional cell division terms, indicating a core association with DNA synthesis and mitotic progression. Some terms (lateral root development, neural precursor proliferation, response to sucrose) appear as non-core annotations but do not override the central replication/cell cycle theme.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006267","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006270","count":1}]},{"hash":"50119684430281998","title":"Diverse Metabolic Biosynthesis and Development","description":"The GO terms are dominated by biosynthetic and metabolic processes (glucan, glycogen, long-chain fatty acids, and fatty-acyl-CoA biosynthesis; valine catabolism; regulation of gluconeogenesis) with occasional developmental signals (post-embryonic development and heart/cardiac muscle differentiation). There isn\u2019t a single coherent functional theme tying all terms, so the cluster appears to reflect a mix of metabolic biosynthesis/showing some developmental roles rather than a specific pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006078","count":1},{"id":"GO:0042546","count":1},{"id":"GO:0006574","count":1},{"id":"GO:0009791","count":1},{"id":"GO:0055007","count":1}]},{"hash":"962622055832139108","title":"Isoprenoid and CoA Biosynthesis with Redox Balance","description":"This cluster is dominated by GO terms tied to biosynthesis of isoprenoid and lipid-derived compounds (coenzyme A biosynthesis, cholesterol biosynthesis, monoterpene biosynthesis, farnesyl diphosphate biosynthesis), suggesting a shared role in lipid/isoprenoid production. The presence of redox-related terms (glutathione metabolic process, cell redox homeostasis) indicates coordination with cellular redox balance, consistent with lipid metabolism requiring redox regulation. ER unfolded protein response hints at a connection to cellular stress related to protein folding, which can intersect with redox status. Overall, the proteins appear to function together in lipid/isoprenoid biosynthesis with redox homeostasis.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0015937","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006749","count":2}]},{"hash":"1714240813805785913","title":"Retinoid metabolism and craniofacial development","description":"The cluster is dominated by retinol and retinal metabolic processes, plus several craniofacial morphogenesis terms (face development, olfactory pit development, inner ear morphogenesis), suggesting a coherent theme where retinoid signaling influences facial and head structure development. Some other catabolic biosynthesis terms are present but do not override the core craniofacial/retinoid pattern.","confidence":"High","size":12,"edges":56,"triangles":144,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":8},{"id":"GO:0042574","count":8},{"id":"GO:0009258","count":5},{"id":"GO:1901023","count":5},{"id":"GO:0060324","count":5}]},{"hash":"1501796220709768185","title":"Diverse carbon and lipid metabolism","description":"The top GO terms indicate metabolism of various carbon sources (glycerol, methanol, glycolysis, 3-chlorocatechol) and lipid biosynthesis/degradation (glycerophospholipid metabolism, phospholipid biosynthetic). This pattern points to a cluster of proteins involved in processing a range of carbon substrates and lipids, rather than a single pathway. Some terms are marked obsolete, reflecting historical annotations, but the overall theme is broad carbon and lipid metabolism.","confidence":"Medium","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0015976","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0019564","count":1},{"id":"GO:0015946","count":1},{"id":"GO:0051143","count":1}]},{"hash":"545162296977466045","title":"N-terminal methylation and tRNA modification enzymes","description":"The top GO terms are dominated by specific methylation activities: N-terminal peptidyl-alanine/serine/glycine methylation and general methylation; along with tRNA wobble uridine modification and tRNA methylation. This points to a cluster of methyltransferases and tRNA-modifying enzymes. Additional terms like ubiquinone biosynthesis and stress responses appear less central, but may reflect related enzymatic activities or context-specific roles.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035902","count":4},{"id":"GO:0018012","count":3},{"id":"GO:0035572","count":3},{"id":"GO:0035573","count":3},{"id":"GO:0018013","count":3}]},{"hash":"2171432357190668307","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":11,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006207","count":4},{"id":"GO:0044205","count":4},{"id":"GO:0006541","count":4},{"id":"GO:0006526","count":3},{"id":"GO:0070365","count":3}]},{"hash":"1933903613880503750","title":"Embryonic and placental development","description":"The Top Terms cluster around developmental processes, especially embryogenesis and placental formation (endocrine system development, trophoblast giant cell differentiation, gestational regulation of placental development, left/right patterning, EMT in heart cushion formation, cartilage and organogenesis). While individual terms touch on specific tissues (pancreatic, germ-line), the common theme is organismal development and placental/differential lineage programs, so a label focused on embryonic and placental development is representative.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003323","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0003198","count":1},{"id":"GO:0035270","count":1}]},{"hash":"1249148276056659616","title":"Large Subunit Ribosome Biogenesis","description":"Top GO terms point to ribosome biogenesis, especially maturation of 5.8S rRNA and large subunit assembly, indicating the proteins are primarily involved in assembling the large ribosomal subunit. Other terms appear peripheral and do not define a single cohesive function for the cluster.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003014","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0030097","count":1}]},{"hash":"1319980184447906723","title":"Developmental transcription and RNA splicing","description":"The proteins show a core link to DNA-templated transcription and mRNA splicing by the spliceosome, with developmental terms such as eye-antennal disc development and embryonic syncytial blastoderm indicating a developmental regulatory module. Some peripheral terms (mannitol response, GABA catabolic regulation, vitamin D signaling, pyrimidine biosynthesis) are less central but do not override the main theme.","confidence":"Medium","size":12,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0010555","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0035214","count":1},{"id":"GO:0016567","count":1}]},{"hash":"1928087078133315278","title":"Plant Energy Metabolism Across Organelles","description":"This cluster's GO terms span mitochondrial protein insertion and general transport, along with diverse metabolic pathways like photorespiration, glycolate oxidation, fatty acid oxidation, and isoprenoid biosynthesis, suggesting a broad plant energy metabolism theme involving multiple organelles rather than a single specific pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032979","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0015031","count":1},{"id":"GO:0009854","count":1},{"id":"GO:0009853","count":1}]},{"hash":"1896103985420320171","title":"Transcriptional Regulation of Metabolic Pathways","description":"The terms center on DNA-templated transcription and regulation of transcription from RNA Pol II promoter, with several entries indicating positive regulation of transcription in response to metabolic signals (oleic acid, carbon source, etc.) and links to biosynthetic and respiration-related processes (pyrimidine, leucine, lysine, ergosterol, cellular respiration). This suggests a cluster of proteins involved in regulating metabolic gene expression rather than a single metabolic enzyme or pathway, i.e., a transcriptional regulatory module tied to metabolism.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035948","count":4},{"id":"GO:0061429","count":3},{"id":"GO:0061415","count":3},{"id":"GO:0035961","count":3}]},{"hash":"1195328953071714724","title":"Diverse biosynthesis and metabolite catabolism","description":"The cluster shows several GO terms tied to biosynthetic and catabolic metabolism (antibiotic biosynthesis, phosphinothricin biosynthesis, carnitine, allantoin, purine, oxalate metabolism), suggesting a broad metabolic theme. A couple of terms (DNA-templated transcription, plasmodesmata transport) are less cohesive with this theme, but the dominant signal is metabolism. Confidence: Low.","confidence":"","size":12,"edges":11,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0045329","count":3},{"id":"GO:0000256","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006145","count":2}]},{"hash":"2054384084272306854","title":"Neuronal Synaptic Transmission Regulation","description":"This cluster is dominated by GO terms tied to synaptic signaling and plasticity, including negative regulation of excitatory postsynaptic potential, negative regulation of cholinergic transmission, positive regulation of inhibitory postsynaptic potential, presynaptic membrane assembly, and postsynaptic density clustering. A few terms imply broader neuronal regulation (circadian wakefulness, chromatin remodeling, xenobiotic response), but the core pattern points to synaptic transmission control and synapse structure. Name reflects the prevailing function across the proteins.","confidence":"High","size":12,"edges":27,"triangles":33,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0042136","count":2},{"id":"GO:0097119","count":2}]},{"hash":"660807216176423648","title":"Nutrient-responsive Transcriptional Regulation","description":"The top GO terms revolve around regulation of transcription from RNA polymerase II promoter in response to metabolic cues (oleic acid and carbon sources) and tie into biosynthetic and respiration-related processes, suggesting a common theme of transcriptional control by nutrient status and associated metabolism.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061429","count":2},{"id":"GO:0061415","count":2},{"id":"GO:0035961","count":2},{"id":"GO:2001196","count":2},{"id":"GO:0043457","count":2}]},{"hash":"1521104135833634926","title":"Mitochondrial energy metabolism and amino acid biosynthesis","description":"This cluster is dominated by GO terms for mitochondrial electron transport (NADH to ubiquinone) and cell redox homeostasis, along with several amino acid and cofactor biosynthetic processes (thiamine, beta-alanine, L-glutamate, and 2-oxoglutarate metabolism). Together, these suggest a coherent theme around mitochondrial energy production and associated biosynthesis rather than a single functional specialization. Some unrelated developmental terms appear in the list, but the core signal points to metabolism-related functions.","confidence":"Medium","size":12,"edges":31,"triangles":32,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":10},{"id":"GO:0009228","count":10},{"id":"GO:0019483","count":9},{"id":"GO:0006120","count":9},{"id":"GO:0045454","count":9}]},{"hash":"1416422961065345621","title":"Ubiquitin-Proteasome Regulation","description":"The top GO terms center on ubiquitination/deubiquitination, SUMO modification, and ER-associated degradation, together with proteasomal control, pointing to a proteostasis-focused cluster concerned with protein turnover and quality control. Additional terms like nucleotide-excision repair and cytoskeletal/ribosomal assembly may reflect broader cellular processes or pleiotropic GO annotations, but the dominant signal is ubiquitin-proteasome\u2013mediated regulation.","confidence":"Medium","size":11,"edges":25,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0016579","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0000226","count":2},{"id":"GO:0000028","count":2}]},{"hash":"869657363327738412","title":"Unknown","description":"The top GO terms are highly disparate, with a few hints toward neural myelination but many unrelated processes (sorocarp differentiation, pancreatic cell development, glycogen metabolism, etc.). There is no clear, cohesive function that binds the cluster as a whole, so a single representative label cannot be confidently assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":1},{"id":"GO:0031643","count":1},{"id":"GO:0022010","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0031285","count":1}]},{"hash":"2176571716156053170","title":"Spliceosome and RNA Processing","description":"Dominant signals are mRNA splicing via spliceosome, spliceosomal complex and snRNP assembly, along with P-body assembly and tRNA processing, indicating core RNA processing/splicing machinery in the nucleus. Additional terms for nuclear import and histone mRNA metabolism reinforce the RNA processing context.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":9},{"id":"GO:0009414","count":6},{"id":"GO:1990141","count":6},{"id":"GO:0051170","count":6},{"id":"GO:0008334","count":6}]},{"hash":"2178506238958113993","title":"Membrane Transport of Nutrients and Ions","description":"Based on the top GO terms, the cluster is enriched for various transmembrane transport activities (nitrite, nitrate, phosphate, arabinose, fucose, potassium ions) and vitamin transport, along with nitrate assimilation and an osmotic stress response. This combination points to a cohesive role in moving diverse nutrients and ions across membranes and managing osmotic balance, suggesting a shared transporter/solute-uptake function across the proteins.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0042891","count":2}]},{"hash":"431998680444806791","title":"Translation and Ribosome Biogenesis","description":"The top terms are dominated by translation (GO:0006412) and ribosomal large subunit biogenesis (GO:0042273), suggesting a core function in protein synthesis and ribosome assembly. The presence of several transport-related terms appears secondary, indicating some membrane transport roles among cluster members but not defining the main theme. Overall, the cluster seems centered on translation machinery with ancillary transport-related proteins.","confidence":"Medium","size":11,"edges":12,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042273","count":2},{"id":"GO:0015707","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0071805","count":1}]},{"hash":"54636724870353330","title":"DNA replication and mitotic cell cycle","description":"The top GO terms are dominated by DNA replication, DNA repair, and mitotic cell cycle processes (G1/S transition, kinetochore localization, cell division), suggesting the cluster mainly centers on DNA replication and mitosis; a few outliers (cerebellar differentiation, cocaine response) are likely incidental. ","confidence":"Medium","size":11,"edges":13,"triangles":5,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0021697","count":4},{"id":"GO:0034501","count":4}]},{"hash":"961368486599983985","title":"Unknown","description":"The GO terms span innate immune response and phagocytosis, but also chromatin organization, DNA repair, and cell polarity, with no single unifying function across all proteins. The lack of edges and the diverse, seemingly unrelated processes suggest a mixed set rather than a coherent biological module, so Unknown is the best label.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0030702","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0097510","count":1},{"id":"GO:0006284","count":1}]},{"hash":"216674266142688562","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0000920","count":2},{"id":"GO:0000480","count":2}]},{"hash":"397007741176367055","title":"Large subunit ribosome biogenesis and export","description":"This cluster is dominated by GO terms tied to ribosome biogenesis, especially maturation and assembly of the large ribosomal subunit and export from the nucleus, suggesting a cohesive function in large subunit maturation and ribosome assembly. A few other terms (GTPase regulation and amino acid transport) may reflect ancillary associations, but the core signal points to large subunit biogenesis. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000466","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0000463","count":1}]},{"hash":"276468656853388835","title":"RNA processing and chromatin regulation","description":"The top GO terms point to post-transcriptional mRNA regulation (P-body assembly, deadenylation-dependent decapping, negative regulation of translational initiation) together with chromatin remodeling/organization, suggesting the proteins participate in broad gene expression control at both RNA and chromatin levels. Some developmental terms appear but the core signal is RNA processing plus chromatin regulation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045947","count":1},{"id":"GO:0000290","count":1},{"id":"GO:0010607","count":1},{"id":"GO:0033962","count":1},{"id":"GO:0003007","count":1}]},{"hash":"288687255905665446","title":"Membrane raft signaling and stress response","description":"The top GO terms emphasize membrane-associated processes (protein localization to membrane raft, PKC signaling, phospholipid catabolic process) and stress-related dynamics (stress-induced mitochondrial fusion, regulation of proteolysis). The mix suggests proteins involved in membrane signaling and cellular stress responses rather than a single highly specific function. Some terms are obsolete or unrelated (podocyte development, acid-sensing channel regulation), indicating a somewhat loose clustering. Overall, the theme is membrane-anchored signaling with stress adaptation, leading to a moderate level of confidence.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001302","count":2},{"id":"GO:0009395","count":2},{"id":"GO:0072249","count":1},{"id":"GO:0030433","count":1},{"id":"GO:1903044","count":1}]},{"hash":"695305842308003170","title":"Membrane Transport of Nutrients and Xenobiotics","description":"Many proteins in this cluster are annotated with transmembrane transport of various substrates (nitrite, D-xylose, fructose, vitamins, xenobiotics), indicating a shared role in import/export of small molecules. While some terms relate to biosynthetic pathways, the transport-related terms are most prominent, supporting a transport-focused cluster label.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":2},{"id":"GO:0019835","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0015707","count":1}]},{"hash":"682714434740993997","title":"LPS and cell-wall biosynthesis with glycosylation","description":"The cluster is enriched for lipopolysaccharide biosynthetic processes, lipid A biosynthesis, spore wall assembly, and protein N-linked glycosylation, all pointing to construction and modification of the cell envelope. Additional terms like biofilm formation and response to antibiotic further link these surface-related processes to community behavior and surface resilience. While one term is an obsolete fungal-specific ascospore wall note, the core theme is cohesive around envelope biosynthesis and surface polysaccharide modification, justifying a label focused on cell envelope biogenesis.","confidence":"High","size":11,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0034232","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0042710","count":2},{"id":"GO:0019428","count":2}]},{"hash":"2027828606427224075","title":"Developmental transcription regulators","description":"The cluster shows broad developmental processes across several tissues (gonads, inner ear, pituitary, uterus, pancreas, forebrain neurons) with core involvement in transcriptional control (DNA-templated transcription and negative regulation of RNA polymerase II), suggesting these proteins act as regulators steering development through transcriptional regulation rather than a single tissue-specific function.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008584","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0032496","count":2}]},{"hash":"2025959463159960628","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":15,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000447","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000398","count":3}]},{"hash":"1103496333401984814","title":"Neural development and stress response","description":"This cluster is dominated by GO terms related to neural development and brain formation (forebrain development, brain development, neural tube closure), suggesting a core theme of neural development. Additional terms point to cellular stress responses (ER-stress\u2013induced apoptotic signaling, response to cadmium) and RNA processing activities (rRNA maturation, RNA guanine-N7 methylation) that may accompany or reflect general cellular functions in these proteins. The mix implies a neural-developmental program with ancillary stress and RNA-processing roles rather than a single, tightly bound pathway. ","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0070059","count":3}]},{"hash":"41333390366823249","title":"ER-associated proteostasis and proteolysis","description":"The top GO terms cluster around endoplasmic reticulum quality control, ubiquitin-dependent ERAD pathways, proteolysis, and responses to misfolded proteins, with related ER processes such as ER polarization. A few terms about extracellular matrix disassembly or respiration appear less central and may be incidental noise, but the dominant theme points to ER-associated protein quality control and turnover.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0022617","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0071218","count":1},{"id":"GO:0000733","count":1}]},{"hash":"1946207210806279304","title":"Vertebrate neurodevelopment and organogenesis with Wnt/Hippo signaling","description":"The top GO terms span neural development (forebrain, cerebellar cortex, visual perception), heart development, and keratinocyte differentiation, plus signaling pathways like Hippo and canonical Wnt. This pattern suggests a set of vertebrate developmental regulators functioning across tissues, coordinated by Wnt and Hippo signaling and supported by general transcription and cell-cycle processes.","confidence":"Medium","size":11,"edges":21,"triangles":15,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":8},{"id":"GO:0007601","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0030900","count":6},{"id":"GO:0007507","count":6}]},{"hash":"1086021981734163008","title":"Core Growth and Metabolic Biosynthesis","description":"The set of terms centers on fundamental cellular processes: ribosome biogenesis and DNA-templated transcription indicate core gene expression, while multiple biosynthetic processes (menaquinone, biotin, antibiotic biosynthesis) and cell division-related terms point to growth and metabolism. The combination suggests a broad, housekeeping cluster rather than a single precise pathway, hence a label around core growth and metabolism is appropriate though not perfectly specific.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0009234","count":2}]},{"hash":"869979094852784697","title":"Translation initiation machinery","description":"This cluster is dominated by GO terms related to translation initiation and preinitiation complex assembly (formation of translation preinitiation complex, formation of cytoplasmic translation initiation complex, cap-dependent translational initiation), including IRES-dependent and viral translation initiation pathways. While a few terms touch on mRNA binding or splicing regulation, the central theme is proteins involved in initiation of translation, suggesting a coherent translation initiation machinery cluster.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075525","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0001732","count":1}]},{"hash":"1953613071170226609","title":"RNA Pol III Transcription Machinery","description":"This cluster is centered on GO terms for transcription by RNA polymerase III, its preinitiation complex assembly, and related regulatory activities, indicating a cohesive role in Pol III transcription machinery. A CENP-A\u2013containing chromatin assembly term is also present but appears secondary to the core Pol III transcription theme.","confidence":"High","size":11,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034766","count":1},{"id":"GO:0032463","count":1},{"id":"GO:0044030","count":1},{"id":"GO:2000774","count":1},{"id":"GO:0034080","count":1}]},{"hash":"535828554364561913","title":"Calcium-regulated vesicle exocytosis","description":"This cluster is dominated by GO terms for vesicle fusion and calcium-dependent exocytosis, supported by membrane-related processes such as phosphatidylethanolamine biosynthesis and Rho signaling that influence vesicle trafficking. The zinc/cadmium transport terms point to membrane transport roles that can intersect with signaling, while developmental terms likely reflect broader roles of vesicle trafficking and signaling in organ development. Overall, the key theme is calcium-regulated vesicle trafficking/exocytosis.","confidence":"Medium","size":11,"edges":10,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":3},{"id":"GO:0071577","count":3},{"id":"GO:0001501","count":2},{"id":"GO:0006906","count":2},{"id":"GO:0006646","count":2}]},{"hash":"1173821229457452418","title":"Chitin-based Cuticle Development and Molting","description":"Dominant GO terms center on chitin-based cuticle formation and molting (chitin-based cuticle development, chitin catabolic process, ecdysis), with supportive notes on secretory trafficking (ER to Golgi transport) and inflammatory signaling (NF-kappaB activation, IL-6/IL-8 responses). This combination suggests the cluster mainly comprises proteins involved in arthropod cuticle synthesis/remodeling and molting, with some ancillary signaling roles.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006032","count":1},{"id":"GO:0070741","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0051216","count":1}]},{"hash":"1026858156437209370","title":"Embryonic tissue development and differentiation","description":"Top GO terms show development across multiple tissues (spinal cord development; mesonephric and metanephric duct development; cartilage condensation; hair cell differentiation) along with transcriptional regulation and signaling-related terms. This pattern suggests proteins involved in general embryonic development and tissue differentiation rather than a single pathway, so the label reflects a broad developmental role for the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":3},{"id":"GO:0071320","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042391","count":2},{"id":"GO:0031659","count":2}]},{"hash":"343516428379448867","title":"Diverse metabolite biosynthesis","description":"The top GO terms cluster around biosynthetic processes for many different substrates (galactose, retinol, PHB, phylloquinone, propylene, melanin, alkaloids, antibiotics), with sporulation appearing as an outlier. The lack of edges suggests the proteins participate in varied, loosely connected metabolic pathways rather than a single pathway, so a general label of diverse metabolite biosynthesis fits best.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0030435","count":4},{"id":"GO:0006012","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0042619","count":3}]},{"hash":"2242176568125299631","title":"Glutathione-dependent redox homeostasis and detoxification","description":"The GO terms point to redox biology and detoxification: glutathione metabolism, protein glutathionylation, cellular oxidant detoxification, and redox homeostasis are prominent, with additional stress-response terms (aluminum, ethanol, herbicide). This pattern suggests proteins functioning to maintain redox balance and detoxify oxidative stress via the glutathione system.","confidence":"High","size":11,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0010044","count":2},{"id":"GO:0019835","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0006749","count":2}]},{"hash":"577810659935193282","title":"Membrane Transporters (ions and metabolites)","description":"The top GO terms are dominated by transmembrane transport of ions and small molecules (sodium, potassium, nitrite, phosphate, arabinose, fucose, vitamins) and a vesicle-related process (neurotransmitter loading), suggesting a cluster of transporter proteins rather than metabolic enzymes. The diversity of substrates points to a general membrane transport function rather than a single nutrient pathway. Therefore, a label like Membrane Transporters (ions and metabolites) captures the common theme across the cluster.","confidence":"High","size":10,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0015707","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0098700","count":2}]},{"hash":"706511158371705183","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The enrichment is dominated by GO terms for mRNA splicing via the spliceosome, including positive regulation and alternative splicing, indicating the cluster primarily represents spliceosome-mediated splicing regulation. Some translation-related and transcription-related terms appear, but the core signal points to RNA processing via splicing.","confidence":"High","size":10,"edges":11,"triangles":7,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1793896315000684044","title":"Liver metabolism and development","description":"The presence of hepatocyte differentiation, bile acid biosynthetic process, and vitamin D catabolic process strongly points to liver-related metabolism and development. Methylation and oxidative demethylation reflect epigenetic regulation common in metabolically active tissues. Some terms like uterus development and maternal processes appear less connected and may be annotation noise, but the dominant signals are hepatic metabolic functions.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":3},{"id":"GO:0060137","count":3},{"id":"GO:1903715","count":2},{"id":"GO:0002677","count":2},{"id":"GO:0042369","count":2}]},{"hash":"1863301581571075097","title":"Nuclear RNA processing and splicing machinery","description":"The top GO terms are dominated by RNA processing and splicing-related activities (tRNA processing, transcription termination, mRNA splicing and spliceosome/ spliceosomal complex assembly, P-body assembly, histone mRNA metabolism) and coupled nuclear import, suggesting a cluster centered on nuclear RNA processing and mRNA metabolism. Chromatin-related and stress-response terms are present but appear secondary to the strong RNA-processing signal. ","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":7},{"id":"GO:0006369","count":7},{"id":"GO:0009414","count":6},{"id":"GO:1990141","count":6},{"id":"GO:0051170","count":6}]},{"hash":"1010850353975706471","title":"ER Stress\u2013Linked Translation and Folding","description":"High confidence: The terms are dominated by translation processes and ER-associated protein folding, including regulation of translation initiation in response to ER stress and ER protein folding, pointing to a cohesive theme of ER quality control under stress.","confidence":"","size":10,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0036494","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0034975","count":2}]},{"hash":"93332646147880055","title":"Metal Ion Homeostasis and Detoxification","description":"The proteins share a clear enrichment for zinc handling (zinc ion transport and homeostasis), cadmium detoxification, and cobalt/iron ion balance, indicating a cohesive role in metal ion homeostasis and detoxification rather than a single pathway. Some terms like intestinal development or ER-Golgi transport appear peripherally, but the core theme is metal ion regulation and detoxification.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060576","count":1},{"id":"GO:0060628","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0055072","count":1},{"id":"GO:0071577","count":1}]},{"hash":"2298580652709557100","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":4,"triangles":1,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0000472","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0000480","count":5}]},{"hash":"1689454555236459181","title":"GTPase Regulation and Protein Oligomerization","description":"This cluster is driven by terms for positive regulation of GTPase activity and protein complex/oligomerization, with additional hints of protein folding. Together these suggest a theme of regulatory proteins that modulate signaling via GTPases and coordinate assembly/folding of multi-protein complexes. A concise label capturing this common thread is \u201cGTPase Regulation and Protein Oligomerization.\u201d Some terms (e.g., cell-cycle and tissue-specific proliferation) appear peripheral but do not dominate the cluster\u2019s core signal.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0097428","count":1}]},{"hash":"50841192983828736","title":"Unknown","description":"The GO terms are scattered across diverse biological processes (cannabinoid biosynthesis, MHC II antigen presentation, renin-angiotensin, amyloid-beta metabolism, development, protein processing), with no clear shared function among the proteins. The graph is sparse (Edges 4, no triangles), so a cohesive functional label cannot be assigned.","confidence":"","size":10,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901696","count":1},{"id":"GO:1901697","count":1},{"id":"GO:0070305","count":1},{"id":"GO:0019886","count":1},{"id":"GO:0033619","count":1}]},{"hash":"1528426748058371478","title":"Energy metabolism and redox processes","description":"The dominant terms relate to electron transport and respiration (mitochondrial electron transport, aerobic respiration) and photosynthetic electron transport, indicating a cluster of proteins involved in energy production via redox reactions. Other listed processes are peripheral metabolic activities, but the shared theme is energy metabolism and redox chemistry.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006123","count":2},{"id":"GO:0006086","count":1},{"id":"GO:0019483","count":1},{"id":"GO:0019684","count":1}]},{"hash":"2029871848348771252","title":"Cellular Stress Response and Signaling","description":"The GO terms cluster around cellular responses to xenobiotic and hormone stimuli, oxidative stress (hydrogen peroxide, redox homeostasis), fatty acid signaling, and general signaling pathways (cAMP, phosphatidylinositol dephosphorylation), suggesting a group of proteins involved in sensing and transducing environmental and metabolic stress signals rather than a single metabolic process. The renal water transport term, while specific, can relate to hormonal and signaling contexts in physiology, reinforcing a signaling/stress-response theme.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0070542","count":2},{"id":"GO:0090502","count":1},{"id":"GO:0071375","count":1},{"id":"GO:0006308","count":1}]},{"hash":"2156743319208760390","title":"Plant cell wall polysaccharide biosynthesis and glycosylation","description":"The top GO terms converge on plant cell wall biogenesis and polysaccharide production (glucuronoxylan, homogalacturonan, mucilage, plant-type secondary cell wall) and protein O-linked glycosylation pathways, indicating a cluster of cell wall\u2013related biosynthetic enzymes and glycosyltransferases. An outlier term for skeletal muscle regeneration is likely annotation noise, but the dominant signal clearly points to plant cell wall biosynthesis and glycosylation.","confidence":"High","size":10,"edges":12,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0010417","count":1},{"id":"GO:0035269","count":1}]},{"hash":"155030930291187214","title":"Lipid metabolism and sterol biosynthesis","description":"The top GO terms are dominated by lipid-related processes: mannosyl-inositol phosphorylceramide metabolic process, unsaturated fatty acid biosynthetic process, and regulation of ergosterol biosynthetic process, pointing to fungal lipid pathways and membrane sterol homeostasis. Other terms (nitrate assimilation, nitric oxide biosynthesis, myelin maintenance, sebaceous gland differentiation, insulin catabolism) seem more peripheral or cross-species annotations, but the clearest theme is lipid metabolism and sterol biosynthesis.","confidence":"Medium","size":10,"edges":27,"triangles":31,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:0006636","count":3},{"id":"GO:0032443","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0042128","count":3}]},{"hash":"740408010062746300","title":"Amino acid biosynthesis","description":"Most GO terms point to biosynthetic pathways for several amino acids (isoleucine, threonine, cysteine, tryptophan) and related steps such as transsulfuration and 2-oxobutyrate formation, suggesting the proteins function in amino acid production rather than degradation or signaling. The presence of related precursor and catabolic terms is secondary to the dominant biosynthetic theme. Therefore the label \"Amino acid biosynthesis\" is appropriate.","confidence":"Medium","size":10,"edges":36,"triangles":65,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":5},{"id":"GO:0009097","count":4},{"id":"GO:0006535","count":4},{"id":"GO:0019346","count":4},{"id":"GO:0046360","count":4}]},{"hash":"2239855716690312479","title":"Chromatin-regulated transcription","description":"GO terms indicate control of transcription by RNA polymerase II and chromatin-related processes (histone methylation and localization to chromatin), pointing to chromatin-regulated transcription as the core function of this cluster. A few terms reference tissue development and stress responses, which are less central but present in the set.","confidence":"Medium","size":10,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0031018","count":2},{"id":"GO:0009409","count":2}]},{"hash":"1368265970976966349","title":"Unknown","description":"The GO terms show no cohesive theme; they include mitotic cell cycle transition, metal and oxidative stress responses, interferon signaling, protein modification regulation, hormone receptor assembly, morphine response, plant cytokinin signaling, and gluconeogenesis regulation, indicating a heterogeneous cluster without a single shared function.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007091","count":1},{"id":"GO:0071276","count":1},{"id":"GO:0071357","count":1},{"id":"GO:0070301","count":1},{"id":"GO:0031400","count":1}]},{"hash":"379486690973974205","title":"Unknown","description":"The top terms are scattered across DNA replication and cell cycle, transcription elongation, and protein degradation, but also include photosynthesis and bacteriochlorophyll biosynthesis as well as ER polarization. This mix lacks a single cohesive function or pathway to define the cluster, making a precise label inappropriate.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0015979","count":3},{"id":"GO:0030494","count":3},{"id":"GO:0030163","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1383978515933787259","title":"Amino Acid Biosynthesis and Nitrogen Metabolism","description":"This cluster shows strong representation of amino acid biosynthesis and related nitrogen-handling processes, including arginine and citrulline biosynthesis, carbamoyl phosphate synthesis, and cellular responses to amino acids, amines, and ammonium ions. While hepatocyte differentiation appears, the dominant theme is amino acid metabolism and nitrogen homeostasis across proteins.","confidence":"Medium","size":10,"edges":28,"triangles":32,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0006526","count":2},{"id":"GO:0070365","count":2},{"id":"GO:1903718","count":2},{"id":"GO:0043200","count":2}]},{"hash":"261933907046757401","title":"Hepatic Vitamin D and Bile Acid Metabolism","description":"Dominant GO terms cluster around liver-specific metabolic processes, including hepatocyte differentiation, bile acid biosynthesis, calcitriol biosynthesis, and vitamin D catabolic processes, as well as epoxygenase P450 pathways involved in xenobiotic/metabolic processing. While some terms (endothelial adhesion, nematode response) are more general, the core signal points to hepatic vitamin D and bile acid metabolism and related P450 activity.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002677","count":7},{"id":"GO:0042369","count":7},{"id":"GO:0070989","count":7},{"id":"GO:0009624","count":7},{"id":"GO:0070365","count":7}]},{"hash":"1758732502504962441","title":"Amino acid biosynthesis and catabolism","description":"Most of the GO terms are directly tied to amino acid metabolism, including L-isoleucine, L-leucine, and L-valine biosynthesis, as well as D-amino acid biosynthetic and catabolic processes. While there are a couple of other signals (folic acid biosynthesis and mitochondrial matrix protein import) that are less central, the dominant pattern points to amino acid production and breakdown. This makes \"Amino acid biosynthesis and catabolism\" a concise, representative label for the cluster.","confidence":"Medium","size":10,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":1},{"id":"GO:0009099","count":1},{"id":"GO:0046437","count":1},{"id":"GO:0006550","count":1},{"id":"GO:0019478","count":1}]},{"hash":"1495668977912201162","title":"Redox and sulfur metabolism cofactors","description":"This cluster\u2019s top GO terms cluster around redox homeostasis, sulfur-containing pathways (transsulfuration), selenocysteine/tRNA modification, and molybdenum cofactor biosynthesis, pointing to a shared theme in redox biology and cofactor metabolism. A few terms (e.g., mitotic M phase, epithelial differentiation) seem less related, and the absence of edges among proteins suggests the connection is not through direct interactions. Overall, the dominant signal is redox/sulfur metabolism and cofactors, giving a coherent but broad functional theme. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0009097","count":2},{"id":"GO:0000087","count":2},{"id":"GO:0006071","count":2},{"id":"GO:0030855","count":2}]},{"hash":"157471094728579104","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009243","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0009242","count":1},{"id":"GO:0097171","count":1}]},{"hash":"809102449354001653","title":"DNA Replication and Cell Cycle Regulation","description":"The top GO terms are dominated by mitotic sister chromatid cohesion, cell cycle, and DNA replication, with additional signals for ubiquitin ligase activity regulation, which together point to a core theme of DNA replication and cell cycle control. Some terms (cytokine production, neuron projection development) seem ancillary or context-dependent, but they do not override the primary nuclear DNA processing signature.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":2},{"id":"GO:0007049","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0035753","count":1},{"id":"GO:1900264","count":1}]},{"hash":"373520777218471917","title":"Immune signaling and antigen presentation","description":"This cluster is dominated by GO terms reflecting immune receptor signaling (T cell receptor, Fc receptor, and C-type lectin receptor signaling) and the antigen presentation pathway via MHC class I, TAP-dependent, plus regulatory processes like deubiquitination that commonly modulate signaling cascades. While a few terms touch on other processes (hypoxia-related transcription, Wnt signaling, metabolism), the strongest and most coherent theme is immune signaling and antigen processing/presentation.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":8},{"id":"GO:0061418","count":6},{"id":"GO:0090090","count":6},{"id":"GO:0002223","count":6},{"id":"GO:0002479","count":6}]},{"hash":"173309220070844308","title":"Membrane Solute Transporters","description":"The top GO terms are dominated by multiple transmembrane transport activities for diverse solutes (phosphate, nitrite, D-xylose, fructose, vitamins, xenobiotics), pointing to a cluster of membrane transport proteins handling solute uptake/efflux. Osmotic stress response further supports a transport-centric role in maintaining cellular solute balance. Other terms may be context-specific or ancillary but do not override the transport theme.","confidence":"High","size":9,"edges":10,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":6},{"id":"GO:0015707","count":5},{"id":"GO:0015753","count":5},{"id":"GO:1990539","count":5},{"id":"GO:0035461","count":5}]},{"hash":"448583981478232240","title":"Transmembrane nutrient and xenobiotic transporters","description":"The top GO terms cluster around membrane transport of nitrite, sugars, vitamins, and xenobiotics, indicating a common function as transmembrane nutrient/xenobiotic transporters; a few non-transport terms appear but are less representative.","confidence":"Medium","size":9,"edges":30,"triangles":50,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":4},{"id":"GO:0015753","count":4},{"id":"GO:1990539","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0042908","count":4}]},{"hash":"2006010042234256440","title":"Unknown","description":"The GO terms are highly diverse, spanning keratinocyte differentiation, chitin localization, hydrogen peroxide\u2013regulated cell death, cholesterol and lipid metabolism, amino acid biosynthesis, hormone response, flavonoid metabolism, and iron-sulfur cluster assembly. There is no clear single pathway or function tying all nine proteins together, so a cohesive, intuitive label cannot be determined from these terms alone.","confidence":"","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030216","count":2},{"id":"GO:0006033","count":1},{"id":"GO:1901300","count":1},{"id":"GO:0045542","count":1},{"id":"GO:0019344","count":1}]},{"hash":"725994853907992281","title":"ECM Adhesion and Remodeling","description":"Many top GO terms cluster around extracellular matrix interactions and remodeling: hyaluronan metabolic process, integrin-mediated signaling, and calcium-independent cell-matrix adhesion, along with positive regulation of metallopeptidase activity. This points to a coherent theme of ECM binding and remodeling. Some other terms (transcription, plant-specific processes, ubiquitin-dependent catabolism, complement activation) seem less related and may reflect cross-annotation or multifunctionality. Overall, the label captures the predominant function of the cluster.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030212","count":2},{"id":"GO:0007229","count":2},{"id":"GO:1905050","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0048455","count":1}]},{"hash":"1240816213709582690","title":"Ribosome Biogenesis and Translation","description":"The GO terms cluster around core translation machinery: cytoplasmic translation, ribosome biogenesis, threonyl-tRNA aminoacylation, and tRNA modification. Other terms related to cell growth and stress response (cell cycle, septum assembly, and amino acid starvation response) support a theme of growth-linked regulation of translation. The strongest common thread is ribosome function and protein synthesis.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":1},{"id":"GO:0055072","count":1},{"id":"GO:0006435","count":1},{"id":"GO:0000747","count":1},{"id":"GO:0002181","count":1}]},{"hash":"465636596534538015","title":"Cell Cycle, DNA Replication, and Chromosome Assembly","description":"The cluster is dominated by GO terms related to cell division, DNA replication, microtubule severing, and CENP-A chromatin assembly, pointing to mitosis and genome maintenance as the main shared function. While there are a few additional terms (ER-Golgi transport, heat acclimation, extracellular matrix) with lower representation, the core function ties to cell-cycle progression and chromosome biology.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2}]},{"hash":"626294326640929920","title":"Transcription and Translation Initiation","description":"This cluster contains GO terms for both DNA-templated transcription regulation and initiation (regulation of transcription, transcription initiation at RNA Pol II promoter) and for translation initiation and ribosome assembly (translation initiation complexes, cytoplasmic translation initiation, ribosome biogenesis). The co-occurrence suggests proteins involved in gene expression control at both transcriptional and translational levels, i.e., core components of transcription initiation and the formation of translation initiation machinery. The single viral process term is likely incidental. Overall, the label reflects the cluster\u2019s focus on transcription and translation initiation and related biogenesis.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2}]},{"hash":"734538567270129612","title":"DNA replication and cell cycle in development","description":"The cluster is dominated by GO terms for DNA replication, cell division, meiosis I, and cell proliferation, pointing to core roles in genome duplication and cell-cycle progression. Additional terms related to DNA repair during transcription-coupled processes and developmental events (neural tube closure, embryonic skeletal morphogenesis) suggest these proteins function in proliferative, developmentally active contexts. Taken together, the group seems to capture replication/mitotic machinery with developmental associations.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0019079","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0060303","count":2}]},{"hash":"1276357212729267","title":"Unknown","description":"The terms point to several distinct processes (Notch signaling, amino acid metabolism, transcription, lipid/sphingolipid biosynthesis, vitamin biosynthesis, insulin response). With no dominant shared function, the cluster appears heterogeneous or noisy rather than tied to a single pathway, so Unknown is appropriate.","confidence":"","size":9,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":5},{"id":"GO:0097053","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0046511","count":3}]},{"hash":"1256241478630149375","title":"RNA Pol II Transcription Regulation & Chromatin Remodeling","description":"Most terms cluster around regulation of transcription by RNA polymerase II, including preinitiation complex assembly, and chromatin processes such as nucleosome mobilization and histone H3 acetylation, suggesting a co-regulatory module of transcription control via chromatin state. A few terms mention photomorphogenesis or metabolism, but the dominant signal is transcription regulation with chromatin remodeling.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0042766","count":1},{"id":"GO:1900446","count":1},{"id":"GO:2000306","count":1},{"id":"GO:0043457","count":1}]},{"hash":"529532785169811993","title":"Glycan biosynthesis and cell envelope assembly","description":"The cluster is dominated by GO terms for polysaccharide and lipid-linked glycan biosynthesis and envelope assembly (capsule polysaccharide biosynthesis, cell wall polysaccharide biosynthesis, mycolate layer assembly, dolichol-linked oligosaccharide and GPI anchor biosynthesis, and UDP-galactose metabolism), suggesting a shared function in glycan construction and cell-surface components. A couple terms relate to telomere maintenance and DNA recombination, which appear less connected to the main theme and may be incidental.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0052573","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0070592","count":1},{"id":"GO:0071769","count":1}]},{"hash":"1902738822909194441","title":"RNA processing and splicing regulation","description":"This cluster shows strong representation of spliceosome-related terms (cis splicing, alternative splicing, and their regulation) and other post-transcriptional controls (mRNA stability, translational initiation, and poly(A) tail regulation), suggesting a cohesive module of RNA processing and post-transcriptional gene regulation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0060211","count":1}]},{"hash":"1972163517486518289","title":"Stress and nutrient-responsive transcription regulation","description":"The top GO terms reveal a pattern of transcriptional regulation by RNA polymerase II in response to various signals (hypoxia, oleic acid, carbon source) along with associated metabolic regulatory processes (respiration, amino acid and nucleotide biosynthesis, sterol-related regulation). This points to a theme where proteins coordinate transcriptional responses to environmental and metabolic cues, i.e., stress- and nutrient-responsive transcription.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:1990416","count":2},{"id":"GO:0035961","count":2},{"id":"GO:0061415","count":2},{"id":"GO:0061429","count":2}]},{"hash":"903100749153139755","title":"Developmental signaling and reproductive processes","description":"The top GO terms point to diverse signaling and developmental roles, including Wnt pathway regulation and collagen receptor signaling, along with responses to peptide hormones and processes tied to development and reproduction (forebrain development, ovulation cycle, budding growth) and hormone-related metabolism (vitamin D3). While the terms span several aspects, they collectively suggest proteins involved in signaling networks governing development and reproductive/hormonal processes rather than a single, narrow function. ","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090090","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0043277","count":3},{"id":"GO:0010800","count":3},{"id":"GO:0032298","count":3}]},{"hash":"774199973863893336","title":"T cell activation and lymphoid development","description":"The top GO terms converge on T cell biology and lymphoid tissue development, including T cell homeostasis, regulation of T cell proliferation, and lymph node development, with supporting signals from the p38MAPK cascade and GM-CSF response. Although RNA processing terms are present, the most representative and recurring themes are immune-related, centering on T cell activation/regulation and lymphoid tissue formation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0038066","count":1},{"id":"GO:0043029","count":1},{"id":"GO:2000766","count":1}]},{"hash":"906423460012737639","title":"Unknown","description":"The top terms span several unrelated biological areas (cellulose/oligosaccharide catabolic processes, lipid metabolism, transcription regulation, calcium homeostasis, reproduction, and behavior) with no clear, cohesive function tying them together. The absence of edges also suggests no shared pathway or interaction pattern, so there isn\u2019t a single interpretable theme for this cluster. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0045944","count":1},{"id":"GO:0009313","count":1},{"id":"GO:0006874","count":1}]},{"hash":"212632566591995633","title":"Bacterial central metabolism and quinone biosynthesis","description":"The cluster centers on energy-production pathways and redox cofactors: glycine cleavage and lipoylation, valine and phenylacetate catabolism, fatty acid beta-oxidation, and biosynthesis of menaquinone and phylloquinone. Translation terms appear due to housekeeping proteins, but the dominant GO terms point to core bacterial metabolism and electron-transport-related processes, with a note of antibiotic biosynthesis/response that can accompany metabolic states in bacteria.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0009249","count":1},{"id":"GO:0019464","count":1},{"id":"GO:0006574","count":1}]},{"hash":"136135014548974301","title":"Membrane Transport and Secretion","description":"The cluster is dominated by GO terms related to transport across membranes (vitamin, thiamine, branched-chain amino acids, xenobiotics) and lipid/phospholipid translocation, along with vesicle docking and protein secretion activities. These connect to membrane-associated transport and secretion processes, suggesting the group functions in moving molecules across membranes or through secretory pathways, even though some terms are metabolic or stress-related. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042760","count":2},{"id":"GO:0015888","count":2},{"id":"GO:0006904","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0046689","count":2}]},{"hash":"258927036953950894","title":"TGF-beta driven collagen synthesis and stress responses","description":"This cluster centers on collagen biosynthesis and a response to TGF-beta stimulus, pointing to extracellular matrix production regulated by TGF-beta. The accompanying terms reflect oxidative and metal ion-related stress responses and metabolic adjustments (e.g., hydrogen peroxide, manganese/selenium ions, amino acids, and putrescine biosynthesis), suggesting coordinated remodeling during stress or repair. Overall, the theme combines ECM production with stress-responsive remodeling.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":3},{"id":"GO:0071560","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0033197","count":2},{"id":"GO:0032964","count":2}]},{"hash":"197543051798926534","title":"Embryonic organogenesis and tissue development","description":"The terms point to developmental and morphogenetic processes across multiple tissues (kidney structures like mesonephric duct and proximal tubule, cartilage condensation, placenta, lymph vessel morphogenesis, and neuromast hair cell differentiation), indicating a general theme of embryonic organ development rather than a specific molecular function. A few terms (heme transport, UDP-xylose metabolism) are less representative but do not override the overall pattern.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035351","count":2},{"id":"GO:0031659","count":1},{"id":"GO:0072177","count":1},{"id":"GO:0072205","count":1},{"id":"GO:0048903","count":1}]},{"hash":"326556421515451100","title":"Glycosylation and specialized metabolite biosynthesis","description":"Top terms indicate a biosynthesis-focused cluster, with strong signals for glycosylation processes (GPI anchor biosynthesis, dolichol-linked oligosaccharide biosynthesis) and for specialized metabolite pathways (ergothioneine, selenoneine, alkaloid metabolism), plus a protein methylation term. A pollen tube guidance term appears but does not dominate, suggesting the primary theme is diverse biosynthetic/modification roles rather than a single pathway. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0010183","count":1},{"id":"GO:0006488","count":1},{"id":"GO:1903253","count":1},{"id":"GO:0052704","count":1}]},{"hash":"1820790321236875253","title":"Plant protein turnover and catabolic metabolism","description":"The cluster\u2019s top GO terms are dominated by proteolysis and peptide catabolic processes, indicating a core theme of protein degradation/turnover in plants; additional terms suggest plant-specific metabolic activities (xylan/ureide catabolism, iron import, folic acid metabolism) and growth regulation, collectively aligning around plant-centered catabolic metabolism with some breadth.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0006526","count":1},{"id":"GO:0043171","count":1},{"id":"GO:0006898","count":1}]},{"hash":"1948801886601198078","title":"Unknown","description":"The top GO terms are highly diverse, centering on various negative regulatory processes (miRNA processing, EMT, DNA damage checkpoint, chromosome condensation) and broad regulatory roles (glucocorticoid signaling, differentiation), with one outlier lipid A biosynthesis term. This makes it hard to identify a single cohesive function tying the proteins together, suggesting no clear common theme.","confidence":"","size":8,"edges":11,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1903799","count":3},{"id":"GO:0070940","count":3},{"id":"GO:0009245","count":3},{"id":"GO:1905213","count":3},{"id":"GO:0010719","count":3}]},{"hash":"1319252344855198823","title":"Ubiquitin-mediated protein regulation","description":"The top GO term is protein deubiquitination, with related terms pointing to ubiquitin-dependent ERAD and broader regulation of protein homeostasis. Other terms hint at downstream effects on transcription, ribosome assembly, and nuclear bodies, suggesting this cluster centers on ubiquitin-related regulation of protein fate and cellular processes.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":7},{"id":"GO:0071276","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0045944","count":4},{"id":"GO:1901896","count":4}]},{"hash":"901300543618948656","title":"Gene Expression and RNA Processing","description":"The cluster centers on core gene-expression activities: translation, transcription elongation, and mRNA export, indicating proteins involved in the flow from transcription to protein synthesis. Additional terms like spindle assembly and DNA integration suggest broader roles in cell cycle and genome dynamics, but the dominant theme remains gene expression machinery. The presence of an unrelated olfactory development term hints at annotation noise rather than a true functional module. Overall, the label reflects the main shared functions with moderate confidence.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042766","count":1},{"id":"GO:2000270","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0021553","count":1}]},{"hash":"951698751361436044","title":"Neuronal receptor trafficking and signaling","description":"The top GO terms are dominated by endocytosis, endocytic recycling, and transport of neurotransmitter receptors to the postsynaptic membrane, with related neuronal signaling (GABAergic transmission and ephrin receptor signaling). This points to a common theme of receptor trafficking and synaptic signaling in neurons. A few terms relate to broader cellular processes (mitotic cycle, mitochondrial inheritance, heart contraction) but do not override the prominent synaptic trafficking signal.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0048013","count":2}]},{"hash":"607538613805649010","title":"Unknown","description":"The top GO terms span apoptotic clearance, skin differentiation, GPCR signaling, UV-B response, inflammation, DNA repair, proteostasis, and coagulation, a highly diverse mix with no single cohesive function tying the proteins together. Because there isn\u2019t a clear shared pathway or biological role among these terms, a precise label is not supported.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043277","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0007200","count":1},{"id":"GO:0060662","count":1},{"id":"GO:0010224","count":1}]},{"hash":"111545446445401300","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0030420","count":2},{"id":"GO:0034414","count":2},{"id":"GO:0031126","count":2}]},{"hash":"257702468320559745","title":"Mitotic Cell Cycle and Cytokinesis","description":"The top GO terms cluster around the mitotic cell cycle, septin ring organization, and DNA replication initiation, indicating a focus on cell division and cytokinesis. Supporting terms like budding growth and cell-cycle regulation reinforce a cohesive theme of cell division, with a few RNA processing and signaling entries likely reflecting regulatory cross-talk.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060211","count":3},{"id":"GO:0032186","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0090090","count":2},{"id":"GO:0071375","count":2}]},{"hash":"610244510392821026","title":"Mitochondrial metabolite transporters","description":"The GO terms indicate transport of various metabolites and ions across the mitochondrial membranes (e.g., Mn2+, Mg2+, NAD, alpha-ketoglutarate, pyrimidine nucleotides), suggesting a core function as mitochondrial metabolite/ion transporters. Some metabolic signaling terms (insulin response, adaptive thermogenesis) reflect broader metabolic context rather than different function. Therefore, the cluster is best described as mitochondrial metabolite transporters.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0035352","count":2},{"id":"GO:1990616","count":2},{"id":"GO:1990519","count":2}]},{"hash":"2215887325696943953","title":"Mitochondrial ion and metabolite transport","description":"These proteins appear to cluster around mitochondrial transport and metabolism. The top GO terms describe transport of manganese, alpha-ketoglutarate, NAD across membranes, and magnesium export from mitochondrion, as well as import of pyrimidine nucleotides into mitochondria, all highlighting mitochondrial metabolite flux. Some terms related to insulin signaling and adaptive thermogenesis imply involvement in energy regulation, reinforcing the focus on mitochondrial transport and metabolism.","confidence":"High","size":8,"edges":11,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0035352","count":4},{"id":"GO:1990616","count":4},{"id":"GO:1990519","count":4}]},{"hash":"812701453051508287","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034473","count":1},{"id":"GO:0034475","count":1},{"id":"GO:0071051","count":1},{"id":"GO:0071035","count":1},{"id":"GO:0016120","count":1}]},{"hash":"447037393797739780","title":"ER\u2013Golgi trafficking and vesicle budding","description":"This cluster is dominated by GO terms for ER-to-Golgi transport, COPI-coated vesicle budding, Golgi ribbon formation, and ER lumen protein retention, pointing to a secretory pathway/ER quality control theme. Energy metabolism terms appear less central.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006122","count":1}]},{"hash":"587878434555207879","title":"DNA Replication and Repair","description":"This cluster is dominated by terms linked to DNA replication initiation and elongation, DNA synthesis in UV-damage repair, RNA-templated DNA biosynthesis, and translesion synthesis, plus telomere maintenance via recombination. Together they point to genome maintenance, DNA synthesis, and damage tolerance as core functions of this group. A few terms are obsolete or seem unrelated (e.g., pancreatic development), likely noise or annotation artifacts.","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":1},{"id":"GO:0000722","count":1},{"id":"GO:1904161","count":1},{"id":"GO:0006270","count":1},{"id":"GO:0006271","count":1}]},{"hash":"332043528421055354","title":"Neuronal Stress Response and Protein Homeostasis","description":"The cluster's GO terms cluster around cellular stress responses (acidic pH, hydrogen peroxide, toxic substances) and neuronal processes (neuron maturation/homeostasis). They also include protein quality control mechanisms (ubiquitination, regulation of protein complex assembly) and stress-associated translational regulation. Together, these terms point to neurons mounting stress responses while maintaining protein homeostasis, making this a coherent label for the cluster.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1990451","count":1},{"id":"GO:1903377","count":1},{"id":"GO:0072755","count":1},{"id":"GO:0031333","count":1},{"id":"GO:0070301","count":1}]},{"hash":"2292136827353654368","title":"Spliceosome-Mediated RNA Splicing and Processing","description":"The cluster\u2019s terms are dominated by mRNA splicing via the spliceosome, including alternative splicing and regulation of splicing, as well as related post-transcriptional controls (mRNA stability, regulatory ncRNA-mediated silencing). A couple of terms about ER-Golgi transport appear, which may reflect multifunctional proteins or annotation noise, but the core signal points to spliceosome-driven RNA processing.","confidence":"High","size":8,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042147","count":2},{"id":"GO:0006888","count":2},{"id":"GO:1901407","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0048026","count":1}]},{"hash":"1684727085168459604","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006223","count":2},{"id":"GO:0045007","count":1},{"id":"GO:0071276","count":1},{"id":"GO:1901291","count":1},{"id":"GO:0006296","count":1}]},{"hash":"664124017594555878","title":"Unknown","description":"GO terms across the proteins span immune antigen presentation, renin-angiotensin/kidney biology, proteolysis, development, and amyloid-beta metabolism, with no single cohesive function tying all members together. This lack of a unifying theme makes a specific, meaningful cluster label inappropriate.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070305","count":1},{"id":"GO:0019886","count":1},{"id":"GO:0033619","count":1},{"id":"GO:0001823","count":1},{"id":"GO:0002016","count":1}]},{"hash":"247461092051843018","title":"DNA Replication and Repair Machinery","description":"This cluster\u2019s GO terms center on DNA replication and genome maintenance, including nucleotide-excision repair, DNA-templated replication, pre-replicative complex assembly, replication initiation, translesion synthesis (both error-free and error-prone), and cellular responses to UV-induced damage, as well as mitotic chromosome condensation. Together these suggest proteins that function in DNA replication initiation, repair, and damage tolerance, i.e., a replication/repair machinery group.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006297","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0070987","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0071494","count":1}]},{"hash":"1790429045401238207","title":"Craniofacial development and retinoid metabolism","description":"Top GO terms indicate strong retinol/retinal metabolic activity, pointing to retinoid metabolism as a core function. This is complemented by development-related terms such as face development, olfactory pit development, and inner ear morphogenesis, suggesting involvement in craniofacial and sensory organ formation. Other catabolic and biosynthetic terms appear supplementary, but do not detract from the central theme tying metabolism to head/sensory morphogenesis.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":8},{"id":"GO:0042574","count":8},{"id":"GO:0009258","count":7},{"id":"GO:1901023","count":7},{"id":"GO:0060324","count":7}]},{"hash":"2289417119944086655","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0000466","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000398","count":3}]},{"hash":"2210853965446504413","title":"Developmental Regulation and Morphogenesis","description":"Top terms point to embryonic development and tissue patterning (cranial skeletal system development, embryonic body morphogenesis, midbrain dopaminergic neuron differentiation) with accompanying regulatory processes (negative regulation of Wnt signaling, chromatin remodeling, mRNA transport) and cell growth. The common thread is a broad developmental program coordinated by gene expression control, rather than a single, cohesive pathway. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904888","count":1},{"id":"GO:0060769","count":1},{"id":"GO:0010909","count":1},{"id":"GO:0051211","count":1},{"id":"GO:0090090","count":1}]},{"hash":"1248813534489042017","title":"Unknown","description":"The GO terms are highly diverse, spanning lipopolysaccharide biosynthesis, proton and calcium transport, mitochondrial translation, fatty acid catabolism, tRNA biosynthesis, ER organization, sporopollenin biosynthesis, and transcription regulation. With only a single edge and no clear shared function across these terms, there is no cohesive theme linking the proteins, so the label Unknown with no confidence is most appropriate.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0019876","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0009062","count":2}]},{"hash":"2214686906787840839","title":"ER protein folding and quality control","description":"The top GO terms cluster around endoplasmic reticulum\u2013related processes: protein folding in the ER, ER-targeting and maturation, ER-associated degradation, and translation initiation changes in response to ER stress, suggesting a focus on proteostasis in the secretory pathway, with some ancillary links to redox balance and nuclear transport as broader proteostasis factors.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036494","count":5},{"id":"GO:0006626","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0034975","count":5},{"id":"GO:0045454","count":5}]},{"hash":"709407904147546766","title":"Carbohydrate Catabolism and Sugar Metabolism","description":"The Top Terms indicate a cohesive theme around sugar processing and carbohydrate metabolism, including glycolysis via fructose-6-phosphate, lactose and ribose catabolic pathways, carbohydrate phosphorylation, and responses to sucrose and fructose, with additional related biosynthetic processes. This suggests the cluster represents a module focused on sugar metabolism and energy-yielding pathways.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902777","count":1},{"id":"GO:0061615","count":1},{"id":"GO:0097171","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0019512","count":1}]},{"hash":"803598676275827361","title":"Membrane Solute Transporters","description":"This cluster is dominated by GO terms for transmembrane transport of various solutes (nitrite, D-xylose, fructose, vitamins, xenobiotics, nitrate assimilation), indicating a coherent role in membrane-based uptake and export of nutrients and xenobiotics. A few terms about stress response and host interaction appear ancillary but do not override the central theme of solute transport across membranes.","confidence":"High","size":7,"edges":16,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":5},{"id":"GO:0015753","count":5},{"id":"GO:1990539","count":5},{"id":"GO:0035461","count":5},{"id":"GO:0042908","count":5}]},{"hash":"1707673145135801732","title":"Golgi-ER Vesicle Trafficking and Docking","description":"The terms cluster around vesicle trafficking and docking/fusion across the secretory pathway, notably ER\u2013Golgi organization, Golgi-to-vacuole transport, and vesicle docking/fusion to membranes, pointing to a coherent membrane-transport theme rather than a single enzyme. A lipid metabolism term is present but does not redefine the main function. Overall, the proteins appear to participate in vesicle formation, targeting, and fusion within Golgi/ER and related compartments.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:0097111","count":2},{"id":"GO:0016081","count":2},{"id":"GO:0033194","count":2},{"id":"GO:0006896","count":2}]},{"hash":"1943905112674262248","title":"Adipose lipid metabolism","description":"This cluster is enriched for GO terms related to lipid handling and energy metabolism, including adipose tissue development, cholesterol and lipid metabolic processes, and acetyl-CoA/propionyl-CoA catabolic and biosynthetic activities. The recurring theme across terms points to lipid metabolism and associated energy pathways, with a secondary note of brain development that may reflect broader metabolic roles. Confidence: High","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0060612","count":5},{"id":"GO:1901373","count":5},{"id":"GO:0019619","count":5},{"id":"GO:0006550","count":5},{"id":"GO:0046356","count":5}]},{"hash":"678399746016482390","title":"Mitochondrial Transport and Energy Metabolism","description":"Most top GO terms point to transport of ions and metabolites across mitochondrial membranes (manganese, alpha-ketoglutarate, NAD, magnesium export, pyrimidine nucleotides) and energy regulation (insulin response, adaptive thermogenesis). This suggests the cluster reflects proteins involved in mitochondrial metabolite transport and energy homeostasis, rather than a single isolated pathway. ","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":3},{"id":"GO:0015742","count":3},{"id":"GO:0035352","count":3},{"id":"GO:1990616","count":3},{"id":"GO:1990519","count":3}]},{"hash":"1562719927400469255","title":"Nucleolar transcription and ribosome biogenesis","description":"The GO terms cluster around transcription by RNA polymerases I/II/III, plus transcription elongation and termination by Pol III and RNA-templated transcription, together with ribosome biogenesis, all characteristic of nucleolar RNA synthesis and ribosome assembly. The fatty acid elongation and pheromone metabolic terms appear peripheral, likely reflecting multifunctional proteins or annotation noise.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0006385","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0001172","count":1}]},{"hash":"2109882974000776961","title":"ERAD and ribosome-associated protein quality control","description":"The cluster\u2019s top GO terms center on misfolded protein handling and degradation pathways: retrograde transport from ER to cytosol, ER-associated degradation (cytoplasm protein quality control by ubiquitin-proteasome system), ribosome-associated ubiquitin-dependent proteolysis, and nonfunctional rRNA decay. Together they suggest a functional module focused on maintaining proteome integrity via ERAD and ribosome-associated quality control.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":2},{"id":"GO:0071712","count":1},{"id":"GO:0051974","count":1},{"id":"GO:1900182","count":1},{"id":"GO:0071629","count":1}]},{"hash":"46992092804546416","title":"DNA Repair and Genome Maintenance","description":"The cluster\u2019s GO terms cluster around DNA repair pathways (base-excision repair, nucleotide-excision repair), DNA replication, and recombination resolution and sister chromatid cohesion, pointing to a core theme of preserving genome integrity. A couple terms (tRNA wobble uridine modification, aging) are less central but do not negate the primary repair/recombination signal.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0006289","count":1},{"id":"GO:0045190","count":1}]},{"hash":"987007412891718643","title":"Polysaccharide biosynthesis and metabolism","description":"The terms mainly describe biosynthesis and turnover of polysaccharides (starch/amylopectin, glycogen, maltose, trehalose, and alpha-glucan), indicating a carbohydrate synthesis and energy-storage cluster. The ovarian follicle development term appears unrelated and may be noise, but the dominant theme is polysaccharide metabolism.","confidence":"Medium","size":7,"edges":12,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001541","count":2},{"id":"GO:0019252","count":1},{"id":"GO:0010021","count":1},{"id":"GO:0005993","count":1},{"id":"GO:0000023","count":1}]},{"hash":"1240103999444626420","title":"Neural development and embryogenesis","description":"Top GO terms indicate a developmental program focused on neural formation (forebrain development, neural tube closure) and broader embryogenesis (multicellular organism development, skeletal system development), with transcriptional regulation as a supporting mechanism (DNA-templated transcription, gene expression regulation). Although some stress and cell cycle terms appear, the dominant theme is neural/embryonic development.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006349","count":2}]},{"hash":"2086231490268617743","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000480","count":2}]},{"hash":"1601759571672015943","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster is driven by terms related to large subunit ribosome biogenesis, maturation of 5.8S and LSU rRNA, and assembly of large subunit preribosome, indicating a core function in ribosome assembly and rRNA maturation. A secondary signal is mRNA splicing via spliceosome, suggesting broader RNA-processing context in the nucleus. Taken together, the dominant theme centers on ribosome biogenesis with associated RNA-processing activities.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000463","count":3},{"id":"GO:1902626","count":3}]},{"hash":"1155117386960231520","title":"Nucleotide and amino acid metabolism with signaling cues","description":"The GO terms show nucleotide/nucleoside metabolism (purine nucleobase biosynthesis, uracil salvage, nucleoside metabolic process, xanthine metabolism) and amino acid biosynthesis (L-asparagine), plus signaling-related processes (dopamine metabolism, cellular response to insulin) and neural/immune development and proliferation. This pattern points to a cluster centered on core metabolic pathways with broader regulatory signaling roles in neural and immune contexts, rather than a single, tight pathway.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009113","count":1},{"id":"GO:0021954","count":1},{"id":"GO:0045982","count":1},{"id":"GO:0006223","count":1},{"id":"GO:0032869","count":1}]},{"hash":"2144272237060690447","title":"Hepatic vitamin D and bile acid biosynthesis","description":"The top GO terms cluster around liver metabolism and P450 activity: bile acid biosynthesis, calcitriol biosynthesis, vitamin D catabolic process, and epoxygenase P450 pathway, together with hepatocyte differentiation, all pointing to hepatic metabolic/detoxification roles. Immune-related terms are present but appear less central to the primary theme. Overall, the cluster seems to represent hepatic vitamin D and bile acid metabolic processes.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002677","count":3},{"id":"GO:0042369","count":3},{"id":"GO:0070989","count":3},{"id":"GO:0009624","count":3},{"id":"GO:0070365","count":3}]},{"hash":"725434205747735155","title":"Prostaglandin and lipid metabolism with detoxification","description":"This cluster centers on prostaglandin biosynthesis and lipid metabolism, with supporting signals from insulin response and fatty acid regulation, plus detoxification and inflammatory regulation. The recurring themes point to lipid-mediated signaling and cellular protective/metabolic stress responses rather than unrelated functions.","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0045892","count":2},{"id":"GO:0031100","count":2},{"id":"GO:0009636","count":2}]},{"hash":"1551841914859944370","title":"DNA Damage Response and Repair","description":"The proteins are enriched for DNA repair and damage signaling processes (double-strand break repair via synthesis-dependent strand annealing, DNA recombination, SOS response, transcription-coupled NER), with some RNA processing terms suggesting coordination of nuclear maintenance activities; together these point to a DNA damage response/repair-focused cluster.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045003","count":2},{"id":"GO:0006268","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0042766","count":1}]},{"hash":"346665675515647649","title":"Organelle Autophagy Pathways","description":"The GO terms cluster around autophagy-driven turnover of organelles, including mitophagy, nucleophagy, glycophagy, and Cvt-mediated vacuolar targeting, as well as autophagosome assembly, indicating a cohesive theme of organelle-specific autophagy; additional terms on cell cycle regulation and programmed cell death relate to autophagy's broader cellular remodeling roles.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000422","count":2},{"id":"GO:0006501","count":2},{"id":"GO:0044805","count":2},{"id":"GO:0034727","count":2},{"id":"GO:0032258","count":2}]},{"hash":"1267800129666113080","title":"Unknown","description":"Top terms show a mix of RNA processing/modification and broad nucleotide/cofactor catabolic processes, with an odd inclusion of cobalamin biosynthesis; no single cohesive function emerges, so a reliable, specific label cannot be assigned.","confidence":"","size":7,"edges":15,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0046067","count":1}]},{"hash":"1179632213662227706","title":"Neurotransmitter Regulation and Stress Responses","description":"This cluster shows enrichment for regulatory effects on neurotransmitters (positive regulation of dopamine metabolism; negative regulation of serotonin secretion) plus responses to various chemical and environmental stresses (lipopolysaccharide, corticosterone, ethanol) and a quinolinate biosynthetic process. The mix points to a theme where neural signaling is modulated under stress and metabolic conditions, so the label reflects both neurotransmitter regulation and stress-related responsiveness.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0010269","count":2},{"id":"GO:0010044","count":2},{"id":"GO:0014063","count":2},{"id":"GO:0019805","count":2}]},{"hash":"1423921298626622193","title":"Nutrient-responsive transcriptional regulation","description":"The top terms cluster around transcriptional control (DNA-templated transcription, transcription from RNA polymerase II promoter) and regulation by carbon sources and oleic acid, suggesting a theme of nutrient- or condition-responsive gene expression. Some terms are disparate or marked obsolete, but the core signal points to transcriptional regulation in response to nutrients/metabolic cues.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1901717","count":2},{"id":"GO:0061429","count":2},{"id":"GO:0061415","count":2}]},{"hash":"902084355113205993","title":"Neuronal ubiquitin\u2013proteasome stress response","description":"The cluster centers on ubiquitin-dependent proteolysis and proteasomal degradation, with several terms tied to oxidative stress signaling in neurons and neuronal homeostasis. Additional signals point to mitophagy-related transport and chromatin turnover, suggesting a role in neuronal proteostasis and stress-induced survival pathways.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903378","count":3},{"id":"GO:0042787","count":3},{"id":"GO:1903377","count":2},{"id":"GO:0042551","count":2},{"id":"GO:0097039","count":2}]},{"hash":"1285666989129338733","title":"Membrane Solute Transporters","description":"The cluster shows a strong emphasis on transport across membranes for a variety of solutes (nitrite, D-xylose, fructose, vitamins, xenobiotics). While a couple of unrelated terms appear, the dominant pattern is membrane transport, suggesting these proteins primarily function as solute transporters. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":1},{"id":"GO:0015753","count":1},{"id":"GO:1990539","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0042908","count":1}]},{"hash":"2229344089445600929","title":"NF-kappaB\u2013driven immune regulation","description":"The top terms cluster around regulation of NF-kappaB signaling and immune/inflammatory processes (positive regulation of canonical NF-kappaB signaling; negative regulation of inflammatory response; regulation of lymphocyte differentiation; negative regulation of IL-4 production; negative regulation of type 2 immune response; regulation of myeloid leukocyte differentiation). While there are a few terms related to Ca2+ detection, transport, and ubiquitination, the dominant theme is immune signaling control via NF-kappaB, justifying this label as representative of the cluster.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043123","count":2},{"id":"GO:0050728","count":2},{"id":"GO:0005513","count":2},{"id":"GO:0007034","count":1},{"id":"GO:0032410","count":1}]},{"hash":"1817571818096802798","title":"B cell activation and cytokine production","description":"The GO terms are dominated by B cell\u2013centric activities: cytokine production, IL-6 regulation, inflammatory response, and IgG isotype switching, pointing to a B cell\u2013driven immune activation module. Some terms (telomere maintenance, scaRNA localization) seem less related and may reflect annotation noise or secondary roles, but the primary signal supports a B cell\u2013focused immune function. ","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0002368","count":6},{"id":"GO:0032212","count":6},{"id":"GO:0048291","count":6},{"id":"GO:0050729","count":6},{"id":"GO:2000778","count":6}]},{"hash":"1018552341743212381","title":"Mitotic Cell Cycle and Ribosome Biogenesis","description":"The GO terms point to processes in cell division and mitosis (cell cycle, mitotic cell cycle, exit from mitosis) as well as ribosome biogenesis and export, plus protein complex formation and cell polarity, suggesting a theme around coordinating cell division with ribosome assembly and protein interactions.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0010458","count":2},{"id":"GO:0030011","count":2}]},{"hash":"1649744123953497042","title":"Transmembrane Transport of Ions and Metabolites","description":"This cluster is dominated by GO terms describing movement of ions and small molecules across membranes (and vesicle loading), suggesting a group of transmembrane transport proteins with diverse substrates. Name reflects this broad transport function.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0035725","count":2}]},{"hash":"1003530424244322512","title":"Unknown","description":"The listed GO terms are highly heterogeneous, spanning iron-sulfur cluster biology, transcription regulation in response to iron, translation, innate immune responses, and plant cutin biosynthesis, with many obsolete annotations. There are no edges or shared functional terms linking the proteins, suggesting there is no coherent, single function uniting the cluster. Therefore, a specific, representative label cannot be determined.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097428","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0036086","count":1},{"id":"GO:0051220","count":1},{"id":"GO:0034396","count":1}]},{"hash":"1745396537846299478","title":"Ribosome Biogenesis and rRNA Processing","description":"The GO terms are centered on ribosome assembly and RNA maturation, including maturation of SSU-rRNA, rRNA processing, and ribosomal large subunit biogenesis, which together point to a shared role in ribosome biogenesis. Nuclear division appears related to cellular growth linked to ribosome production, and a few terms about mitochondria or apoptosis may be ancillary. Overall, the dominant theme is ribosome biogenesis and rRNA maturation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030490","count":1},{"id":"GO:0000280","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0006364","count":1},{"id":"GO:1903638","count":1}]},{"hash":"278407539397163718","title":"Ribosome biogenesis and translation","description":"The GO terms show a clear ribosome/translation focus: translation, ribosome biogenesis, and rRNA maturation/assembly, indicating a cluster of ribosome-related biogenesis and protein synthesis factors.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":2},{"id":"GO:0000470","count":2},{"id":"GO:0000028","count":1},{"id":"GO:0030490","count":1}]},{"hash":"1767106885644971861","title":"Innate Immune Response and Antiviral Regulation","description":"GO terms indicate innate immune activity and antiviral regulation (innate immune response, negative regulation of viral transcription, T cell homeostasis), suggesting a defense-focused cluster, with a few obsolete or epigenetic terms appearing as noise.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046597","count":2},{"id":"GO:0051092","count":2},{"id":"GO:2000620","count":2},{"id":"GO:0060816","count":2},{"id":"GO:1900095","count":2}]},{"hash":"1207659744256961094","title":"Aromatic Compound Catabolism and Metabolic Regulation","description":"The top GO terms emphasize aromatic compound degradation (catechol, 3,4-dihydroxybenzoate) and regulation of metabolic processes (cellular respiration and transcriptional control by carbon sources), suggesting a metabolism-driven regulatory theme rather than a single enzyme function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0019615","count":1},{"id":"GO:0019619","count":1},{"id":"GO:1901717","count":1}]},{"hash":"1549173285297833078","title":"Cross-tissue developmental organogenesis","description":"The top GO terms cover developmental processes across both plants and animals\u2014flower and seed/ovule formation in plants, and nephron, cardiac vascular smooth muscle, tracheal cartilage, and primitive streak formation in animals\u2014along with related differentiation and formation processes (platelet formation, germinal center regulation). This pattern points to a shared theme of tissue and organ development across diverse lineages, rather than a single specialized pathway.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048459","count":1},{"id":"GO:0072160","count":1},{"id":"GO:0060947","count":1},{"id":"GO:0060534","count":1},{"id":"GO:0090009","count":1}]},{"hash":"429422832161757884","title":"Diverse Compound Catabolism","description":"The top GO terms show multiple distinct catabolic/metabolic processes (prostaglandin, stilbene, glucuronoside, 3-phenylpropionate catabolism, and PHB biosynthesis), with only a few outliers (response to toxic substance, endocannabinoid signaling regulation). The lack of a single cohesive pathway and the presence of diverse substrates suggest a cluster of proteins involved in various metabolic degradation tasks rather than one tight function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905344","count":1},{"id":"GO:0019740","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0046272","count":1}]},{"hash":"1330990865671587048","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009650","count":1},{"id":"GO:0006296","count":1},{"id":"GO:0016579","count":1},{"id":"GO:0033314","count":1},{"id":"GO:1990506","count":1}]},{"hash":"2058556900170566545","title":"Hepatic Vitamin D and Bile Acid Biosynthesis","description":"The cluster centers on vitamin D metabolism (calcitriol and vitamin D catabolic processes) and bile acid biosynthesis, with supporting signals from hepatic differentiation and P450 epoxygenase activity, pointing to a liver-centric metabolic module.","confidence":"Medium","size":6,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002677","count":4},{"id":"GO:0042369","count":4},{"id":"GO:0070989","count":4},{"id":"GO:0009624","count":4},{"id":"GO:0070365","count":4}]},{"hash":"1226858187057535279","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by translation and ribosome-related processes: translation in cytoplasm, ribosomal large subunit assembly/biogenesis, export from the nucleus, and RNA modification via pseudouridine synthesis for rRNA and snRNA. These collectively point to proteins involved in ribosome maturation and protein synthesis, making this the most coherent cluster theme. Some scattered terms on growth or telomere maintenance are less central to the core function here, but do not override the ribosome-centric signal.","confidence":"High","size":6,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0031120","count":2},{"id":"GO:0031118","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0000027","count":1}]},{"hash":"1336806721963831435","title":"Hepatic vitamin D and bile acid metabolism","description":"The cluster centers on liver-related metabolism, highlighted by hepatocyte differentiation, bile acid biosynthesis, calcitriol biosynthesis, and vitamin D catabolism, all of which involve P450 enzymes (epoxygenase pathway, oxidative demethylation). Immune-modulatory terms like negative regulation of chronic inflammatory response and response to nematode fit with vitamin D\u2019s immunomodulatory roles, supporting a cohesive hepatic vitamin D and bile acid metabolism theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002677","count":6},{"id":"GO:0042369","count":6},{"id":"GO:0070989","count":6},{"id":"GO:0009624","count":6},{"id":"GO:0070365","count":6}]},{"hash":"1755552004098622202","title":"Calcium signaling and muscle contraction regulation","description":"The cluster shows a consistent theme around calcium ion transport and homeostasis (intracellular Ca2+, Ca2+ transport to ER) and modulation of muscle activity (negative regulation of heart and striated muscle contraction), with related steroid hormone responses, suggesting a calcium-dependent muscle function module with hormonal regulation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0051001","count":3},{"id":"GO:1903515","count":3},{"id":"GO:0098736","count":3},{"id":"GO:0002028","count":3}]},{"hash":"1531985270174261805","title":"Redox stress and mitochondrial metabolism","description":"The cluster\u2019s terms cluster around redox biology and energy metabolism: hydrogen peroxide biosynthesis, cell redox homeostasis, and mitochondrial electron transport (NADH to ubiquinone) point to oxidative stress management and mitochondrial respiration as core themes. Additional terms like response to lipopolysaccharide and response to toxic substances support a broader stress-response context, though several other terms (neuron maturation, splicing, histone deacetylation, propylene catabolism) appear more incidental. Overall, the redox/mitochondrial angle best ties the set together.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":1},{"id":"GO:0046098","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0006120","count":1}]},{"hash":"273388381308420528","title":"Angiogenesis and vascular regulation","description":"The GO terms cluster around blood vessel formation and endothelial behavior (angiogenesis, endothelial cell migration) and proteolytic/blood-pressure\u2013related pathways (plasma kallikrein-kinin cascade, regulation of arterial blood pressure), suggesting a vascular signaling/regulatory theme. Some metabolic terms appear, but the dominant signal is vascular development and homeostasis.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060055","count":1},{"id":"GO:0042593","count":1},{"id":"GO:0002353","count":1},{"id":"GO:0002155","count":1},{"id":"GO:0003085","count":1}]},{"hash":"124748764234613289","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0039702","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0010587","count":1}]},{"hash":"1707544332715602182","title":"Unknown","description":"No GO terms are listed and there are no edges or triangles among the 5 proteins, so there is no detectable shared function to base a label on.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1322351024493231061","title":"Unknown","description":"The listed GO terms cover a wide range of processes (mitotic cell cycle, innate immune response, Wnt signaling regulation, hormone response, apoptotic clearance, phosphorylation, DNA replication initiation, bud growth, vitamin D metabolism, and ovulation). There isn\u2019t a single coherent theme connecting these functions, so a concise, representative label cannot be confidently assigned.  ","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0090090","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0043277","count":2}]},{"hash":"686988033974405546","title":"Meiosis Chromatin and Cohesion","description":"The top GO terms cluster around meiotic processes (microsporogenesis, meiotic chromosome condensation, meiotic sister chromatid cohesion) and chromatin-related activities (DNA replication-dependent chromatin assembly, heterochromatin formation, rDNA maintenance). This suggests a coherent theme of meiosis linked with chromatin remodeling, chromosomal condensation, and cohesion, with a few broader signals like cell division that support the overall context.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0009959","count":4},{"id":"GO:0043007","count":4},{"id":"GO:0042518","count":4},{"id":"GO:0051028","count":4}]},{"hash":"1579335555413098991","title":"Golgi-Associated Vesicle Trafficking","description":"The top terms are centered on Golgi functions (Golgi transport, Golgi inheritance, vesicle docking/targeting) along with related processes like ER inheritance and acrosome assembly, pointing to a coherent theme of Golgi-mediated vesicle trafficking and organelle inheritance across the proteins in this cluster.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055108","count":1},{"id":"GO:0048313","count":1},{"id":"GO:0006896","count":1},{"id":"GO:0006904","count":1},{"id":"GO:0048309","count":1}]},{"hash":"1981228793361995451","title":"DNA Repair and Genome Maintenance","description":"The GO terms cluster around DNA damage response and repair pathways, including NHEJ, global genome NER, translesion synthesis (both error-prone and error-free), and telomere maintenance via recombination, with additional protein modification processes (ubiquitination/ISG15 conjugation) linked to proteostasis during repair. This cohesive theme suggests a module dedicated to genome stability and DNA repair mechanisms.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043524","count":5},{"id":"GO:1901044","count":5},{"id":"GO:0000722","count":5},{"id":"GO:1903955","count":5},{"id":"GO:0006303","count":5}]},{"hash":"1977216167185998768","title":"Nutrient-regulated transcription","description":"This cluster features GO terms tied to transcription control in response to nutrient signals, including nitrogen catabolite activation and transcription from RNAP II promoters under different carbon sources, suggesting a shared role in coordinating gene expression with metabolic state. Additional terms point to general transcription and some RNA/protein modification activities that may accompany regulation. Overall, it reflects transcriptional regulation linked to nutrient sensing, likely in a eukaryotic context.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901717","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1900399","count":2},{"id":"GO:0001080","count":2},{"id":"GO:1901714","count":2}]},{"hash":"1399892011633445847","title":"Transmembrane Transporters for Ions and Metabolites","description":"The GO terms highlight transmembrane transport activities for a variety of substrates and ions (nitrite, sugars like arabinose and fucose, phosphate, vitamins) and also neurotransmitter loading into synaptic vesicles. This converges on a common function: membrane transporters handling diverse substrates, rather than a single substrate. Hence the label Transmembrane Transporters for Ions and Metabolites. ","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0035725","count":1}]},{"hash":"1950126441795378472","title":"Neural development and axon guidance signaling","description":"This cluster is enriched for terms tied to nervous system development and signaling pathways, notably Roundabout signaling (axon guidance) and Smoothened signaling, alongside related processes like cell polarity and neuronal survival. While there is a noisy signal from T cell receptor signaling, the strongest themes center on neural development and axon guidance, with supporting roles for trafficking and polarity.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":3},{"id":"GO:0035385","count":3},{"id":"GO:0006893","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0000747","count":2}]},{"hash":"1494685873582688890","title":"Unknown","description":"The GO terms are heterogeneous, spanning ubiquitin/proteasome regulation (ubiquitinase activity, SCF complex), secretory pathway processes (ER polarization, Golgi retention), and other unrelated functions (transcription elongation, DNA damage tolerance, transformation competence). There isn\u2019t a single cohesive theme tying all terms together, so a precise label isn\u2019t justifiable.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903007","count":2},{"id":"GO:0061166","count":2},{"id":"GO:1903715","count":2},{"id":"GO:1990171","count":2},{"id":"GO:0032968","count":2}]},{"hash":"1900459810271137589","title":"Unknown","description":"The terms are a mix of nucleotide/nucleoside metabolism (uracil salvage, nucleoside metabolic process, xanthine metabolic process) and nervous system development/ neurotransmitter related processes (CNS neuron development, striatum development, dopamine metabolic process), along with a few immune/metabolic signals. With no edges and no clear single function tying all proteins together, there isn\u2019t a cohesive theme to label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006223","count":2},{"id":"GO:0021954","count":1},{"id":"GO:0045982","count":1},{"id":"GO:0032869","count":1},{"id":"GO:0046651","count":1}]},{"hash":"246991517355118282","title":"Nuclear RNA Processing and Chromatin Regulation","description":"This set centers on nuclear RNA processing (mRNA splicing via spliceosome, tRNA processing, P-body guidance) and chromatin-related functions (histone mRNA metabolism, pericentric heterochromatin formation, import into nucleus), suggesting a shared theme of RNA metabolism linked to chromatin maintenance. A few terms like apoptotic process and T cell differentiation appear peripheral to the main theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":1},{"id":"GO:0033081","count":1},{"id":"GO:0009414","count":1},{"id":"GO:1990141","count":1},{"id":"GO:0051170","count":1}]},{"hash":"2059051433663164680","title":"DNA Replication and Repair","description":"The GO terms are dominated by DNA replication and repair processes, including leading/lagging strand elongation, premeiotic replication, mitotic lagging strand elongation, nucleotide-excision repair, proofreading, and translesion synthesis, plus gene conversion. This points to a genome-maintenance function for the cluster, with only one lipid catabolic term likely representing noise.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016042","count":2},{"id":"GO:0006272","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0035822","count":1},{"id":"GO:0006297","count":1}]},{"hash":"2255091683841862617","title":"Unknown","description":"The top terms are a mix of RNA and protein methylation (several methylation-related GO terms) plus transcription regulation and disparate processes like immune response and metabolism, with no clear single pathway or function tying them together, and the cluster has no edges. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010197","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0018012","count":2},{"id":"GO:0070555","count":2},{"id":"GO:0002347","count":2}]},{"hash":"1015018462575862619","title":"Mitochondrial Metabolite Transport","description":"The cluster centers on transport of various metabolites into or out of mitochondria (manganese, alpha-ketoglutarate, NAD, magnesium, pyrimidine nucleotides) and includes energy-metabolism related terms (insulin response, adaptive thermogenesis). This points to a cohesive theme of mitochondrial transport and energy regulation, despite a few broader/outdated terms. ","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0035352","count":2},{"id":"GO:1990616","count":2},{"id":"GO:1990519","count":2}]},{"hash":"944589925208236020","title":"Mitochondrial transport and dynamics","description":"The terms converge on mitochondria, including membrane fission and cytochrome c release, and a variety of metabolite/ion transports across mitochondrial membranes, with secondary associations to insulin signaling and adaptive thermogenesis. This suggests a cohesive theme of mitochondrial metabolism, dynamics, and signaling.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090149","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0001836","count":2},{"id":"GO:0006828","count":1},{"id":"GO:0015742","count":1}]},{"hash":"1649105285243497791","title":"DNA Repair and Genome Maintenance","description":"The top GO terms center on nucleotide-excision repair, DNA repair, DNA replication, telomere maintenance via recombination, and regulation of double-strand break repair, indicating a cohesive role in genome integrity and damage response; transcription-related terms seem ancillary. Overall, the cluster is best described by DNA repair and genome maintenance functions.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0031571","count":2},{"id":"GO:0006360","count":1}]},{"hash":"452379730197941653","title":"APC-Dependent Mitosis and Ubiquitination","description":"The top terms point to cell division and mitotic control, including anaphase-promoting complex-dependent catabolic process, mitotic cell cycle, and protein ubiquitination (K11-linked), indicating these proteins are tied to ubiquitin-mediated regulation of mitosis via APC-driven proteolysis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2001162","count":2}]},{"hash":"1104432536324254495","title":"Endosome-to-lysosome Transport","description":"Most of the top GO terms point to intracellular trafficking of vesicles between endosomes and lysosomes and related localization to vesicular membranes, including early-to-late endosome transport and endosome-to-lysosome routes. While a few terms touch on cytoskeletal regulation and nuclear processes, the dominant theme is endosomal/vesicular transport, suggesting the cluster represents endosome-lysosome trafficking machinery.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0008333","count":2}]},{"hash":"697291833430327839","title":"Amino acid import across plasma membrane","description":"The cluster\u2019s terms overwhelmingly point to transport of amino acids across the plasma membrane (L-lysine, methionine, arginine, ornithine, and D- forms), suggesting a shared function in amino acid import. A few related terms (nitric oxide production, neuron apoptotic regulation, sodium transport) may reflect broader regulatory roles, but the dominant signal is amino acid import activity.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0097639","count":1},{"id":"GO:0044690","count":1},{"id":"GO:0006527","count":1},{"id":"GO:0002537","count":1},{"id":"GO:0042941","count":1}]},{"hash":"1670829734456280962","title":"Translation-Linked Stress Signaling","description":"Based on the data, translation (GO:0006412) is the most represented term, suggesting components of the translation machinery. The presence of multiple signaling and stress-related terms (ER stress-induced apoptotic signaling, interferon production, STAT phosphorylation regulation, ubiquitin sorting, insulin signaling, macrophage differentiation) indicates the cluster may comprise proteins that link translation to cellular stress and immune signaling rather than a single cohesive pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045650","count":1},{"id":"GO:1902741","count":1},{"id":"GO:1902237","count":1},{"id":"GO:0018192","count":1}]},{"hash":"2265581786327824381","title":"Metabolic Pathways with Nutrient Stress","description":"The GO terms cluster around glycolysis and several catabolic processes (glycolytic, L-alanine, propylene, oxaloacetate, retinol) and other metabolic activities, with additional terms for nutrient- and hypoxia-related responses. This suggests a metabolic emphasis with adaptive regulatory responses to environmental conditions rather than a single, specific pathway, hence a label capturing both metabolism and nutrient-stress regulation.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006096","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0042208","count":2}]},{"hash":"560022211714734111","title":"Amino acid and porphyrin biosynthesis","description":"The top terms are dominated by biosynthetic processes for several amino acids (beta-alanine, proline, ectoine) and a porphyrin biosynthetic step, indicating the proteins in this cluster are mainly involved in amino acid metabolism and related metabolite production. A couple of terms like cell wall organization and flooding response are present but less central to the cluster\u2019s core theme.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0019878","count":1},{"id":"GO:0006593","count":1},{"id":"GO:0009413","count":1},{"id":"GO:0019483","count":1}]},{"hash":"753343707289803584","title":"Metabolic and Environmental Stress Response","description":"This cluster mixes metabolic processes (aerobic respiration, cholesterol and triglyceride metabolism) with diverse stimulus-response terms (response to lead ion, ethanol, insulin, UV protection), suggesting proteins involved in metabolism that also participate in environmental responses. The pattern is broad but centers on metabolism coupled with responsiveness to external cues, justifying a label that captures both aspects.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":3},{"id":"GO:0008203","count":3},{"id":"GO:0010288","count":3},{"id":"GO:0051781","count":3},{"id":"GO:0007568","count":3}]},{"hash":"1143797365944029197","title":"Fungal Cell Wall Biogenesis and Growth","description":"The top GO terms cluster around fungal-type cell wall biogenesis/assembly, ascospore wall biosynthesis, beta-glucan formation, and related filamentous growth and budding processes, pointing to a shared role in constructing and remodeling fungal cell walls during growth and sporulation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030447","count":2},{"id":"GO:0009272","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0051692","count":1},{"id":"GO:0000917","count":1}]},{"hash":"17691947682217822","title":"Spliceosome-driven mRNA processing","description":"The GO terms cluster around spliceosome-mediated mRNA splicing and its regulation (cis and alternative splicing), plus associated post-transcriptional controls such as mRNA stability, poly(A) tail regulation, and translational initiation. Together these suggest a shared function in post-transcriptional gene regulation centered on RNA processing rather than transcriptional control.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0060211","count":1}]},{"hash":"417515352541000208","title":"Mitochondrial Metabolite Transporters","description":"The top GO terms point to transport of diverse metabolites across the mitochondrial membranes (manganese, alpha-ketoglutarate, NAD, magnesium, pyrimidine nucleotides), which is characteristic of mitochondrial carrier proteins that shuttle metabolites into and out of the organelle. Some terms also touch on metabolic regulation (insulin response, adaptive thermogenesis), supporting a broader energy-metabolism context. Overall, these proteins likely belong to mitochondrial metabolite transporters rather than a signaling pathway cluster.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0035352","count":4},{"id":"GO:1990616","count":4},{"id":"GO:1990519","count":4}]},{"hash":"1155154180134187559","title":"Unknown","description":"The top GO terms are spread across chromatin assembly, miRNA processing, dephosphorylation, photoreceptor recovery, mRNA transport, protein localization, endocytic recycling, and apoptosis, with no single shared function or pathway linking the proteins; there are no edges or cohesive interactions to define a common role.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":2},{"id":"GO:1903799","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0036368","count":1},{"id":"GO:0010800","count":1}]},{"hash":"304892690618435080","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0019878","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0006531","count":1},{"id":"GO:0009097","count":1}]},{"hash":"865179533646125701","title":"Metabolic Transcriptional Regulation","description":"This cluster\u2019s terms predominantly describe regulation of transcription from RNA polymerase II by metabolic signals (e.g., oleic acid, carbon source) and link to biosynthetic pathways (amino acids, nucleotides, sterols) and respiration, indicating a common theme of transcriptional control of metabolism (likely in yeast).","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0061429","count":4},{"id":"GO:0061415","count":4},{"id":"GO:0035961","count":4},{"id":"GO:2001196","count":4},{"id":"GO:0043457","count":4}]},{"hash":"2228378838281563437","title":"Ubiquitin-mediated regulation of apoptosis","description":"The cluster\u2019s top GO terms center on ubiquitination (autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent catabolic processes) and apoptosis regulation (apoptotic processes, regulation of neuron apoptosis), with additional links to JNK signaling and transcriptional regulation. This suggests a cohesive theme around ubiquitin signaling governing cell fate and stress responses, despite some developmental terms present. Therefore, a label focusing on ubiquitin pathways and apoptosis best summarizes the cluster.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060669","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0046328","count":2}]},{"hash":"1908067282257537125","title":"Nuclear gene expression regulation and differentiation","description":"The top GO terms point to a mix of nuclear-level processes (transcription-coupled repair, RNA processing, chromatin regulation, RNA Pol II tethering) and differentiation/cell-cycle related events (stem cell differentiation, Meiosis I, G2/M regulation). While the terms span multiple specific functions, they collectively reflect regulation of gene expression at the nuclear level and cues for cell fate decisions, rather than a single narrow pathway. Confidence: Medium","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006283","count":1},{"id":"GO:0090054","count":1},{"id":"GO:0001732","count":1},{"id":"GO:0000973","count":1},{"id":"GO:0008283","count":1}]},{"hash":"904048179177852535","title":"Phosphate Transport and Regulation","description":"This cluster\u2019s strongest signals are phosphate ion transport and its regulation, pointing to proteins that move phosphate across membranes and control this process. The single term for protein maturation is less directly linked, so the main theme remains phosphate handling rather than a unified maturation function. Given the small size and lack of interactions, the label reflects the dominant function with moderate confidence.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":1},{"id":"GO:2000185","count":1},{"id":"GO:0051604","count":1}]},{"hash":"1122483342962316326","title":"Neural development and GABAergic signaling","description":"The top GO terms point to neural development (midbrain dopaminergic neuron differentiation, neural fold elevation formation) and synaptic function (GABAergic transmission), suggesting a cluster tied to neuronal differentiation and inhibitory signaling. Several other terms appear unrelated (xenobiotic response, telomerase assembly, heterocyst development) and may reflect annotation noise, but the core pattern supports a neuronal development and signaling theme.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0048532","count":1},{"id":"GO:1904948","count":1},{"id":"GO:1901389","count":1},{"id":"GO:0043158","count":1}]},{"hash":"2062094458287586696","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006526","count":1},{"id":"GO:0070365","count":1}]},{"hash":"1275180802497167892","title":"Peroxisomal photorespiration and lipid metabolism","description":"The top GO terms cluster around photorespiration, oxidative photosynthetic carbon metabolism, glycolate catabolism, and fatty acid alpha-oxidation, all of which are linked to peroxisomal metabolism and related lipid/terpenoid pathways in plants. The presence of isoprenoid biosynthetic process supports broader plastid/peroxisome-associated metabolism. One insulin-response term is likely incidental. Overall, the theme is peroxisomal processing of photorespiratory and lipid-related pathways.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009854","count":2},{"id":"GO:0009853","count":2},{"id":"GO:0046296","count":2},{"id":"GO:0001561","count":2},{"id":"GO:0008299","count":2}]},{"hash":"774623805711492383","title":"Unknown","description":"The top GO terms are heterogeneous, spanning central metabolism (gluconeogenesis, glycolysis, amino acid catabolism) as well as development and cellular processes (pituitary development, muscle regeneration, splicing, vacuole fusion), with no clear single unifying function for all proteins. This makes it difficult to assign a coherent, specific label to the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":1},{"id":"GO:0032889","count":1},{"id":"GO:0043403","count":1},{"id":"GO:0061621","count":1},{"id":"GO:0009405","count":1}]},{"hash":"96267880285184687","title":"Nuclear import and transcription regulation","description":"This cluster is characterized by GO terms tied to nuclear processes: DNA-templated transcription, import into nucleus, and negative regulation of protein export from nucleus, suggesting a common theme in nuclear transport and gene expression. Some terms (potassium ion transport, dendrite morphogenesis, lymphocyte proliferation, fatty acid biosynthetic process) appear peripheral or noisy; overall, the label reflects the strongest shared function.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0006351","count":2}]},{"hash":"615008469907977838","title":"Telomere maintenance and DNA replication","description":"GO terms cluster around DNA replication and telomere-related processes (telomere capping and localization), suggesting a role in genome maintenance. Some terms (translation-related and obsolete ones) may be annotation noise, but the dominant theme ties to nucleic acid metabolism and chromosome end protection.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0006430","count":1},{"id":"GO:0006260","count":1}]},{"hash":"2006927834376475715","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0006541","count":1},{"id":"GO:0008614","count":1},{"id":"GO:0000304","count":1},{"id":"GO:0042823","count":1}]},{"hash":"347573978691783727","title":"Embryonic organogenesis","description":"The top GO terms point to multiple developmental processes across embryonic tissues\u2014kidney structures (mesonephric duct, metanephric components), cartilage condensation, placenta formation, lymph vessel morphogenesis, and sensory hair cell differentiation\u2014suggesting a broad theme of organogenesis rather than a single molecular function.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031659","count":1},{"id":"GO:0072177","count":1},{"id":"GO:0072205","count":1},{"id":"GO:0048903","count":1},{"id":"GO:0033319","count":1}]},{"hash":"1150925048653065726","title":"Unknown","description":"The GO terms are highly diverse, spanning neuronal apoptosis, ion transport, mitochondrial depolarization, cell polarity, development, muscle migration, lipoprotein assembly, lymphocyte aggregation, and unrelated cell-wall processes, with no clear shared function tying the proteins together.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043524","count":1},{"id":"GO:1902307","count":1},{"id":"GO:0051900","count":1},{"id":"GO:0035088","count":1},{"id":"GO:0021861","count":1}]},{"hash":"2022294690574222490","title":"Virus-modulated host signaling and lipid metabolism","description":"The GO terms cluster around host signaling pathways (Rho signaling, JNK cascade, NF-kappaB signaling) and lipid biosynthesis (fatty acid elongation, very long-chain fatty acid biosynthesis, sphingolipid biosynthesis). A couple terms point to viral modulation of host processes, suggesting the proteins participate in virus-host interactions; a few outliers (cementum mineralization, G1/S transition) are less connected but do not override the core theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":1},{"id":"GO:0030497","count":1},{"id":"GO:0007254","count":1},{"id":"GO:0045070","count":1},{"id":"GO:0042761","count":1}]},{"hash":"1733975368696787184","title":"Transmembrane Transport of Small Molecules","description":"The top GO terms are dominated by various transmembrane transport processes (nitrite, D-xylose, fructose, vitamin, and xenobiotic transport), with osmotic stress and nitrate assimilation also present. This suggests the proteins in this cluster function broadly as transporters for small molecules across membranes. The lack of edges and the small cluster size means the evidence is modest, so a cautious Medium confidence.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":1},{"id":"GO:0015753","count":1},{"id":"GO:1990539","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0042908","count":1}]},{"hash":"325532510954706290","title":"Unknown","description":"The terms are highly diverse, spanning insect cuticle pigmentation, stress response transcription regulation, several differentiation and developmental processes across different organisms, and several obsolete GO terms. There isn\u2019t a clear, shared biological theme tying these proteins together, so a cohesive label cannot be determined.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048085","count":2},{"id":"GO:0006990","count":1},{"id":"GO:0032915","count":1},{"id":"GO:1903694","count":1},{"id":"GO:2000693","count":1}]},{"hash":"1337225945115023735","title":"Actin-driven cytoskeleton remodeling and cell migration","description":"The proteins\u2019 GO terms cluster around actin cytoskeleton dynamics: phagocytosis, actin cortical patch localization, contractile ring/muscle filament assembly, and mesenchyme migration, pointing to actin filament organization and actin-based cellular movement. This suggests a cohesive theme of actin remodeling and cell motility, with some related processes like endocytosis regulation tying in. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":3},{"id":"GO:0006909","count":3},{"id":"GO:0051666","count":3},{"id":"GO:0030240","count":3},{"id":"GO:1903475","count":3}]},{"hash":"603507828390975064","title":"Unknown","description":"The terms span telomere maintenance and cell-cycle\u2013related regulation, temperature sensing, muscle and epithelial biology, hormone secretion, and immune signaling, with no single dominant function tying the proteins together. With only 3 proteins and 2 edges, there isn\u2019t a cohesive shared pathway to define a meaningful label.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904908","count":2},{"id":"GO:0050960","count":2},{"id":"GO:0035508","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0043403","count":2}]},{"hash":"499499955013763605","title":"Unknown","description":"The GO terms are highly diverse with no single dominant function or pathway linking the proteins; they span stress responses, metal/ion responses, and various metabolic processes, making a coherent label unlikely.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":1},{"id":"GO:0050665","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0010269","count":1},{"id":"GO:0009688","count":1}]},{"hash":"1199539338411216614","title":"Neuronal synaptic vesicle cycling and calcium signaling","description":"These proteins show a coherent pattern around neuronal communication: synaptic vesicle budding and endocytic recycling, regulation of calcium channel activity, and ephrin signaling\u2014all key aspects of synaptic vesicle cycling and calcium-dependent signaling in neurons. The auditory sensory term is related context, but the dominant theme is neural synaptic function, with some broader cellular processes (apoptosis, mitochondrial organization) that may reflect general cellular roles. Overall, a medium level of confidence that this label captures the cluster's core function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0006915","count":2},{"id":"GO:1900756","count":1},{"id":"GO:0007006","count":1},{"id":"GO:0016185","count":1}]},{"hash":"1547218009803122250","title":"Unknown","description":"Top terms across the cluster are a mix of podocyte development, ERAD, membrane raft localization, T cell polarity, proteolysis regulation, mitochondrial fusion/inner membrane organization, PKC signaling, and TLR3 signaling, with only single-term representations and no shared functional thread. There isn\u2019t a cohesive, interpretable theme binding these terms for a concise label, given the disparate biological processes involved. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072249","count":1},{"id":"GO:0030433","count":1},{"id":"GO:1903044","count":1},{"id":"GO:1903905","count":1},{"id":"GO:0045861","count":1}]},{"hash":"2294821392850035249","title":"B Cell Activation and Cytokine Production","description":"The top GO terms are dominated by B cell\u2013specific immune functions: cytokine production by B cells, isotype switching to IgG, and regulation of inflammatory responses including IL-6 production. Although a few unrelated terms appear, the prevailing signal centers on B cell activation and antibody-related cytokine activity, justifying this label.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002368","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0048291","count":3},{"id":"GO:0050729","count":3},{"id":"GO:2000778","count":3}]},{"hash":"1059204885680556459","title":"Neuronal development and neurotransmitter metabolism","description":"This cluster centers on neural processes: neuron projection development, neurotransmitter biosynthesis (GABA) and amino acid catabolism (glutamate), calcium signaling, and memory, suggesting involvement in neuronal signaling and neurotransmitter metabolism. Some terms like circadian rhythm and pigmentation are less specific, but the dominant theme is neural function.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0042136","count":1},{"id":"GO:0007623","count":1},{"id":"GO:0009449","count":1},{"id":"GO:0048085","count":1}]},{"hash":"1953560703315954148","title":"Unknown","description":"The top GO terms are highly diverse and include regulatory processes (negative regulation of miRNA processing; negative regulation of EMT; negative regulation of DNA damage checkpoint) alongside unrelated or disparate functions (lipid A biosynthetic process; meiotic checkpoint signaling; lung epithelial differentiation; AMP catabolic process; glucocorticoid signaling). The lack of a clear, shared biological theme across the three proteins suggests there is no coherent common function to name, so the cluster is best labeled Unknown. ","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1903799","count":3},{"id":"GO:0070940","count":3},{"id":"GO:0009245","count":3},{"id":"GO:1905213","count":3},{"id":"GO:0010719","count":3}]},{"hash":"368643660198865516","title":"ER-Golgi trafficking and calcium signaling","description":"The top GO terms cluster around intracellular vesicle transport from the ER to the Golgi and calcium regulation within organelles, pointing to a shared function in organelle trafficking and Ca2+ homeostasis. While vascular morphogenesis and cell division terms appear, the strongest signal is ER-Golgi transport with associated calcium release control, suggesting this cluster centers on intracellular trafficking and calcium signaling. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0009636","count":1},{"id":"GO:0001886","count":1},{"id":"GO:0010880","count":1}]},{"hash":"1655594022477258225","title":"Broad Metabolic Pathways and Mitochondrial Translation","description":"The terms are dominated by varied catabolic processes across different substrates (carbohydrates, lipids, nucleotides, and amino acids) and include mitochondrial translation, plus a few ancillary aspects of cell metabolism (ER organization, amino acid biosynthesis). This suggests a broad metabolic cluster rather than a single specific pathway, with a notable but secondary link to mitochondrial protein synthesis.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019876","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0009062","count":1},{"id":"GO:0070681","count":1},{"id":"GO:0007029","count":1}]},{"hash":"1251229841525947791","title":"Unknown","description":"The three top GO terms point to disparate processes (ion transport, water homeostasis, and riboflavin biosynthesis) with no clear shared function. With no edges or cohesive signaling among the proteins, there isn\u2019t a single representative theme to name the cluster beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034220","count":1},{"id":"GO:0009992","count":1},{"id":"GO:0009231","count":1}]},{"hash":"636693796524420002","title":"Gluconeogenesis and glycolysis regulation","description":"This cluster is dominated by GO terms related to gluconeogenesis and its regulation, plus adjacent carbohydrate metabolism and glycolytic regulation (e.g., fructose-6-phosphate and fructose-1,6-bisphosphate pathways). While there are a few broader terms (dephosphorylation, xenobiotic response), the core theme is control of glucose production and glycolytic flux.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":1},{"id":"GO:0030388","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0030308","count":1},{"id":"GO:0051289","count":1}]},{"hash":"1824056810480656902","title":"DNA Repair and Genome Maintenance","description":"The dominant GO terms point to DNA damage response and genome maintenance, including nucleotide-excision repair, DNA replication, recombination, and the SOS response. While a couple terms pertain to plant development and host interaction (likely incidental), the core signal across this cluster is genome integrity preservation and DNA repair/replication processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0090305","count":1},{"id":"GO:0009432","count":1},{"id":"GO:0039657","count":1}]}]