[{"hash":"1773877964653157895","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":382,"triangles":3099,"max_degree":28,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1905490","count":12},{"id":"GO:0051301","count":12},{"id":"GO:0043547","count":12},{"id":"GO:1905608","count":12},{"id":"GO:0031291","count":12}]},{"hash":"2297690330061338715","title":"Immunometabolic Regulation and Transcription","description":"This cluster shows a blend of immune-related terms (cellular response to interleukin-4, lymphocyte proliferation) with core metabolic processes (gluconeogenesis, carbohydrate metabolism, serine and homocysteine catabolism, transsulfuration) and transcriptional activity (DNA-templated transcription), plus protein interaction complexity (protein homotetramerization). The dominant theme appears to be proteins involved in coordinating immune signaling with metabolic regulation and transcriptional control, though the retina development term is an outlier in this context. Overall, the label reflects a family of proteins linking immune responses to metabolism and gene regulation.","confidence":"Medium","size":29,"edges":339,"triangles":2267,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071353","count":13},{"id":"GO:0006351","count":10},{"id":"GO:0045722","count":8},{"id":"GO:0051289","count":8},{"id":"GO:0046651","count":8}]},{"hash":"540418590324250001","title":"Neurodevelopment with DNA replication and stress signaling","description":"The cluster prominently features neural development terms (forebrain development, neural tube closure) alongside cell cycle and DNA replication terms (mitotic cell cycle, DNA replication, DNA-templated transcription) and stress-associated pathways (ER stress\u2013related apoptotic signaling, DNA damage response). This mix suggests proteins functioning in neural development that are coupled to genome maintenance and cellular stress responses during proliferation, rather than a single discrete function. Confidence: Medium","confidence":"","size":29,"edges":396,"triangles":3402,"max_degree":28,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0006260","count":8},{"id":"GO:0030900","count":7},{"id":"GO:0009636","count":7},{"id":"GO:0001843","count":7}]},{"hash":"1635954286376945188","title":"Fatty acid biosynthesis and transport","description":"The top GO terms are dominated by fatty acid metabolism and lipid biosynthesis, including medium-, long-, and very long-chain fatty acids, fatty acid transport/import, and lipoteichoic acid and menaquinone biosynthesis. This points to a cohesive cluster centered on lipid metabolism, with a few peripheral terms (seed coat development, nonribosomal peptide activation) that are less central to the core theme. ","confidence":"High","size":29,"edges":313,"triangles":2146,"max_degree":27,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0036112","count":10},{"id":"GO:0070395","count":10},{"id":"GO:0010214","count":10},{"id":"GO:0044539","count":10},{"id":"GO:0006633","count":10}]},{"hash":"2183579219898955584","title":"Metal Ion Transport and Detoxification","description":"This cluster is dominated by metal ion transport and detoxification terms (cadmium, mercury, copper, zinc) plus mercury detox and copper homeostasis, indicating a shared function in metal ion handling; the ER-to-Golgi transport terms suggest a trafficking context that may coordinate metal ion management with secretory pathway processes.","confidence":"High","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0070574","count":4},{"id":"GO:0046689","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0050787","count":3}]},{"hash":"259596396047599025","title":"Unknown","description":"The GO terms are a mosaic of metabolism, transcription, RNA processing, and ER/chaperone-related activities, with no single unifying function across the cluster and no edges to tie them together, so a specific label isn't justifiable.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0034975","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0006564","count":2}]},{"hash":"2180341168997680402","title":"Plastid heme/chlorophyll biosynthesis and gene expression","description":"The terms cluster around plastid-associated pathways: heme biosynthesis and protoporphyrinogen IX biosynthesis, energy generation via proton-motive force-driven ATP synthesis in the plastid thylakoid membranes, and plastid transcription/translation. This combination strongly suggests a chloroplast-focused module involved in pigment biosynthesis and organelle gene expression.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006783","count":3},{"id":"GO:0099132","count":2},{"id":"GO:0015986","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0006355","count":1}]},{"hash":"2083580555855580969","title":"Chloroplast Translation and Biogenesis","description":"The cluster centers on chloroplast/plastid functions: plastid translation, chloroplast organization, and protein import into chloroplast stroma, plus de-etiolation and fatty acid biosynthesis within plastids. tRNA methylation also occurs in chloroplasts, supporting a plastid-centric theme. A bacterial biosynthetic term likely reflects plastid ancestry or annotation noise, consistent with the endosymbiotic origin of chloroplasts. ","confidence":"High","size":29,"edges":364,"triangles":2696,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0055114","count":2},{"id":"GO:0006633","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0097171","count":2}]},{"hash":"1737357598339677568","title":"ERAD and Ubiquitin-Mediated Protein Quality Control","description":"The cluster is dominated by terms for ERAD and ubiquitination, including protein ubiquitination, deglycosylation, and aggrephagy, pointing to a cohesive module of ER-associated protein quality control and ubiquitin\u2011proteasome\u2013mediated turnover, with some related cell-cycle ubiquitination signaling.","confidence":"High","size":29,"edges":111,"triangles":127,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":8},{"id":"GO:0006517","count":5},{"id":"GO:2000157","count":5},{"id":"GO:0016567","count":5},{"id":"GO:1903094","count":5}]},{"hash":"2077045866155642428","title":"Pseudohyphal growth and mitosis","description":"The top GO terms show strong representation for filamentous/invasive growth under nutrient limitation (invasive growth in response to glucose limitation and pseudohyphal growth) together with cell cycle processes (cell division, mitotic cell cycle). While a few other terms (retina development, visual perception) appear, they are low in frequency and likely noise. Overall, the cluster appears to group proteins involved in nutrient-responsive filamentous growth and cell division, justifying a label focused on growth form and cell cycle.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001403","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0007124","count":3}]},{"hash":"1332612300227305521","title":"DNA Replication and Repair","description":"The top GO terms are dominated by DNA metabolism: DNA replication (GO:0006260, GO:0006261), DNA repair (GO:0006281), and DNA recombination (GO:0006310). While there are plant cell wall and glycosylation terms present (GO:0071555, GO:0009834, GO:0016266), these likely reflect multifunctional or co-expressed proteins with secondary annotations rather than a primary cell wall-focused function. Thus, the cluster most coherently maps to genome maintenance processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071555","count":6},{"id":"GO:0006281","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0009834","count":4},{"id":"GO:0016266","count":4}]},{"hash":"1748111018629239414","title":"Plant seed development and hormone-regulated transcription","description":"This cluster is dominated by DNA-templated transcription and its regulation, with seed development as a prominent process, and includes ABA- and ethylene-activated signaling terms plus defense-related responses, suggesting coordinated transcriptional control of developmental programs and hormone-mediated signaling in plants. The ER-to-Golgi transport term may reflect general cellular logistics linked to secretion during development.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0048316","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0060982","count":3}]},{"hash":"478426665289651562","title":"Neurodevelopment and ER-stress\u2013induced apoptosis","description":"The Top Terms are dominated by nervous system development and related processes (nervous system development, forebrain development, neural tube closure, neuron cellular homeostasis), with additional signals for innate immune defense and ER-stress\u2013triggered apoptotic signaling. This suggests proteins in the cluster are centered on neural development while also engaging cellular stress responses and apoptosis pathways, hence a neural-development\u2013centric cluster with ER-stress\u2013associated signaling.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007399","count":14},{"id":"GO:0051260","count":14},{"id":"GO:0070050","count":13},{"id":"GO:0045087","count":12},{"id":"GO:0051607","count":12}]},{"hash":"1746882345686880888","title":"Sterol biosynthesis and lipid metabolism","description":"The top GO terms cluster around sterol biosynthesis (ergosterol and cholesterol pathways, sterol oxidation steps) and general lipid metabolism (fatty acid, ether lipid, ceramide-related lipid processes), suggesting the proteins share a sterol/lipid biosynthetic function. A few terms (photosynthesis, B cell chemotaxis, CNS myelin maintenance) seem incidental or broader annotations.","confidence":"Medium","size":29,"edges":5,"triangles":1,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0033490","count":3},{"id":"GO:0006696","count":3},{"id":"GO:0080065","count":3},{"id":"GO:0035754","count":3}]},{"hash":"297784713522505709","title":"Neural Synaptic Signaling and Behavior Regulators","description":"The top GO terms point to synaptic function and neural signaling: vocalization and grooming behaviors, GABA secretion, receptor localization to the synapse, and voltage-gated calcium channel complex assembly, all of which are core to neuronal communication. Additional terms like regulation of potassium import and negative regulation of p38/MAPK and JNK cascades further support signaling activity in neurons. The presence of these behavior- and synapse-related terms suggests the proteins cluster around synaptic transmission and neuronal behavior regulation, with a minor metabolic term (PRPP biosynthesis) likely incidental. Overall, the label captures the predominant theme. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0071625","count":5},{"id":"GO:0046328","count":5},{"id":"GO:0014051","count":4},{"id":"GO:0006015","count":4},{"id":"GO:0070978","count":4}]},{"hash":"2210490256721431892","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms around ribosome assembly and function (ribosome biogenesis, ribosomal subunit biogenesis, ribosomal large subunit export from nucleus, cytoplasmic translation), suggesting a cohesive theme of ribosome production and protein synthesis, with cell cycle/division annotations reflecting growth coordination. Minor terms like response to mercury and conjugation appear less representative. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0046689","count":3},{"id":"GO:0090529","count":3},{"id":"GO:0002181","count":3}]},{"hash":"832398731862376779","title":"Type I Interferon Response","description":"The cluster is strongly enriched for interferon-associated and innate antiviral functions: cellular response to type I interferon, cellular response to dsRNA, and innate immune response, plus a response to unfolded protein that can accompany viral infection. These together point to a coherent theme of antiviral defense driven by interferon signaling. Some unrelated GO terms (e.g., gibberellin signaling, prostate development) appear as noise but do not override the main antiviral theme.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071357","count":21},{"id":"GO:0051301","count":19},{"id":"GO:0071360","count":18},{"id":"GO:0045087","count":18},{"id":"GO:0006986","count":18}]},{"hash":"1474547335394229557","title":"Glycan biosynthesis and ECM components","description":"Most top GO terms are about biosynthesis of glycans and extracellular matrix components (xyloglucan/xylogalacturonan/ fucose/ heparan sulfate proteoglycans). Several terms also connect matrix biology to development signaling (BMP signaling, embryonic morphogenesis, skeletal/joint development), suggesting the cluster centers on glycan production and ECM involvement in signaling. This theme coherently links the varied terms better than any single pathway. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009863","count":12},{"id":"GO:0042353","count":12},{"id":"GO:0008101","count":12},{"id":"GO:0009834","count":12},{"id":"GO:0035118","count":12}]},{"hash":"1155489896156446523","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by ribosome biogenesis (GO:0042254, GO:0042273), translation initiation (GO:0001731), translation reinitiation (GO:0002188), and rRNA processing (GO:0000447). This points to proteins involved in assembling ribosomes and initiating protein synthesis, with related rRNA processing. A few terms for vesicle trafficking or signaling are secondary and less representative of the cluster's main function.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0006888","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5}]},{"hash":"1510579957700275998","title":"Unknown","description":"The top GO terms span nuclear transcription (DNA-templated transcription and its regulation) and several membrane transport processes (chloride and basic amino acid transport) plus swim bladder inflation; the proteins show no single cohesive function, and the cluster appears heterogeneous, with no shared pathway tying them together. Therefore a specific label is not reliable.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0045795","count":2},{"id":"GO:0030644","count":2},{"id":"GO:0097638","count":2}]},{"hash":"1684897406775715772","title":"Unknown","description":"The terms are a mix of membrane proteolysis, nucleoside/nucleotide transport, and various developmental or signaling processes with no single cohesive function linking the cluster. This suggests the proteins represent diverse, unrelated roles rather than a unified biological function.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034435","count":2},{"id":"GO:0015862","count":2},{"id":"GO:0035364","count":2},{"id":"GO:0006509","count":2},{"id":"GO:0031293","count":2}]},{"hash":"1862062867076997810","title":"Plant vesicle trafficking and Rac signaling","description":"GO terms cluster around vesicle transport (Golgi to vacuole, docking, fusion) and small GTPase signaling (Rac) with related roles in sugar transport and development, suggesting a group of vesicle trafficking regulators in plants.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035020","count":2},{"id":"GO:0048354","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0006904","count":2},{"id":"GO:0048280","count":2}]},{"hash":"953993605288119502","title":"Developmental Gene Expression and DNA Maintenance","description":"These proteins show strong ties to developmental processes (neural tube closure, forebrain development, multicellular organism development), suggesting roles in vertebrate development. They also cluster around core nuclear activities\u2014DNA-templated transcription and DNA repair\u2014and regulation of gene expression (imprinting). The presence of an ER-stress\u2013related apoptotic signaling term and a cellular cadmium response indicates context of cellular stress affecting development and genome integrity. Overall, the cluster appears to represent developmental gene regulation linked to genome maintenance, with some stress-response connections.","confidence":"Medium","size":28,"edges":40,"triangles":17,"max_degree":11,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0001843","count":27},{"id":"GO:0070059","count":27},{"id":"GO:0006351","count":27},{"id":"GO:0006281","count":27},{"id":"GO:0006349","count":27}]},{"hash":"984683929942690732","title":"Cytokinesis, Cytoskeleton, and Golgi-ER Transport","description":"The cluster is dominated by processes tied to cell division and cytokinesis (cell division, septum digestion after cytokinesis) and is reinforced by cytoskeletal regulation (actin filament capping, GTPase activity) and membrane trafficking between the ER and Golgi, which are essential for successful cytokinesis and vesicle dynamics. Some GO terms (nutrient response, pigmentation, TGF-beta signaling) appear peripheral but may reflect broader cellular remodeling accompanying division. Overall, the theme centers on division-associated cytoskeletal dynamics and intracellular transport.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0007584","count":5},{"id":"GO:0050731","count":5},{"id":"GO:0051016","count":5},{"id":"GO:0043547","count":5}]},{"hash":"2057863631429776820","title":"Plant hormone biosynthesis and fruit ripening","description":"The GO terms are dominated by plant-specific biosynthetic processes such as gibberellin and ethylene biosynthesis, gibberellin catabolic process, fruit ripening, and proanthocyanidin biosynthesis, with hydrogen peroxide\u2013mediated stress responses supporting a developmental/stress-related theme in plants. Some outlier terms (lipopolysaccharide and penicillin biosynthesis) may reflect cross-annotation noise, but the core signal points to plant hormone production and related metabolite synthesis.","confidence":"Medium","size":28,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":14},{"id":"GO:1902987","count":8},{"id":"GO:0009103","count":7},{"id":"GO:0010421","count":7},{"id":"GO:0010023","count":7}]},{"hash":"310140647166064874","title":"Innate Immune Response and Interferon Signaling","description":"Top GO terms are dominated by innate immune and antiviral responses (defense against Gram-positive bacteria, response to exogenous dsRNA, LPS signaling, innate immune response, and interferon-beta production), suggesting this cluster centers on innate immune signaling and antiviral defense. A couple of neural development terms appear less connected to the core theme, potentially reflecting annotation pleiotropy. Overall, this label captures the main functional theme.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050830","count":8},{"id":"GO:0043330","count":7},{"id":"GO:0051965","count":7},{"id":"GO:0031663","count":7},{"id":"GO:0022038","count":7}]},{"hash":"1121582848954021535","title":"Potassium Ion Transport and Homeostasis","description":"The top GO terms are dominated by potassium ion handling (intracellular homeostasis, import/export, transmembrane transport), indicating a cluster of proteins involved in potassium transport and regulation. Although a few terms pertain to transcription and development, these likely reflect broader cellular roles of the included proteins. Overall, a concise label emphasizing potassium transport and homeostasis fits best.","confidence":"High","size":28,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030007","count":9},{"id":"GO:0051260","count":8},{"id":"GO:0006351","count":8},{"id":"GO:1990573","count":8},{"id":"GO:0019233","count":8}]},{"hash":"1678022350551017314","title":"mRNA Processing and Translational Control","description":"These terms cluster around post-transcriptional gene expression: mRNA decay via deadenylation, alternative splicing, and multiple facets of translation initiation and reinitiation (including IRES-dependent viral initiation and formation of the preinitiation complex). The proteins are likely involved in RNA maturation and the regulation of translation rather than transcriptional control, reflecting a cohesive theme of post-transcriptional regulation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":5},{"id":"GO:0000380","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0006446","count":4}]},{"hash":"909571713092721976","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":187,"triangles":503,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0000961","count":4},{"id":"GO:0010019","count":4},{"id":"GO:0009451","count":4},{"id":"GO:1905639","count":4}]},{"hash":"483681512504642469","title":"Neuronal synaptic transmission and brain development","description":"The cluster is enriched for brain development and synaptic signaling terms, including regulation of synaptic vesicle exocytosis, neurotransmitter secretion, and short-term synaptic potentiation, suggesting a cohesive role in neuronal communication and maturation. Additional terms on membrane transport and GTPase signaling point to supporting cytoskeletal and membrane dynamics, though one term about mating projection growth appears less aligned. Overall, the dominant theme is neuronal synaptic function and brain development.","confidence":"High","size":28,"edges":5,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0010796","count":9},{"id":"GO:2000300","count":9},{"id":"GO:0007420","count":9},{"id":"GO:0031384","count":9},{"id":"GO:0007269","count":8}]},{"hash":"33018684511916125","title":"Unknown","description":"The terms span diverse biological areas (brain development, plant hormone signaling, lipid catabolism, oxidative stress responses, DNA repair, unfolded protein response), with no clear single function tying the cluster together. This makes it inappropriate to assign a confident, specific label.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0021762","count":5},{"id":"GO:0006685","count":4},{"id":"GO:0042542","count":4},{"id":"GO:2000378","count":4},{"id":"GO:1990414","count":3}]},{"hash":"641864605564578093","title":"Plant-fungal recognition and cell wall remodeling","description":"These proteins show GO terms tied to plant cell wall biosynthesis and modification (xyloglucan metabolism, fungal-type and plant-type cell wall organization), and detection of molecules of fungal origin, suggesting a plant immune sensing and cell wall remodeling axis in response to fungal cues. The photosynthesis and ER\u2013Golgi transport terms add broader cellular context but the dominant pattern centers on plant-fungal interaction and cell wall dynamics.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0051291","count":3},{"id":"GO:0042546","count":3},{"id":"GO:0032491","count":3},{"id":"GO:0006037","count":3}]},{"hash":"504851029744395177","title":"Xenobiotic and Hormone Metabolism","description":"The top GO terms cluster around catabolic and metabolic processing of diverse organic compounds, including multiple xenobiotics (carbazole, coumarin, camphor, retinoic acid) and hormone-related pathways (progesterone metabolism, prostaglandin biosynthesis, aldosterone-regulated processes). This suggests the proteins function broadly in organic compound breakdown and hormone/lipid mediator metabolism rather than a single, narrow pathway. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046232","count":23},{"id":"GO:0001516","count":21},{"id":"GO:0010193","count":20},{"id":"GO:0034653","count":20},{"id":"GO:0035865","count":20}]},{"hash":"537593621735088261","title":"Gene Expression Regulation and RNA Metabolism","description":"The top GO terms cluster around core gene expression processes: cytoplasmic translation, DNA-templated transcription, mRNA decay and polyadenylation, and related regulatory signals (TGF-beta and glucocorticoid responses) plus differentiation control. This suggests the proteins collectively participate in transcriptional and translational regulation and RNA processing, with context-dependent signaling modulating gene expression and cell differentiation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0045647","count":4},{"id":"GO:0046782","count":4}]},{"hash":"2237130239616119269","title":"Developmental transcriptional regulation","description":"The cluster is dominated by GO terms related to DNA-templated transcription and regulation of transcription by RNA polymerase II, along with multiple development-related terms (multicellular organism development, heart development, seed development, cerebellar cortex development) and DNA binding regulation. While there is a plant-specific ABA signaling term, the overarching theme is transcriptional control driving developmental processes across tissues, suggesting a coherent module of developmental gene regulation.","confidence":"High","size":28,"edges":9,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0007275","count":5},{"id":"GO:0009738","count":4},{"id":"GO:0045944","count":3},{"id":"GO:0007507","count":3}]},{"hash":"2113644568187345223","title":"Membrane Transporters","description":"The top GO terms are all transmembrane transport activities for diverse substrates, including nitrate, phosphate, arabinose, sodium, galactose, sialic acid, 4-hydroxyphenylacetate, and xenobiotics, suggesting this cluster comprises membrane transporter proteins with broad substrate uptake and efflux roles.","confidence":"High","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0035435","count":4},{"id":"GO:0015751","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0035725","count":4}]},{"hash":"298502616734876800","title":"Plant hormone signaling and seed cuticle biosynthesis","description":"The cluster centers on plant hormone signaling (ABA and ethylene) and transcriptional regulation, linked to seed development and the regulation of cutin and wax biosynthesis, with a concurrent response to chitin (defense). This combination points to a cohesive plant-specific regulatory module coordinating hormone signaling, transcription, seed development, and cuticle/wax formation; defense responses are also represented, supporting the overall theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0009738","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0009873","count":5},{"id":"GO:0010200","count":5}]},{"hash":"831549978791131492","title":"Immune signaling and differentiation","description":"The top GO terms include strong signals for immune processes (T cell receptor signaling, natural killer cell differentiation) along with related signaling events (JUN phosphorylation) and additional differentiation and cell-cycle related terms (melanocyte and myoblast differentiation, spindle assembly checkpoints). While not exclusively immune, the prominent immune signaling and differentiation themes suggest proteins acting in immune regulation and developmental signaling cross-talk. Therefore the label reflects the dominant functional threads across the cluster.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":28},{"id":"GO:0097324","count":28},{"id":"GO:0009636","count":28},{"id":"GO:1990801","count":28},{"id":"GO:0014835","count":28}]},{"hash":"459676940735418348","title":"Neural development and transcriptional regulation","description":"The top GO terms are dominated by neural development (neural tube closure, forebrain development) and broad multicellular development, with additional emphasis on DNA-templated transcription and regulation of gene expression. This points to a core function in developmental pathways with transcriptional control, particularly in neural tissues, despite some ancillary terms related to stress or immune responses. Confidence: High","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":27},{"id":"GO:0070059","count":27},{"id":"GO:0006351","count":27},{"id":"GO:0006349","count":27},{"id":"GO:0071276","count":27}]},{"hash":"701923993303214256","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"Top terms center on gibberellin and ethylene biosynthesis and fruit ripening, with related hormone signaling and stress responses (salicylic acid catabolic, hydrogen peroxide\u2013mediated PCD). A few annotations point to secondary metabolism (proanthocyanidin biosynthesis) and odd notes like penicillin biosynthesis or obsolete terms, likely annotation noise. Overall, the cluster seems to group proteins involved in plant hormone production and ripening processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":20},{"id":"GO:0010421","count":11},{"id":"GO:0010023","count":11},{"id":"GO:0009686","count":11},{"id":"GO:0009835","count":11}]},{"hash":"1131042790428777116","title":"Proteoglycan biosynthesis and ECM organization","description":"The top GO terms are dominated by proteoglycan biosynthesis (heparan sulfate, chondroitin sulfate, and related proteoglycan processes) and UDP-xylose metabolism, indicating a focus on glycosaminoglycan/proteoglycan assembly. Additional terms like tissue morphogenesis, cell adhesion molecule production, and extracellular matrix-related processes reinforce a theme of extracellular matrix construction and cell\u2013ECM interactions. This cluster seems centered on proteoglycan synthesis and ECM organization rather than intracellular pathways.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":4},{"id":"GO:0015012","count":4},{"id":"GO:0030210","count":4},{"id":"GO:0050650","count":4},{"id":"GO:0071555","count":3}]},{"hash":"633065455146440957","title":"Neuronal Synaptic Plasticity and Calcium Signaling","description":"The top GO terms cluster around neuronal signaling, synaptic modulation, memory, and calcium-dependent processes (regulation of long-term synaptic plasticity; long-term memory; excitatory postsynaptic potential; calcium ion transport and detection). The amphetamine response and sensory touch terms further point to brain-related signaling, while a couple of terms (bone ossification and obsolete oxidation-reduction) appear as noise. Taken together, the cluster most plausibly represents proteins involved in neuronal synaptic plasticity and calcium signaling.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0048169","count":2},{"id":"GO:0001975","count":2},{"id":"GO:0050975","count":2},{"id":"GO:0007616","count":2}]},{"hash":"98121338531252054","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0000961","count":3}]},{"hash":"1374072662171434440","title":"Pyrimidine Nucleotide Salvage","description":"This cluster is dominated by GO terms for pyrimidine salvage and related pyrimidine metabolism (CTP salvage, uracil salvage, UMP and CMP salvage, and general pyrimidine nucleobase metabolism), indicating a cohesive function around recycling pyrimidine nucleotides. Some additional terms (coenzyme A and chorismate/tyrosine biosynthesis) may reflect broader metabolic context or annotation overlap, but the strongest signal centers on pyrimidine salvage pathways.","confidence":"High","size":28,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044211","count":6},{"id":"GO:0006223","count":6},{"id":"GO:0006206","count":6},{"id":"GO:0015937","count":6},{"id":"GO:0044206","count":6}]},{"hash":"1948940215661258628","title":"RNA and protein methyltransferases","description":"The top GO terms cluster around various methylation activities: rRNA methylation, peptidyl-lysine methylation (and dimethyl/trimethyl variants), N-terminal methylation, RNA guanine-N7 methylation and mRNA cap formation, plus tRNA wobble modification and rDNA heterochromatin formation. This pattern points to a group of enzymes that modify both RNAs and proteins and may link RNA processing with chromatin regulation in the rDNA region. A minor association with spermidine biosynthesis is present but less defining. ","confidence":"High","size":27,"edges":89,"triangles":109,"max_degree":23,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0031167","count":13},{"id":"GO:0018027","count":12},{"id":"GO:0000183","count":11},{"id":"GO:0018013","count":10},{"id":"GO:0018023","count":9}]},{"hash":"2086550034481156202","title":"ESCRT-driven MVB trafficking and protein sorting","description":"The cluster\u2019s top GO terms cluster around ESCRT-mediated multivesicular body assembly, ubiquitin-dependent protein sorting via the MVB pathway, and viral budding via host ESCRT complex, indicating a vesicle-trafficking and ubiquitin-proteolysis theme. Some terms like muscle development and B cell signaling appear peripheral, but the dominant signal is ESCRT/MVB\u2013related processes.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0039702","count":3},{"id":"GO:1902188","count":3},{"id":"GO:0036258","count":3},{"id":"GO:0043162","count":3}]},{"hash":"146473871971455225","title":"Photosynthesis Light-Response and Photoprotection","description":"The top GO terms coalesce around photosynthetic activity and light-associated regulation, including photosynthesis, light harvesting in photosystem I, responses to red and far-red light, low/high light intensity, UV-A response, and nonphotochemical quenching. These together point to a coherent functional theme of photosynthesis with photoprotection and pigment-related processes (phytol/chlorophyll linkage), justifying a label centered on photosynthesis and light response.","confidence":"High","size":27,"edges":345,"triangles":2786,"max_degree":26,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":11},{"id":"GO:1904964","count":5},{"id":"GO:0018298","count":5},{"id":"GO:0009768","count":5},{"id":"GO:0010218","count":5}]},{"hash":"803227382682045198","title":"Glycolysis and carbohydrate catabolism","description":"This cluster is enriched for carbohydrate catabolism and energy-producing pathways, including canonical glycolysis, glycolysis from storage polysaccharides, fructose-6-phosphate metabolism, and glycogen catabolism; the presence of cellulose catabolic process also points to broad carbohydrate breakdown. Some terms relate to vacuolar degradation (piecemeal microautophagy of the nucleus, vacuolar protein processing), consistent with cellular turnover accompanying metabolic remodeling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":5},{"id":"GO:0030245","count":5},{"id":"GO:0042136","count":5},{"id":"GO:0046340","count":5},{"id":"GO:0093001","count":4}]},{"hash":"227742507319580473","title":"Ribosome Biogenesis and Translation","description":"The cluster is enriched for translation and ribosome-related processes (GO:0006412; GO:0042254; GO:0042256) along with rRNA processing and maturation (GO:0006364; GO:0000462), indicating a cohesive group of proteins involved in ribosome assembly and protein synthesis, including translational fidelity maintenance; occasional links to stress responses (e.g., antibiotic response) likely reflect broader regulation but do not redefine the core function.","confidence":"High","size":27,"edges":326,"triangles":2396,"max_degree":26,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":26},{"id":"GO:0042254","count":13},{"id":"GO:0046677","count":8},{"id":"GO:0045903","count":7},{"id":"GO:1990145","count":7}]},{"hash":"383268621023113993","title":"Unknown","description":"The terms span circadian rhythm, xenobiotic and alkaloid responses, pigmentation, memory, calcium signaling, and developmental processes across different species, with no clear shared pathway or function linking them.","confidence":"","size":27,"edges":346,"triangles":2801,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007623","count":8},{"id":"GO:0071312","count":8},{"id":"GO:0048085","count":8},{"id":"GO:0042136","count":8},{"id":"GO:0051454","count":8}]},{"hash":"1760707344943205142","title":"RNA processing and gene expression regulation","description":"This cluster is dominated by GO terms related to RNA metabolism and gene expression, including transcription, splicing, mRNA export, polyadenylation, and initiation/recoding of translation. The combination points to coordinated RNA processing and control of protein synthesis, with additional terms hinting at cell fate regulation via apoptosis in neural/glial contexts. ","confidence":"Medium","size":27,"edges":6,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0002188","count":5},{"id":"GO:0000398","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0006378","count":4}]},{"hash":"1508050892506170594","title":"Exocytosis and vesicle trafficking","description":"The top GO terms cluster around exocytosis and Golgi-to-plasma membrane transport, with exocyst localization/assembly and vesicle tethering pointing to exocytic vesicle docking/secretion. Other terms are ancillary but align with secretory pathway regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006887","count":3},{"id":"GO:0006893","count":3},{"id":"GO:0051601","count":3},{"id":"GO:0001927","count":3},{"id":"GO:0090522","count":3}]},{"hash":"1020142735423412195","title":"Detoxification and redox response","description":"The cluster is dominated by oxidative-reduction and detoxification terms (cellular oxidant detoxification, response to toxic substance, oxidative-reduction process), suggesting a shared role in managing oxidative stress and detoxifying reactive compounds. Some secondary metabolism terms appear, but the central theme is redox balance and detoxification.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":16},{"id":"GO:0042619","count":10},{"id":"GO:0009636","count":9},{"id":"GO:0098869","count":9},{"id":"GO:0046272","count":9}]},{"hash":"2269425165552934448","title":"DNA Replication, Transcription, and Protein Turnover","description":"This cluster is dominated by core genome maintenance and protein homeostasis terms: DNA replication (GO:0006260), DNA-templated transcription (GO:0006351), and ubiquitin-dependent protein catabolic process plus proteasome assembly (GO:0006511; GO:0043248). These indicate a common theme of genetic information processing and protein turnover, even though other biosynthetic or developmental terms present are more peripheral. Confidence in this as a representative label is Medium.","confidence":"","size":27,"edges":9,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0043248","count":7},{"id":"GO:0030212","count":7},{"id":"GO:0015995","count":7},{"id":"GO:0006511","count":7}]},{"hash":"343278960062211711","title":"Plant/Fungal Cell Wall Biogenesis and Microbe Detection","description":"The top GO terms point to plant/fungal cell wall synthesis and modification (cell wall biogenesis, fungal-type cell wall organization, xyloglucan metabolism, plant-type wall modification), with accompanying signals for recognizing microbial components (detection of fungal origin, detection of bacterial lipopeptide) and defense-related responses (antibacterial peptide biosynthesis, cytokine signaling). While a few outliers exist, the dominant theme is cell wall-related processes tied to microbe sensing, supporting this label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042546","count":1},{"id":"GO:0032491","count":1},{"id":"GO:0006037","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0009831","count":1}]},{"hash":"1398656284316413232","title":"Membrane Transporters for Nutrients and Xenobiotics","description":"The term enrichment is dominated by various membrane transport processes\u2014phosphate, nitrate, arabinose, selenite, xenobiotic, and other small-molecule transport\u2014plus related signaling pathways, which together suggest a cohesive set of membrane transport proteins involved in uptake and efflux of nutrients and xenobiotics.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0070562","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0071332","count":1},{"id":"GO:0035435","count":1}]},{"hash":"1789043384077509679","title":"Regulation of Signaling Pathways","description":"The top GO terms cluster around regulation of signaling\u2014especially negative regulation of Rho and Ras pathways\u2014plus ubiquitination, which modulates signaling, and downstream processes like transcription and vesicle priming. The inclusion of context-specific terms (acrosome reaction, neutrophil degranulation, gibberellin signaling) suggests a broad theme of controlling cellular signaling across diverse contexts rather than a single specialized process.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0007340","count":3},{"id":"GO:0016082","count":3}]},{"hash":"1710955677213423734","title":"Plant Hormone Signaling and Transcriptional Regulation","description":"The cluster is dominated by GO terms for plant hormone signaling (cytokinin, gibberellin, salicylic acid) and transcriptional control (DNA-templated transcription and its regulation), alongside two-component/phosphorelay signaling typical of plant signal transduction. Additional terms related to leaf senescence and secondary cell wall biogenesis fit within hormone-regulated development and growth, supporting a cohesive theme of hormone-triggered transcriptional responses in plants.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0009739","count":7},{"id":"GO:0009751","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0000160","count":5}]},{"hash":"1054951084762927476","title":"Ubiquitin\u2013proteasome\u2013dependent degradation in meiosis","description":"The top terms are focused on ubiquitin-dependent catabolic processes, polyubiquitination, and SCF-directed proteasomal degradation, pointing to components of the ubiquitin-proteasome system. The inclusion of oocyte maturation and spindle assembly in female meiosis I indicates a link to meiotic regulation, with microtubule polymerization further tying to spindle dynamics. Together, they describe a cohesive theme of ubiquitin-mediated protein turnover governing meiosis and cell-cycle control.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:0000209","count":10},{"id":"GO:0031146","count":10},{"id":"GO:0001556","count":8},{"id":"GO:0021678","count":8}]},{"hash":"280305815112027093","title":"Unknown","description":"The terms span DNA replication and transcription alongside development and neural signaling (myoblast fusion, Schwann cell development, glutamatergic synaptic transmission and plasticity) without a single coherent biological theme, so a specific functional label isn\u2019t justified.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0001324","count":2},{"id":"GO:0060963","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007520","count":2}]},{"hash":"1720597611667988588","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033696","count":2},{"id":"GO:0006337","count":2},{"id":"GO:0060765","count":2},{"id":"GO:0080185","count":1},{"id":"GO:0031069","count":1}]},{"hash":"233470715482793051","title":"Nuclear transcription and RNA processing","description":"This cluster is dominated by GO terms related to transcription, especially regulation and initiation by RNA polymerase II, along with mRNA processing and RNA-related transcription processes. A single ribosome biogenesis term is present but does not outweigh the central theme of nuclear gene expression control and RNA maturation. Therefore the name reflects the core shared function of the proteins.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006397","count":2},{"id":"GO:0090116","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001172","count":1}]},{"hash":"1799578194874461109","title":"Unknown","description":"The GO terms span diverse, cross-kingdom processes (lipid signaling, plant biosynthesis, plant defense, and animal development) with no single cohesive function, so a concise, representative label cannot be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":8},{"id":"GO:0019433","count":8},{"id":"GO:2000124","count":8},{"id":"GO:0009863","count":8},{"id":"GO:0042353","count":8}]},{"hash":"525381395908864726","title":"Vesicle trafficking and Golgi\u2013vacuole transport","description":"This cluster centers on intracellular membrane trafficking, especially Golgi\u2013vacuole transport: Cvt pathway targeting, Golgi organization, retrograde vesicle recycling, and vacuolar acidification, with proton transport supporting membrane dynamics. Plant-specific processes like pollen tube growth and chloroplast movement appear as context rather than changing the theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":3},{"id":"GO:0007112","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0009904","count":2},{"id":"GO:0009903","count":2}]},{"hash":"1739653482380677912","title":"Lipid metabolism and detoxification cluster","description":"This cluster centers on lipid catabolism and detoxification processes, with multiple terms for triglyceride and monoacylglycerol breakdown, phosphatidylserine catabolism, and cellular detoxification of oxidants and toxic substances, plus related lipid signaling (endocannabinoid) and alkaloid metabolism. While some terms are obsolete, the dominant theme ties to lipid-based metabolism and small-molecule detoxification. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0009820","count":6},{"id":"GO:0009636","count":6},{"id":"GO:0019433","count":6}]},{"hash":"1609773578522883806","title":"Plant hormone signaling and defense transcription regulators","description":"This cluster centers on transcription-related GO terms (DNA-templated transcription and its regulation) paired with ABA- and ethylene-activated signaling and defense responses (including chitin response and cuticle/wax biosynthesis regulation). The combination suggests proteins that regulate gene expression in response to plant stresses and hormones, shaping defense and cuticle-related processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006355","count":5},{"id":"GO:0009738","count":5},{"id":"GO:0016525","count":4},{"id":"GO:0009873","count":4}]},{"hash":"1943632924499583748","title":"Mitotic Cell Cycle and Spindle Checkpoint","description":"The top GO terms are dominated by mitosis-related processes (mitotic cell cycle, DNA replication, mitotic spindle assembly, G2 DNA damage checkpoint signaling, JUN phosphorylation, and related regulatory steps), indicating a cohesive cluster of proteins involved in cell division and genome maintenance. While a few terms point to broader signaling or differentiation pathways (e.g., T cell receptor signaling, melanocyte migration, myoblast differentiation), the mitotic and spindle-associated functions clearly predominate.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":26},{"id":"GO:0006260","count":26},{"id":"GO:0050852","count":25},{"id":"GO:0097324","count":25},{"id":"GO:0009636","count":25}]},{"hash":"1712140420687149420","title":"GPCR-linked apoptosis and NF-\u03baB/NFAT signaling","description":"This cluster is dominated by GO terms for GPCR signaling, regulation of apoptotic processes, and NF-\u03baB/NFAT pathways, with supporting signals from protein phosphorylation and GTPase regulation, suggesting a cohesive role in GPCR-driven signaling that impacts apoptosis and inflammatory responses rather than a single tissue- or process-specific function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":4},{"id":"GO:0070212","count":3},{"id":"GO:0051531","count":3},{"id":"GO:0006468","count":3},{"id":"GO:0043547","count":3}]},{"hash":"951912670889380693","title":"RNA Processing and Chromatin Remodeling in Plants","description":"The Top Terms cluster around RNA biogenesis and chromatin regulation, including box C/D snoRNP assembly, snoRNA localization, tRNA dihydrouridine synthesis, and chromatin remodeling. Translation appears as a secondary signal, suggesting a broader gene-expression machinery cluster. Occasional plant-specific terms (defense response, pollen tube reception) hint at context but are not dominant. Overall, the core theme is RNA processing and chromatin-level regulation in plants.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006952","count":1},{"id":"GO:0010483","count":1},{"id":"GO:0009607","count":1},{"id":"GO:0055114","count":1}]},{"hash":"155764447890040134","title":"Cytokinin Signaling with Metabolic Regulation","description":"The GO terms point to plant cytokinin signaling and broader regulatory/metabolic processes (transcription regulation, proteolysis, thiamine and quinolinate biosynthesis, stress responses). While not a single precise function, they cluster around plant growth signaling and linked metabolism.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045793","count":6},{"id":"GO:0009736","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0006508","count":5},{"id":"GO:0010269","count":4}]},{"hash":"789477554903219986","title":"Translation and Cell Division","description":"The top GO terms center on translation and cell cycle/division, indicating a cluster involved in core growth and proliferation. Additional terms like sporulation and amino acid biosynthesis suggest related metabolic and differentiation readiness, while iron-sulfur cluster assembly points to general housekeeping functions; overall, the dominant theme is the machinery for protein synthesis and cell division.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0009099","count":2}]},{"hash":"14215108033951771","title":"Chloroplast Photosynthesis and PSII Assembly","description":"This cluster is dominated by GO terms for photosynthesis and photosystem II assembly, indicating a chloroplast/PSII-biogenesis\u2013related function. While a few other terms (mitochondrial processes, development) appear, the strongest signal centers on photosynthetic activity and PSII assembly.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":5},{"id":"GO:0010207","count":2},{"id":"GO:0033132","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009107","count":1}]},{"hash":"2233643657746181012","title":"Central carbon metabolism","description":"The cluster shows strong representation of core metabolic processes: glycolysis, the TCA cycle, regulation of pyruvate decarboxylation to acetyl-CoA, branched-chain amino acid catabolism, and thiamine biosynthesis. These together indicate a focus on energy production and carbon flow. Some neural development terms appear, but they are less prominent and may reflect annotation overlap rather than a dedicated neural-function cluster. Thus, Central carbon metabolism is the best overarching label.","confidence":"High","size":26,"edges":57,"triangles":13,"max_degree":11,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006096","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0006099","count":6},{"id":"GO:0009228","count":5},{"id":"GO:0070389","count":5}]},{"hash":"1131805784806033567","title":"Plant pigment and cell-wall polysaccharide biosynthesis","description":"GO terms cluster around anthocyanin pigment production, sporopollenin biosynthesis for pollen walls, and nucleotide-sugar\u2013dependent biosynthesis (rhamnose, xylose, galacturonate) used in cell-wall polysaccharides, suggesting a cohesive theme of plant pigment and cell-wall polymer biosynthesis.","confidence":"High","size":26,"edges":23,"triangles":2,"max_degree":6,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":14},{"id":"GO:0009718","count":12},{"id":"GO:0016126","count":11},{"id":"GO:0006012","count":10},{"id":"GO:0019305","count":10}]},{"hash":"1809208979982955781","title":"Plant Hormone Signaling and Secondary Metabolite Biosynthesis","description":"The top GO terms emphasize plant hormone signaling (cytokinin-activated signaling, response to gibberellin) and biosynthetic processes for flavonols and lignin, suggesting the cluster groups proteins involved in hormone signaling and phenylpropanoid metabolism; some chromatin-related annotations appear as incidental regulatory links.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":12},{"id":"GO:0035522","count":12},{"id":"GO:0009739","count":11},{"id":"GO:1901430","count":11},{"id":"GO:1905839","count":11}]},{"hash":"871676940988572406","title":"Plant stress signaling and membrane transport","description":"The Top Terms cluster around plant-specific responses (abscisic acid response, plant-type cell wall) and membrane transport processes (sodium and fatty acid transmembrane transport), with additional hints from ubiquitination and RNA processing that often modulate stress responses. The combination suggests proteins involved in coordinating plant stress signaling with membrane-associated transport and metabolism.","confidence":"Medium","size":26,"edges":31,"triangles":5,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0019076","count":2}]},{"hash":"399398379830727446","title":"Renal Solute Transport","description":"The cluster is dominated by transmembrane transport terms for ions and solutes (potassium, urea, methylammonium, hydrogen peroxide) and kidney-related processes (renal water absorption, metanephric proximal tubule development, excretion, salt stress response), indicating transporter proteins functioning in renal tubule epithelia, especially the proximal tubule, with a possible detox-response component.","confidence":"High","size":26,"edges":48,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":15},{"id":"GO:0070295","count":12},{"id":"GO:0072232","count":12},{"id":"GO:0071288","count":12},{"id":"GO:0085018","count":12}]},{"hash":"1670026954270620431","title":"Plant transcription regulation and chromatin remodeling","description":"The top GO terms cluster around regulation of DNA-templated transcription and chromatin state (heterochromatin formation, histone acetylation, telomeric D-loop dynamics, meiotic recombination regulation), with additional plant-specific signals such as responses to gibberellin and salicylic acid and lignin biosynthesis regulation. This suggests proteins that control gene expression by modulating chromatin structure in plants, integrating developmental and hormonal cues.","confidence":"High","size":26,"edges":15,"triangles":1,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":10},{"id":"GO:0009739","count":8},{"id":"GO:0000183","count":8},{"id":"GO:0009751","count":8},{"id":"GO:1901430","count":7}]},{"hash":"1368159035196492949","title":"Oocyte meiosis and neural development","description":"Cluster terms strongly point to meiotic processes in oocytes (oocyte maturation, spindle assembly in female meiosis I) and early neural development (third ventricle development, initiation of neural tube closure), with supporting roles for ubiquitin-mediated proteolysis and microtubule dynamics that drive meiosis and cell-cycle progression. This combination suggests a cohesive theme around oogenesis coupled with initial neural development.","confidence":"High","size":26,"edges":198,"triangles":769,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":23},{"id":"GO:0001556","count":22},{"id":"GO:0021678","count":22},{"id":"GO:0051436","count":22},{"id":"GO:0046785","count":22}]},{"hash":"1982313323864192935","title":"Phenylpropanoid and alkaloid biosynthesis","description":"The top GO terms cluster around secondary metabolite production, notably phenylalanine-derived pathways like cinnamic acid biosynthesis (phenylpropanoids) and alkaloid biosynthesis, with related hints of antibiotic and toxin biosynthesis. L-phenylalanine catabolic activity supports the phenylpropanoid connection, and the zinc stress term aligns with stress-related regulation of secondary metabolism. Some terms are obsolete, but the prevailing theme is phenylpropanoid/alkaloid biosynthesis and related defense metabolites, possibly with enzyme complexes (homotetramerization) involved.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006559","count":4},{"id":"GO:0019557","count":4},{"id":"GO:0019556","count":4},{"id":"GO:1990359","count":3}]},{"hash":"2177253605708068349","title":"Core transcription and translation machinery","description":"The cluster is enriched for transcription (DNA-templated transcription; RNA polymerase I/II/III assembly; regulation of Pol II elongation) and translation (translational initiation; translation), suggesting a core gene expression machinery. Protein folding and tubulin complex assembly terms appear but do not change the overall theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:1990115","count":1},{"id":"GO:0032968","count":1}]},{"hash":"1493085301041456323","title":"Fungal filamentous growth and secretion","description":"The terms point to nutrient-triggered filamentous growth (pseudohyphal/invasive growth in response to glucose limitation) alongside secretion and protein trafficking (ER exit, lysosomal enzyme secretion), suggesting a coordinated fungal program that links nutrient sensing to morphogenesis and secretory pathways. Some terms are less specific or cross-kingdom, so confidence is moderate.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061060","count":3},{"id":"GO:0070863","count":2},{"id":"GO:0033299","count":2},{"id":"GO:0007124","count":2},{"id":"GO:2000010","count":2}]},{"hash":"1665980761017379333","title":"Embryonic Morphogenesis and Neural Development","description":"The cluster\u2019s top GO terms cluster around morphogenesis across tissues (face, lung, nerve branching, axonal fasciculation) and development, with supporting cellular processes such as Golgi organization, nuclear protein import, and transcription, suggesting involvement in embryonic tissue shaping and neural patterning.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007030","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0034605","count":2},{"id":"GO:0006606","count":2},{"id":"GO:2000172","count":2}]},{"hash":"1675606320819443028","title":"Endomembrane Vesicle Trafficking","description":"Top GO terms indicate multiple endomembrane transport routes (ER-Golgi, Golgi-ER, endocytosis, endosome-to-melanosome, and synaptic vesicle transport), suggesting proteins specialized for intracellular vesicle movement. While nitrogen utilization and CO2 transport terms appear, the dominant theme is vesicle trafficking within the endomembrane system.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035646","count":2},{"id":"GO:0030100","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0048490","count":2}]},{"hash":"945026761714406875","title":"Ubiquitin-Proteasome Regulation in Meiosis","description":"The cluster is dominated by ubiquitin-dependent proteolysis terms (SCF- and general proteasomal pathways) and meiosis/ovarian development terms (oocyte maturation, spindle assembly in female meiosis I), suggesting proteins that function in ubiquitin-proteasome\u2013mediated regulation during meiosis and early development.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":20},{"id":"GO:0031146","count":20},{"id":"GO:0001556","count":18},{"id":"GO:0021678","count":18},{"id":"GO:0051436","count":18}]},{"hash":"518682403242432668","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0000056","count":4},{"id":"GO:0008033","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006281","count":2}]},{"hash":"671336731544853504","title":"Peroxisome Biogenesis and Inheritance","description":"The cluster is dominated by GO terms tied to peroxisomes: inheritance, membrane biogenesis, protein import into the peroxisomal membrane, and ER-dependent peroxisome organization, with ceramide biosynthesis regulation suggesting peroxisomal lipid metabolism involvement; a lone cell division term is still compatible but does not define the cluster\u2019s main theme.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0045033","count":4},{"id":"GO:0045046","count":3},{"id":"GO:0016557","count":3},{"id":"GO:2000304","count":3}]},{"hash":"222083926190049361","title":"Development and Immune Signaling Network","description":"This cluster combines signals tied to development (thymus and placenta development, melanocyte migration) with immune signaling (T cell receptor pathway) and cell-cycle regulation (CDK/MAPK activity), suggesting a thematic grouping of development- and immunity-related signaling pathways, with broader metabolic and stress response terms as context.","confidence":"Medium","size":25,"edges":273,"triangles":1937,"max_degree":24,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0034501","count":22},{"id":"GO:0045736","count":22},{"id":"GO:0000187","count":20},{"id":"GO:0071276","count":20},{"id":"GO:0048538","count":20}]},{"hash":"967607761426993398","title":"Microtubule spindle dynamics and nuclear migration","description":"This cluster is dominated by terms related to microtubule-driven processes: spindle assembly/elongation, kinetochore attachments, minus-end\u2013directed sliding, and nuclear migration along microtubules, with an additional related term on karyogamy. The common thread is microtubule dynamics governing mitosis and nuclear positioning.","confidence":"High","size":25,"edges":138,"triangles":401,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":24},{"id":"GO:1990535","count":22},{"id":"GO:0001560","count":22},{"id":"GO:0072092","count":22},{"id":"GO:0031534","count":22}]},{"hash":"908096410054401367","title":"mRNA processing and translation regulation","description":"The Top Terms are dominated by mRNA splicing, export, and poly(A) tail regulation, plus translation preinitiation and reinitiation, and regulatory ncRNA-mediated gene silencing. This points to a cohesive module centered on maturation and processing of mRNA in the nucleus and its coordination with translation regulation, i.e., a coordinated mRNA processing/translation control cluster.","confidence":"High","size":25,"edges":196,"triangles":793,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":16},{"id":"GO:0001731","count":16},{"id":"GO:0048026","count":16},{"id":"GO:0031047","count":16},{"id":"GO:0006406","count":16}]},{"hash":"98366538779587429","title":"Translation Initiation and mRNA Processing","description":"The proteins are enriched with translation initiation and reinitiation processes, including formation of the preinitiation complex, IRES-mediated viral translation, and regulation of translational initiation, alongside RNA processing/export signals and ncRNA-mediated gene silencing, suggesting a cohesive module around RNA metabolism that controls mRNA translation. ","confidence":"Medium","size":25,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":10},{"id":"GO:0001731","count":10},{"id":"GO:0002188","count":10},{"id":"GO:0048026","count":9},{"id":"GO:0031047","count":9}]},{"hash":"292222745123318754","title":"Neuronal Development and Excitatory Synaptic Signaling","description":"The cluster\u2019s top GO terms center on nervous system development, hippocampus development, and dendrite morphogenesis, along with excitatory postsynaptic potential and dopamine response, pointing to proteins involved in neuronal differentiation and excitatory synaptic function; other terms suggest general cellular processes like trafficking and transcription that support neuronal activity.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0000060","count":4},{"id":"GO:0050852","count":3},{"id":"GO:0031647","count":3}]},{"hash":"304407315440852914","title":"Chloroplast Translation and Photosynthesis","description":"This cluster is best described as chloroplast gene expression and photosynthetic machinery, evidenced by translation, tRNA processing, and photosynthesis terms, with supporting redox balance and molybdenum cofactor biosynthesis; some unrelated terms may reflect annotation noise.","confidence":"High","size":25,"edges":297,"triangles":2234,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0006777","count":2}]},{"hash":"657480991315783899","title":"Auxin Transport and Root Development","description":"The cluster is dominated by GO terms tied to auxin biology: auxin-activated signaling, polar transport, and export across the plasma membrane, plus ER-Golgi\u2013associated transport related to auxin. Adventitious root development and transmembrane transport further support a role in auxin-mediated root growth and transporter trafficking. Altogether, these terms point to a coherent functional theme around auxin transport/signaling driving root development.","confidence":"High","size":25,"edges":45,"triangles":14,"max_degree":10,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0009734","count":3},{"id":"GO:0080162","count":3},{"id":"GO:0009926","count":3},{"id":"GO:0010315","count":3}]},{"hash":"141521928608954701","title":"Mitochondrial Translation & Fe-S Cluster Maturation","description":"Top GO terms reveal a concerted mitochondrial focus: mitochondrial translation and related rRNA import into mitochondrion, alongside general translation. Fe-S cluster maturation and iron ion homeostasis indicate involvement in mitochondrial iron-sulfur protein assembly and redox balance, which often accompany mitochondrial gene expression and genome maintenance. Overall, this cluster appears to group proteins tied to mitochondrial protein synthesis and Fe-S cluster machinery, with ancillary roles in mitochondrial iron handling and DNA replication.","confidence":"High","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0097428","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0035928","count":2},{"id":"GO:0030433","count":2}]},{"hash":"2091722971524079157","title":"Unknown","description":"The top GO terms cover a mix of insect developmental processes (eye cone and wing cell fate), signaling (EGFR ligand maturation, phosphorylation), stress and protein handling (unfolded protein response, ER-to-cytosol proteolysis), immunity, and metabolism, with no single unifying function linking most terms. Because the cluster spans diverse biological themes, there isn\u2019t a coherent, shared function to label beyond Unknown. ","confidence":"","size":25,"edges":20,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042676","count":4},{"id":"GO:0038005","count":4},{"id":"GO:0034620","count":4},{"id":"GO:0035311","count":4},{"id":"GO:0032815","count":4}]},{"hash":"1560543973258771032","title":"Developmental Transcriptional Regulation","description":"The top GO terms cluster around development of various organs (pituitary gland, cerebellum, eye, primitive streak) and neural structures, combined with strong signals of transcriptional control (RNA polymerase II\u2013mediated transcription and its negative regulation). This pattern suggests proteins function as transcription regulators that coordinate developmental programs, with a plant-related cytokinin signaling term illustrating broader signaling roles in development. Overall, the shared theme is transcriptional regulation during organismal development.","confidence":"High","size":25,"edges":66,"triangles":22,"max_degree":11,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0006355","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0009736","count":5},{"id":"GO:0008045","count":5}]},{"hash":"740535004976973067","title":"Glucocorticoid-responsive muscle and heart development","description":"This cluster centers on transcriptional regulation linked to glucocorticoid signaling (dexamethasone response), with support from RNA Pol II\u2013mediated transcription and chromatin remodeling (nucleosome assembly). It also features heart and myotube (muscle) development, suggesting a theme of steroid-responsive gene regulation driving muscle and cardiac development.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0032781","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0007507","count":2}]},{"hash":"2123766648094321471","title":"Sodium/Potassium Ion Transport and Salt Stress","description":"The dominant GO terms describe sodium and potassium ion movement across membranes, ion homeostasis, cell volume regulation, vacuolar acidification, and salt-stress response, indicating a cohesive role in ion transport and osmoregulation. An outlier term related to BDNF receptor signaling appears incidental and does not alter the overall theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036376","count":4},{"id":"GO:0030007","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0009651","count":3},{"id":"GO:0006884","count":3}]},{"hash":"487838175419446604","title":"Plant Hormone Signaling and Development","description":"The top GO terms center on responses to multiple plant hormones (cytokinin, gibberellin, ABA, salicylic acid) and development, suggesting this cluster comprises components of hormone signaling pathways that regulate growth and development. While a few chromatin-related terms appear, the dominant theme is hormone-mediated regulation of plant development, justifying the chosen name.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0009739","count":7},{"id":"GO:0009737","count":7},{"id":"GO:0009751","count":7},{"id":"GO:0007275","count":6}]},{"hash":"738516347510500433","title":"N-terminal acetylation and polyamine biosynthesis","description":"The top GO terms cluster around acetylation events at N-termini (N-terminal acetylation, N-terminal peptidyl-methionine acetylation, N-terminal propionylation) and acetylation of polyamines (spermidine, putrescine), plus related amino acid biosynthesis processes. Despite a few outliers (angiogenesis, melatonin biosynthesis), the shared pattern is protein N-terminal modification and polyamine metabolism, justifying this label.","confidence":"Medium","size":25,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045150","count":12},{"id":"GO:0061606","count":11},{"id":"GO:0006526","count":11},{"id":"GO:0032918","count":11},{"id":"GO:0017196","count":11}]},{"hash":"1809604335688154615","title":"Vacuolar amino acid transporters","description":"This cluster shows multiple GO terms for amino acid transport across membranes with emphasis on transport into or out of the vacuole (asparagine, arginine, histidine, glutamate, proline), suggesting a cohesive function as vacuolar amino acid transporters. Some annotations like lithium ion transport or obsolete terms may be less specific noise but do not override the main theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006867","count":3},{"id":"GO:1990818","count":3},{"id":"GO:0090452","count":3},{"id":"GO:0089708","count":3},{"id":"GO:1901481","count":3}]},{"hash":"1948626507283448056","title":"Ubiquitin-Dependent Protein Degradation and TNF Signaling","description":"These proteins are dominated by ubiquitin-related processes: ubiquitin-dependent protein catabolic process and protein autoubiquitination are highly represented, pointing to proteasomal turnover. Additionally, TNF-mediated signaling and its regulation appear prominently, suggesting the cluster centers on ubiquitin-regulated signaling pathways that intersect immune processes (e.g., V(D)J recombination). Some terms are obsolete, but the core theme remains ubiquitin-proteasome regulation linked to inflammatory signaling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0051865","count":11},{"id":"GO:1901253","count":11},{"id":"GO:1903762","count":11},{"id":"GO:2000620","count":10}]},{"hash":"1086819766564452765","title":"Developmental Signaling and Transcription","description":"Top GO terms center on transcriptional control and development, with several signaling pathways (ABA, ethylene, parathyroid hormone, neural patterning) represented, plus basic regulatory processes like DNA replication and kinase activity modulation. The mix points to proteins that coordinate development through gene expression regulation and signaling, rather than a single pathway. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0007275","count":9},{"id":"GO:0009738","count":8},{"id":"GO:0006469","count":7},{"id":"GO:0071374","count":6}]},{"hash":"2207001599569289130","title":"Proteoglycan/ECM Biosynthesis and Morphogenesis","description":"These proteins cluster around extracellular matrix (ECM) components and assembly: proteoglycan biosynthesis (heparan sulfate proteoglycans, UDP-D-xylose), ECM-related processes (cell adhesion molecule production, tissue morphogenesis), and lens maintenance, plus related glycosylation. While some terms (insulin response, mucosal immunoglobulin production) are less directly tied, the dominant pattern supports ECM and tissue development functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042403","count":3},{"id":"GO:0006486","count":3},{"id":"GO:0033319","count":3},{"id":"GO:0048729","count":3},{"id":"GO:0060352","count":3}]},{"hash":"1738990450145791790","title":"ER-Golgi Vesicle Trafficking","description":"The top GO terms show strong enrichment for vesicle transport between the ER and Golgi in both directions (Golgi to ER and ER to Golgi), plus related vesicle trafficking activities, which indicates a cohesive cluster of proteins involved in ER-Golgi trafficking. A few terms related to translation initiation and transcription regulation appear, but they seem secondary to the main trafficking theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0008283","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0000122","count":3}]},{"hash":"736235625308962882","title":"Ubiquitin-Dependent Protein Turnover and NF-\u03baB Signaling","description":"The cluster is dominated by ubiquitination-related terms (ubiquitin-dependent protein catabolic process, autoubiquitination, K48- and K6-linked ubiquitination) and signaling pathways like NF-\u03baB activation and regulation of apoptosis, pointing to a cohesive role in ubiquitin-driven protein degradation and downstream survival/apoptotic signaling, with some immune-related terms (V(D)J recombination) reflecting broader relevance to immune regulation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0051865","count":8},{"id":"GO:0036205","count":8},{"id":"GO:0070936","count":8},{"id":"GO:0085020","count":8}]},{"hash":"665335075962988519","title":"Ubiquitin-Proteasome Degradation","description":"Dominant GO terms reflect ubiquitin-dependent proteolysis and polyubiquitination, pointing to proteasome-mediated protein turnover as the core function; secondary terms suggest stress responses and development/cell-cycle links that are peripheral.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0000209","count":10},{"id":"GO:0031146","count":10},{"id":"GO:1903378","count":7},{"id":"GO:0046685","count":7}]},{"hash":"436992189641602872","title":"Ubiquitin-mediated proteolysis in oocyte meiosis","description":"The terms converge on ubiquitin-proteasome\u2013driven protein degradation, especially SCF-dependent ubiquitination, linked to mitotic cell cycle regulation, oocyte maturation, and meiosis I spindle assembly. The combination of proteolysis and meiotic/spindle processes suggests a cluster focused on ubiquitin-regulated meiotic progression in oocytes.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":18},{"id":"GO:0042787","count":15},{"id":"GO:0051436","count":14},{"id":"GO:0008285","count":14},{"id":"GO:0031571","count":13}]},{"hash":"352338168596806403","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0006508","count":2},{"id":"GO:2000344","count":1},{"id":"GO:0052889","count":1},{"id":"GO:0016042","count":1}]},{"hash":"522350168962432527","title":"GA-regulated transcription of secondary cell wall biosynthesis","description":"This cluster\u2019s top terms focus on regulation of DNA-templated transcription and plant-type secondary cell wall biogenesis, with links to lignin biosynthesis and a gibberellin response. This suggests transcription factors that mediate GA-responsive expression of genes driving lignin-rich secondary cell wall formation in plants. Some epigenetic terms appear, but the dominant signal is transcriptional control of cell wall biosynthesis.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0009834","count":6},{"id":"GO:1901348","count":6},{"id":"GO:0009739","count":4}]},{"hash":"498853902419950106","title":"Membrane transport of nutrients and cofactors","description":"The cluster is enriched for multiple transmembrane transport processes, including phosphate ion, coenzyme A, thiamine pyrophosphate, manganese ion, and mitochondrial nucleotide import, pointing to a shared role in moving essential nutrients and cofactors across membranes. Additional terms related to amino acid starvation response, adaptive thermogenesis, insulin secretion regulation in response to glucose, and liver regeneration support a broader theme of metabolic regulation and energy homeostasis tied to these transport activities.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":23},{"id":"GO:0034198","count":23},{"id":"GO:1990845","count":23},{"id":"GO:0061179","count":23},{"id":"GO:1990519","count":23}]},{"hash":"909949651679881346","title":"Ubiquitin-Dependent Cell Cycle Regulation","description":"The top GO terms strongly point to ubiquitin-mediated protein turnover (K11-linked ubiquitination; ubiquitin-dependent protein catabolic process) and mitotic control (metaphase/anaphase transition; cell division), suggesting the cluster centers on regulation of the cell cycle by ubiquitination. Some terms related to prostate development or interferon response may reflect broader or tissue-specific annotations rather than defining the core function. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071357","count":10},{"id":"GO:0046661","count":9},{"id":"GO:0030850","count":9},{"id":"GO:0006463","count":9},{"id":"GO:0000492","count":8}]},{"hash":"228022444922665713","title":"Plant Chromatin Regulation","description":"These proteins are linked mainly by chromatin-related processes: nucleosome assembly, histone modification, and subtelomeric heterochromatin formation/telomere dynamics, with secondary ties to plant developmental signaling (root meristem growth, gibberellin response). This suggests a chromatin-regulation theme governing genome organization and transcription in plants.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0010082","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0009739","count":2},{"id":"GO:1901430","count":2}]},{"hash":"2131147183795275049","title":"Membrane Transport and Metabolic Processes","description":"The top GO terms are dominated by transport across membranes (antimonite/arsenite transport, sodium-dependent organic anion transport, plasma membrane pyruvate transport) along with basic metabolic steps (coenzyme A biosynthesis, phosphorylation/dephosphorylation, methylation). Despite some obsolete terms, the common thread is involvement in membrane transport and core metabolism, justifying this label for the cluster.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0015937","count":1},{"id":"GO:1904251","count":1},{"id":"GO:0016311","count":1}]},{"hash":"623196110349992770","title":"Ubiquitin-Proteasome\u2013Mediated Regulation of Cell Signaling","description":"The top terms include protein polyubiquitination and proteasome regulatory particle assembly, suggesting a role in protein turnover. Coupled with keywords for apoptosis, cell migration, epithelial polarity, and intracellular signaling, the cluster likely represents regulators of diverse cellular processes driven by ubiquitin-proteasome pathways rather than a single pathway. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033028","count":4},{"id":"GO:0097284","count":4},{"id":"GO:0090162","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0000209","count":3}]},{"hash":"1625301430756951926","title":"C4 photosynthesis and plant carbon metabolism","description":"This cluster is dominated by terms tied to photosynthesis and carbon metabolism in plants, including photosynthesis, C4 photosynthesis, oxaloacetate metabolism, and the TCA cycle. The nitrate response and pigmentation terms support a plant-specific photosynthetic context, while some other terms (transcription, vesicle coating) appear ancillary. Overall, the core signal points to C4 photosynthesis and related carbon metabolism, with supportive plant physiology context.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0010167","count":4},{"id":"GO:0006107","count":4},{"id":"GO:0015979","count":4},{"id":"GO:0009760","count":4},{"id":"GO:0006099","count":4}]},{"hash":"510158460979299651","title":"Energy metabolism and nutrient-stress signaling","description":"The top GO terms cluster around central energy production (pyruvate and ATP biosynthesis) and broad nutrient/energy signaling (glucose, nutrient, insulin stimulus) alongside stress responses (hypoxia, heat) and cell fate (programmed cell death). This suggests a cohesive module that links energy metabolism with nutrient sensing and stress-induced responses, rather than a single pathway. Confidence: Medium","confidence":"","size":24,"edges":167,"triangles":655,"max_degree":20,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0042866","count":9},{"id":"GO:0001666","count":8},{"id":"GO:0012501","count":7},{"id":"GO:0006754","count":7},{"id":"GO:0033198","count":7}]},{"hash":"1486495756740126225","title":"Plant secondary metabolite and pollen-wall biosynthesis","description":"These GO terms cluster around biosynthetic processes in plants, including sterol, anthocyanin-containing compound, galactose, rhamnose, xylose, and UDP-sugar synthesis, as well as sporopollenin production for the pollen exine. While a couple of terms are broad (oxidation-reduction, cytolysis), the dominant theme is plant-specific metabolite and structural polymer biosynthesis, especially related to pollen walls and cell-surface components.","confidence":"Medium","size":24,"edges":7,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":17},{"id":"GO:0019835","count":14},{"id":"GO:0016126","count":10},{"id":"GO:0009718","count":10},{"id":"GO:0006012","count":9}]},{"hash":"437208502832799810","title":"Unknown","description":"The top GO terms span a broad range of processes from transcription and DNA replication to metabolism and various cellular responses (sperm capacitation, chemotaxis, response to cocaine). There is no single cohesive function linking all 24 proteins, and the lack of edges supports a heterogeneous set rather than a module. Confidence: None.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":7},{"id":"GO:0009636","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0033160","count":7},{"id":"GO:0006935","count":7}]},{"hash":"495075043700034947","title":"Neuronal transcription and dendrite morphogenesis","description":"This cluster shows strong enrichment for DNA-templated transcription and nuclear transport terms, plus dendrite morphogenesis and neuronal responses (e.g., response to cocaine, potassium ion transport, glucose metabolism). Together these point to neuronal gene regulation and structural development of dendrites, with metabolic and signaling support. Some outlier terms exist, but the neural theme is the most coherent thread.","confidence":"High","size":24,"edges":196,"triangles":747,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":20},{"id":"GO:0006351","count":14},{"id":"GO:0048813","count":14},{"id":"GO:0043552","count":14},{"id":"GO:0033160","count":14}]},{"hash":"1184563568835270613","title":"DNA replication and nucleotide catabolism","description":"The top GO terms cluster around DNA metabolism, including DNA replication, DNA unwinding, and various nucleotide catabolic processes (ADP, CDP, GDP, UDP), with karyogamy linking to nuclear events. Some plant-specific terms appear but likely represent broader gene annotations; overall the dominant theme is DNA metabolism and nucleotide turnover.","confidence":"Medium","size":24,"edges":186,"triangles":751,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":9},{"id":"GO:0032508","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0071405","count":5},{"id":"GO:0046032","count":5}]},{"hash":"2262273255236605586","title":"Ribosome biogenesis and translation machinery","description":"This cluster is dominated by GO terms related to protein synthesis and ribosome assembly, including translation, cytoplasmic translation, ribosome biogenesis, and initiation/elongation/termination of translation, with additional terms pointing to ribosomal subunit export and mRNA turnover; together these indicate a cohesive group centered on the ribosome and translational machinery.","confidence":"High","size":24,"edges":150,"triangles":469,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0042254","count":13},{"id":"GO:0002181","count":6},{"id":"GO:0000055","count":6},{"id":"GO:0000288","count":6}]},{"hash":"1873301560277488983","title":"Glutathione-dependent xenobiotic and aromatic amino acid catabolism","description":"Top GO terms indicate glutathione metabolism, xenobiotic and aromatic amino acid (phenylalanine/tyrosine) catabolism, consistent with detoxification pathways; other terms are sparsely represented and do not disrupt the main theme.","confidence":"High","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006749","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0042178","count":2},{"id":"GO:0006559","count":2}]},{"hash":"180204046002444100","title":"Oxidative Stress Response and ER Protein Folding","description":"The cluster is dominated by GO terms related to redox biology and oxidative stress (oxidation-reduction process, redox homeostasis, oxidant detoxification, cellular response to oxidative stress) and endoplasmic reticulum\u2013specific protein folding, suggesting a cohesive theme around maintaining protein quality under oxidative conditions. Additional terms on protein repair and transcription regulation support a broader stress-response context, but redox/homeostasis and ER folding are the central connection. ","confidence":"High","size":24,"edges":119,"triangles":278,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":15},{"id":"GO:0045454","count":12},{"id":"GO:0098869","count":11},{"id":"GO:0034975","count":10},{"id":"GO:0016032","count":10}]},{"hash":"815357129467469395","title":"Neural development, cell-cycle control, and apoptosis","description":"The cluster centers on neural development signals (forebrain development, neural tube closure) and includes strong links to cell-cycle regulation (APC/C- and SCF-dependent proteasomal pathways) and apoptosis (ER-stress\u2013triggered intrinsic pathway and glial apoptosis), suggesting a cohesive module that coordinates neural development with proteostasis and programmed cell death. ","confidence":"High","size":24,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0051260","count":4},{"id":"GO:0046835","count":4},{"id":"GO:0007565","count":3},{"id":"GO:0031145","count":3}]},{"hash":"1058035080625767780","title":"Epigenetic regulation of differentiation","description":"Top GO terms indicate involvement in differentiation across multiple lineages (granulocytes, erythrocytes, cerebral cortex development, sperm capacitation) and histone methylation/demethylation regulation, pointing to an epigenetic layer controlling lineage specification. Additional terms like cellular response to cAMP and redox homeostasis suggest broader signaling and metabolic readiness accompanying differentiation. This combination supports a label around epigenetic regulation guiding differentiation.","confidence":"Medium","size":24,"edges":189,"triangles":833,"max_degree":22,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021987","count":14},{"id":"GO:0009228","count":14},{"id":"GO:0034720","count":14},{"id":"GO:0071320","count":14},{"id":"GO:0030851","count":14}]},{"hash":"2087399119218107260","title":"Ribosome and Translation Machinery","description":"This cluster is dominated by translation-related functions, with GO:0006412 (translation) appearing most strongly and entries like ribosomal large subunit assembly and translational termination supporting a core role in protein synthesis. While a few transcription- and DNA metabolism-related terms are present, they are less represented and likely reflect secondary associations. Overall, the proteins cluster around ribosome function and translation processes.","confidence":"High","size":24,"edges":267,"triangles":1855,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":19},{"id":"GO:0046677","count":5},{"id":"GO:0006353","count":4},{"id":"GO:0046898","count":3},{"id":"GO:0006259","count":3}]},{"hash":"82890139924067285","title":"Metabolic Biosynthesis Pathways","description":"The top GO terms cluster around biosynthetic and metabolic processes, including amino acid biosynthesis (serine, glutamine), methionine salvage, and cobalamin and lipopolysaccharide biosynthesis, plus carbon utilization and transcription. This pattern points to a group of proteins involved in fundamental biosynthesis and metabolism rather than a single specific function, so the name \u201cMetabolic Biosynthesis Pathways\u201d captures the overarching theme. Some terms (like stomatal development) seem outliers, likely due to cross-species annotations, contributing to only partial coherence.","confidence":"Medium","size":24,"edges":68,"triangles":51,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019509","count":4},{"id":"GO:0009236","count":4},{"id":"GO:2000122","count":3},{"id":"GO:0015976","count":3},{"id":"GO:0071244","count":3}]},{"hash":"2070849936533385810","title":"Methylation-Driven Biosynthesis and RNA/Protein Modification","description":"There is a clear set of GO terms centered on methylation: multiple N-terminal peptidyl methylations (serine, glycine, alanine), plus tRNA and rRNA methylation, all within broader biosynthetic contexts such as ubiquinone, cobalamin, and antibiotic biosynthesis. This points to a theme of methyltransferase enzymes functioning across various biosynthetic pathways and post-translational/RNA modifications in microbes, supporting a cohesive label around methylation-driven biosynthesis.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":3},{"id":"GO:0035572","count":3},{"id":"GO:0035573","count":3},{"id":"GO:0070476","count":3},{"id":"GO:0017000","count":3}]},{"hash":"1710409238334126621","title":"Neuronal RNA Processing and Synapse Development","description":"This cluster centers on RNA metabolism: mRNA splicing via the spliceosome, mRNA export, regulation of translational initiation, and ncRNA-mediated gene silencing, with additional signals for dendrite extension and synapse assembly, suggesting a link between RNA processing and neuronal development/synaptogenesis.","confidence":"Medium","size":24,"edges":53,"triangles":18,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3}]},{"hash":"2198101426362204273","title":"Aromatic xenobiotic catabolism and stress response","description":"Based on the top GO terms, the cluster is dominated by catabolic processes for various xenobiotics (carbazole, coumarin, camphor, retinoic acid) and by stress-response terms (response to ozone, immobilization stress), suggesting a functional theme of detoxification/metabolism of environmental compounds plus stress signaling. A few outliers (e.g., tongue muscle differentiation) appear incidental, but the overall pattern supports xenobiotic metabolism with a stress-response component.","confidence":"Medium","size":24,"edges":23,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":14},{"id":"GO:0010193","count":13},{"id":"GO:0034653","count":13},{"id":"GO:0035865","count":13},{"id":"GO:0046226","count":13}]},{"hash":"998283797854327586","title":"Calcium-responsive transcription and developmental signaling","description":"This cluster centers on transcriptional activity (DNA-templated transcription, RNA polymerase II) and calcium signaling (cellular response to calcium ion), with additional links to developmental processes (dorsal closure, primitive streak formation) and rhythm (circadian rhythm). The common thread appears to be transcriptional regulation tied to calcium-responsive signaling during development and timing. Confidence: Medium","confidence":"","size":24,"edges":249,"triangles":1545,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0071277","count":10},{"id":"GO:0006366","count":7},{"id":"GO:0009737","count":7},{"id":"GO:0090009","count":7}]},{"hash":"1371145582990604638","title":"Skeletal Muscle Differentiation and Calcium Signaling","description":"The cluster is strongly enriched for skeletal muscle\u2013related terms, especially positive regulation of skeletal muscle cell differentiation and skeletal muscle fiber adaptation, along with cellular responses to calcium ions. This points to a core theme of muscle development and calcium-dependent regulation, with other terms (neuron/lung differentiation) likely reflecting broader developmental programs but not dominating the cluster. ","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001016","count":17},{"id":"GO:0006366","count":15},{"id":"GO:0071277","count":12},{"id":"GO:0032933","count":10},{"id":"GO:0043503","count":10}]},{"hash":"975080362784839882","title":"Gibberellin/cytokinin signaling and secondary cell wall biosynthesis","description":"The cluster shows strong representation of plant hormone signaling terms (gibberellin, cytokinin, salicylic acid) alongside processes related to secondary cell wall formation and lignin biosynthesis (syringal lignin biosynthetic process), with supporting chromatin remodeling signals, suggesting a coordinated program governing hormone responses and cell wall biosynthesis in plants.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009739","count":7},{"id":"GO:0009736","count":7},{"id":"GO:0043044","count":7},{"id":"GO:1901348","count":7},{"id":"GO:0009751","count":7}]},{"hash":"1983814465069762175","title":"Plant phenylpropanoid and lignan biosynthesis","description":"This cluster is enriched for GO terms tied to phenylpropanoid metabolism and lignan biosynthesis (pinoresinol and secoisolariciresinol), as well as anthocyanin biosynthesis, which together point to a shared role in plant secondary metabolism. A few terms like DNA repair and transcription are present but less representative of the core function. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0031162","count":2},{"id":"GO:0006012","count":1},{"id":"GO:0009718","count":1}]},{"hash":"1160890621004579611","title":"Plant Hormone Signaling and Transcription Regulation","description":"The cluster is dominated by GO terms for plant hormone responses (gibberellin, salicylic acid, cytokinin signaling) and transcriptional regulation, suggesting proteins that act in hormone-triggered transcriptional control. While a few terms touch on chromatin-related processes, the central theme aligns with hormone signaling guiding transcriptional activity.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009739","count":5},{"id":"GO:0009751","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0009736","count":4}]},{"hash":"1465729030848599758","title":"Unknown","description":"The GO terms span chromatin regulation (rDNA heterochromatin formation, histone H2A deubiquitination, deneddylation, ubiquitin-dependent catabolic processes) and translation control (preinitiation complex formation, regulation of translational initiation, IRES-dependent initiation), plus diverse developmental processes (neural crest differentiation, germ-line cyst encapsulation) and even plant-specific signaling. This mix suggests no single coherent functional theme for the cluster, but rather a heterogeneous set of regulatory processes, making a concise, specific label inappropriate.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0035522","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0000338","count":2}]},{"hash":"776531636659367141","title":"Cell division and vesicle trafficking","description":"The top GO terms show a strong emphasis on regulation of the cell cycle and mitotic cytokinesis, along with vesicle-related processes such as Cvt vesicle assembly and nucleus-vacuole junction assembly, suggesting a core theme of intracellular organization during division and trafficking. Additional terms touch on cytoskeleton regulation and developmental contexts, but the dominant signals point to cell division and vesicle transport as the defining features of this cluster.","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007050","count":22},{"id":"GO:1904793","count":20},{"id":"GO:0071562","count":20},{"id":"GO:0015991","count":20},{"id":"GO:0090138","count":20}]},{"hash":"1111612489560819889","title":"Proteoglycan and Glycosylation Biosynthesis","description":"The cluster is enriched for heparan sulfate and chondroitin sulfate proteoglycan biosynthetic processes, along with UDP-D-xylose metabolism and general protein glycosylation, indicating a shared focus on assembling glycosaminoglycan/proteoglycan components and related glycoconjugates. Additional terms related to tissue morphogenesis and cell adhesion molecule production align with extracellular matrix remodeling and cell\u2013matrix interactions, while insulin and thyroid hormone metabolic terms may reflect broader metabolic regulation. Overall, the common theme is proteoglycan and glycosylation biosynthesis driving ECM-related functions.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015012","count":6},{"id":"GO:0050650","count":6},{"id":"GO:0005978","count":4},{"id":"GO:0042403","count":4},{"id":"GO:0006486","count":4}]},{"hash":"439153054117329235","title":"Developmental signaling and proliferation control","description":"These proteins cluster around regulatory signaling (positive regulation of GTPase activity and serine/threonine kinase activity with autophosphorylation) and processes linked to growth and development (mitotic cell cycle, multicellular organism development, transcription). The presence of skin development and cellular response to hypoxia suggests tissue-specific developmental programs that coordinate proliferation and gene expression. Overall, the shared theme is signaling-driven control of development and cell proliferation.","confidence":"Medium","size":24,"edges":56,"triangles":0,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":13},{"id":"GO:0031954","count":12},{"id":"GO:0051028","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0007275","count":12}]},{"hash":"1893089964445924441","title":"Actin Cytoskeleton Remodeling and Signaling","description":"This cluster features terms focused on regulation of GTPase activity, Arp2/3-mediated actin nucleation, and kinase activity, all pointing to signaling pathways that drive actin dynamics. The presence of mitotic cell cycle and protein phosphorylation regulation supports coordinated control during cell growth and division. While mRNA transport and hypoxia response are broader processes, they may reflect general cellular signaling contexts linked to cytoskeletal regulation. Overall, the dominant theme is actin-cytoskeleton remodeling governed by signaling cascades.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0030433","count":7},{"id":"GO:0031954","count":7},{"id":"GO:2000601","count":7},{"id":"GO:0051028","count":7}]},{"hash":"1483849123638631428","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0009409","count":2},{"id":"GO:0015970","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0009086","count":2}]},{"hash":"435277045237081549","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0000961","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0009451","count":2},{"id":"GO:1905639","count":2}]},{"hash":"992603433944123492","title":"Bacterial carbohydrate metabolism and cell-wall biosynthesis","description":"This cluster centers on carbohydrate metabolism (glycogen, starch, glucose) and cell-wall organization, with associated biosynthesis of thiol cofactors (bacillithiol, mycothiol) that support envelope-related processes, plus stress-related responses (water deprivation, flooding). The mix suggests a cohesive theme of metabolic and cell-wall biosynthesis in bacteria, with some stress-responsive elements.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":4},{"id":"GO:0009414","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0019252","count":3},{"id":"GO:0071793","count":3}]},{"hash":"1485019195557002588","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042403","count":2},{"id":"GO:0048702","count":2},{"id":"GO:0015015","count":2},{"id":"GO:0009812","count":2},{"id":"GO:0050427","count":2}]},{"hash":"1169082872429265240","title":"Plant defense signaling and transcriptional regulation","description":"Based on the prominent GO terms, this cluster centers on regulation of gene expression (DNA-templated transcription, miRNA-mediated silencing) and plant-specific signaling pathways (abscisic acid-activated, ethylene-activated) that govern defense responses, development, and cell communication (response to chitin, cell adhesion, centrosome maintenance). The combination suggests a module coordinating transcriptional and post-transcriptional control with hormone signaling and defense, rather than a single enzymatic process.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035278","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0051661","count":2}]},{"hash":"1433459174502830648","title":"Translation initiation and regulation","description":"Based on the Top Terms, several GO terms clearly center on translation initiation and its control, including translation reinitiation, formation of the translation preinitiation complex, and regulation of translational initiation, along with IRES-dependent viral initiation and related viral translation events. While there are a few outliers (neural development, ER-stress\u2013related apoptosis), these are less frequent and may reflect multifunctional annotations rather than a core cluster feature. The strongest cohesive theme is translational initiation and its regulatory steps, justifying this label.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":4},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1099922731883514578","title":"Neural development and GTPase signaling regulation","description":"Top GO terms cluster around neural development processes (axonogenesis, myelination in PNS, regulation of long-term synaptic potentiation) and signaling control via Rho GTPases and kinase activity. While a couple of terms (auxin-activated signaling, blastocyst development) are less neural, the overall pattern points to neuronal differentiation and regulation of signal transduction as the cluster's theme.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":2},{"id":"GO:0006355","count":2},{"id":"GO:1900271","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0043547","count":2}]},{"hash":"113862014455788707","title":"Diverse Catabolic Metabolism","description":"The terms show widespread catabolic activity across diverse substrates (cellulose, diacylglycerol, chlorophyll, acetylcholine). While some biosynthetic and detoxification terms appear, there is no single cohesive pathway; the common thread is broad catabolic metabolism.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":5},{"id":"GO:0042136","count":5},{"id":"GO:0046340","count":5},{"id":"GO:0015996","count":5},{"id":"GO:0098869","count":5}]},{"hash":"1298489593566765662","title":"Glutamatergic Synaptic Transmission and Ion Transport","description":"These terms cluster around neuronal signaling, dominated by ion transport (sodium, potassium, phosphate) and glutamatergic synaptic transmission, consistent with involvement in excitatory neurotransmission and postsynaptic potentials. The presence of 'response to morphine' and 'positive regulation of calcineurin-NFAT signaling' may reflect modulatory pathways or non-neuronal roles, but the strongest signal connects ion transport with glutamatergic synapse function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0006817","count":3},{"id":"GO:0035249","count":2},{"id":"GO:0043278","count":2}]},{"hash":"189623981297459202","title":"Autophagy\u2013lysosome and Fe-S cluster biogenesis","description":"Dominant signals are autophagy and lysosome processes (autophagosome assembly; lysosome organization), with weaker signals for iron-sulfur (Fe-S) cluster assembly/maturation, suggesting a cluster of proteins tied to organelle turnover and Fe-S biogenesis rather than transcriptional regulation. Note that some terms are obsolete, reflecting annotation history rather than core function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000045","count":2},{"id":"GO:0033197","count":2},{"id":"GO:0007040","count":2},{"id":"GO:1900026","count":2},{"id":"GO:1903026","count":1}]},{"hash":"2038408849524735326","title":"Lysosome and Autophagy Regulation","description":"The top terms are dominated by autophagy and lysosome/vacuole trafficking (negative regulation of autophagosome assembly, lysosome localization, Golgi to vacuole transport, contractile vacuole discharge), with a few broader terms. This suggests a functional theme around degradation pathways and organelle trafficking, despite some non-specific GO terms present.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":3},{"id":"GO:1902902","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1252205539735394507","title":"Ubiquitin-Proteasome Regulation in Oocyte Meiosis","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein degradation and polyubiquitination, including SCF-dependent ubiquitin-mediated proteolysis, and with strong links to spindle assembly and oocyte maturation in female meiosis. These suggest proteins that regulate meiotic progression via ubiquitin-proteasome\u2013mediated turnover and spindle dynamics, with additional connections to circadian and microtubule functions.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":17},{"id":"GO:0000209","count":12},{"id":"GO:0031146","count":10},{"id":"GO:0042752","count":10},{"id":"GO:0001556","count":8}]},{"hash":"477318786957767413","title":"Oocyte meiosis and spindle assembly","description":"The top GO terms are dominated by spindle assembly in female meiosis I, oocyte maturation, and microtubule polymerization, with supportive signals from ubiquitin\u2013proteasome\u2013mediated protein catabolic processes during the cell cycle. This pattern points to proteins involved in oocyte development and spindle dynamics rather than general metabolism, hence the label.","confidence":"High","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007057","count":13},{"id":"GO:0008285","count":13},{"id":"GO:0001556","count":13},{"id":"GO:0021678","count":13},{"id":"GO:0021993","count":13}]},{"hash":"964170926845697456","title":"Chromatin remodeling and histone modification","description":"The proteins cluster around epigenetic regulation of chromatin: histone modifications (methylation and acetylation), nucleosome assembly, and chromatin remodeling, with links to DNA repair/recombination in chromatin contexts. Some GO terms are obsolete in current ontologies, but the recurrent theme is chromatin state maintenance and remodeling.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034773","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0031397","count":2}]},{"hash":"2279504295324820969","title":"TLR-Driven Antiviral Transcriptional Response","description":"The cluster overwhelmingly features innate immune and antiviral defense signals (innate immune response, defense response to virus) and Toll-like receptor signaling (TLR3/7/9), coupled with regulation of DNA-templated transcription. This suggests proteins that link pathogen sensing to transcriptional activation during antiviral responses, with some cross-talk signals (ABA/ethylene) that may reflect broader defense signaling. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0034154","count":3}]},{"hash":"638215505353559875","title":"CAAX-box protein maturation and turnover","description":"The cluster centers on CAAX-box and prenylated protein processing/maturation, ubiquitin-dependent degradation, and deneddylation, indicating a theme of post-translational modification and controlled turnover of prenylated proteins. Some terms like nuclear envelope organization may reflect membrane-associated roles, but the strongest signals are CAAX maturation, prenylation-related catabolism, and protein degradation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071432","count":2},{"id":"GO:0006998","count":2},{"id":"GO:0030327","count":2},{"id":"GO:0080120","count":2},{"id":"GO:0071586","count":2}]},{"hash":"1091325308704756396","title":"Cofactor biosynthesis and xenobiotic metabolism","description":"The top GO terms cluster around biosynthesis of cofactors like biotin and ubiquinone, plus related biosynthetic processes (antibiotic biosynthesis). There is also a clear redox/xenobiotic signal (oxidation-reduction, P450 epoxygenase pathway, cellular oxidant detoxification, cellular response to xenobiotic stimulus) and some protein modification terms (methylation, trimethylation, hydroxylation). Taken together, the proteins appear linked to metabolic/cofactor biosynthesis with an accompanying redox and xenobiotic processing dimension, rather than a single narrow function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0009102","count":8},{"id":"GO:0055114","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0032259","count":6}]},{"hash":"960863744801190691","title":"ER-Golgi trafficking and glycosylation","description":"The strongest recurring themes are ER-to-Golgi vesicle transport, GPI anchor biosynthesis, and O-linked glycosylation, pointing to secretory pathway components and membrane-associated protein processing. Proton transmembrane transport also fits with membrane transport, while photosynthesis/light-response terms are present but less represented, suggesting they are less central to this cluster\u2019s core function. Overall, the cluster seems to group proteins involved in secretion and protein modification rather than core photosynthetic processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0006506","count":2},{"id":"GO:0035269","count":2},{"id":"GO:1904964","count":1}]},{"hash":"1085754237358360198","title":"Carbohydrate and Nucleotide Biosynthesis","description":"This cluster centers on carbohydrate metabolism (starch, glycogen, and sucrose biosynthesis) and nucleotide-related processes (AMP salvage), with accompanying biosynthetic themes like phosphatidylinositol metabolism and bacillithiol biosynthesis. Some terms (brain development, response to flooding, obsolete mannosylation) seem out of place and may reflect annotation noise, but the dominant GO terms consistently point to carbohydrate and nucleotide biosynthesis. ","confidence":"Medium","size":23,"edges":207,"triangles":1102,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019252","count":7},{"id":"GO:0005978","count":7},{"id":"GO:0005985","count":7},{"id":"GO:0046488","count":5},{"id":"GO:0044209","count":4}]},{"hash":"1830937523322087179","title":"Unknown","description":"The top GO terms reflect diverse metabolic processes (amino acid biosynthesis and catabolism, vitamin K biosynthesis, fatty acid oxidation) plus an outlier Notch signaling term, yielding no single cohesive functional theme. This heterogeneity makes a concise, representative label difficult to justify beyond Unknown.","confidence":"","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006564","count":8},{"id":"GO:0017000","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0007219","count":7},{"id":"GO:0097053","count":7}]},{"hash":"2286278843609735280","title":"Amino acid catabolic pathways","description":"The top GO terms are dominated by multiple amino acid\u2013specific catabolic processes (L-alanine, L-kynurenine, L-cysteine, glycine, tryptophan to acetyl-CoA, glyoxylate, and related organic acid/phosphonate catabolism), with a secondary signal for glucocorticoid response and Notch signaling that may reflect multifunctional proteins or annotation noise. This pattern points to a coherent metabolic module focused on amino acid degradation rather than a single signaling pathway.","confidence":"Medium","size":23,"edges":55,"triangles":49,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":8},{"id":"GO:0007219","count":8},{"id":"GO:0097053","count":8},{"id":"GO:0019448","count":6},{"id":"GO:0051384","count":6}]},{"hash":"142645226540125259","title":"Light-Related Development and Stress Response","description":"The top GO terms point to light-associated processes (photosynthesis, retina development) alongside cellular stress and apoptosis responses (hypoxia, cadmium, myeloid/hepatocyte apoptosis), with additional regulation terms (ubiquitination, homooligomerization) suggesting a broader regulatory cluster. While there isn\u2019t a single clear function, the shared theme centers on light-related biology and stress response, rather than a specific enzymatic activity or pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0060041","count":4},{"id":"GO:0071456","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0043547","count":4}]},{"hash":"36509484865628137","title":"Unknown","description":"The GO terms span photosynthesis, virus lifecycle steps, DNA repair, various metabolic processes, and stress responses, with no single dominant function tying the cluster together; therefore a cohesive, specific label cannot be determined.","confidence":"","size":23,"edges":252,"triangles":1750,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006284","count":1}]},{"hash":"2229107189063951553","title":"Light-responsive photosynthesis and photoprotection","description":"The cluster centers on photosynthesis and light-response processes, including light harvesting in photosystem I, responses to red/far-red light and various light intensities, photosynthesis in general, nonphotochemical quenching, and chlorophyll/chromophore-related processes, suggesting a cohesive group of chloroplast light-reaction and photoprotection proteins.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:1904964","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0009768","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0010114","count":2}]},{"hash":"2237422429925490303","title":"Chloroplast RNA turnover and chlorophyll degradation","description":"The top GO terms cluster around chloroplast-associated processes: chloroplast-nucleus signaling, chlorophyll catabolic/degradation pathways, and chloroplast-related translation and RNA modification, with a few mitochondrial RNA turnover hints. This suggests a plastid-centered module focused on RNA metabolism and chlorophyll breakdown, with supporting notes on organellar signaling.","confidence":"Medium","size":23,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006412","count":2},{"id":"GO:0006212","count":2},{"id":"GO:1902777","count":2},{"id":"GO:0015996","count":2}]},{"hash":"778596671276562571","title":"Plant photosynthesis and chlorophyll turnover","description":"The cluster is dominated by GO terms tied to photosynthesis, nonphotochemical quenching, and chlorophyll catabolic processes, suggesting proteins involved in chloroplast light reactions and pigment turnover. Additional terms related to plant development appear but are secondary; a few annotations (like insulin response) may reflect cross-plant annotation noise. Overall, the set centers on photosynthetic and pigment-processing functions in plants.","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0010196","count":2},{"id":"GO:0006206","count":2},{"id":"GO:0016310","count":2}]},{"hash":"1547734569198115201","title":"Mitochondrial inner membrane protein import and assembly","description":"Based on the GO terms, the cluster centers on mitochondrial protein handling: insertion of proteins into the mitochondrial inner membrane, assembly of the respiratory chain complex IV, and various aspects of intracellular/membrane-associated protein transport. While some plant-specific terms (stomatal opening, salt response) appear, the strongest signals are mitochondrial import and membrane insertion processes, suggesting a cohesive mitochondrial membrane assembly/transport function.","confidence":"High","size":23,"edges":43,"triangles":30,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":3},{"id":"GO:0033617","count":3},{"id":"GO:0009306","count":2},{"id":"GO:0043953","count":2},{"id":"GO:0065002","count":2}]},{"hash":"439800015587545916","title":"Metal ion transport and detoxification","description":"The GO terms point to a core focus on transport and homeostasis of metal ions (mercury, copper, zinc) and detoxification, including mercury detoxification, mercury transport, copper ion export, and copper/zinc ion transport. Oxidative stress (superoxide metabolism) often accompanies metal handling. While there are a few development-related terms (bud growth, axon guidance, cell-matrix adhesion), these appear secondary, making metal ion transport/detoxification the most representative shared function.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007118","count":2},{"id":"GO:0060396","count":2},{"id":"GO:0008045","count":2},{"id":"GO:0007160","count":2},{"id":"GO:0050787","count":2}]},{"hash":"256476904145376768","title":"Plant hormone signaling and chromatin regulation","description":"Top GO terms reveal strong links to plant-specific signaling (cytokinin-activated, gibberellin response) together with chromatin remodeling and histone acetylation regulation, plus processes in lignin and flavonol biosynthesis and subtelomeric/meiotic chromatin regulation. This points to a cluster of proteins coordinating developmental hormone cues with epigenetic control and secondary metabolism in plants, rather than a single enzymatic pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":10},{"id":"GO:0043044","count":10},{"id":"GO:0009739","count":9},{"id":"GO:1901430","count":9},{"id":"GO:1905839","count":9}]},{"hash":"2104772525968839312","title":"Plant Flower Development and Transcription Regulation","description":"The cluster is dominated by plant-focused terms: flower development, anther development, vegetative phase change, and cytokinin-activated signaling, along with regulation of DNA-templated transcription. Together these point to coordinated transcriptional control during plant developmental programs. Some animal-related terms appear as noise and do not fit the main plant theme, reinforcing the plant development interpretation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009908","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0010321","count":2},{"id":"GO:0048653","count":2}]},{"hash":"1399734081067858961","title":"Nucleotide Metabolism and DNA Maintenance","description":"The top GO terms point to nucleotide-related processes (dephosphorylation; nucleoside monophosphate phosphorylation; NAD+ and CoA biosynthesis) along with DNA-centric activities (DNA repair, DNA replication). A viral process term and other metabolic terms are present, suggesting a broader metabolic/DNA-processing theme rather than a tight, single pathway. The sparse connectivity (edge 1, no triangles) implies a loose association, so this label captures the overall theme rather than a tightly defined module.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016311","count":5},{"id":"GO:0006281","count":4},{"id":"GO:0016032","count":4},{"id":"GO:0009435","count":3},{"id":"GO:0015937","count":3}]},{"hash":"302704826072953909","title":"Mitochondrial nutrient transport and energy regulation","description":"The cluster is dominated by transmembrane transport GO terms for various metabolites and cofactors (phosphate, CoA, thiamine pyrophosphate, pyrimidine nucleotides into mitochondrion, manganese), plus terms tied to nutrient stress responses and energy homeostasis (amino acid starvation response, adaptive thermogenesis, insulin secretion regulation, fatty acid response, liver regeneration). This pattern suggests a cohesive role in mitochondrial transport of nutrients/cofactors and linked energy metabolism, justifying a label focused on mitochondrial metabolite transport and energy regulation.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":19},{"id":"GO:0034198","count":19},{"id":"GO:1990845","count":19},{"id":"GO:0061179","count":19},{"id":"GO:1990519","count":19}]},{"hash":"2200065035802507549","title":"Unknown","description":"The GO terms are highly diverse: several hint at muscle/neural roles (diaphragm contraction, neuromuscular process controlling posture, heart morphogenesis) but many others cover general metabolism, RNA/protein processing, DNA repair, and even fungal cell wall synthesis. There is no single coherent function tying all terms together, and the network shows no edges, so a specific, representative label isn\u2019t justifiable. ","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":5},{"id":"GO:0006281","count":3},{"id":"GO:0050884","count":2},{"id":"GO:0006491","count":2},{"id":"GO:0003007","count":2}]},{"hash":"141140035105636201","title":"Cell Stress Response and Apoptosis","description":"These proteins show enrichment in both transcriptional and cell-cycle related processes (DNA-templated transcription and G1/S transition) along with multiple stress-related proteostasis and apoptotic terms (extrinsic apoptotic signaling, regulation of protein folding and degradation, inclusion body assembly, and stress fiber dynamics). The common theme appears to be cellular stress response coordinating transcription, cell cycle, and apoptosis.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0032435","count":1},{"id":"GO:1903215","count":1}]},{"hash":"1349905872957788752","title":"Mitotic cell division and cytoskeleton dynamics","description":"Based on the dominance of mitosis- and cytoskeleton-related GO terms (cell division, chromosome segregation, mitotic cell cycle, sister chromatid cohesion, microtubule regulation, Arp2/3-mediated actin nucleation, actin patch assembly) and the presence of intracellular protein and protein transport terms, the cluster appears to collect proteins coordinating spindle function, chromosomal motions, and actin-driven remodeling during cell division. The occasional placental development term likely reflects broader roles in proliferative tissues rather than a distinct function for this cluster.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007059","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0007062","count":2}]},{"hash":"623751353672763161","title":"RNA processing and translation initiation","description":"The cluster is enriched for mRNA processing (splicing, splice-site recognition, polyadenylation and tail regulation, RNA modification) and translation initiation/reinitiation, plus small-subunit processome assembly, indicating a cohesive set of post-transcriptional gene expression machineries connecting RNA maturation to translation start.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":12},{"id":"GO:0002188","count":12},{"id":"GO:0006378","count":11},{"id":"GO:0045292","count":10},{"id":"GO:0006376","count":9}]},{"hash":"2119472254579614487","title":"ABA and Ethylene Signaling in Plant Defense and Cuticle","description":"Top GO terms show ABA- and ethylene-activated signaling with transcriptional regulation, plus responses to chitin, seed development, and regulation of wax/cutin biosynthesis and cuticle formation. This points to a plant-specific program integrating hormone signaling, defense, and epidermal barrier development.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1928863900589698079","title":"Gene Expression Regulation and Cell Cycle Control","description":"This cluster's top GO terms include DNA-templated transcription and translation initiation/reinitiation, implying regulation of gene expression at both transcriptional and translational levels, alongside terms about cell cycle transitions (G0 to G1, CDK activity). The mix suggests a cohesive theme around coordinating transcription, translation, and cell-cycle control, with a few outliers such as platelet activating factor biosynthesis that may be less central.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045736","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070317","count":2},{"id":"GO:0006663","count":2}]},{"hash":"1574618923085242187","title":"Plant oxidative stress-driven lignin catabolism","description":"The terms cluster around oxidative stress response and detoxification (cellular oxidant detoxification, response to oxidative stress, hydrogen peroxide catabolic process) together with plant-type cell wall organization and lignin catabolic process, implying proteins involved in ROS defense and lignin remodeling/degradation in plants; a few terms like visual perception and pyruvate import are less central but do not negate the overall theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009664","count":2},{"id":"GO:0046274","count":2},{"id":"GO:0006979","count":2}]},{"hash":"1511458511561762713","title":"Mitochondrial respiration and proteostasis","description":"Reasoning: The terms most represented are mitochondrial processes (mitochondrial electron transport, aerobic respiration) and protein handling/assembly (ubiquitin recycling, negative regulation of proteolysis, protein homotetramerization/heterooligomerization, protein targeting to mitochondrion). This pattern points to a cluster centered on energy production in mitochondria and maintenance of proteostasis.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0008340","count":2}]},{"hash":"69208063798180890","title":"Floral Meristem Identity and Transcription Regulation","description":"This cluster centers on plant development, notably floral/inflorescence meristem identity and determinacy, alongside transcription-related processes such as mRNA capping and transcriptional regulation. The presence of meristem maintenance and determinacy terms suggests a core developmental module, while associated terms (protein methylation, arginine hydroxylation, ubiquitin biosynthesis) indicate regulatory layers at the level of transcription and protein turnover in plants.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0010077","count":1},{"id":"GO:0010582","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0001887","count":1}]},{"hash":"1212394342495124908","title":"Cell Cycle Proliferation and Developmental Signaling","description":"The cluster is dominated by core cell-cycle processes (DNA replication, DNA-templated transcription, cell division, centrosome cycle), indicating strong involvement in proliferation. It also includes multiple signaling pathways (Wnt, ERK/MAPK, Hippo) and development-related terms (nervous system development, T cell receptor signaling), suggesting a broader program linking growth control with developmental signaling. Overall, the proteins appear to coordinate cell growth, division, and developmental signaling networks.","confidence":"High","size":22,"edges":11,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0006351","count":9},{"id":"GO:0090263","count":8},{"id":"GO:0051301","count":7},{"id":"GO:1903715","count":7}]},{"hash":"1320272293200469388","title":"Central carbon metabolism and lipid biosynthesis","description":"The GO terms show strong representation of glycolysis, the TCA cycle, the glyoxylate cycle, and related oxaloacetate/2-oxoglutarate metabolism, plus pathways for malonyl-CoA and long-chain fatty acid biosynthesis. This indicates a cluster of proteins involved in core energy production and lipid biosynthesis, with hypoxia response as a potential ancillary adaptation signal.","confidence":"High","size":22,"edges":228,"triangles":1481,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":13},{"id":"GO:0006103","count":8},{"id":"GO:0006097","count":7},{"id":"GO:0006096","count":7},{"id":"GO:0019878","count":6}]},{"hash":"356777402669743093","title":"Triglyceride and Phospholipid Catabolism","description":"The cluster is dominated by GO terms for lipid breakdown and remodeling: triglyceride catabolic process, triglyceride mobilization, triglyceride acyl-chain remodeling, and phosphatidylcholine/phosphatidylethanolamine catabolic processes. This indicates a cohesive lipid catabolic/remodeling function, possibly coordinating membrane lipid turnover and energy mobilization. Other terms like plant-type cell wall organization and ion transport are present but appear peripheral to the main lipid-focused theme.","confidence":"High","size":22,"edges":37,"triangles":27,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0034638","count":4},{"id":"GO:2000480","count":4},{"id":"GO:0046338","count":3},{"id":"GO:0006642","count":3},{"id":"GO:0010898","count":3}]},{"hash":"1230570445841270272","title":"Ribosome biogenesis and cell proliferation","description":"The cluster shows strong signals for ribosome biogenesis and cell cycle progression (ribosome biogenesis, ribosomal large subunit biogenesis, cell division, positive regulation of cell population proliferation). Brain development terms appear as secondary associations, suggesting possible involvement in neurodevelopmental contexts but not changing the core theme of growth and protein synthesis.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0008284","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0000747","count":3}]},{"hash":"2167322658629300117","title":"Bacterial secondary metabolism and LPS biosynthesis","description":"The cluster is enriched for diverse bacterial biosynthetic processes: antibiotic biosynthesis, lipopolysaccharide (LPS) biosynthesis, phosphinothricin and PHB biosynthesis, and related core metabolic/serine biosynthetic activities. While some catabolic terms appear (ureide, purine, allantoin) the dominant theme centers on production of secondary metabolites and cell-envelope components typical of bacteria, suggesting a cohesive label around bacterial metabolism and envelope biosynthesis.","confidence":"Medium","size":22,"edges":112,"triangles":282,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0009103","count":7},{"id":"GO:1901766","count":6},{"id":"GO:0010136","count":6},{"id":"GO:0006145","count":6}]},{"hash":"1273965957570761006","title":"Embryonic transcriptional regulation and organogenesis","description":"These terms cluster around RNA polymerase II\u2013driven transcription and its regulation, plus several embryonic organogenesis processes (primitive streak formation, midbrain and pituitary development, tooth dentin odontogenesis, Purkinje cell differentiation, and digestive tract morphogenesis). The recurring theme is transcriptional control guiding diverse tissues through embryogenesis, with broader developmental roles rather than a single organ. The ABA response term appears as an outlier, likely due to cross-species annotation rather than a core function of this cluster.","confidence":"Medium","size":22,"edges":117,"triangles":181,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":8},{"id":"GO:0000122","count":7},{"id":"GO:0090009","count":7},{"id":"GO:0030901","count":6},{"id":"GO:0021983","count":6}]},{"hash":"720153256056685913","title":"Redox detoxification and calcium-regulated muscle signaling","description":"The terms point strongly to oxidative stress responses and detoxification (cellular oxidant detoxification, redox homeostasis, glutathionylation, toxin catabolism, arsenic response, vitamin C metabolism) with additional signals of calcium-mediated muscle regulation (positive regulation of calcium release affecting skeletal muscle contraction). This suggests a cluster focused on redox/detox pathways with some involvement in muscle calcium signaling.","confidence":"Medium","size":22,"edges":228,"triangles":1483,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":15},{"id":"GO:0045454","count":15},{"id":"GO:0014810","count":10},{"id":"GO:0009407","count":10},{"id":"GO:0010731","count":10}]},{"hash":"642697381696589292","title":"Ribosome biogenesis and translation machinery","description":"Dominant GO terms center on translation, ribosome assembly, and rRNA processing, with signals for mitochondrial translation termination and ITS2 rRNA processing, indicating core involvement in ribosome production and protein synthesis; some virus- and toxin-response terms likely reflect translational regulation during stress.","confidence":"High","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0070126","count":6},{"id":"GO:0046677","count":6},{"id":"GO:0042255","count":4},{"id":"GO:0000448","count":4}]},{"hash":"40437113165066597","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":6},{"id":"GO:1905639","count":5},{"id":"GO:0070129","count":5},{"id":"GO:0042793","count":5},{"id":"GO:0000961","count":5}]},{"hash":"1928914867467192101","title":"Unknown","description":"The top terms span metabolism (aromatic amino acid biosynthesis, molybdopterin cofactor biosynthesis), sulfur-related RNA modification (tRNA wobble thiolation, urmylation, cysteine persulfide formation), redox homeostasis, signaling (peptidyl-tyrosine dephosphorylation), and developmental processes (epithelial differentiation, spinal cord development) plus a yeast morphology term (regulation of pseudohyphal growth). This wide mix suggests no single cohesive function or pathway tying all proteins together, so there isn\u2019t a clear, specific label beyond Unknown.","confidence":"","size":22,"edges":19,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009073","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0018192","count":2},{"id":"GO:0035335","count":2},{"id":"GO:0045454","count":2}]},{"hash":"2289314082571777791","title":"Redox-Linked tRNA Modification and Urmylation","description":"The cluster is dominated by GO terms connecting redox homeostasis with tRNA wobble uridine thiolation and Urm1-mediated protein modification (urmylation), plus a link to molybdopterin cofactor biosynthesis involved in redox enzymes. This points to a cohesive theme around redox-regulated RNA modification and protein urmylation, rather than disparate tissue- or development-specific roles, though some terms like mitotic M phase and developmental processes are present but less central.","confidence":"Medium","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":2},{"id":"GO:0018192","count":2},{"id":"GO:0035335","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0030855","count":2}]},{"hash":"1866249441557538897","title":"Ubiquitin-ERAD proteostasis and aggrephagy","description":"The cluster is dominated by ubiquitin-related processes (deubiquitination, sumoylation, autoubiquitination) and ERAD pathways, plus an autophagy angle (aggrephagy) for clear protein quality-control function. Together these terms point to a module coordinating ubiquitin signaling, ER-associated degradation, and selective autophagic clearance of misfolded proteins, hence the label. Some terms are obsolete, but the core theme remains proteostasis via ubiquitin/SUMO modification and ERAD- and aggrephagy-related processes.","confidence":"High","size":22,"edges":226,"triangles":1442,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":11},{"id":"GO:0016925","count":10},{"id":"GO:0030433","count":9},{"id":"GO:1904049","count":7},{"id":"GO:1902283","count":7}]},{"hash":"2111576889386219166","title":"Plant defense and chloroplast processes","description":"The top GO terms are dominated by plant-specific processes: thylakoid membrane organization, chlorophyll catabolic process, seedling development, defense response to other organism, and regulation of plant-type hypersensitive response, suggesting the proteins cluster around chloroplast function and plant immunity. A few terms about heart development appear as outliers, likely cross-species annotation noise, but do not override the overall plant-focused theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009271","count":1},{"id":"GO:0010027","count":1},{"id":"GO:0090351","count":1},{"id":"GO:0015996","count":1},{"id":"GO:0009814","count":1}]},{"hash":"1255168148122795261","title":"Peptidoglycan synthesis and cell wall remodeling","description":"The dominant terms describe peptidoglycan biosynthesis, cell wall organization and catabolic processes, plus a cellular response to chitin, pointing to cell wall dynamics as the cluster's core function. Occasional nuclear processes (RNA polymerase transcription/repair) may reflect multifunctional proteins or annotation spillover, but do not redefine the main theme. Therefore, label reflects cell wall synthesis and remodeling.","confidence":"Medium","size":22,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006360","count":3},{"id":"GO:0070816","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0009252","count":2},{"id":"GO:0071555","count":2}]},{"hash":"146898876249237144","title":"Plant Cell Wall Biosynthesis and Modification","description":"This cluster is dominated by GO terms related to plant-type secondary cell wall biogenesis, xylan and xyloglucan metabolism, and cell wall modification, pointing to a shared role in plant cell wall biosynthesis and remodeling. Some unrelated terms (e.g., infection structure, insect development) appear but are likely annotation noise. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":4},{"id":"GO:0075015","count":2},{"id":"GO:0001744","count":2},{"id":"GO:0042248","count":2},{"id":"GO:0007299","count":2}]},{"hash":"785082561027002327","title":"Transcriptional Regulation in Neural Development","description":"Top GO terms indicate broad transcriptional control using RNA Pol II and DNA-templated transcription, while many terms describe neural development and cell fate specification (interneurons, motor neurons, oligodendrocytes). The mixture suggests a cluster of transcriptional regulators coordinating neural development, with some additional developmental roles in other tissues.","confidence":"High","size":22,"edges":178,"triangles":716,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":9},{"id":"GO:0006366","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0021892","count":6},{"id":"GO:0021520","count":6}]},{"hash":"1720360463683315892","title":"Strigolactone Biosynthesis and Shoot Formation","description":"This cluster is dominated by GO terms for strigolactone biosynthetic process and secondary shoot formation, pointing to plant hormone\u2013regulated shoot development. Other terms hint at plastid-related transcription and general protein processing, supporting a plant-specific functional theme centered on strigolactone production and its developmental effects.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010223","count":2},{"id":"GO:1901601","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042793","count":2},{"id":"GO:0050821","count":1}]},{"hash":"1753013570110713409","title":"Plant Hormone Signaling and Metabolic Regulation","description":"This cluster is driven by GO terms for plant hormone signaling (cytokinin-activated signaling pathway, response to gibberellin) and secondary metabolism (lignin and flavonol biosynthesis), suggesting a cohesive theme around growth regulation and metabolism in plants, despite some noisy or ancillary terms. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":10},{"id":"GO:0009739","count":9},{"id":"GO:1901430","count":9},{"id":"GO:1905839","count":9},{"id":"GO:0010520","count":9}]},{"hash":"1347625937000401318","title":"Cardiac Development and Transcription Regulation","description":"This cluster is dominated by GO terms tied to transcriptional regulation (DNA-templated transcription, positive regulation of transcription by RNA polymerase II, chromatin binding regulation, transcription factor activity) and cardiac-related development processes (heart development, cardiac muscle hypertrophy in response to stress, embryonic placenta morphogenesis). While gluconeogenesis appears, the strongest signals point to gene expression control during heart development and related chromatin/modulatory mechanisms, suggesting a group of proteins coordinating transcription in cardiac development contexts.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":4},{"id":"GO:0045944","count":3},{"id":"GO:0035562","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0060669","count":2}]},{"hash":"962420630151282748","title":"Unknown","description":"The top terms show a mix of prokaryotic biosynthetic processes (PHB, lipid A/LPS, polycistronic mRNA processing) and eukaryotic proteoglycan biosynthesis, plus a DNA damage checkpoint and toxin response. This combination does not reveal a single cohesive function or pathway tying the proteins together, suggesting the cluster is heterogeneous rather than a distinct, interpretable module.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0009245","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0031573","count":2}]},{"hash":"1274090521089551307","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0000961","count":3},{"id":"GO:0010019","count":3},{"id":"GO:0009451","count":3},{"id":"GO:1905639","count":3}]},{"hash":"1913374108685713036","title":"Neurodevelopment and Brain Angiogenesis","description":"The top GO terms cluster around brain development (GO:0007420), neural tube patterning (GO:1901621), mesoderm formation (GO:0001707), and angiogenesis (GO:0045766), with supporting signals for synaptic activity (GO:0060079). This pattern suggests proteins involved in early neural development and associated vascularization, possibly coordinating brain structure formation with neural connectivity and blood vessel growth. Some terms are obsolete or peripheral (e.g., ERAD, NF-kappaB regulation), but the core theme points to developmental signaling in neuro-vascular contexts.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0071374","count":2}]},{"hash":"1203624747910853732","title":"mRNA processing and translational regulation","description":"The top GO terms indicate both RNA processing (splicing/spliceosome, splice-site recognition, mRNA polyadenylation) and translation control (preinitiation complex formation, translational initiation, reinitiation, stress-related mRNA stability, viral translation). This suggests a cluster of proteins involved in coordinating RNA processing with regulation of translation, including response to stress and viral mechanisms.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0006446","count":4},{"id":"GO:0006376","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0002188","count":3}]},{"hash":"422155166985253462","title":"Immune signaling and mitotic regulation","description":"This cluster includes immune signaling terms (T cell receptor signaling; natural killer cell differentiation) and mitosis-related terms (mitotic spindle assembly, spindle checkpoint, G2 DNA damage checkpoint, JUN phosphorylation), plus differentiation/migration terms (myoblast differentiation, melanocyte migration). The shared theme seems to be signaling that links immune differentiation with cell cycle regulation, rather than a single cohesive pathway.","confidence":"Medium","size":22,"edges":10,"triangles":1,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":5},{"id":"GO:0097324","count":5},{"id":"GO:0009636","count":5},{"id":"GO:1990801","count":5},{"id":"GO:0014835","count":5}]},{"hash":"1483667399520128046","title":"Unknown","description":"The Top Terms are a highly diverse mix including membrane repair, immune response, chromatin remodeling and transcription regulation, various signaling pathways (vitamin D receptor, jasmonic acid), and even neuronal and metabolic processes. With no edges connecting nodes, there isn't a clear, single functional module tying these proteins together, so a concise, unified label isn\u2019t evident. Confidence: None","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":3},{"id":"GO:0030154","count":2},{"id":"GO:0002250","count":2},{"id":"GO:0045815","count":2},{"id":"GO:0070562","count":2}]},{"hash":"1558634099867045546","title":"Amino acid and ion transmembrane transport","description":"The top GO terms point to transport across membranes for various amino acids (asparagine, arginine, histidine, glutamate, proline) and ions (lithium, potassium), with some vacuolar export/import activity and membrane maintenance context, suggesting a transporter-focused cluster involved in amino acid and ion movement across membranes.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":2},{"id":"GO:0006867","count":2},{"id":"GO:1990818","count":2},{"id":"GO:0090452","count":2},{"id":"GO:0089708","count":2}]},{"hash":"975302759484747851","title":"Unknown","description":"The terms span transcription, vesicle trafficking (COPII), protein ubiquitination, actin dynamics, ribosome biogenesis, and development in diverse tissues, with no single cohesive function or pathway linking them all. This makes it difficult to assign a concise, representative label.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0090114","count":4},{"id":"GO:0032933","count":3},{"id":"GO:1902525","count":3}]},{"hash":"494729138455706779","title":"Plant immune signaling and defense responses","description":"Top GO terms point to defense responses to bacteria and fungi, respiratory burst in defense, SA-mediated signaling, and plant-specific hypersensitive response. While there are a few general terms like intracellular signal transduction and stress responses to heat/ozone, the plant immunity signals dominate, suggesting the cluster represents plant immune signaling and defense pathways.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002679","count":1},{"id":"GO:0009817","count":1},{"id":"GO:1900034","count":1},{"id":"GO:0009816","count":1},{"id":"GO:0035556","count":1}]},{"hash":"1829253287937488153","title":"Pectin biosynthesis and cell wall remodeling","description":"The top GO terms are dominated by mucilage pectin biosynthetic process, pectin catabolic process, and cell wall modification, indicating involvement in pectin metabolism and cell wall remodeling in plants. A few terms like cytoplasmic translation and NF-kappaB signaling appear less relevant or general annotations, likely background noise. Overall, the cluster appears to represent proteins involved in pectin production and remodeling of the plant cell wall.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048358","count":8},{"id":"GO:0045490","count":8},{"id":"GO:0042545","count":8},{"id":"GO:0002181","count":2},{"id":"GO:1903833","count":2}]},{"hash":"1048275452372959814","title":"Gluconeogenesis and amino acid metabolism","description":"This cluster centers on central carbon metabolism, with multiple terms for gluconeogenesis, glycogen regulation, and biosynthesis/metabolism of several amino acids (arginine, citrulline, glutamine). Additional terms for glucocorticoid signaling (response to dexamethasone) and cAMP response suggest hormonal regulation of metabolic pathways, supported by ER-Golgi transport and a cell cycle term that may reflect broader cellular growth context. Overall, the shared theme appears to be carbohydrate and amino acid metabolic processes with regulatory signaling.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0005981","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0005979","count":2}]},{"hash":"1865443123974733931","title":"Golgi-ER vesicle transport and SNARE assembly","description":"The cluster is dominated by GO terms for ER-to-Golgi and intra-Golgi vesicle transport, Golgi-to-vacuole pathways, and SNARE complex assembly, all central to Golgi-associated vesicle trafficking and membrane fusion. This cohesive set supports a label of Golgi-ER vesicle transport with SNARE-mediated fusion.","confidence":"High","size":22,"edges":15,"triangles":5,"max_degree":6,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006896","count":16},{"id":"GO:0048280","count":16},{"id":"GO:0006891","count":16},{"id":"GO:0090161","count":16},{"id":"GO:0006888","count":16}]},{"hash":"69794636656219526","title":"Plant cell wall organization and plasmodesmata regulation","description":"This cluster is dominated by GO terms related to plant cell wall structure and modification (cell wall organization, plant-type cell wall cellulose biosynthetic process, plasmodesma organization, plant-type cell wall modification), suggesting proteins involved in wall assembly and intercellular transport through plasmodesmata. Some terms (phospholipid catabolic process, glucose-6-phosphate transport) and obsolete Wnt pathway entries are likely annotation noise, but the central theme is plant cell wall architecture and plasmodesmatal regulation.","confidence":"Medium","size":22,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0016266","count":2},{"id":"GO:2001009","count":2},{"id":"GO:0009831","count":2},{"id":"GO:0009663","count":2}]},{"hash":"2001085937881345395","title":"TLR-mediated innate immune signaling and antimicrobial peptide regulation","description":"This cluster shows multiple GO terms centered on innate immune responses, including toll-like receptor signaling (TLR8, TLR10), cytokine signaling, detection of bacterial lipopeptides, and regulation of antibacterial peptide biosynthesis and interferon production, suggesting a cohesive theme around immune sensing and antimicrobial defense. Some development-related terms are present but appear less representative of the main function. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019221","count":2},{"id":"GO:0070340","count":2},{"id":"GO:0006963","count":2},{"id":"GO:0072287","count":2},{"id":"GO:0045078","count":2}]},{"hash":"885575257998639352","title":"Membrane Ion Transport and Thermosensation","description":"This cluster centers on membrane-associated ion transport (sodium import, potassium export), membrane hyperpolarization, and thermosensory behavior, pointing to a theme of ion homeostasis coupled with temperature-responsive signaling. Some outlier terms like nucleotide-excision repair and metal detox exist but are less representative of the main function.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0051262","count":3},{"id":"GO:0060081","count":3},{"id":"GO:0040040","count":3},{"id":"GO:0098719","count":3}]},{"hash":"675112385881606347","title":"ER-Golgi Vesicle Transport and Neural Development","description":"This cluster is dominated by GO terms for ER-Golgi vesicle transport and retrograde Golgi-ER transport, indicating a core role in vesicle trafficking. The presence of brain/forebrain development terms suggests these trafficking proteins may be particularly relevant in neural contexts. Additional terms related to transcription, GTPase regulation, pigmentation, and SREBP signaling imply broader regulatory or membrane-related roles that can accompany trafficking functions. Overall, the shared theme appears to be vesicle transport proteins with a neural development association.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0006351","count":4}]},{"hash":"657614039258710302","title":"Core transcription and translation machinery","description":"This cluster's top GO terms cluster around gene expression: DNA-templated transcription (and termination/antitermination), translation, and rRNA pseudouridine synthesis. While a couple plant-specific terms appear (embryo sac development, homogalacturonan biosynthesis), they are less representative than the central transcription/translation processes, suggesting proteins mainly participate in fundamental gene expression rather than a specialized pathway.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0009553","count":2},{"id":"GO:0010289","count":2}]},{"hash":"697451910618278895","title":"Membrane transporters for xenobiotics and lipids","description":"The cluster\u2019s top GO terms center on various transmembrane transport activities: xenobiotic and daunorubicin transport, cobalt and molybdate ion transport, bacteriocin transport, and lipid translocation (phospholipid, ceramide). This points to proteins involved in moving xenobiotics, metals, and lipids across membranes, i.e., detox/transport functions. Some SOS response and transcription elongation regulation terms suggest broader stress responses, but the shared function appears to be membrane transport/ detox roles, justifying this label.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034244","count":3},{"id":"GO:0006824","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0043215","count":3},{"id":"GO:0006855","count":3}]},{"hash":"1875338148156093998","title":"Developmental vesicle trafficking and cytoskeleton","description":"This cluster blends vesicle trafficking/autophagy-related terms (Cvt vesicle assembly, nucleus-vacuole junction) with cytoskeletal regulation via cell-cell adhesion, pointing to morphogenetic processes. It also includes tissue-specific development terms (glial cell fate, CNS vasculogenesis, renal development, larval cuticle formation), suggesting a broad developmental program. The common thread appears to be development coordinated with intracellular trafficking and cytoskeletal remodeling, justifying the label.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:1904793","count":18},{"id":"GO:0071562","count":18},{"id":"GO:0015991","count":18},{"id":"GO:0090138","count":18},{"id":"GO:0007403","count":18}]},{"hash":"1793092559852828423","title":"Mammary gland development and lactation genes","description":"This cluster centers on mammary gland biology, with GO terms such as lactation, mammary gland alveolus development, and regulation of mammary gland epithelial cell proliferation, complemented by transcriptional regulation (DNA-templated transcription) and cell-cycle controls (G2/M transition and re-entry into mitosis) as well as ER unfolded protein response, all consistent with transcriptional coordination and secretory activity during mammary development and lactation.","confidence":"High","size":21,"edges":7,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0007595","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0030968","count":6},{"id":"GO:0000411","count":5}]},{"hash":"1680522619837383023","title":"Plant signaling regulators and meristem maintenance","description":"The top GO terms point to broad regulation of signaling pathways (TGF-beta/BMP, NF-kappaB), alongside processes that control intracellular trafficking and phosphorylation (vacuole fusion, nuclear protein export, peptidyl-threonine dephosphorylation). The presence of meristem identity maintenance and photosystem adjustment hints at a plant-development context. Together, these terms suggest a cluster of regulators coordinating signaling and growth in plants rather than structural components. ","confidence":"Medium","size":21,"edges":51,"triangles":37,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030512","count":10},{"id":"GO:0061191","count":10},{"id":"GO:0042347","count":10},{"id":"GO:0000173","count":10},{"id":"GO:0046827","count":10}]},{"hash":"1341068855644044441","title":"Quinone biosynthesis and related metabolism","description":"Proteins in this cluster are enriched for biosynthetic and catabolic metabolic processes, notably phylloquinone and menaquinone biosynthesis and fatty acid beta-oxidation, along with several amino acid catabolic pathways. This points to a metabolism-centric module tied to redox biology and energy production, rather than a single specialized function.","confidence":"High","size":21,"edges":31,"triangles":14,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0042372","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0006635","count":3}]},{"hash":"1150783757583643569","title":"Neuronal development and synaptic signaling","description":"This cluster centers on neuronal-related processes: dendrite morphogenesis, excitatory postsynaptic potential, transcriptional regulation in neurons, and responses to neural stimuli such as glucose and cocaine, all pointing toward neuronal development, transcriptional control, and synaptic function. A couple terms (immune/angiogenesis) are less aligned and may reflect pleiotropic roles, but the dominant signal is neural development and signaling. ","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0048813","count":11},{"id":"GO:0071333","count":10},{"id":"GO:0050830","count":10},{"id":"GO:0042220","count":10}]},{"hash":"1029711953664036085","title":"Wnt and Hippo signaling in keratinocyte differentiation","description":"This cluster is enriched for positive regulation of canonical Wnt signaling, hippo signaling, and keratinocyte differentiation, suggesting a coherent theme of signaling pathways guiding epidermal cell fate. While other terms (apoptotic process, xenobiotic transport) indicate broader stress-response processes, the strongest shared signal is Wnt/Hippo\u2013driven skin differentiation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":5},{"id":"GO:0035329","count":5},{"id":"GO:0030216","count":5},{"id":"GO:0060044","count":5},{"id":"GO:0006915","count":5}]},{"hash":"1208428107306971494","title":"Unknown","description":"The GO terms span a wide range of unrelated processes (transcription, placenta development, nucleocytoplasmic transport regulation, chemotaxis, metabolism, responses to drugs and hormones, immune signaling, and ion transport). There is no clear, singular function or pathway tying these proteins together, and the cluster has no edges or triangles, suggesting heterogeneity or a spurious grouping. Therefore I cannot assign a specific, coherent label beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":18},{"id":"GO:0001890","count":18},{"id":"GO:0033160","count":18},{"id":"GO:0006935","count":18},{"id":"GO:0006006","count":18}]},{"hash":"1436897092419267050","title":"Neural development with ER stress and cell-cycle signals","description":"The cluster blends neural development terms (forebrain development, neural tube closure) with core cellular processes (mitotic cell cycle, cell division, transcription, ribosome biogenesis, ER-Golgi transport) and stress-induced apoptosis (ER stress\u2013related). This suggests a cohesive theme where neurodevelopment is linked to cell proliferation and ER-stress signaling, despite a few broader terms like defense response that appear less tightly connected. Confidence: Medium","confidence":"","size":21,"edges":176,"triangles":791,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0006888","count":5}]},{"hash":"945604700394112649","title":"Proteostasis and protein quality control","description":"This cluster aggregates functions related to proteostasis: protein processing, ER unfolded protein response, proteasome assembly, endosomal microautophagy, oxidative stress response, and RNA/protein quality control. The mix of degradation, autophagy, and stress signaling suggests a proteostasis/stress-response module rather than a single pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0070651","count":4},{"id":"GO:0061738","count":4},{"id":"GO:0016485","count":4},{"id":"GO:0070682","count":4}]},{"hash":"1608034532075619161","title":"Nuclear transcription and mitotic regulation","description":"Predominant signals are nuclear processes: transcription, nuclear export regulation, kinetochore localization, and mitotic/meiotic cell cycle control, plus CDK activity regulation; a few immune and migration terms are likely noise.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":12},{"id":"GO:0046826","count":11},{"id":"GO:0051321","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0034501","count":10}]},{"hash":"1569796223144409074","title":"DNA Metabolism and Protein Quality Control under Oxidative Stress","description":"Top GO terms show nucleic acid processes (DNA-templated transcription, DNA replication, cell division) alongside redox/oxidative stress responses and ER-related protein folding/ERAD. This suggests a cluster where DNA metabolism and cell cycle functions co-occur with protein quality control in the endoplasmic reticulum under oxidative conditions, hence a combined label.","confidence":"Medium","size":21,"edges":31,"triangles":21,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0034599","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":3}]},{"hash":"477247169036601246","title":"Transcription Regulation and ER Stress Response","description":"It features transcription-related terms (DNA-templated transcription, RNA polymerase II regulation), translation, ER stress response, and redox/modification processes, suggesting a theme of transcriptional control coupled with oxidative and ER-stress signaling.","confidence":"Medium","size":21,"edges":206,"triangles":1256,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0034976","count":3},{"id":"GO:1903026","count":3}]},{"hash":"477548732659337535","title":"Nucleic Acid Methylation and Transcription Regulation","description":"This cluster is enriched for methylation-related activities (peptidyl-lysine methylation/dimethylation, N-terminal peptidyl-glycine methylation, rRNA methylation) and chromatin/transcription-related terms (DNA-templated transcription, rDNA heterochromatin formation) as well as DNA repair. Together these imply a group of proteins involved in shaping chromatin state and transcription through methylation of proteins and RNA, with potential links to genome maintenance. Some metabolic terms (sulfate assimilation, dGTP/IDP catabolic processes) appear as incidental associations rather than core functions.","confidence":"Medium","size":21,"edges":33,"triangles":10,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0018023","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0000103","count":2}]},{"hash":"1058871515952483404","title":"Diverse Small-Molecule Metabolism","description":"The GO terms span oxidation-reduction, lignin biosynthesis, retinol and prostaglandin metabolism, various sugar and aldehyde catabolic processes, and responses to chemical stimuli and physiological signals. There isn\u2019t a single cohesive function, but a broad involvement in metabolism of small molecules and related chemical responses, justifying a label that reflects diverse metabolic processes rather than a specific pathway.","confidence":"Medium","size":21,"edges":45,"triangles":18,"max_degree":10,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":12},{"id":"GO:0009809","count":10},{"id":"GO:0042572","count":10},{"id":"GO:0051160","count":9},{"id":"GO:0033498","count":9}]},{"hash":"1167268235407403656","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009231","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0000961","count":1}]},{"hash":"1129283104548880552","title":"Spliceosome-Mediated mRNA Processing","description":"Most of the top terms center on mRNA splicing and its regulation via the spliceosome (including standard, alternative, and cis-splicing). Additional terms touch on ribophagy, stress-related regulation of mRNA stability, and translation elongation, which together point to a theme of RNA processing and its regulation under cellular stress. While a couple of terms (e.g., viral release) are less directly connected, they do not override the dominant spliceosome/splicing signal. Confidence: High","confidence":"","size":21,"edges":42,"triangles":23,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0034517","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0006414","count":3}]},{"hash":"2262808960542784026","title":"Muscle Redox Homeostasis and Calcium Signaling","description":"The cluster is enriched for antioxidant and detox-related processes (cellular oxidant detoxification, redox homeostasis, glutathione metabolism) plus toxin catabolic and starvation response terms, indicating a general metabolic stress and detox capability. The concurrent calcium-handling terms (regulation of calcium-release channels and muscle contraction regulation) suggest a link to calcium signaling in muscle, a redox-sensitive facet of muscle function. Together, these patterns point to a theme of muscle-associated redox balance coupled with calcium signaling.","confidence":"Medium","size":21,"edges":185,"triangles":910,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":16},{"id":"GO:0045454","count":16},{"id":"GO:1902476","count":15},{"id":"GO:0009072","count":15},{"id":"GO:0009407","count":15}]},{"hash":"2009564995768436714","title":"Mitochondrial lipid biosynthesis and energy metabolism","description":"Most of the top GO terms point to lipid biosynthesis (CDP-diacylglycerol, triglyceride, ether lipids, cardiolipin remodeling) and mitochondrial energy production (mitochondrial ATP synthesis). Cardiolipin remodeling is a mitochondrially localized lipid essential for inner membrane function, linking lipid metabolism to respiration. While a few terms touch on development or immune regulation, the lipid/mitochondrial theme is dominant, suggesting this cluster reflects mitochondrial lipid biosynthesis and energy metabolism.","confidence":"Medium","size":21,"edges":41,"triangles":20,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010143","count":14},{"id":"GO:0042775","count":14},{"id":"GO:0021587","count":14},{"id":"GO:0070236","count":14},{"id":"GO:0016024","count":14}]},{"hash":"1997423940240115492","title":"Cell envelope and surface polysaccharide biosynthesis","description":"The top GO terms cluster around cell wall organization and biosynthesis of surface components (O antigen, lipopolysaccharide) and related sugar metabolism, suggesting these proteins function in building or modifying the cell envelope. Some terms (cilia/photoreceptor localization and certain cell cycle terms) appear as outliers, but the dominant theme is surface biosynthesis. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0090526","count":4},{"id":"GO:0045842","count":4},{"id":"GO:1905515","count":4}]},{"hash":"450564648597378886","title":"Glutathione-Dependent Detoxification and Redox Homeostasis","description":"This cluster is dominated by GO terms related to cellular oxidant detoxification, redox homeostasis, glutathione metabolism, toxin catabolic processes, and responses to arsenic, indicating a core function in antioxidant defense and xenobiotic detoxification. Additional terms about starvation and aromatic amino acid metabolism fit broader metabolic context, while calcium signaling and chloride transport appear peripheral to the main detox/redox theme.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":19},{"id":"GO:0045454","count":19},{"id":"GO:1902476","count":13},{"id":"GO:0014810","count":13},{"id":"GO:0060316","count":13}]},{"hash":"1202365994511417054","title":"Light- and hormone-regulated transcription signaling","description":"The top GO terms cluster around DNA-templated transcription and its regulation, plus light-related pathways (far-red signaling, long-day photoperiodism/flowering) and cytokinin signaling, suggesting a module of transcription factors and signaling proteins controlled by light and hormones in plants.","confidence":"Medium","size":21,"edges":52,"triangles":6,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0032094","count":3},{"id":"GO:0070365","count":3},{"id":"GO:0048579","count":3},{"id":"GO:0010018","count":3}]},{"hash":"324757538449760238","title":"Multisubstrate membrane transporters","description":"The high representation of GO terms for transmembrane transport across diverse substrates (ions, sugars, nitrate, xenobiotics) suggests this cluster groups transporter proteins that ferry multiple substrates across membranes, rather than a single substrate type or non-transport function. The presence of xenobiotic transport, nitrate transmembrane transport, and sugar transport terms indicates broad specificity.","confidence":"High","size":21,"edges":79,"triangles":5,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":9},{"id":"GO:0035435","count":8},{"id":"GO:0015751","count":8},{"id":"GO:0006855","count":8},{"id":"GO:0042128","count":8}]},{"hash":"743619300617894910","title":"Lipid hormone and xenobiotic metabolism","description":"The top GO terms cluster around metabolism and signaling of lipid-derived hormones (prostaglandin biosynthesis, progesterone metabolism, retinoic acid catabolism, vitamin D response, female gonad development) alongside xenobiotic detoxification (carbazole, coumarin, camphor catabolic processes). This points to a coherent theme of enzymes that handle endogenous lipid signaling molecules and external detox substrates, likely through shared metabolic pathways such as cytochrome P450\u2013mediated processes. Some terms like cellular response to potassium ion are broader, but overall the link to lipid hormone and xenobiotic metabolism is strong.","confidence":"Medium","size":21,"edges":17,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":9},{"id":"GO:0046232","count":8},{"id":"GO:0008585","count":8},{"id":"GO:0033280","count":8},{"id":"GO:0010193","count":7}]},{"hash":"545948839236278191","title":"Unknown","description":"The GO terms are too heterogeneous (biosynthesis of several compounds, lipid-related processes, P450 pathways, and stress response) and several terms are obsolete, giving no single coherent function to label this cluster. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0042619","count":10},{"id":"GO:0017000","count":7},{"id":"GO:0046272","count":7},{"id":"GO:0097755","count":7}]},{"hash":"1262239018079411651","title":"Glycolysis, Gluconeogenesis, and PPP Regulation","description":"The cluster is dominated by central carbohydrate metabolism: glycolysis (and its regulation), gluconeogenesis, fructose metabolism, carbohydrate phosphorylation, and pentose-phosphate pathway regulation, with serine biosynthesis tied to glycolytic flux. A few outlier terms (cobalt response, NF-kappaB) are minor and do not disrupt the overall theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045820","count":5},{"id":"GO:0006000","count":5},{"id":"GO:0006094","count":5},{"id":"GO:0016311","count":5},{"id":"GO:0006564","count":4}]},{"hash":"1223513753823458363","title":"Plant Hormone Signaling and Transcription Regulation","description":"GO terms point to plant-specific signaling and transcription control, with cytokinin-activated signaling, DNA-templated transcription and its regulation, and responses to gibberellin and salicylic acid. Additional terms on cell wall biogenesis, chitin response, and epidermal differentiation (atrichoblast) suggest a theme of growth\u2013defense coordination and developmental programs governed by hormone signaling. Despite zero edges, the shared plant regulatory themes indicate a coherent functional cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0009739","count":4},{"id":"GO:0009751","count":4}]},{"hash":"1633897623777508651","title":"Endocytic trafficking and vesicle signaling","description":"This cluster is dominated by terms tied to endocytosis and endosome-to-lysosome transport (including regulation of multivesicular body size), plus exocytosis and related vesicle trafficking. Additionally, there are terms linking to signaling pathways (JNK cascade) and stimulus responses (mechanical stimulus, immune signaling), suggesting the proteins function together in endomembrane trafficking with coordinated signaling roles and responses to external cues. ","confidence":"Medium","size":21,"edges":20,"triangles":6,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":8},{"id":"GO:2000300","count":8},{"id":"GO:0071260","count":8},{"id":"GO:0042088","count":8},{"id":"GO:0031384","count":8}]},{"hash":"1582844699428099755","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:0019740","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2}]},{"hash":"43585379585672134","title":"Metal Ion Transport and Detoxification","description":"The terms point to detoxification and transport of various metal ions (mercury, copper, zinc, cadmium, iron), including detoxification of mercury, mercury/copper/zinc transport, copper homeostasis, and iron regulation. This shared motif indicates a cluster centered on metal ion handling and detox processes.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":2},{"id":"GO:0006801","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0060003","count":2},{"id":"GO:0015694","count":2}]},{"hash":"2072016191519380815","title":"Membrane Transport of Ions, Xenobiotics, and Lipids","description":"The cluster is strongly enriched for various membrane transport terms, including cobalt and molybdate ion transport, daunorubicin and xenobiotic transmembrane transport, phospholipid and ceramide translocation, and long-chain fatty acid import into peroxisomes, suggesting these proteins act together as transporters or trafficking components for metals, drugs/xenobiotics, and lipids. Some terms like cytochrome complex assembly also point to membrane-associated processes, but the dominant theme appears to be diverse membrane transport functions. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006824","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0043215","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0017004","count":4}]},{"hash":"1087119732581506723","title":"Plant ABA and ethylene signaling with cuticle biosynthesis","description":"The cluster is enriched for plant hormone signaling terms (ABA and ethylene) and defense-related responses (response to chitin), plus regulatory processes affecting cutin and wax biosynthesis. This combination suggests a coherent module coordinating hormonal signaling, defense responses, and epidermal cuticle formation, likely governed by transcriptional regulators.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0009873","count":3}]},{"hash":"1306514880737123224","title":"Neural and Lens Development","description":"This cluster\u2019s top GO terms cluster around developmental processes, especially neural development (forebrain development, neural tube closure) and ocular differentiation (lens fiber cell differentiation). Additional terms point to broad development (multicellular organism development) and gene regulation (DNA-templated transcription), consistent with a set of developmental regulators. Some annotations (defense response to Gram-positive bacterium, cellular response to cadmium ion, regulation of gene expression by genomic imprinting) may reflect pleiotropy or annotation noise, but the dominant theme remains neural/eye development and transcriptional control during development.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070306","count":10},{"id":"GO:0030900","count":10},{"id":"GO:0001843","count":10},{"id":"GO:0070059","count":10},{"id":"GO:0006351","count":10}]},{"hash":"1831271505725600085","title":"ER-associated RNA processing and stress response","description":"The top GO terms point to endoplasmic reticulum (ER) functions such as ER-to-Golgi transport and ER-associated degradation, alongside RNA metabolism activities like mRNA capping, guanine-N7 methylation, nonsense-mediated decay, and mRNA export. This suggests a cluster of proteins involved in ER quality control and processing/handling of mRNA, with an ER-stress\u2013elicited apoptosis component. Some terms like osteoblast differentiation and cell division may be incidental but do not override the dominant ER/RNA processing theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0036265","count":3},{"id":"GO:0006370","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070059","count":3}]},{"hash":"964611332075675922","title":"CDK-regulated cell cycle and transcription","description":"This cluster is dominated by GO terms for DNA-templated transcription, DNA replication initiation, cell division, and regulation of G2/M with CDK activity, pointing to a core theme of cell cycle control and transcriptional regulation. Some tissue-specific terms appear, but the central pattern aligns with CDK-mediated cell cycle progression and transcription.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045737","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0006270","count":2},{"id":"GO:0010444","count":2}]},{"hash":"311966670678432206","title":"Unknown","description":"The terms span plant-specific processes (chlorophyll and cellulose catabolism) and diverse biological areas (hypoxia response, detoxification, endothelial migration, T cell costimulation, and neural/behavioral traits), with no edges linking members, indicating no cohesive, shared function. This lack of a unifying theme makes a precise label inappropriate, so Unknown is appropriate. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0015996","count":5},{"id":"GO:0008284","count":4},{"id":"GO:0030245","count":4},{"id":"GO:0001666","count":4},{"id":"GO:0031295","count":4}]},{"hash":"1730161978962205799","title":"Plant secondary metabolite biosynthesis and catabolism","description":"This cluster is enriched for diverse secondary metabolism pathways (stilbene, alkaloids, antibiotic biosynthesis) and glycoside processing, along with detoxification and stress responses (oxidant detoxification, response to hypoxia, response to toxic substances). The combination suggests a cohesive theme around production and turnover of plant defensive metabolites and their processing, with some accompanying core metabolic activities such as biotin biosynthesis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0001666","count":3}]},{"hash":"839045760583562337","title":"ABA/Cytokinin/GA Plant Hormone Signaling","description":"The cluster is dominated by GO terms for abscisic acid-, cytokinin-, and gibberellin-activated signaling, pointing to plant hormone signaling pathways as the unifying function. Additional terms related to biotic responses (defense, nodulation) and regulatory processes (protein phosphatase activity regulation) fit with signaling networks and hormone cross-talk in plants. While a few terms (e.g., synapse assembly) may be less directly connected, the strongest signals are clearly plant hormone signaling, making this a cohesive, interpretable cluster.","confidence":"High","size":21,"edges":24,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":5},{"id":"GO:0009736","count":3},{"id":"GO:0043086","count":3},{"id":"GO:0080163","count":3},{"id":"GO:0009740","count":3}]},{"hash":"2068724187693240833","title":"Detox and Strigolactone Metabolism","description":"The predominant terms are detoxification-related (oxidation\u2013reduction, cellular oxidant detoxification, response to toxic substance) together with strigolactone biosynthesis and response, suggesting a functional cluster around detox pathways and strigolactone metabolism in plants.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009086","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0019391","count":2}]},{"hash":"1600419615912977991","title":"Unknown","description":"The top GO terms span DNA-templated transcription, multiple stress responses (SOS, antibiotic, nutrient), development processes (plant vascular patterning and multicellular development), and diverse metabolic/transport roles (cobalt transport, lipoprotein response, sorocarp morphogenesis), with no clear single theme linking them. Therefore a concise, representative label is not evident.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0010222","count":3}]},{"hash":"295115495995097275","title":"Endosome\u2013lysosome trafficking","description":"The proteins are associated with vesicular transport between the Golgi, endosomes, and lysosomes, including endosome-to-lysosome transport, Golgi-to-endosome transport, vesicle docking in exocytosis, and lysosome organization, pointing to a cohesive role in endolysosomal trafficking.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0008333","count":6},{"id":"GO:0051291","count":4},{"id":"GO:0006895","count":4},{"id":"GO:0006904","count":4},{"id":"GO:0043524","count":4}]},{"hash":"2171535259621671894","title":"Nuclear transcription and cell cycle in development","description":"The cluster shows strong signals for DNA-templated transcription, multicellular development, and mitotic spindle assembly, indicating a focus on nuclear transcriptional regulation and cell division during development. Some metabolic terms appear, but the core theme centers on transcription and cell-cycle processes in a developmental context, justifying this label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1856835646469323928","title":"Plant detoxification and secondary metabolite catabolism","description":"The top GO terms point to a set of catabolic and detoxification processes across plant metabolites and xenobiotics (glucuronoside, stilbene, uracil, dichloroethane catabolism) and include detoxification via cellular oxidant pathways and P450 epoxygenases, along with strigolactone biosynthesis and response. This pattern suggests a cohesive theme around breakdown and detoxification of diverse plant-derived compounds and xenobiotics, rather than a single, narrow function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0019391","count":1},{"id":"GO:1901601","count":1}]},{"hash":"1189808721818037114","title":"Ion and nutrient starvation signaling with transport","description":"The GO terms point to cellular responses to potassium and nitrogen starvation, ABA-activated signaling, transcriptional and splicing regulation, and calcium-regulated secretory/exocytic processes, along with intracellular protein transport. This suggests a cohesive stress-signaling and trafficking program coordinating nutrient/ion stress with transcription and secretion.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051365","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006376","count":2}]},{"hash":"2074307368118277789","title":"Fatty acid biosynthesis and diverse metabolism","description":"The top GO terms show fatty acid biosynthetic processes (fatty acid biosynthesis and long-chain fatty-acyl-CoA metabolism) as dominant, suggesting lipid biosynthesis is the central theme of this cluster. The presence of several catabolic and fermentation terms (inositol, mandelate, pyruvate fermentation to ethanol, butanediol) indicates additional, diverse metabolic activities associated with this cluster. Altogether, the cluster appears to center on fatty acid biosynthesis with broader metabolic capabilities.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":8},{"id":"GO:0035336","count":8},{"id":"GO:0090180","count":5},{"id":"GO:0032923","count":5},{"id":"GO:0000951","count":5}]},{"hash":"467546690144619477","title":"DNA replication and cell cycle regulation","description":"The top GO terms are dominated by nuclear processes: DNA replication, DNA-templated transcription, the centrosome cycle, and regulation of the nuclear cell cycle, pointing to a core theme of DNA replication and cell cycle control. A few terms relate to development and signaling (embryonic cranial skeleton morphogenesis, T cell receptor signaling, melanocyte migration, response to toxic substances), which may reflect pleiotropic roles or broader cellular context in these proteins. Overall, the cluster appears centered on DNA replication and cell cycle regulation with some peripheral functional associations.","confidence":"Medium","size":20,"edges":11,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006813","count":11},{"id":"GO:0006260","count":10},{"id":"GO:0006351","count":8},{"id":"GO:0007098","count":8},{"id":"GO:0048701","count":8}]},{"hash":"2124342914876495475","title":"Viral budding via ESCRT/MVB pathways","description":"The top GO terms center on viral release/budding and host ESCRT machinery, including viral life cycle and multivesicular body (MVB) sorting pathways, with related vesicle transport to vacuoles. While some cell-cycle terms are present, the strongest and most coherent theme is viral budding dependent on ESCRT and MVB trafficking, indicating a cluster of host\u2013virus interaction processes.","confidence":"High","size":20,"edges":32,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:1902187","count":7},{"id":"GO:0043328","count":7},{"id":"GO:0051301","count":7},{"id":"GO:1902188","count":7},{"id":"GO:0010458","count":7}]},{"hash":"206763890032547698","title":"Unknown","description":"The GO terms mix immune signaling (T cell receptor signaling, NK differentiation), development/differentiation (melanocyte, myoblast), and cell cycle/checkpoint processes (mitotic spindle assembly, G2 checkpoint) with other signaling terms, and there isn\u2019t a single cohesive function linking all proteins. None","confidence":"","size":20,"edges":18,"triangles":3,"max_degree":5,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":20},{"id":"GO:0097324","count":20},{"id":"GO:0009636","count":20},{"id":"GO:1990801","count":20},{"id":"GO:0014835","count":20}]},{"hash":"1412458203467298095","title":"mRNA Splicing, Processing, and Export","description":"This cluster centers on spliceosome-mediated mRNA splicing, mRNA export from the nucleus, and various aspects of mRNA modification and polyadenylation, indicating a cohesive role in mRNA maturation and trafficking. The presence of regulatory ncRNA-mediated gene silencing and translation reinitiation terms suggests additional post-transcriptional control mechanisms but remain connected to RNA processing.","confidence":"High","size":20,"edges":60,"triangles":71,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":13},{"id":"GO:0031047","count":13},{"id":"GO:0006378","count":11},{"id":"GO:0045292","count":11},{"id":"GO:0006406","count":11}]},{"hash":"1796509873491831033","title":"Iron-sulfur cluster biogenesis & iron-responsive transcription","description":"This cluster is dominated by GO terms related to [2Fe-2S] cluster assembly and maturation, iron-regulated transcription from RNA polymerase II, and responses to iron availability. The presence of chloroplast-nucleus signaling and mitochondrial RNA processes suggests coordination of Fe-S biogenesis with organellar signaling and transcriptional regulation, pointing to a cohesive function in Fe-S cluster maturation coupled to iron-responsive gene expression.","confidence":"High","size":20,"edges":188,"triangles":1105,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0034396","count":2},{"id":"GO:0044571","count":2}]},{"hash":"2210780763383266211","title":"Glycan and polysaccharide biosynthesis","description":"The cluster is characterized by multiple carbohydrate biosynthesis GO terms (starch, amylopectin, glycogen, alpha-glucan) and related glycosylation processes, indicating a core function in building and decorating glycans and cell-wall polysaccharides, with ancillary links to thiol-based biosynthesis and lipid biosynthesis; overall, this points to a cohesive theme of glycan/polymer biosynthesis and glycosylation. ","confidence":"Medium","size":20,"edges":14,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019252","count":3},{"id":"GO:0010021","count":3},{"id":"GO:0071793","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0097502","count":3}]},{"hash":"608895956408304009","title":"Mitochondrial Metabolism and Xenobiotic Detox","description":"The top GO terms cluster around mitochondria-related processes (mitochondrial translation, fatty acid catabolic process) and detox/molecule-processing pathways (cellular oxidant detoxification, response to xenobiotic/toxic substances, prostaglandin biosynthesis). This suggests a coherent module focused on mitochondrial energy metabolism coupled with detox signaling and lipid handling; scattered terms like nylon catabolic process and transamidation-related tRNA biosynthesis may be annotations hitching to mitochondrial contexts, but the overall theme remains mitochondria-centered metabolism and stress response.","confidence":"High","size":20,"edges":42,"triangles":10,"max_degree":9,"top_function":"autophagy","top_go_terms":[{"id":"GO:0032543","count":5},{"id":"GO:0046835","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0009410","count":5},{"id":"GO:0009062","count":4}]},{"hash":"1336471400506668576","title":"Renal development and steroid hormone metabolism","description":"The cluster centers on kidney development and hormone-related metabolism, with strong representation of renal system development and inner medullary collecting duct development, alongside C21-steroid hormone biosynthesis and progesterone metabolic process. The presence of thyroid hormone response and prostaglandin signaling further suggests coordinated hormonal regulation, with tissue homeostasis as a broader context. Retinal/retinol metabolism terms are present but likely secondary to the renal-hormonal theme.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":20},{"id":"GO:0042572","count":20},{"id":"GO:0001894","count":19},{"id":"GO:2000353","count":19},{"id":"GO:0097066","count":19}]},{"hash":"897202068317376276","title":"Unknown","description":"The terms cover nucleotide biosynthesis (dATP, AMP salvage, adenosine salvage), various carbohydrate-related pathways (tagatose-6-phosphate catabolism, sucrose response, carbohydrate phosphorylation) and mitochondrial translation, which do not point to a single cohesive theme. The cluster has only a single edge and no triangles, indicating weak functional connectivity among members. Because there is no clear shared function uniting the proteins, a precise label could not be assigned. ","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097171","count":7},{"id":"GO:0032543","count":6},{"id":"GO:0019512","count":6},{"id":"GO:0006175","count":6},{"id":"GO:0006169","count":6}]},{"hash":"1060282355115225790","title":"APC/C-Mediated Mitosis and Ubiquitination","description":"These proteins cluster around mitotic progression and ubiquitin-dependent proteolysis: strong signals for mitotic cell cycle, APC/C-dependent catabolic processes, and K11-linked ubiquitination imply regulation of chromosome segregation via ubiquitin-mediated degradation. Additional terms about GTPase activity and histone methylation suggest supportive roles in spindle dynamics and chromatin remodeling during division. Some terms (cadmium response, growth hormone response) appear peripheral, but do not alter the dominant mitotic/ubiquitin theme. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007568","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0070979","count":4},{"id":"GO:0000278","count":4}]},{"hash":"1788874573015492191","title":"Unknown","description":"The terms span nuclear processes (DNA replication, DNA-templated transcription, negative regulation of protein export from nucleus), metabolism (glucose metabolic process), intracellular transport and localization (protein localization to microtubule), development (cerebellar cortex development, melanocyte migration), and immune signaling (innate immune response, T cell receptor signaling). There isn\u2019t a single clear function or pathway that unites these terms, so a cohesive label is not evident.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006006","count":7},{"id":"GO:0021695","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0045087","count":7}]},{"hash":"1029042983825513932","title":"Heavy Metal Transport and Homeostasis","description":"This cluster's top GO terms center on transport and detoxification of metal ions (mercury, copper, zinc, cadmium) and related ion homeostasis, suggesting proteins that move and regulate metal ions and respond to metal exposure.","confidence":"High","size":20,"edges":57,"triangles":74,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":3},{"id":"GO:0006801","count":3},{"id":"GO:0006878","count":3},{"id":"GO:0060003","count":3},{"id":"GO:0015694","count":3}]},{"hash":"876216139880143644","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060716","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0034965","count":2},{"id":"GO:0001682","count":2},{"id":"GO:0000294","count":2}]},{"hash":"1810448816685961765","title":"Unknown","description":"The top GO terms cover extracellular matrix remodeling, chromatin organization, ribosome biogenesis and rRNA processing, cell morphogenesis/division, and even cellular fusion, with a few obsolete terms. There isn\u2019t a single coherent function tying these together, so a unified label isn\u2019t reliable.","confidence":"","size":20,"edges":21,"triangles":4,"max_degree":7,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0030574","count":3},{"id":"GO:0035551","count":3},{"id":"GO:0034724","count":3},{"id":"GO:0034396","count":3},{"id":"GO:0046677","count":3}]},{"hash":"1747048606153739476","title":"Flavonoid Biosynthesis and Xenobiotic Metabolism","description":"The top GO terms point strongly to flavonoid/anthocyanin biosynthesis (kaempferol and quercetin O-glucoside, anthocyanin-containing compounds) and related detoxification/modification (glucuronidation, xenobiotic processing), suggesting a cohesive theme of aromatic secondary metabolite production and processing. Some terms (e.g., paranode localization) appear as noise, but the flavonoid-related signals are dominant.","confidence":"Medium","size":20,"edges":29,"triangles":16,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0009718","count":8},{"id":"GO:0002175","count":5},{"id":"GO:0071412","count":5},{"id":"GO:0016999","count":5}]},{"hash":"765893805933148555","title":"Plant cell wall biogenesis and xyloglucan metabolism","description":"The top GO terms are dominated by plant cell wall-related processes (cell wall biogenesis, fungal/plant cell wall organization, plant-type cell wall modification) and xyloglucan metabolism, with an additional plant development term (stamen filament development) supporting a cell wall remodeling/development theme in plants. A few terms related to transporter activities appear as outliers, but do not define the cluster's core function. Thus the label reflects the main signal: plant cell wall biosynthesis and modification, especially xyloglucan metabolism. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042546","count":5},{"id":"GO:0032491","count":5},{"id":"GO:0006037","count":5},{"id":"GO:0031505","count":5},{"id":"GO:0009831","count":5}]},{"hash":"295135559327179421","title":"Ubiquitin-dependent TNF signaling and NF-kB regulation","description":"This cluster centers on ubiquitin-dependent protein catabolic processes and autoubiquitination, with consistent links to TNF-mediated signaling and regulation of I-kappaB phosphorylation. Together these terms indicate a cohesive theme of ubiquitin-driven control of the TNF/NF-kB inflammatory signaling axis. While a term like V(D)J recombination appears, the dominant pattern is ubiquitin-proteasome\u2013linked regulation of TNF/NF-kB signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":14},{"id":"GO:0051865","count":9},{"id":"GO:2000620","count":9},{"id":"GO:0033209","count":9},{"id":"GO:0070512","count":9}]},{"hash":"382753372506632743","title":"Mesodermal Muscle and Cardiovascular Differentiation","description":"The top GO terms cluster around skeletal muscle differentiation and adaptation, paraxial mesoderm differentiation, and cardiovascular morphogenesis (aorta) plus heart-rate regulation, pointing to mesoderm-derived muscle and heart development. Additional neural/neuroendocrine terms appear as broader lineage ties but do not outweigh the core mesodermal differentiation theme.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":11},{"id":"GO:2001016","count":10},{"id":"GO:0032933","count":8},{"id":"GO:0043503","count":8},{"id":"GO:0061103","count":8}]},{"hash":"1433994564136611563","title":"Photosynthesis and light-reaction proteins","description":"Most represented terms are photosynthesis and light-reaction processes, indicating these proteins are tied to photosynthetic energy capture. Other terms are sporadic or obsolete (uracil catabolic process, menaquinone biosynthesis, etc.), suggesting some annotation noise. Therefore, name reflects the dominant signal: Photosynthesis and light-reaction proteins.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0019684","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0009234","count":2}]},{"hash":"1982612181960895279","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":17},{"id":"GO:0031047","count":17},{"id":"GO:0006369","count":15},{"id":"GO:0000398","count":15},{"id":"GO:0071031","count":14}]},{"hash":"2202050216279927284","title":"Plant cell wall remodeling and plasmodesmata signaling","description":"This cluster centers on plant-specific cell wall biology, notably regulation of cellulose biosynthesis and plasmodesma organization, suggesting a module for cell wall remodeling and intercellular transport. The presence of light-responsive and hormone-related terms indicates associated signal transduction and stress response aspects in plants, tying these processes together as a functional plant cell wall signaling cluster.","confidence":"High","size":20,"edges":87,"triangles":132,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2001009","count":5},{"id":"GO:0009831","count":5},{"id":"GO:0009663","count":5},{"id":"GO:0032355","count":3},{"id":"GO:0045008","count":3}]},{"hash":"344678716582486119","title":"Ribosome biogenesis and RNA processing","description":"The proteins are enriched for translation, rRNA processing, preribosome assembly, and tRNA maturation terms, pointing to involvement in ribosome biosynthesis and RNA maturation. Although a few terms touch on DNA metabolism, the strongest theme centers on ribosome assembly and protein synthesis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006364","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1588953957104685449","title":"Plant Hormone Signaling and Transcription Regulation","description":"These proteins are enriched for regulation of DNA-templated transcription and hormone signaling terms (ABA- and ethylene-activated pathways), with additional terms for defense, development, and cuticle biosynthesis (response to chitin, seed development, cutin and wax biosynthesis). This suggests a set of plant transcriptional regulators that integrate hormone signals to control development, defense responses, and cuticle formation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0009738","count":4},{"id":"GO:0009873","count":4},{"id":"GO:0010200","count":4}]},{"hash":"1421094890813187870","title":"Membrane trafficking and signaling","description":"The listed GO terms cluster around vesicle transport and membrane dynamics\u2014late endosome to vacuole sorting, protein transport, abscission, and plasma membrane repair\u2014together with signaling processes such as thrombin-activated receptor signaling and axon guidance. Developmental terms also tie to cellular processes that depend on membrane trafficking. Some viral-related terms may reflect host\u2013virus interactions rather than core protein function, but the dominant theme is membrane trafficking and associated signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":2},{"id":"GO:0048672","count":1},{"id":"GO:0046745","count":1},{"id":"GO:0009838","count":1},{"id":"GO:0032511","count":1}]},{"hash":"1882035487522939567","title":"Proteostasis and Oxidative Stress Response","description":"This cluster is dominated by GO terms tied to protein quality control, proteolysis, and responses to oxidative stress, including peroxisomal protein import and chaperone-mediated assembly. The convergence on proteostasis mechanisms under oxidative conditions suggests a shared function in maintaining protein homeostasis when cells experience oxidative stress, with peroxisomal involvement.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0070407","count":3},{"id":"GO:0034766","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0006515","count":3},{"id":"GO:0016558","count":3}]},{"hash":"2050519186336824366","title":"Unknown","description":"The terms span diverse processes (DNA replication and mitotic checkpoints, T/NK cell signaling, melanocyte migration, myoblast differentiation, and stress responses) with no single dominant function, so there isn\u2019t a cohesive label that clearly fits the cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":19},{"id":"GO:0050852","count":17},{"id":"GO:0097324","count":17},{"id":"GO:0009636","count":17},{"id":"GO:1990801","count":17}]},{"hash":"1198402175683317897","title":"Auxin-responsive transcription and plant development","description":"The cluster\u2019s GO terms center on DNA-templated transcription and plant developmental processes driven by auxin, including response to auxin, auxin-activated signaling, sepal development, and somatic embryogenesis. While there are general terms like ribosome biogenesis and protein homooligomerization, the highlighted auxin-related transcriptional regulation and developmental programs best capture the cluster\u2019s theme. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0001403","count":2}]},{"hash":"1409985933770927621","title":"Kinase signaling regulators","description":"The terms cluster around regulation of phosphorylation and signaling (positive regulation of serine/threonine kinase activity, autophosphorylation, and GTPase activity regulation), along with TORC1 and SREBP signaling, ubiquitination, and related processes like mRNA transport. This pattern suggests a group of proteins that modulate signaling cascades and post-translational modification rather than a single pathway, justifying a concise label focused on phosphorylation-driven signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":10},{"id":"GO:0070317","count":9},{"id":"GO:0031954","count":9},{"id":"GO:0051028","count":9},{"id":"GO:0038202","count":9}]},{"hash":"1406051208844295266","title":"ER-Golgi trafficking and RNA processing regulators","description":"The cluster\u2019s top GO terms mix ER-to-Golgi and Golgi-to-ER vesicle transport with RNA processing (splicing, RNA transport, RNA methylation) and related regulatory activities (TORC1 signaling, GTPase regulation, serine dephosphorylation, actin nucleation control). This suggests a cohesive theme around intracellular trafficking coupled to RNA metabolism and signal-regulatory processes, rather than a single isolated function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0051028","count":3}]},{"hash":"2257046988977439714","title":"Ubiquitin-Proteasome-Driven Protein Degradation","description":"Most enriched GO terms describe ubiquitin-dependent protein catabolic processes and SCF-dependent proteasomal degradation (ERAD, polyubiquitination). This indicates a cohesive function in ubiquitin-proteasome\u2013mediated protein turnover, including cell-cycle regulation. A few other terms appear incidental. Overall, the cluster centers on ubiquitin-proteasome\u2013driven degradation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0030433","count":6},{"id":"GO:0000209","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0060041","count":5}]},{"hash":"432969799917483512","title":"Eicosanoid biosynthesis and inflammatory signaling","description":"This cluster is characterized by GO terms tied to lipid mediator production\u2014prostaglandins, leukotrienes, and lipoxygenase pathways\u2014as well as immune and oxidative stress responses (response to cytokine, response to LPS, cellular oxidant detoxification, lipid hydroperoxide response). While a couple terms (Leydig cell differentiation, cornification) are less clearly connected, the dominant pattern is biosynthesis of lipid-derived inflammatory mediators and related signaling. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070207","count":2},{"id":"GO:0034097","count":2},{"id":"GO:0071449","count":2},{"id":"GO:0033327","count":2},{"id":"GO:0098869","count":2}]},{"hash":"2105323526817118663","title":"Protein oligomerization and complex assembly","description":"The cluster is enriched for GO terms related to protein oligomerization and assembly\u2014positive regulation of oligomerization, homotetramerization, and heterooligomerization\u2014indicating a shared function in forming protein complexes. Other terms like insulin receptor signaling and aerobic respiration appear but are broader contexts and do not override the central oligomerization signal.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032461","count":3},{"id":"GO:0008286","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0051291","count":2}]},{"hash":"671118463002394185","title":"Cellular Regulation and Metabolism","description":"The cluster shows GO terms spanning transcription, signaling (insulin receptor), energy metabolism (aerobic respiration), protein complex formation (homotetramerization/heterooligomerization), lifespan determination, and catabolic/proteostasis processes (bradykinin catabolic, amyloid-beta metabolic, negative regulation of proteolysis). This mix points to a broad coordination of cellular regulation and metabolic processes rather than a single, specific pathway. Some terms appear less coherent with the core theme (e.g., bud site selection), indicating annotation heterogeneity; overall, the label captures the common functional thread. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0051291","count":2}]},{"hash":"203226394000583733","title":"Meiotic DNA Repair and Recombination Machinery","description":"This cluster centers on DNA replication and meiosis-specific genome maintenance, with multiple terms for recombination and repair (SDSA, heteroduplex formation, reciprocal meiotic recombination) and telomere maintenance via recombination. The presence of protein oligomerization terms supports assembly into multi-subunit meiotic complexes, and germline/oocyte fate terms suggest a meiosis-focused context. Overall, these proteins likely function together in meiotic DNA repair and recombination pathways.","confidence":"High","size":19,"edges":136,"triangles":534,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0006268","count":8},{"id":"GO:0045003","count":7},{"id":"GO:0030491","count":6},{"id":"GO:0007131","count":6}]},{"hash":"1244237559968984326","title":"Immune Signaling and Cell Differentiation","description":"The top GO terms cluster around T cell receptor signaling, NK cell differentiation, and differentiation of other lineages (myoblasts, melanocytes), as well as related signaling events like JUN phosphorylation. This indicates a theme of immune activation coupled with broader cell differentiation processes, even though some mitosis-related terms are present, they likely reflect shared regulatory signaling rather than a single mitotic function.","confidence":"Medium","size":19,"edges":38,"triangles":23,"max_degree":10,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":19},{"id":"GO:0097324","count":19},{"id":"GO:0009636","count":19},{"id":"GO:1990801","count":19},{"id":"GO:0014835","count":19}]},{"hash":"1365907565068226679","title":"Mitotic spindle and microtubule organization","description":"Most top terms describe microtubule-based processes essential for mitosis and spindle function: mitotic spindle assembly, minus-end directed microtubule sliding, spindle elongation, kinetochore-microtubule attachment, and nuclear migration along microtubules. A few terms touch on microtubule stability in other contexts (e.g., neuron projection maintenance), but the dominant signal is spindle dynamics and microtubule organization during cell division.","confidence":"High","size":19,"edges":140,"triangles":642,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:1990535","count":19},{"id":"GO:0001560","count":19},{"id":"GO:0072092","count":19},{"id":"GO:0031534","count":19},{"id":"GO:0000022","count":19}]},{"hash":"2292312081896484876","title":"Kinetochore-Mitosis and DNA Replication Regulators","description":"This cluster is dominated by mitosis- and DNA replication-related terms: kinetochore localization, centrosome cycle and separation, DNA replication, and regulation of CDK activity, all pointing to cell-cycle control during mitosis. Developmental and proliferation terms fit within this core theme, while potassium transport appears as a minor outlier. Overall, the set represents proteins involved in mitotic regulation and DNA replication.","confidence":"High","size":19,"edges":36,"triangles":70,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":8},{"id":"GO:0006260","count":7},{"id":"GO:0045736","count":7},{"id":"GO:0035335","count":7},{"id":"GO:0007098","count":6}]},{"hash":"2045300452816684187","title":"Neural development and dendrite morphogenesis","description":"The top GO terms are centered on nervous system development, neural tube closure, forebrain development, and dendrite morphogenesis, indicating a cohesive theme of neural formation and neuronal morphology. Some terms (e.g., T cell signaling, melanocyte migration, ER-stress\u2013related apoptosis) are peripheral but do not override the dominant neurodevelopmental signal. Thus, the cluster is best described as neural development and dendrite morphogenesis.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0001843","count":8},{"id":"GO:0070059","count":8},{"id":"GO:0007399","count":8},{"id":"GO:0048813","count":8},{"id":"GO:0030900","count":8}]},{"hash":"678231490283856350","title":"Immune signaling and mitotic regulation","description":"The top GO terms show strong representation of immune-related signaling (T cell receptor signaling, NK cell differentiation, JUN phosphorylation) alongside mitosis-related processes (mitotic spindle assembly, spindle assembly checkpoint, G2 DNA damage checkpoint signaling, protein import regulation). This suggests a cluster of proteins involved in signaling pathways that govern immune responses and also regulate cell cycle progression, with some differentiation-related terms likely reflecting broader developmental signaling. Confidence: Medium","confidence":"","size":19,"edges":62,"triangles":62,"max_degree":11,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":19},{"id":"GO:0097324","count":19},{"id":"GO:0009636","count":19},{"id":"GO:1990801","count":19},{"id":"GO:0014835","count":19}]},{"hash":"400863120010398148","title":"Amino acid transport across plasma membrane","description":"Many GO terms emphasize import of amino acids across the plasma membrane (arginine, ornithine, lysine, leucine), suggesting the proteins are primarily membrane transporters for amino acids. The presence of lipoprotein transport and macrophage activation terms hints at additional membrane-associated roles and possible immune-related connections, but the dominant pattern is amino acid uptake across the membrane. Confidence: Medium","confidence":"","size":19,"edges":16,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042953","count":2},{"id":"GO:0043030","count":2},{"id":"GO:0097638","count":2},{"id":"GO:0098713","count":2},{"id":"GO:0010923","count":2}]},{"hash":"2172928445683422273","title":"Bacterial Fatty Acid Biosynthesis and Lipoteichoic Acid Production","description":"The top GO terms are dominated by fatty acid metabolism and transport (medium-/long-/very long-chain fatty acids, import/transport), plus lipoteichoic acid biosynthesis and related lipid biosynthesis pathways, indicating a bacterial lipid metabolism and cell envelope biosynthesis module. Some peripheral terms (seed coat development, phenylacetate catabolism) appear ancillary, but the core signal is lipid metabolism. ","confidence":"High","size":19,"edges":25,"triangles":5,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0036112","count":9},{"id":"GO:0070395","count":9},{"id":"GO:0010214","count":9},{"id":"GO:0044539","count":9},{"id":"GO:0006633","count":9}]},{"hash":"2121208458391220490","title":"Retinal and neural development via retinoic acid","description":"The top GO terms emphasize retinal and retinol metabolism, retinoic acid signaling, forebrain development, and axis patterning (anterior/posterior, proximal/distal), pointing to a cohort involved in retinal biology and early neural patterning guided by retinoic acid. GABA catabolism supports neural maturation, aligning with this theme.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":18},{"id":"GO:0042572","count":18},{"id":"GO:0009952","count":17},{"id":"GO:0055129","count":17},{"id":"GO:0030900","count":17}]},{"hash":"1728791829812683579","title":"RNA Processing and Decay","description":"The GO profile is dominated by RNA metabolism: mRNA deadenylation and decay (deadenylation-dependent/independent), decapping, exoribonuclease activity, and splicing, with transcription also present but secondary; a mitochondrial import term appears incidental. Overall, the cluster centers on RNA processing and turnover.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0000290","count":1},{"id":"GO:0000288","count":1},{"id":"GO:0050850","count":1}]},{"hash":"332889072495965008","title":"Photosynthetic ROS Detox and Redox Homeostasis","description":"This cluster is enriched for GO terms related to removal of reactive oxygen species (superoxide radicals, hydrogen peroxide), glutathione metabolism, and cellular redox homeostasis, alongside photosynthesis and light-stress responses (UV-A, high light). The combination of detoxification, antioxidant pathways, and photosynthetic processes points to proteins involved in photoprotection and ROS scavenging in chloroplasts. An outlier term like white fat cell differentiation is likely noise, but the overall theme is coherent around redox control in photosynthetic tissues.","confidence":"High","size":19,"edges":151,"triangles":686,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0019430","count":3},{"id":"GO:0050787","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0050665","count":3},{"id":"GO:0042554","count":3}]},{"hash":"2103166626684170722","title":"Diverse Biosynthetic Pathways","description":"The top GO terms are dominated by biosynthetic and metabolic processes across a wide range of compound classes (poly-hydroxybutyrate, mycolic acid, tropane alkaloids, retinal, estrogens, testosterone, melanin). This suggests the cluster represents proteins involved in diverse biosynthetic pathways rather than a single, unified function. A couple of terms (response to methotrexate, lung development) are broader or unrelated, but do not overturn the overall theme of biosynthesis.","confidence":"Medium","size":19,"edges":125,"triangles":410,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":18},{"id":"GO:0042619","count":18},{"id":"GO:0009710","count":16},{"id":"GO:0071768","count":16},{"id":"GO:0031427","count":16}]},{"hash":"923105177737601820","title":"ER Stress, Protein Folding, and Redox Homeostasis","description":"The cluster is defined by GO terms for ER stress response and protein folding in the endoplasmic reticulum, with redox-related processes such as redox homeostasis and deglutathionylation also represented, indicating participants in ER proteostasis under stress; some transcription-related terms appear but the dominant theme is ER folding and redox regulation.","confidence":"High","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034976","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0034975","count":4},{"id":"GO:0006351","count":3}]},{"hash":"1608654364828937974","title":"Protein acetylation and amino acid biosynthesis","description":"The top GO terms are dominated by various protein acetylation events (peptidyl-lysine N6-acetylation, N-terminal acetylation, propionylation, and acetylation of spermidine/putrescine), suggesting a core function centered on acetylation. The presence of several biosynthetic processes (arginine, mycothiol, ectoine) indicates linked metabolic pathways in this cluster. Overall, the acetylation theme best captures the shared functions of these proteins, with related metabolic processes accompanying them.","confidence":"High","size":19,"edges":40,"triangles":11,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":15},{"id":"GO:0017198","count":15},{"id":"GO:0061606","count":14},{"id":"GO:0006526","count":14},{"id":"GO:0032918","count":14}]},{"hash":"1847852271206716817","title":"Cell cycle and organelle biogenesis","description":"This cluster shows strong representation of cell cycle and division terms (cell division, cell cycle) alongside organelle biogenesis processes (Golgi organization, ER membrane fusion) and translation-related terms (cytoplasmic translation, ribosomal subunit biogenesis), suggesting proteins involved in cell growth and coordinated assembly of cellular compartments, with a possible outlier defense response to protozoan. ","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0016320","count":5},{"id":"GO:0007030","count":4},{"id":"GO:0051260","count":4}]},{"hash":"102378771308775921","title":"Proteostasis: Ubiquitination and Proteasome Assembly","description":"The top GO terms are dominated by protein ubiquitination and proteasome regulatory particle assembly, pointing to a core theme of protein turnover and ubiquitin-mediated degradation. Additional terms reference stress- and signaling-related processes, and some tissue-specific contexts, which may reflect broader pleiotropy in the annotations. Overall, the strongest common thread is proteostasis through ubiquitination and proteasome function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0071260","count":5},{"id":"GO:0061408","count":5},{"id":"GO:0070198","count":4},{"id":"GO:0098907","count":4}]},{"hash":"939384851561777596","title":"Heavy metal transport and homeostasis","description":"The cluster shows recurring GO terms for transport and homeostasis of several metal ions (mercury, copper, zinc, iron, cadmium) and a mercury response, indicating a coherent group of proteins involved in metal ion transport and detoxification/detoxification-related homeostasis.","confidence":"High","size":19,"edges":135,"triangles":549,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":4},{"id":"GO:0006801","count":4},{"id":"GO:0006878","count":4},{"id":"GO:0060003","count":4},{"id":"GO:0015694","count":4}]},{"hash":"948357604114710745","title":"Broad-substrate membrane transporters","description":"The GO terms show transmembrane transport of diverse substrates (phosphate, arabinose, nitrate, sodium, galactose, sialic acid, 4-hydroxyphenylacetate, xenobiotics), suggesting broad-substrate membrane transport rather than a single-specific function.","confidence":"High","size":19,"edges":107,"triangles":299,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":6},{"id":"GO:0015751","count":6},{"id":"GO:0006855","count":6},{"id":"GO:0042128","count":6},{"id":"GO:0035725","count":6}]},{"hash":"1008022168723745957","title":"Mitotic control and apoptosis signaling","description":"This cluster centers on cell cycle regulation (G2/M transition, mitotic cell cycle) and apoptotic pathways (ER-stress\u2013induced intrinsic apoptosis, positive regulation of apoptosis), with supportive terms for transcription and phosphorylation control. The combination suggests a module coordinating cell division with stress-induced death signals, despite a developmental term (neural tube closure) that may reflect broader transcriptional roles. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":14},{"id":"GO:0000278","count":12},{"id":"GO:0001843","count":11},{"id":"GO:0070059","count":11},{"id":"GO:0043065","count":11}]},{"hash":"1665823824947724072","title":"Neural and Mesodermal Differentiation","description":"This cluster is enriched for terms related to development and differentiation across neural and mesoderm-derived tissues (neuron development, paraxial mesoderm differentiation, skeletal muscle adaptation, carotid body glomus cells, lung neuroendocrine cells, heart rate regulation by chemical signals). The shared theme is lineage specification and tissue formation rather than a single biochemical pathway, supporting a developmental label.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:2001038","count":17},{"id":"GO:0048712","count":17},{"id":"GO:0006366","count":17},{"id":"GO:0032933","count":16},{"id":"GO:0043503","count":16}]},{"hash":"1837473343718666524","title":"Muscle and neuroendocrine differentiation regulators","description":"This cluster is enriched for transcription-related GO terms (RNA polymerase II transcription, DNA-templated transcription) and differentiation processes in skeletal muscle and neuroendocrine tissues (skeletal muscle fiber adaptation, positive regulation of muscle differentiation, neuron development, lung and carotid body neuroendocrine differentiation), suggesting a group of transcriptional regulators coordinating muscle and neuroendocrine development. Some metabolic signaling terms (SREBP pathway) may reflect linked regulation of differentiation via metabolism.","confidence":"High","size":19,"edges":167,"triangles":907,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":11},{"id":"GO:2001016","count":9},{"id":"GO:0071277","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0009737","count":6}]},{"hash":"437399882488777615","title":"Transcriptional regulation and lineage differentiation","description":"The top GO terms cluster around regulation of transcription (DNA-templated transcription) and multiple differentiation/fate specification events across tissues (forebrain neurons, thymic T cells, eosinophils, club cells, ureter, hemopoiesis). This suggests a set of proteins broadly coordinating gene expression programs that drive developmental lineage decisions, with transcriptional control being a unifying theme. Some terms extend to nutrient-responsive transcription in other organisms, supporting a general transcription-regulatory role in development. ","confidence":"Medium","size":19,"edges":165,"triangles":878,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:2000032","count":12},{"id":"GO:0006355","count":12},{"id":"GO:0045061","count":7},{"id":"GO:0090295","count":7},{"id":"GO:2000977","count":7}]},{"hash":"51517139783583411","title":"Histone modification and chromatin assembly","description":"The top GO terms cluster around histone modifications (H3 methylation/acetylation), nucleosome assembly, and epigenetic programming of gene expression, pointing to chromatin regulation as the core function. A non-epigenetic term (uterine gland development) is present but unlikely to define the group; overall, the pattern supports chromatin remodeling and histone modification as the main theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090309","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0098532","count":2},{"id":"GO:1903709","count":2},{"id":"GO:0051573","count":2}]},{"hash":"1143213426348066221","title":"N-terminal acetylation and polyamine biosynthesis","description":"Top GO terms are dominated by N-terminal post-translational modifications (propionylation and acetylation) and polyamine biosynthesis pathways (putrescine, spermidine) fed by L-arginine biosynthesis. Other biosynthetic processes (melatonin, ectoine, mycothiol) are present but less central. The core theme appears to be protein N-terminal modifications linked with polyamine metabolism, with broader metabolism signals. Angiogenesis appears as an annotation artifact rather than defining the cluster. ","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":19},{"id":"GO:0006526","count":19},{"id":"GO:0032918","count":19},{"id":"GO:0017196","count":19},{"id":"GO:0001525","count":19}]},{"hash":"194161301262065685","title":"Organ development and muscle function","description":"This cluster shows several terms linked to organogenesis (heart morphogenesis, placenta development) and muscle-related activity (diaphragm contraction, neuromuscular process controlling posture), alongside transcriptional regulation, suggesting a theme around developmental processes that include muscle function. Some terms appear noisy (e.g., plant cytokinin signaling, glycan processing), but the dominant pattern is development and muscle physiology.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0003007","count":5},{"id":"GO:0009736","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3}]},{"hash":"2273379460114655060","title":"Developmental transcriptional regulation","description":"The cluster is enriched for multiple development-related terms (petal development, phloem development, organ boundary specification, forebrain development, chondrocyte differentiation) along with DNA-templated transcription and its regulation, suggesting a broad focus on developmental processes and transcriptional control across species rather than a single pathway. Confidence: Medium","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048441","count":6},{"id":"GO:0010199","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0030900","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1119691060952859693","title":"mRNA Processing and Splicing Regulation","description":"Most of the top terms center on post-transcriptional RNA processing: splicing via the spliceosome, regulation of splicing, mRNA polyadenylation/stability, and related TOR-like processes, plus translation reinitiation. This pattern points to a cohesive group of proteins involved in RNA maturation and fate rather than transcription, hence the label \"mRNA Processing and Splicing Regulation.\"","confidence":"High","size":19,"edges":170,"triangles":952,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":12},{"id":"GO:0010610","count":11},{"id":"GO:0045292","count":11},{"id":"GO:1901407","count":10},{"id":"GO:0048026","count":10}]},{"hash":"997831031667237774","title":"DNA replication and repair","description":"Most terms center on DNA metabolism: replication, repair, recombination, plasmid maintenance, and helicase regulation. A few terms (viral process, vacuole targeting) seem incidental, but the dominant theme is genome maintenance.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0051096","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0006269","count":1}]},{"hash":"1835409361838251420","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":131,"triangles":459,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006986","count":2}]},{"hash":"1798719944990634689","title":"Rho/Rac GTPase-driven actin remodeling","description":"The proteins show strong enrichment for Rho/Rac/Ras signaling and actin cytoskeleton-related GO terms (lamellipodium assembly, actin cytoskeleton organization, small GTPase-mediated signaling), indicating this cluster centers on cytoskeletal remodeling and cell motility driven by GTPase pathways; insulin signaling and immune-related terms may reflect broader signaling contexts but do not alter the core theme.","confidence":"High","size":19,"edges":21,"triangles":3,"max_degree":14,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0008286","count":6},{"id":"GO:0035023","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0035020","count":6},{"id":"GO:0046580","count":6}]},{"hash":"956405683468492987","title":"RNA processing and translation control","description":"This cluster centers on regulation of gene expression at multiple levels: mRNA splicing (spliceosome), translation initiation and reinitiation, formation of the translation preinitiation complex, miRNA-mediated translational silencing, and transcriptional activity, with supporting signals from TORC1 pathway. While some developmental GO terms appear, the dominant theme is RNA processing and control of translation/transcription, indicating a cohesive function in regulating gene expression.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":6},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0007568","count":4}]},{"hash":"535211671748667612","title":"Neural development and transcriptional regulation","description":"The cluster features strong signals for DNA-templated transcription and regulation of transcription, plus nucleosome assembly, suggesting chromatin-level control of gene expression. It also includes neural-linked terms such as somatic motor neuron differentiation, neurofilament cytoskeleton organization, neuromuscular process controlling posture, and glutamate reuptake, pointing to involvement in neural development and synaptic maintenance. Some broader developmental terms (heart development, visual perception) may reflect shared regulatory programs across tissues, but the neural-focused terms support a cohesive theme of neural development coupled with transcriptional control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0006334","count":2}]},{"hash":"1840022985465968318","title":"Neural development and synaptic plasticity","description":"The top GO terms cluster around neuronal development (substantia nigra development, multicellular organism development) and synaptic signaling/plasticity (ephrin receptor signaling, long-term synaptic potentiation), with supporting but secondary stress- and apoptosis-related terms (apoptotic process, cellular response to cadmium ion). This suggests a coherent theme of brain development and synaptic function, with some ancillary stress responses.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048013","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0021762","count":2}]},{"hash":"630833233873019476","title":"Immune signaling and cell cycle checkpoints","description":"The cluster is enriched for immune-related signaling terms (T cell receptor signaling, NK cell differentiation, JUN phosphorylation) suggesting active immune signaling pathways. It also includes differentiation and migration terms (melanocyte migration, myoblast differentiation), pointing to broader developmental processes. Additionally, cell cycle\u2013related terms (mitotic G2 DNA damage checkpoint signaling, spindle assembly\u2013associated phosphorylation, nuclear import regulation during spindle checkpoint) indicate coordinated control of division. Overall, it represents proteins balancing immune signaling with cell cycle regulation and differentiation programs.","confidence":"Medium","size":19,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":18},{"id":"GO:0097324","count":18},{"id":"GO:0009636","count":18},{"id":"GO:1990801","count":18},{"id":"GO:0014835","count":18}]},{"hash":"604376008143588068","title":"Ubiquitin-Dependent Cell Cycle and Meiotic Spindle Regulation","description":"The top GO terms point to ubiquitin-dependent proteolysis and regulation of ubiquitin ligase activity in the mitotic cell cycle, along with microtubule polymerization and spindle assembly in female meiosis I, plus oocyte maturation. This suggests a core theme of coordinating protein degradation with spindle/microtubule dynamics during meiosis and cell cycle progression, despite some peripheral terms on immunity or development. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051436","count":10},{"id":"GO:0008285","count":10},{"id":"GO:0045087","count":9},{"id":"GO:0051607","count":9}]},{"hash":"880769463757650726","title":"RNA Methylation and RNA Modification","description":"The top GO terms predominantly reflect RNA post-transcriptional modifications (rRNA and tRNA methylation, mRNA 7-methylguanosine cap, wobble uridine modification), suggesting a cohesive theme around RNA modification enzymes. Some peripheral terms (antibiotic/biotin biosynthesis, cellular senescence) appear less central, but do not override the main RNA-modification signal.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":10},{"id":"GO:0009102","count":8},{"id":"GO:0070476","count":7},{"id":"GO:0036265","count":7},{"id":"GO:0006370","count":7}]},{"hash":"1376159267163580563","title":"Organelle transcription and ribosome assembly","description":"The top GO terms cluster around transcription and ribosome biogenesis in organelles\u2014mitochondria and chloroplasts/plastids\u2014including mitochondrial transcription, chloroplast organization, plastid rRNA transcription, regulation of mitochondrial transcription, and mitochondrial ribosome assembly, with supporting RNA splicing. This points to a cohesive theme of organelle gene expression and ribosome assembly rather than cytosolic processes.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0009658","count":2},{"id":"GO:0006393","count":2},{"id":"GO:0008380","count":2},{"id":"GO:0042794","count":2}]},{"hash":"2044586226744424592","title":"Regulators of receptor signaling and endocytosis","description":"The term set indicates proteins that modulate multiple receptor-initiated pathways (B/T cell signaling, insulin signaling) and related processes like endocytosis and actin remodeling (Rac/Rho, ruffle assembly, caveolin-mediated endocytosis), plus regulatory layers such as ubiquitination and translation initiation, pointing to a cohesive theme of signaling modulation rather than a single pathway. Confidence reflects this broad, multi-pathway regulatory focus.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035020","count":4},{"id":"GO:0097178","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0031397","count":2},{"id":"GO:0008286","count":2}]},{"hash":"737870662991404965","title":"Neural apoptosis and protein turnover","description":"The top GO terms center on neural/glial apoptotic processes and neuronal development, paired with ubiquitin-proteasome\u2013mediated protein catabolism and regulation of ubiquitination, suggesting a theme of neural development coupled with protein homeostasis. Additional terms related to cytoskeletal remodeling and ribosome biogenesis imply broader cellular remodeling in neural contexts. Thus, a concise label focusing on neural cell death and protein turnover is appropriate.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034349","count":4},{"id":"GO:0051402","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0051092","count":3},{"id":"GO:0032933","count":3}]},{"hash":"1810927197347453875","title":"Wnt signaling and development","description":"This cluster is best labeled by its developmental theme: the top GO terms are centered on Wnt signaling, cell differentiation, and multicellular organism development, each with notable representation. While there are also terms for ribosome biogenesis and mitotic spindle processes, these appear less cohesive with the main developmental signal. The lack of edges suggests a broad rather than tightly connected functional module, but the strongest shared signal across members points to developmental signaling and differentiation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2160862030201703870","title":"Ubiquitin-Proteasome Degradation","description":"The top GO terms are dominated by ubiquitin-related processes: polyubiquitination, SCF-dependent proteasomal degradation, ubiquitin-dependent protein catabolic processes, and autoubiquitination, plus ERAD, which together point to proteins involved in tagging substrates for proteasomal turnover. A few other terms (suberin/cutin biosynthesis and MHC class II antigen processing) likely reflect annotation noise or cross-species contexts rather than core function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":4},{"id":"GO:0060348","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0051865","count":3}]},{"hash":"1035443228743546998","title":"Synaptic vesicle exocytosis and neurotransmitter release","description":"This cluster is dominated by terms tied to vesicle trafficking and exocytosis at synapses, including vesicle fusion, presynaptic dense core vesicle exocytosis, synaptic vesicle maturation, neurotransmitter secretion, and calcium-regulated exocytosis, as well as short-term synaptic potentiation. These co-occurring GO terms point to a cohesive role in neurotransmitter release machinery, despite the presence of some peripheral annotations like ABA signaling which may reflect broader or cross-species annotations.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":6},{"id":"GO:0009738","count":4},{"id":"GO:0035249","count":4},{"id":"GO:0006906","count":4},{"id":"GO:0099525","count":4}]},{"hash":"328550955804354323","title":"Transcription Regulation and Ubiquitin-Dependent Degradation","description":"The proteins cluster around DNA-templated transcription and its regulation, complemented by ubiquitin-related processes (deubiquitination and ubiquitin-dependent degradation), suggesting a coherent theme of transcriptional control linked to protein turnover; a few outlier terms (histone modification, ERAD, necroptosis) exist but do not dominate, supporting a moderate confidence in this label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035523","count":1},{"id":"GO:1901026","count":1},{"id":"GO:0051568","count":1}]},{"hash":"1518580196519415219","title":"Gene Expression Regulation and RNA Processing","description":"The top GO terms are dominated by DNA-templated transcription and its regulation, with additional signals for mRNA export, ribosome biogenesis, and protein monoubiquitination, suggesting a cluster focused on controlling gene expression at transcription and RNA handling levels. Some neural/developmental terms may reflect broader roles of involved factors. Overall, this cluster aligns with gene expression regulation rather than a single specific pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0032933","count":1},{"id":"GO:1902525","count":1},{"id":"GO:0030900","count":1}]},{"hash":"2189726398632576711","title":"Unknown","description":"The Top Terms are highly diverse, spanning transcription regulation, development (forebrain and prostate gland development), ribosome biogenesis, cytoskeleton dynamics, ubiquitination, and stress-responsive mRNA export, with no single dominant function or pathway, and no interactions among proteins, making a coherent label unlikely.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035019","count":1},{"id":"GO:0043486","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0032933","count":1},{"id":"GO:1902525","count":1}]},{"hash":"182845846881158656","title":"Unknown","description":"The GO terms span plant reproductive processes (self pollen rejection), carbohydrate biosynthesis (starch, glycogen, glucose) and stress/defense pathways, and bacterial cofactors biosynthesis (ubiquinone, bacillithiol, mycothiol), showing no single cohesive function. With zero edges and mostly singleton terms, there is no clear shared theme to define a specific cluster label.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060320","count":1},{"id":"GO:0006744","count":1},{"id":"GO:0019252","count":1},{"id":"GO:0071793","count":1},{"id":"GO:0009413","count":1}]},{"hash":"1044035904254535690","title":"Plant vesicle trafficking and chloroplast movement","description":"The cluster\u2019s GO terms center on intracellular transport and organelle dynamics, especially Golgi-ER related vesicle trafficking, Golgi organization, and retrograde transport, alongside chloroplast movement and related plant-specific processes like Cvt pathway targeting and peroxisome autophagy. This combination suggests a cohesive theme of vesicle trafficking and organelle dynamics in plant cells, though some terms (transcription, cell division) are broader and less directly tied. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009904","count":1},{"id":"GO:0009903","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0048213","count":1},{"id":"GO:0032258","count":1}]},{"hash":"1479791938732555770","title":"Neuroendocrine and mesodermal differentiation","description":"This cluster centers on development and differentiation across neural/astrocytic lineages, neuron development, and mesoderm-derived tissues (paraxial mesoderm, skeletal muscle) plus neuroendocrine differentiation (lung neuroendocrine cells, carotid body glomus cells). Transcription by RNA polymerase II and signaling pathways like SREBP, along with regulation of heart rate by chemical signals, suggest overarching regulatory programs guiding tissue-specific differentiation and maturation. The cohesive theme is tissue-specific differentiation with neuroendocrine and mesodermal emphasis.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:2001038","count":10},{"id":"GO:0048712","count":10},{"id":"GO:0006366","count":10},{"id":"GO:0032933","count":8},{"id":"GO:0043503","count":8}]},{"hash":"295612033905873801","title":"Neuronal actin remodeling and synaptic vesicle regulation","description":"We see strong signals for neuronal function: regulation of synaptic vesicle exocytosis and brain development, coupled with multiple terms describing actin cytoskeleton remodeling (formin-nucleated actin, polymerization, stress fibers) and mechanical signaling. This pattern indicates a cohesive module of proteins coordinating actin dynamics to support synaptic transmission and neuronal growth, with a few unrelated terms (immune response, obsolete annotations) present but not dominant.","confidence":"High","size":18,"edges":130,"triangles":513,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":13},{"id":"GO:0010796","count":11},{"id":"GO:0007420","count":11},{"id":"GO:0031384","count":11},{"id":"GO:0090338","count":8}]},{"hash":"1400165774208318557","title":"Muscle and neural development with cell cycle control","description":"The cluster centers on developmental processes in muscle and nervous system, highlighted by myoblast fusion, response to muscle activity, and axonogenesis, along with angiogenesis and synaptic activity. It also includes cell cycle-related terms (G2/M transition, mitotic cell cycle, kinetochore localization) and signaling (peptidyl-threonine phosphorylation), suggesting a coordinated program of tissue development and proliferation/differentiation rather than a single pathway. Therefore, the label captures the shared theme of muscle and neural development intertwined with cell cycle regulation.","confidence":"Medium","size":18,"edges":75,"triangles":130,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043065","count":6},{"id":"GO:0014850","count":6},{"id":"GO:0007520","count":6},{"id":"GO:0000086","count":6},{"id":"GO:0000278","count":6}]},{"hash":"2110257017143910149","title":"Photosynthesis light harvesting and photoprotection","description":"This cluster centers on photosynthesis and light response, including light harvesting, responses to red/far-red light, low light, UV-A, and nonphotochemical quenching, indicating chloroplast photoprotective machinery.","confidence":"High","size":18,"edges":81,"triangles":138,"max_degree":16,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":6},{"id":"GO:1904964","count":3},{"id":"GO:0018298","count":3},{"id":"GO:0009768","count":3},{"id":"GO:0010218","count":3}]},{"hash":"998708951830915722","title":"Cobalamin Biosynthesis and Cobalt-Responsive Metabolism","description":"The cluster centers on cobalamin (vitamin B12) biosynthesis and cobalt ion response, with links to central carbon metabolism (pentose-phosphate shunt regulation, glycolytic regulation, carbohydrate phosphorylation) and photosynthesis, pointing to cobalt-dependent, B12-producing, photosynthetic bacteria. Some terms are obsolete or noisy (e.g., brain development), but the core theme ties B12 biosynthesis with cobalt regulation and metabolic flux control.","confidence":"Medium","size":18,"edges":76,"triangles":134,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0071279","count":2}]},{"hash":"1167514405679992167","title":"Mitochondrial translation and energy production","description":"The top terms center on translation and mitochondrial processes, including rRNA import into mitochondrion and proton motive force-driven ATP synthesis, plus ATP synthesis overall. This points to mitochondrial gene expression and bioenergetics as the core function of the cluster, with other terms likely reflecting ancillary cellular or behavioral contexts rather than defining the main theme.","confidence":"High","size":18,"edges":148,"triangles":743,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0099132","count":3},{"id":"GO:0042777","count":2},{"id":"GO:0015986","count":1},{"id":"GO:0035928","count":1}]},{"hash":"1794132435657086578","title":"Chloroplast Photosynthesis Machinery","description":"Most of the top GO terms point to chloroplast photosynthesis and related processes: photosynthesis, PSII oxygen evolving complex assembly, carbon fixation, and photorespiration. This pattern suggests the cluster comprises proteins involved in chloroplast energy capture and carbon metabolism. A few terms related to mitochondrial respiratory complex assembly and aerobic respiration are present, which may reflect broader energy-related functions or annotation cross-talk, but the dominant signal is chloroplast photosynthesis. ","confidence":"High","size":18,"edges":57,"triangles":90,"max_degree":16,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":7},{"id":"GO:0009735","count":3},{"id":"GO:0010270","count":3},{"id":"GO:0009060","count":2},{"id":"GO:1902600","count":2}]},{"hash":"371601316661042609","title":"Unknown","description":"The terms cover translation, snoRNP assembly, cell division, metabolism, cilium-related processes, photoreceptor organization, interferon response, and development; they do not converge on a single coherent function for this cluster, suggesting a mixed or context-specific set of roles rather than a tightly linked pathway.","confidence":"","size":18,"edges":24,"triangles":9,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0000492","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0090526","count":1}]},{"hash":"2142308925611790863","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000961","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0009451","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0090617","count":2}]},{"hash":"2188676877942613524","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":149,"triangles":755,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":16},{"id":"GO:0031047","count":16},{"id":"GO:0006369","count":11},{"id":"GO:1903608","count":11},{"id":"GO:0034476","count":10}]},{"hash":"425376459241262892","title":"Mesodermal Muscle Development and Transcription","description":"The cluster is enriched for transcription-related GO terms (RNA polymerase II transcription, DNA-templated transcription) and skeletal muscle/mesoderm differentiation (paraxial mesodermal differentiation, skeletal muscle fiber adaptation, positive regulation of muscle differentiation), suggesting a shared regulatory program for muscle development. It also includes neural and neuroendocrine differentiation terms (neuron development, carotid body glomus cell differentiation, lung neuroendocrine cell differentiation), indicating broader developmental transcription across mesodermal and neural lineages.","confidence":"High","size":18,"edges":147,"triangles":724,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":10},{"id":"GO:2001016","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0032933","count":6},{"id":"GO:0043503","count":6}]},{"hash":"484801459627770615","title":"Developmental cell fate specification network","description":"This cluster centers on GO terms about development and cell fate decisions across multiple lineages, especially neuronal differentiation (cerebral cortex GABAergic interneurons, spinal motor neurons, subpallium neurons) and other organ lineages (oligodendrocyte, bronchiole, pancreas), with transcription by RNA polymerase II indicating active gene expression during these differentiation programs. The cohesive theme is coordinated tissue- and lineage-specific differentiation rather than a single pathway, justifying a label around developmental cell fate specification.","confidence":"Medium","size":18,"edges":147,"triangles":728,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":13},{"id":"GO:0021892","count":8},{"id":"GO:0021520","count":8},{"id":"GO:0060435","count":8},{"id":"GO:0060163","count":8}]},{"hash":"2197806069822025992","title":"Oxidative and xenobiotic stress response","description":"This cluster centers on responses to xenobiotic stimuli and oxidative stress (hydrogen peroxide) and apoptosis, suggesting a common theme of stress signaling and cell fate decisions, despite some disparate terms.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0006915","count":3},{"id":"GO:2000327","count":2},{"id":"GO:0071320","count":2}]},{"hash":"148425754672436814","title":"Spliceosome Assembly and RNA Processing","description":"The top GO terms are dominated by spliceosome- and RNA processing-related processes (mRNA splicing via spliceosome, spliceosomal snRNP/complex assembly, deadenylation-dependent decapping, histone mRNA metabolism). There are also terms tied to transcription termination and chromatin context (pericentric heterochromatin formation, hair cycle), suggesting these proteins function primarily in RNA processing with links to transcriptional regulation and chromatin state. Overall, the cluster is best characterized as spliceosome-driven RNA processing with related regulatory connections.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":17},{"id":"GO:0006369","count":13},{"id":"GO:0070317","count":13},{"id":"GO:1990141","count":13},{"id":"GO:0000387","count":13}]},{"hash":"2052650136145090148","title":"RNA splicing and mRNA processing regulators","description":"The cluster is enriched for nuclear mRNA processing terms\u2014splicing via spliceosome, small-subunit processome assembly, poly(A) tail regulation, and related post-transcriptional control (including translation and miRNA-mediated silencing)\u2014suggesting a cohesive group of proteins involved in RNA maturation and turnover rather than a single downstream function.","confidence":"Medium","size":18,"edges":149,"triangles":753,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":7},{"id":"GO:1900363","count":6},{"id":"GO:0006376","count":5},{"id":"GO:0060211","count":5},{"id":"GO:0006378","count":5}]},{"hash":"1933609112424352321","title":"Unknown","description":"The top GO terms span disparate processes (negative regulation of kinase activity; unfolded protein response/ERAD; DNA replication; redox homeostasis; translational frameshifting; iron-sulfur protein maturation), with no clear shared function or interaction pattern. The absence of edges among proteins further suggests this is a non-cohesive set rather than a single pathway.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:1901621","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1489635223163866654","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006620","count":2},{"id":"GO:0051083","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0048366","count":2},{"id":"GO:0007008","count":1}]},{"hash":"1665722906120079810","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0048568","count":5},{"id":"GO:0002188","count":5}]},{"hash":"856564052204916173","title":"Plant defense signaling and cuticle biosynthesis","description":"The cluster features GO terms for plant hormone signaling (abscisic acid and ethylene), transcriptional regulation (DNA-templated transcription and its regulation), defense responses (response to chitin and positive regulation of cellular defense), and cuticle formation (positive regulation of cutin biosynthetic process and regulation of wax biosynthetic process). Together, these point to a coherent module where hormone signaling modulates transcription to drive defense responses and reinforce the plant cuticle. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010200","count":2}]},{"hash":"645470232324467485","title":"Plant transcriptional regulation and development","description":"Based on the top GO terms, most of the proteins are linked to DNA-templated transcription, its regulation, and the assembly of RNA polymerase II preinitiation complexes, with multiple terms pointing to transcription initiation and plant development (including lateral root morphogenesis). While a couple terms touch on vesicle trafficking and vacuole fusion, the dominant signal is transcriptional control guiding development in plants.","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:0007275","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0090114","count":2},{"id":"GO:2000648","count":1}]},{"hash":"1471649041314761157","title":"Plant Hormone Signaling and Seed/Cuticle Development","description":"This cluster centers on plant-specific signaling and development: ABA- and ethylene-activated pathways, transcriptional regulation of these processes, seed development, and regulation of wax/cutin biosynthesis and cuticle-related defenses (with chitin response). These together point to coordinated plant hormone signaling driving seed/epidermal development and barrier formation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009738","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009873","count":3},{"id":"GO:0010200","count":3},{"id":"GO:0007275","count":3}]},{"hash":"122587370202240781","title":"Plant cell wall biosynthesis and remodeling","description":"This cluster is dominated by plant-focused terms such as cell wall biogenesis, xyloglucan metabolic process, plant-type cell wall modification, fungal-type cell wall organization, and endosperm cellularization, indicating proteins involved in constructing and remodeling the plant cell wall and related growth processes. An outlier term like skeletal muscle fiber development appears unrelated, but the overarching theme clearly points to plant cell wall biology and tissue development, including reproductive structures like stamen filaments. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0042546","count":2},{"id":"GO:0080086","count":2},{"id":"GO:0032491","count":2},{"id":"GO:0006037","count":2}]},{"hash":"940543776502120301","title":"Lipid catabolism and autophagy-lysosome trafficking","description":"The top GO terms are dominated by lipid catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine) alongside autophagy- and endomembrane- trafficking processes (piecemeal microautophagy of the nucleus, multivesicular body disassembly, vacuum/vacuolar protein processing). This points to a shared role in lipid turnover linked to vesicle-mediated degradation and endomembrane remodeling, with some stress-related terms (UV-B response) reflecting broader cellular context. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":8},{"id":"GO:2000124","count":8},{"id":"GO:0006660","count":8},{"id":"GO:0052651","count":8},{"id":"GO:0030245","count":6}]},{"hash":"1882519259240167334","title":"Plant cell wall biogenesis and fungal detection","description":"The top terms are centered on plant cell wall biosynthesis/remodeling (cell wall biogenesis, xyloglucan metabolism, plant-type and fungal-type wall organization, wall modification) and recognition of fungal molecules, plus a plant structure term (stamen filament development). A few outliers exist (iron homeostasis, antibiotic response, IL-2 production), but the dominant theme is plant cell wall formation with fungal detection/defense.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060586","count":4},{"id":"GO:0042546","count":4},{"id":"GO:0080086","count":4},{"id":"GO:0032491","count":4},{"id":"GO:0006037","count":4}]},{"hash":"1324877164998897239","title":"Synaptic Endocytosis and Vesicle Recycling","description":"The GO terms cluster around membrane remodeling and vesicle trafficking at synapses, including clathrin-dependent endocytosis, GPCR internalization, and positive regulation of synaptic vesicle recycling, as well as GABAergic synaptic transmission. Dynamin-related processes linked to membrane fission/scission appear alongside, suggesting a focus on vesicle cycling and receptor internalization at neuronal synapses. Sphingomyelin catabolism may reflect membrane lipid remodeling supporting these processes. Overall, the dominant theme is synaptic membrane trafficking and vesicle recycling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000266","count":3},{"id":"GO:0006685","count":3},{"id":"GO:0007114","count":3},{"id":"GO:1903526","count":2},{"id":"GO:0002031","count":2}]},{"hash":"367803690655462623","title":"Ribosome maturation and mRNA transport","description":"Dominant terms include maturation of 5.8S rRNA and LSU/SSU rRNA, pointing to ribosome biogenesis, while mRNA transport supports RNA handling; TORC1 signaling and GTPase activity regulation suggest coordination with growth. The vesicle trafficking terms seem supportive of general intracellular transport but do not outweigh the ribosome/RNA processing theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0038202","count":4}]},{"hash":"2031938752508491175","title":"Cell growth and division with cytoskeleton dynamics","description":"These GO terms cluster around core growth/division processes and structural organization: translation initiation and preinitiation complex formation point to increased protein synthesis, while cell division and spindle pole body separation regulation reflect mitotic control. Actin filament depolymerization and intraciliary transport indicate cytoskeletal remodeling and trafficking, with nuclear pore localization highlighting nucleocytoplasmic transport. The presence of regulation of dendrite development and SREBP signaling adds a growth and biosynthetic context. Overall, the set suggests a theme of cell growth and division coupled with cytoskeletal and transport processes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002188","count":7},{"id":"GO:0001731","count":7},{"id":"GO:0032933","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0030042","count":6}]},{"hash":"2195746590395339241","title":"Ubiquitin-Mediated Proteolysis","description":"This cluster is strongly enriched for GO terms related to ubiquitination and ubiquitin-dependent protein catabolic processes (including protein ubiquitination, autoubiquitination, and specific ubiquitin linkages like K48), indicating a cohesive function in tagging proteins for degradation. Some related terms touching chromatin regulation and cell cycle checkpoints (e.g., histone ubiquitination, mitotic spindle checkpoint signaling) support a broader role of ubiquitin signaling in regulating chromatin and cell division. Overall, the dominant theme is ubiquitin-driven protein turnover.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0051865","count":6},{"id":"GO:0016567","count":6},{"id":"GO:1903265","count":6},{"id":"GO:0085020","count":6}]},{"hash":"1370868431829897795","title":"Oocyte meiosis and neural tube development","description":"The cluster includes GO terms tied to female meiosis (oocyte maturation, spindle assembly in female meiosis I) and neural tube development (initiation of neural tube closure, third ventricle development), alongside ubiquitin-proteasome\u2013mediated protein catabolism, suggesting a development-focused group that spans gametogenesis and neural development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0001556","count":9},{"id":"GO:0021678","count":9},{"id":"GO:0051436","count":9},{"id":"GO:0046785","count":9}]},{"hash":"1108041465304582614","title":"TLR-Driven Antiviral Immunity and Macrophage Activation","description":"Most of the prominent GO terms point to innate immune responses against pathogens, especially antiviral pathways: TLR8 and TLR10 signaling, dsRNA response, interferon production, defense against virus, and macrophage activation. A few plant-development terms appear as outliers, likely noise, but do not override the antiviral immune theme. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":9},{"id":"GO:0006963","count":8},{"id":"GO:0045078","count":8},{"id":"GO:0034158","count":8},{"id":"GO:0034166","count":8}]},{"hash":"1234096282379327733","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1835949812990973566","title":"TLR-Mediated Innate Immune Signaling","description":"The cluster is enriched for innate immune terms such as detection of bacterial lipopeptide, TLR8 and TLR10 signaling, cytokine signaling, interferon production, and antimicrobial peptide biosynthesis, suggesting a coordinated response to bacterial components. A few non-immune terms appear among the top GO terms, likely due to noise or broad annotations, but the dominant theme is innate immune sensing and signaling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019221","count":2},{"id":"GO:0070340","count":2},{"id":"GO:0006963","count":2},{"id":"GO:0072287","count":2},{"id":"GO:0045078","count":2}]},{"hash":"1432495819692076333","title":"T/NK Cell Signaling and Differentiation","description":"The top GO terms are dominated by immune-related processes: T cell receptor signaling and natural killer cell differentiation, suggesting the proteins cluster around adaptive immune signaling and lymphoid lineage commitment. Additional terms like JUN phosphorylation indicate activation signaling cascades, with other terms reflecting broader differentiation and checkpoint control. Overall, the strongest theme is immune cell signaling and differentiation, hence this label.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":17},{"id":"GO:0097324","count":17},{"id":"GO:0009636","count":17},{"id":"GO:1990801","count":17},{"id":"GO:0014835","count":17}]},{"hash":"2045050758054614839","title":"Synaptic vesicle trafficking and neurotransmitter exocytosis","description":"The cluster is enriched for terms related to regulated neurotransmitter release (glutamate), calcium-dependent exocytosis, and Rab-mediated vesicle trafficking, plus ER membrane localization and tubular network organization, pointing to presynaptic vesicle cycling and ER remodeling in neurons. Some lipid droplet and amyloid-related terms appear but the dominant signal centers on neuronal secretion and trafficking processes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034389","count":2},{"id":"GO:0032483","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0061646","count":1},{"id":"GO:1990000","count":1}]},{"hash":"529406199532565692","title":"Pollen Recognition and Secretory Trafficking","description":"The Top Terms indicate pollen acceptance and meiosis cytokinesis along with strong signals for Golgi-to-plasma membrane transport, exocytosis, endosome organization, and extracellular matrix disassembly. This pattern points to a module involved in pollen-pistil interaction and the secretory pathway that remodels the cell surface and surrounding matrix, supporting pollen acceptance and cell polarity during reproduction. Some terms reflect general trafficking and polarity mechanisms shared across cell types, reinforcing a trafficking/polarity theme rather than a single niche function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060321","count":4},{"id":"GO:0007111","count":4},{"id":"GO:0006893","count":4},{"id":"GO:0007110","count":4},{"id":"GO:0016049","count":3}]},{"hash":"574916369717910018","title":"Unknown","description":"The top GO terms span very diverse processes (brown fat differentiation, pollen sperm differentiation, cellulose catabolic, hopanoid biosynthesis, cytokine response, fibroblast proliferation, cell cycle transitions), with no single cohesive function or pathway linking the proteins. Edges are absent, and many terms are organism- or process-specific, so there isn\u2019t a consistent theme to name a meaningful cluster.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":2},{"id":"GO:0030245","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0040015","count":1},{"id":"GO:0034097","count":1}]},{"hash":"5124652515595699","title":"Glycosylation and Ubiquitination Machinery","description":"The cluster's strongest signals are glycosylation-related processes (protein N-linked glycosylation, dolichol-linked oligosaccharide biosynthetic process) and protein ubiquitination, pointing to a core theme of post-translational modification and glycan assembly. Other terms such as glycogen biosynthesis and various development-related processes appear as less coherent annotations, suggesting broader or context-dependent roles rather than a single cohesive module.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0006487","count":1},{"id":"GO:0060117","count":1}]},{"hash":"385124377725890797","title":"Unknown","description":"The top GO terms span disparate biology from plant defense and cell wall remodeling to animal heart electrophysiology and neural differentiation, with almost no connectivity among them (no edges, no clear shared function), so there is no cohesive theme to label the cluster beyond Unknown. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0006949","count":2},{"id":"GO:0009828","count":2},{"id":"GO:0019953","count":2},{"id":"GO:0009395","count":2}]},{"hash":"1674855025298031326","title":"Unknown","description":"The top terms are diverse and only loosely cluster around defense/adhesion themes, with additional unrelated terms (lipid transport, DNA methylation, vitamin K response, etc.). There is no single convergent function that clearly ties all 18 proteins together, making a reliable, specific label inappropriate.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":2},{"id":"GO:0006952","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0006869","count":2},{"id":"GO:0010951","count":2}]},{"hash":"1952993544325681569","title":"Unknown","description":"The top terms are scattered across translation, several signaling and immune-regulatory processes, development, and differentiation with no cohesive functional theme. With no edges linking the proteins and no a single shared GO biology, there is no clear module to name beyond Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0035556","count":1},{"id":"GO:2001181","count":1},{"id":"GO:0035171","count":1}]},{"hash":"724059789530610597","title":"Metabolism and protein quality control","description":"This cluster combines metabolic processes (L-glutamine catabolic pathways, gluconeogenesis) with core cellular processes (cell wall organization, cell division) and ER-associated stress responses (unfolded protein response, translation initiation in response to ER stress, chaperone-related refolding). The co-occurrence of metabolism with protein folding/quality control under stress suggests a bundled function around metabolic regulation coupled to protein homeostasis. ","confidence":"Medium","size":17,"edges":72,"triangles":122,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0097428","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2097661451297489043","title":"Spliceosome-mediated mRNA processing and translation initiation","description":"This cluster is enriched for spliceosome-related processes (mRNA splicing, splice site recognition, regulation of splicing) and also includes a term for translation preinitiation complex formation, suggesting a link between mRNA processing and translation initiation.","confidence":"High","size":17,"edges":125,"triangles":535,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":14},{"id":"GO:0045292","count":14},{"id":"GO:0048026","count":14},{"id":"GO:0031047","count":14},{"id":"GO:0010610","count":13}]},{"hash":"2126714937422769270","title":"Ribosome Biogenesis and Nuclear Export","description":"The cluster is strongly characterized by GO terms for ribosomal large subunit biogenesis, preribosome assembly, LSU-rRNA maturation, and export of ribosomal subunits from the nucleus, indicating a cohesive group of proteins involved in ribosome production and nucleocytoplasmic transport. Additional terms for mRNA export and nuclear protein localization support this theme, while a few terms (e.g., embryonic cranial skeleton morphogenesis) may reflect pleiotropy or background noise. Overall, the label captures the dominant function represented.","confidence":"High","size":17,"edges":128,"triangles":581,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0006260","count":4},{"id":"GO:1902626","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000056","count":4}]},{"hash":"1486861956605470028","title":"Steroid hormone biosynthesis and related metabolism","description":"Based on the GO terms, the cluster centers on steroid hormone biosynthesis (C21-steroid hormone biosynthetic process), progesterone metabolism, and thyroid hormone response, with additional signals tying to retinol metabolism and prostaglandin signaling. While there is a kidney development term present, the strongest, cohesive theme is hormone and lipid metabolism pathways, suggesting a group of proteins involved in steroid/hormone biosynthesis and signaling as the core function.","confidence":"Medium","size":17,"edges":106,"triangles":442,"max_degree":16,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0046370","count":7},{"id":"GO:0042572","count":7},{"id":"GO:0001894","count":5},{"id":"GO:2000353","count":5}]},{"hash":"2026602554280012366","title":"Immune differentiation and cell cycle control","description":"The top GO terms show immune-related differentiation (T cell receptor signaling, natural killer cell differentiation) alongside cell-cycle and mitosis-related processes (DNA replication, spindle assembly, G2 checkpoint, JUN phosphorylation). This mix suggests a cluster of genes involved in immune cell development and regulation of cell division, rather than a single narrow function. While some terms reference broader differentiation (melanocyte, myoblast), the core theme centers on immune differentiation and cell-cycle control.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":16},{"id":"GO:0050852","count":15},{"id":"GO:0097324","count":15},{"id":"GO:0009636","count":15},{"id":"GO:1990801","count":15}]},{"hash":"616872334254477450","title":"Neuronal vesicle trafficking and development","description":"The cluster shows strong enrichment for vesicle-related processes (synaptic vesicle exocytosis regulation, Golgi vesicle docking, multivesicular body sorting) and neural development terms (brain development, axon guidance), suggesting a cohesive group of proteins involved in vesicle trafficking in neurons and neural maturation. Some terms (like mating projection growth and T cell signaling) are less central or cross-species, but the dominant pattern is vesicle management in neural contexts.","confidence":"High","size":17,"edges":10,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":7},{"id":"GO:2000300","count":7},{"id":"GO:0007420","count":7},{"id":"GO:0031384","count":7},{"id":"GO:1902902","count":7}]},{"hash":"2164034943064938394","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":130,"triangles":594,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0000961","count":2}]},{"hash":"89223625164172669","title":"Amino acid catabolic metabolism and signaling","description":"The cluster is dominated by amino-acid catabolic processes (L-alanine, L-kynurenine/tryptophan, L-cysteine, glycine) and related metabolic activities like pyruvate biosynthesis and oxalic acid secretion, pointing to a core theme of amino-acid turnover and metabolism. The presence of signaling-related GO terms (Notch signaling, response to cAMP, glucocorticoid response) suggests broader regulatory connections to cellular signaling and hormonal responses. Together these terms imply a cluster centered on amino-acid metabolism with associated signaling pathways, rather than a single, highly specific function.","confidence":"Medium","size":17,"edges":134,"triangles":651,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0042853","count":9},{"id":"GO:0007219","count":9},{"id":"GO:0097053","count":9},{"id":"GO:0042866","count":9},{"id":"GO:0051591","count":9}]},{"hash":"988873558640125846","title":"Organelle protein import and abiotic stress response","description":"The top terms cluster around import of proteins into mitochondria and chloroplasts, indicating organelle targeting as a common function. The presence of ABA biosynthesis regulation and stress-response terms (high light, desiccation, freezing) suggests these proteins participate in plant abiotic stress signaling linked to organelle function, justifying the combined label.","confidence":"High","size":17,"edges":24,"triangles":12,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":5},{"id":"GO:0045037","count":5},{"id":"GO:0030150","count":5},{"id":"GO:0000002","count":5},{"id":"GO:0032094","count":5}]},{"hash":"103290322284356771","title":"Plant Oxidative Metabolism and Detoxification","description":"Explanation: The top GO terms cluster around oxidation-reduction processes, cellular oxidant detoxification, and cytochrome P450\u2013mediated pathways, with additional plant-specific catabolic activities (chlorophyll and stilbene). Although there are some miscellaneous terms, the dominant theme is oxidation-based metabolism and detoxification of plant secondary metabolites, suggesting a loosely connected set of enzymes involved in redox biology and breakdown of plant compounds.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0098869","count":4},{"id":"GO:0015996","count":4},{"id":"GO:0016311","count":4},{"id":"GO:0019373","count":4}]},{"hash":"381495855156229288","title":"Diverse stimulus-response and metabolism cluster","description":"The top GO terms cover responses to a variety of stimuli (zinc, xenobiotics, amino acids, amines, glucagon) and metabolic/regulatory processes (liver development, DNA synthesis regulation, xyloglucan biosynthesis). Although one term is plant-specific, the shared theme is proteins involved in sensing or responding to diverse stimuli and adjusting metabolic pathways, justifying a broad stimulus-response/metabolism label.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0009969","count":3},{"id":"GO:0010043","count":2},{"id":"GO:0042493","count":2}]},{"hash":"262025009548122010","title":"Ribosome biogenesis, RNA processing, and proteostasis","description":"The cluster\u2019s top GO terms strongly point to ribosome assembly (ribosomal large subunit biogenesis; translation; translational initiation) and RNA processing/surveillance (nuclear mRNA surveillance; post-transcriptional tethering of RNA Pol II), complemented by proteostasis (proteasomal ubiquitin-dependent degradation; ERAD). While DNA replication/repair terms are present, the dominant signal centers on ribosome biogenesis and RNA handling with ubiquitin-proteasome\u2013mediated quality control, suggesting a nuclear-coordinated gene-expression/protein-homeostasis module.","confidence":"Medium","size":17,"edges":103,"triangles":324,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000715","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0000122","count":3}]},{"hash":"1538315411524675866","title":"Metal Detox and Ion Homeostasis","description":"The cluster shows strong enrichment for metal detox and ion transport terms (mercury detox, mercury ion transport, copper ion homeostasis, copper ion export/transport) alongside oxidative stress and calcium signaling signals; translation-related terms suggest baseline expression machinery but are less specific. The metal detox/ion homeostasis theme is the most coherent across terms, with metal handling being a unifying axis for the proteins in this cluster.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0000027","count":2}]},{"hash":"849846870032091324","title":"RNA processing and transcriptional regulation","description":"The top GO terms cluster around regulation of transcription by RNA polymerase II, mRNA splicing (cis splicing via the spliceosome and regulation of splicing), mRNA export, and regulation of translation initiation, plus ncRNA-mediated gene silencing. While brain development and liver regeneration appear, the dominant signal is gene-expression control at multiple post-transcriptional steps, justifying the label.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000122","count":2},{"id":"GO:1900363","count":2}]},{"hash":"380238373225495257","title":"Translation initiation regulation and mRNA processing","description":"This cluster is dominated by terms related to translation initiation, preinitiation complex formation, and regulation of translational initiation, including IRES-dependent viral initiation, plus several mRNA processing terms (polyadenylation, splicing, modification). This indicates a cohesive theme around controlling translation initiation and related RNA maturation steps.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":7},{"id":"GO:0001731","count":7},{"id":"GO:0006446","count":7},{"id":"GO:0075522","count":7},{"id":"GO:0075525","count":7}]},{"hash":"1242984414022742733","title":"Neuronal development and migration with metabolism","description":"The cluster is enriched for neural development and migration terms (pyramidal neuron development; tangential migration from SVZ to olfactory bulb) together with metabolic processes (glucose metabolic process; thiamine biosynthetic process) and signaling (intracellular signal transduction, regulation of GTPase activity). This points to proteins involved in neuron formation/migration that are linked to metabolic and signaling regulation. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006006","count":4},{"id":"GO:0016477","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0042144","count":3},{"id":"GO:0098907","count":3}]},{"hash":"1200493011944412496","title":"Developmental transcription and cell cycle","description":"This cluster centers on core processes of gene expression and cell division that are essential during development: DNA-templated transcription, DNA replication, and mitotic cell cycle, alongside developmental processes like forebrain development, neural tube closure, and multicellular organism development. While some stress-related terms appear (cadmium response, ER stress\u2013related apoptosis), the dominant themes are transcriptional regulation and proliferative activity shaping developmental programs, suggesting these proteins cooperate in developmental gene expression and proliferation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0001843","count":6},{"id":"GO:0070059","count":6},{"id":"GO:0006349","count":6}]},{"hash":"354958150740457980","title":"Unknown","description":"The terms span immune signaling, meiosis/mitosis control, DNA damage tolerance, ubiquitination, fungal cell wall organization, histone modification, and transport\u2014hardly a single cohesive function. Because there is no clear unifying theme, Unknown is the appropriate label.","confidence":"","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042138","count":17},{"id":"GO:0038095","count":17},{"id":"GO:0050852","count":17},{"id":"GO:0010458","count":17},{"id":"GO:0043951","count":17}]},{"hash":"498476745697582585","title":"Translational initiation and its regulation","description":"The cluster is dominated by GO terms about initiating translation, including reinitiation, preinitiation complex formation, and IRES-mediated initiation, with additional mRNA processing terms. This points to a cohesive module of proteins involved in starting and modulating protein synthesis at the mRNA level.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0075522","count":4},{"id":"GO:0075525","count":4}]},{"hash":"1214617646551126415","title":"Cell growth and division with metabolism","description":"The cluster centers on core growth and division processes (cell division, mitotic cell cycle) and ribosome biogenesis, which align with protein synthesis and cytoskeletal remodeling needed for division. It also includes metabolic and nutrient signaling terms (response to nutrient, amino acid transport, SREBP signaling, regulation of monoubiquitination), suggesting a broader metabolism-linked growth module. An outlier term for forebrain development and a variety of related processes indicate a general cellular housekeeping group rather than a single pathway, supporting a label around growth and metabolism rather than a narrow pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007584","count":3},{"id":"GO:0061087","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0003333","count":2}]},{"hash":"1992235300480408349","title":"Developmental transcription regulators","description":"The Top Terms show a clear emphasis on DNA-templated transcription and its regulation, together with several development-related processes (multicellular organism development, axon target recognition, trophoblast giant cell differentiation). Despite a couple of obsolete terms, the dominant theme suggests proteins that regulate transcription during developmental programs. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051639","count":2},{"id":"GO:0048016","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1411308211226206100","title":"Cardiac electrical signaling and stress response","description":"The top GO terms are heavily weighted toward heart function and electrophysiology, including regulation of SA node cell action potential, regulation of delayed rectifier potassium channel activity, and positive regulation of cardiac muscle hypertrophy in response to stress. While some terms touch neural signaling (GABA secretion, startle response) and general signaling (cAMP), the strongest and most coherent theme is cardiac electrical activity and the heart\u2019s adaptive response to stress, justifying a label focused on cardiac electrophysiology and stress response.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":4},{"id":"GO:1903244","count":4},{"id":"GO:0006378","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0014051","count":3}]},{"hash":"1197189436314466943","title":"Chromatin Remodeling and Protein Quality Control","description":"These proteins show enrichment for transcription initiation-coupled chromatin remodeling, unfolded protein response/ERAD, regulation of protein export from the nucleus, and aspects of translational control, redox balance, and stress responses. The combination suggests a theme where gene expression regulation is linked to protein folding/quality control under cellular stress, rather than a single specific pathway. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045815","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1940713042201530158","title":"Plant innate immunity and ethylene signaling","description":"The dominant GO terms point to plant defense signaling (innate immune response, ethylene-activated signaling) along with growth/development and transcriptional regulation, suggesting a cluster centered on plant stress responses and hormone signaling. Some terms are less specific (e.g., necroptosis regulation, viral transcription), but the strongest signals are immune and ethylene-related, with transcriptional control and microtubule localization supporting a regulatory, signaling-focused cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0048366","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1451202533977954955","title":"Neural dendrite morphogenesis and ephrin signaling","description":"The top GO terms cluster around dendrite development and morphogenesis, neuronal stem cell maintenance, and ephrin receptor signaling, suggesting a neural development and dendrite formation theme. A couple of plant-related terms appear but do not overwhelm the neural signal, which is the dominant pattern here.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016358","count":2},{"id":"GO:0009955","count":2},{"id":"GO:0097150","count":2},{"id":"GO:0048013","count":2},{"id":"GO:0050775","count":2}]},{"hash":"1143793581104446590","title":"RNA processing and splicing regulation","description":"Dominant GO terms point to mRNA processing and spliceosome-mediated splicing (mRNA cis splicing via spliceosome; regulation of mRNA polyadenylation; pre-mRNA cleavage), indicating a post-transcriptional gene regulation theme. A few terms touch on cell growth or differentiation, which may be peripheral or dataset noise. Overall, the cluster seems best described by RNA processing/splicing regulation.","confidence":"Medium","size":17,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":2},{"id":"GO:1905606","count":2},{"id":"GO:1904761","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0030307","count":2}]},{"hash":"204712134446154595","title":"Embryonic heart and forebrain morphogenesis","description":"This cluster\u2019s top GO terms cluster around developmental processes and morphogenesis, notably heart development, forebrain development, and embryonic cranial skeleton morphogenesis, indicating a shared role in embryonic organ formation. Additional terms touch on cell division and stress-related signaling (ER stress\u2013related apoptosis, calcium signaling modulation, responses to muscle activity/stretch, and ethanol response), suggesting supporting roles in cellular remodeling during development. Overall, the dominant theme is embryonic development and tissue morphogenesis with ancillary regulatory and stress-related processes. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0050849","count":3}]},{"hash":"1978650917812773245","title":"Unknown","description":"The terms are very diverse and only loosely linked via miRNA regulation and transcription; many terms refer to distinct processes (liver regeneration, myotome development, immune signaling, metabolism) with no shared pathway or interaction evident among the proteins. With no edges and a lack of a cohesive function, there isn\u2019t a clear theme to assign a meaningful label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0000022","count":2},{"id":"GO:0044339","count":2},{"id":"GO:0006351","count":2}]},{"hash":"347799995019770443","title":"Metal ion transport and homeostasis","description":"The top GO terms cluster around transport and handling of multiple metal ions (copper, zinc, iron, mercury, cadmium) and detoxification processes, including copper ion homeostasis and mercury detoxification, suggesting a group of metal-transporters/regulators. Ubiquitination appears as a regulatory note rather than the core function. Overall, the shared theme is metal ion transport and maintenance across cellular compartments.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0050787","count":2},{"id":"GO:0006801","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0060003","count":2}]},{"hash":"2027758196019636923","title":"Meiosis Chromosome Cohesion and Segregation","description":"The terms cluster around meiotic sister chromatid cohesion, centromeric localization, biorientation, and septin ring dynamics related to cell division, suggesting a chromosomal segregation module; a few neuron-related terms may be incidental noise.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":5},{"id":"GO:0031175","count":4},{"id":"GO:0051388","count":3},{"id":"GO:0032186","count":3},{"id":"GO:0070199","count":3}]},{"hash":"1302876935171579810","title":"Oocyte Meiosis: Spindle Assembly and Ubiquitin-Proteasome Regulation","description":"This cluster is dominated by GO terms tied to oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, together with SCF-dependent ubiquitin-proteasome\u2013mediated protein degradation. The co-occurrence of these processes suggests a coordinated program controlling meiosis progression and spindle dynamics in oocytes, with ubiquitin-mediated proteolysis enabling timely transitions. Some brain-development terms (third ventricle development, initiation of neural tube closure) may reflect broader developmental roles or shared signaling contexts in early embryogenesis, but the strongest signals center on meiotic and cytoskeletal regulation in oocytes.","confidence":"High","size":17,"edges":14,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":17},{"id":"GO:0001556","count":16},{"id":"GO:0021678","count":16},{"id":"GO:0051436","count":16},{"id":"GO:0046785","count":16}]},{"hash":"905069849735183543","title":"Bacterial cell wall glycan biosynthesis","description":"The top terms cluster around cell wall organization and glycosylation, including teichoic acid biosynthesis, various forms of protein O-linked glycosylation, and lipid-linked sugar biosynthesis, which points to a cohesive theme of bacterial cell envelope polysaccharide synthesis and surface glycan construction. Some terms (insect development) appear less related and may reflect cross-species annotations, but the dominant signal supports cell wall glycan biosynthesis.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0016266","count":4},{"id":"GO:0018242","count":3},{"id":"GO:0019350","count":3},{"id":"GO:0075015","count":3}]},{"hash":"324878572532711839","title":"Vesicle transport and cytoskeletal remodeling","description":"This cluster centers on endomembrane trafficking (endosome-to-lysosome transport, pinocytosis, CVT pathway) and actin/cytoskeleton dynamics (lamellipodium morphogenesis, microvillus assembly) with accompanying GTPase regulation and secretion/remodeling activities (histamine release, ECM disassembly). Together these terms point to a cohesive theme of vesicle trafficking coupled to cytoskeletal remodeling and related secretory and matrix-modifying processes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0008333","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0022617","count":3},{"id":"GO:1903595","count":3}]},{"hash":"2086773916410260959","title":"Mitochondrial protein import and mitophagy regulation","description":"The prominent GO terms center on mitochondrial function\u2014calcium import into mitochondrion, protein import into the mitochondrial matrix, and regulation of autophagy of mitochondrion\u2014coupled with monoatomic anion transport, suggesting mitochondrial protein trafficking and quality control as the shared theme. The neural processes present may reflect mitochondria\u2019s roles in neurons, but the core pattern points to mitochondrial import and mitophagy. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903959","count":1},{"id":"GO:0006820","count":1},{"id":"GO:0036444","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0001662","count":1}]},{"hash":"913887376452676070","title":"DNA Damage Response and p53-Mediated Apoptosis","description":"The top GO terms point to DNA-related processes (DNA-templated transcription, DNA repair) and apoptotic pathways, including intrinsic p53-mediated signaling, suggesting a stress response to DNA damage that can lead to apoptosis. Peripheral terms like nucleotide catabolism and steroid biosynthesis appear less central to the core theme but may reflect ancillary metabolic contexts. Overall, the strongest cohesive theme is DNA damage response with apoptosis.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:2000757","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0006154","count":1},{"id":"GO:0050850","count":1}]},{"hash":"1650907021703655970","title":"Proteoglycan Biosynthesis and ECM Assembly","description":"The cluster shows strong representation of proteoglycan biosynthesis terms (heparan sulfate, heparin, chondroitin sulfate) indicating a common function in producing extracellular matrix components. Immune and developmental terms (neutrophil chemotaxis, mesoderm development) align with ECM roles in cell signaling and tissue remodeling, while the mucilage-related term suggests polysaccharide biosynthesis. Overall, the core theme appears to be proteoglycan biosynthesis and extracellular matrix assembly.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010192","count":2},{"id":"GO:2001200","count":2},{"id":"GO:0030593","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0007114","count":2}]},{"hash":"2064306032038732343","title":"Central metabolism: glycolysis and amino acid biosynthesis","description":"The top GO terms indicate involvement in glycolysis and pyruvate production, along with multiple amino acid biosynthetic and catabolic pathways, plus quinone biosynthesis. This pattern points to a cluster representing broad central metabolism rather than a single pathway, justifying a label around central metabolism with emphasis on glycolysis and amino acid biosynthesis.","confidence":"Medium","size":16,"edges":113,"triangles":468,"max_degree":15,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0042866","count":6},{"id":"GO:0009097","count":5},{"id":"GO:0061621","count":4},{"id":"GO:0042372","count":4},{"id":"GO:0009234","count":4}]},{"hash":"998629710390741441","title":"Negative regulation of TGF-\u03b2/BMP signaling","description":"This cluster is dominated by GO terms about down-regulating SMAD signaling and TGF-\u03b2/BMP pathways, including negative regulation of TGF-\u03b2 receptor signaling and BMP signaling, as well as related cellular responses to TGF-\u03b2. While a few terms touch on meristem identity or vacuole fusion, the overarching theme is inhibition of TGF-\u03b2/BMP signaling, suggesting these proteins act as regulators of this pathway.","confidence":"High","size":16,"edges":71,"triangles":151,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0010991","count":15},{"id":"GO:0042347","count":15},{"id":"GO:0071560","count":15},{"id":"GO:0030514","count":15},{"id":"GO:0046827","count":15}]},{"hash":"1570939182841203306","title":"Vascular ECM Remodeling and Elastin Catabolism","description":"These terms point to vascular ECM remodeling: ECM disassembly, elastin breakdown, smooth muscle migration, and fibrinolysis, with an additional cue from ANP-related blood pressure regulation. The translation/transcription terms seem secondary noise rather than core features.","confidence":"High","size":16,"edges":114,"triangles":481,"max_degree":15,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0030163","count":3},{"id":"GO:0014909","count":2},{"id":"GO:0022617","count":2},{"id":"GO:0060309","count":2}]},{"hash":"2413838071366640","title":"Wnt and Hippo signaling in development","description":"This cluster centers on developmental growth and fate decisions, highlighted by positive regulation of canonical Wnt signaling and Hippo signaling, neural tube closure, multicellular development, and keratinocyte differentiation. It also includes mitotic cell cycle and apoptotic processes, suggesting a coordinated module governing embryonic development and tissue remodeling through these pathways.","confidence":"High","size":16,"edges":37,"triangles":21,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0007275","count":11},{"id":"GO:0090263","count":10},{"id":"GO:0060044","count":10}]},{"hash":"1357576685498334176","title":"NF-\u03baB\u2013driven antiviral innate immunity and ER stress response","description":"Most terms point to innate immune signaling and NF-\u03baB activation (innate immune response, defense response to virus, I-kappaB phosphorylation), complemented by ubiquitination and ER stress responses (unfolded protein response, translation initiation during ER stress, chaperone-dependent refolding) and redox homeostasis. This suggests a cohesive immune- and stress-response module.","confidence":"High","size":16,"edges":16,"triangles":0,"max_degree":11,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0045087","count":4},{"id":"GO:0045842","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0007252","count":4}]},{"hash":"92687922891668054","title":"Transmembrane Transporters","description":"The top GO terms are dominated by various transmembrane transport activities (phosphate, vitamin, arabinose, nitrate, hydroxyphenylacetate, etc.), indicating a cluster of membrane transporter proteins with diverse substrates. Some immune and apoptosis terms appear as secondary annotations, likely due to contextual roles or annotation overlap, but the strongest signal is substrate transport across membranes. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0071222","count":3},{"id":"GO:0097194","count":3},{"id":"GO:0035435","count":3}]},{"hash":"714550314879110378","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":20,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0046512","count":2},{"id":"GO:2000637","count":2},{"id":"GO:0003334","count":2},{"id":"GO:0016479","count":2}]},{"hash":"2017652171890419985","title":"DNA replication, repair, and chromatin regulation","description":"The cluster shows repeated signals for DNA-templated transcription, DNA replication, and DNA repair, along with methylation of histone H4 and arginine residues, indicating a module focused on genome maintenance and transcriptional/chromatin regulation. While xenobiotic response terms appear, the dominant theme is DNA-centric processes and chromatin modification, suggesting a cohesive functional grouping around genomic integrity and gene regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0090398","count":3}]},{"hash":"1489468316692929433","title":"Plant phytochelatin-mediated cadmium detoxification","description":"The defining GO terms are phytochelatin biosynthetic process and phytochelatin-metal complex formation, plus response to cadmium ion, pointing to a plant-specific metal-detoxification pathway. Other terms like photosynthesis or transcription are broader and less diagnostic, but do not undermine the core phytochelatin\u2013cadmium detox theme.","confidence":"High","size":16,"edges":43,"triangles":26,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0035754","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0015979","count":1}]},{"hash":"518508901596928006","title":"Quinone biosynthesis and respiration","description":"The cluster shows strong signals for aerobic respiration and redox-related processes, with specific involvement in ubiquinone and phylloquinone biosynthesis\u2014both central to electron transport and energy metabolism. While a few terms are obscure or transient (e.g., certain PTMs and obsolete GO terms), the core theme ties quinone biosynthesis to respiratory/redox function, justifying the label. ","confidence":"Medium","size":16,"edges":106,"triangles":389,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0001887","count":1},{"id":"GO:0030961","count":1},{"id":"GO:0006744","count":1}]},{"hash":"2139224154198547299","title":"Chloroplast Photosynthesis and Chlorophyll Biosynthesis","description":"This cluster is dominated by GO terms pointing to photosynthesis, light harvesting in photosystem I, and responses to red/far-red light and UV-A, along with phytol/chlorophyll-related biosynthetic processes. Although a couple of terms are obsolete, the consistent theme is chloroplast-driven photosynthetic activity and pigment biosynthesis (phytol/chlorophyll), with related fatty acid biosynthesis linked to chloroplast membranes. Therefore, the cluster likely represents chloroplast photosynthesis and chlorophyll biosynthesis pathways.","confidence":"High","size":16,"edges":111,"triangles":445,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006633","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0009768","count":2}]},{"hash":"430883757656216317","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0014075","count":5},{"id":"GO:0006526","count":5},{"id":"GO:0044210","count":4},{"id":"GO:0006098","count":4},{"id":"GO:0044205","count":4}]},{"hash":"2148439160724090725","title":"Bacterial central carbon metabolism and lipid biosynthesis","description":"The GO terms point to core energy and carbon-flow pathways (glycolysis, gluconeogenesis, TCA cycle, pyruvate decarboxylation to acetyl-CoA) together with lipid biosynthesis (long-chain fatty acids, malonyl-CoA) and cofactors biosynthesis (menaquinone), plus related amino acid catabolism and other biosynthetic processes. This suggests a cluster centered on central metabolism and membrane/lipid biosynthesis in bacteria, hence the label.","confidence":"High","size":16,"edges":98,"triangles":319,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":5},{"id":"GO:0042759","count":4},{"id":"GO:0009234","count":3},{"id":"GO:0006552","count":3},{"id":"GO:0006086","count":3}]},{"hash":"642516553998480735","title":"Unknown","description":"The top GO terms reflect a wide mix of biosynthetic (alkaloids, lipids, steroids, pigment) and developmental or regulatory processes from diverse species, with no single shared molecular function or pathway tying the proteins together. This makes it impossible to assign a cohesive, intuitive label beyond Unknown.","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009710","count":1},{"id":"GO:0071768","count":1},{"id":"GO:0031427","count":1},{"id":"GO:0042574","count":1},{"id":"GO:0006703","count":1}]},{"hash":"1647154919828564416","title":"Amino acid, nucleotide, and antibiotic biosynthesis","description":"These proteins cluster around a set of biosynthetic GO terms, spanning antibiotic biosynthesis (including clavulanic acid), amino acid synthesis (glutamine and asparagine), nucleotide/nucleoside metabolism (nucleoside metabolic process, UDP-N-acetylglucosamine biosynthesis), and related carbohydrate phosphorylation. The common thread is involvement in diverse biosynthetic pathways producing small molecules, rather than a single specific function. Therefore the label reflects a broad biosynthetic role for this cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0006541","count":3},{"id":"GO:0046835","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0097171","count":3}]},{"hash":"704361764005684143","title":"Neural and retinal developmental transcription regulators","description":"The cluster is driven by GO terms tied to transcription (DNA-templated transcription) and broad development, with specific emphasis on neural and visual tissues (cerebellar cortex development, retina development) and neural migration, suggesting these proteins participate in transcriptional control of brain and eye development. Metabolic and signaling terms (glucose metabolism, GTPase activity) appear but seem secondary, and an immune-related term appears as an outlier. Overall, the dominant theme is developmental transcriptional regulation in neural/retinal contexts.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0006006","count":2}]},{"hash":"1211739994562801772","title":"Steroid Hormone Biosynthesis","description":"The top terms are dominated by testosterone, androgen, aldosterone, and cortisol biosynthetic processes, which together define steroidogenesis. Though a few unrelated terms appear (e.g., transcription regulation, antibiotic response), the strongest signal points to enzymes and pathways that produce steroid hormones, justifying the label. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0061370","count":4},{"id":"GO:0008209","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0006351","count":3}]},{"hash":"2261607552418128532","title":"Unknown","description":"The top GO terms cover transcription, nervous system development, mitotic processes, immune signaling, pigment cell migration, muscle differentiation, and spindle/mitosis checkpoints, with no single unifying function across the cluster. This spread suggests the proteins do not share a cohesive biological role, so a clear, specific label is not discernible beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0050852","count":5},{"id":"GO:0097324","count":5}]},{"hash":"208847210438814032","title":"Chloroplast PSII assembly and photosynthesis","description":"This cluster centers on terms tied to photosystem II assembly and the light-driven reactions of photosynthesis, including PSII assembly, stabilization, and photoinhibition, pointing to a chloroplast photosynthetic role. The additional glutathione metabolic process suggests antioxidant protection associated with photosynthetic activity, while xenobiotic/phenylalanine catabolic terms may reflect broader stress-related metabolism linked to chloroplast function. Overall, the proteins appear to be involved in PSII assembly and photosynthetic processes with related stress responses.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010190","count":1},{"id":"GO:0042549","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0019684","count":1},{"id":"GO:0010205","count":1}]},{"hash":"598804183298086604","title":"Sterol biosynthesis and oxidation enzymes","description":"The top GO terms point strongly to sterol metabolism, including cholesterol biosynthesis via lathosterol and ergosterol biosynthesis, plus sterol oxidation steps. There is also a related sphingolipid metabolism term (mannosyl-inositol phosphorylceramide). Although a few terms seem less related, the dominant theme across several terms suggests proteins involved in sterol biosynthesis and oxidative modifications.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035754","count":4},{"id":"GO:0032286","count":4},{"id":"GO:0006675","count":4},{"id":"GO:0001949","count":4},{"id":"GO:0055114","count":4}]},{"hash":"711954837042441497","title":"Chromatin-Driven Transcription Regulation","description":"The cluster is dominated by GO terms tied to transcription by RNA Polymerase II and chromatin biology\u2014chromatin localization, nucleosome dynamics, and histone modifications\u2014plus assembly of transcription preinitiation complexes. This points to a cohesive function in chromatin-mediated control of transcription, with some terms reflecting plant stress and light-responsive regulation. Overall, the proteins likely function in regulating Pol II transcription via chromatin state and remodeling.","confidence":"High","size":16,"edges":84,"triangles":223,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":11},{"id":"GO:0071169","count":9},{"id":"GO:0043457","count":9},{"id":"GO:0043966","count":9},{"id":"GO:0045898","count":9}]},{"hash":"1557884979046526512","title":"Branched-chain amino acid biosynthesis & metabolism","description":"Top terms are dominated by branched-chain amino acid pathways (L-leucine, L-isoleucine, L-valine biosynthesis and related D-amino acid metabolism), with supporting signals from folic acid and carnitine-related metabolism; a few outlier terms (DNA repair, regulation of hormone levels) are present but do not change the overall theme, suggesting the cluster represents amino acid biosynthesis and catabolism activities.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0009098","count":3},{"id":"GO:0046437","count":3},{"id":"GO:0019478","count":3},{"id":"GO:0006550","count":3}]},{"hash":"1406529227531369039","title":"Unknown","description":"The top GO terms span diverse processes (cellular response to virus, glucose response and metabolism, transcription, development, and regulatory activities) with no single cohesive function binding the proteins, and the cluster has no edges, indicating heterogeneity. Therefore, there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098586","count":5},{"id":"GO:0071333","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0033160","count":4}]},{"hash":"1812301891248450383","title":"Chloroplast Pigment Biosynthesis","description":"These proteins are enriched for GO terms tied to photosynthesis and pigment biosynthesis in plastids, including chlorophyll biosynthesis and biosynthesis of quinones (phylloquinone, plastoquinone, menaquinone) as well as vitamin K biosynthesis. The presence of GO:0015979 (photosynthesis) and multiple pigment/quinone biosynthetic terms strongly suggests a functional link to chloroplast pigment production and the photosynthetic electron transport chain. The sebaceous gland differentiation term appears as noise and does not fit the main theme.","confidence":"High","size":16,"edges":5,"triangles":1,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":5},{"id":"GO:0018298","count":4},{"id":"GO:0048034","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0009234","count":2}]},{"hash":"103258112281660489","title":"Radiation-induced apoptosis and mitophagy","description":"This cluster is dominated by GO terms for radiation and UV responses, extrinsic apoptotic signaling, and mitophagy, with supporting signals from protein deubiquitination and proteostasis. Together they point to a cohesive theme of stress-activated cell fate decisions and mitochondrial quality control, even though some terms (like lens morphogenesis and muscle contraction) may reflect broader expression rather than core function.","confidence":"Medium","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":6},{"id":"GO:0008625","count":5},{"id":"GO:0000422","count":5},{"id":"GO:0016579","count":5},{"id":"GO:0032355","count":5}]},{"hash":"2254959342855280706","title":"Plant Hormone Signaling and Phenylpropanoid Biosynthesis","description":"The top GO terms cluster around plant hormone responses (gibberellin and ethylene) and phenylpropanoid metabolism (syringal lignin and flavonol biosynthesis), suggesting a cohesive theme of plant growth regulation and secondary metabolite production. While a few terms touch chromatin or DNA repair processes, the dominant signals point to hormone signaling coupled with lignin/flavonoid biosynthesis in plants.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009739","count":7},{"id":"GO:1901430","count":7},{"id":"GO:1905839","count":7},{"id":"GO:0010520","count":7},{"id":"GO:0035066","count":7}]},{"hash":"1963619554686275226","title":"Plant Secondary Cell Wall Biosynthesis and Metabolism","description":"The top GO terms strongly point to plant-type secondary cell wall biogenesis and its positive regulation, suggesting these proteins are involved in cell wall formation in plants. Supporting terms include polysaccharide catabolic processes and phytochelatin biosynthesis, which relate to carbohydrate remodeling and metal detox pathways common in plant cells, along with nitrate assimilation and nitric oxide biosynthesis reflecting plant-specific metabolism and signaling that accompany cell wall development. Despite no interaction edges, the shared functional theme is coherent around plant cell wall biosynthesis and related metabolic activities.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0009834","count":2},{"id":"GO:1901348","count":2},{"id":"GO:0000272","count":2}]},{"hash":"2253027600696465259","title":"Spliceosome-associated RNA processing factors","description":"The dominant GO terms point to mRNA splicing via the spliceosome, splice-site recognition, and cis-splicing, with additional references to mRNA polyadenylation and regulation of RNA polymerase II CTD phosphorylation. Together, these indicate a cohesive cluster of proteins involved in RNA maturation and spliceosome-mediated processing, with a few viral-related terms likely reflecting incidental associations rather than core function. ","confidence":"Medium","size":16,"edges":115,"triangles":497,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":8},{"id":"GO:0006378","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0045292","count":6}]},{"hash":"2126191017908778683","title":"Neural vesicle trafficking and axonogenesis regulation","description":"The cluster\u2019s top terms cluster around vesicle transport and signaling (Rab protein signaling, regulation of synaptic vesicle exocytosis, Golgi to plasma membrane transport) and neural development (brain development, regulation of axonogenesis). This suggests a coherent theme of vesicle trafficking processes shaping neural development and axon growth, with some germline-related development terms that may reflect shared trafficking roles. ","confidence":"High","size":16,"edges":64,"triangles":82,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":8},{"id":"GO:2000300","count":8},{"id":"GO:0007420","count":8},{"id":"GO:0031384","count":8},{"id":"GO:0032482","count":7}]},{"hash":"1339028993321728805","title":"RNA Modification and Protein Ubiquitination","description":"The cluster is dominated by RNA modification terms (tRNA N2-guanine methylation; RNA guanine-N7 methylation; rRNA guanine-N7 methylation) and a ubiquitination term set (protein ubiquitination; peptidyl-arginine hydroxylation). These recurrent themes point to a core function in RNA and protein post-translational modifications, with additional lipid metabolism and xenobiotic response terms present but less central. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002940","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0001300","count":2}]},{"hash":"1770313533644891511","title":"Transmembrane Transport of Cofactors and Metabolites","description":"This cluster is dominated by GO terms describing transmembrane transport of various cofactors and ions (heme, phosphate, CoA, TPP, manganese, pyrimidine nucleotides), plus related metabolic regulation signals (adaptive thermogenesis, fatty acid response, amino acid starvation). The shared theme is membrane transport of metabolism-related molecules, linking energy metabolism and nutrient sensing.","confidence":"High","size":16,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":5},{"id":"GO:0035435","count":4},{"id":"GO:0034198","count":4},{"id":"GO:1990845","count":4},{"id":"GO:0061179","count":4}]},{"hash":"1082293713885814916","title":"Plant cell wall biosynthesis and plasmodesmata organization","description":"Most of the top GO terms center on plant cell wall biology\u2014cellulose biosynthesis, cell wall organization, and plasmodesma organization\u2014with related glycosylation, suggesting this cluster reflects plant cell wall formation and intercellular transport. A few terms about DNA repair/recombination appear, likely as incidental annotations, but they do not define the main theme. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":3},{"id":"GO:0006310","count":2},{"id":"GO:2001009","count":2},{"id":"GO:0009831","count":2},{"id":"GO:0009663","count":2}]},{"hash":"1216060613436212811","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000961","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0009451","count":2},{"id":"GO:1905639","count":2},{"id":"GO:0090617","count":2}]},{"hash":"644792101569221386","title":"Neural tube and embryonic development","description":"The cluster is dominated by terms tied to neural/embryonic development (neural tube closure, forebrain development, multicellular organism development, skeletal system development) along with general transcriptional and cell cycle processes (DNA-templated transcription, mitotic cell cycle) that support development. Additional terms reflect stress responses (ER stress\u2013related apoptosis, cadmium response) and immune defense, which may accompany development or represent co-expressed genes. Overall, the central theme is neural and embryonic tissue formation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":7},{"id":"GO:0070059","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0006349","count":7},{"id":"GO:0071276","count":7}]},{"hash":"2134411283422082276","title":"Chloroplast RNA Processing and Metabolism","description":"The top GO terms are strongly enriched for chloroplast-related RNA processing (chloroplast mRNA processing, polycistronic mRNA processing) and plastid-associated metabolic processes (ubiquinone biosynthesis, carbon dioxide transport, nitrogen utilization). Although there is a plant development term (meristem development), the plastid-centric terms dominate, suggesting a cluster of chloroplast gene expression and metabolic functions rather than a single signaling pathway. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043086","count":1},{"id":"GO:0080163","count":1},{"id":"GO:0010239","count":1},{"id":"GO:0048507","count":1},{"id":"GO:0006744","count":1}]},{"hash":"617227520991830175","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0007283","count":2},{"id":"GO:2000344","count":2},{"id":"GO:0052889","count":2},{"id":"GO:0016042","count":2}]},{"hash":"1713147568779777588","title":"Ubiquitin-Proteasome Degradation and Cell Cycle Regulation","description":"The cluster is dominated by ubiquitin-dependent proteolysis terms (ubiquitin-dependent protein catabolic process and SCF-dependent proteasomal ubiquitin-dependent protein degradation) and signals promoting ubiquitination, pointing to a core theme of proteostasis via the ubiquitin-proteasome system. Additional terms related to cell cycle control (mitotic G1 DNA damage checkpoint signaling) and circadian regulation suggest coordination between proteolysis, cell cycle regulation, and rhythmic processes. While some developmental and stress-response terms are present, the central motif is ubiquitin-mediated protein degradation tied to cell-cycle and stress-aware regulation.","confidence":"High","size":16,"edges":15,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0031146","count":8},{"id":"GO:0031571","count":6},{"id":"GO:1902916","count":6},{"id":"GO:0042752","count":6}]},{"hash":"1509487947774718549","title":"Unknown","description":"The top GO terms span transcription, transcription regulation, protein ubiquitination regulation, ribosome biogenesis, actin dynamics, and distinct developmental processes (forebrain and prostate gland). With no clear shared function linking these proteins and no edges connecting them, there isn\u2019t a cohesive theme to name the cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035948","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0032933","count":2}]},{"hash":"1784629700794621163","title":"Unknown","description":"The top GO terms cover very different processes (drug response, ion transport, selenium metabolism, various post-translational modifications, ubiquinone biosynthesis, stress response, aging), with no clear shared function or pathway tying the proteins together. Edges are absent, so a cohesive theme cannot be determined.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0006813","count":2},{"id":"GO:0001887","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0006744","count":2}]},{"hash":"1425319231615952869","title":"Nuclear transport and transcription regulation under stress","description":"The cluster is dominated by terms tied to DNA-templated transcription and regulation of nuclear import/export, pointing to a core theme of nuclear signaling and transcription control. Supporting terms like hypoxia detection and glucose metabolism suggest associated stress and metabolic signaling. Some terms (placenta development, chemotaxis) may reflect broader contexts or annotation noise but do not overwhelm the core theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001890","count":5},{"id":"GO:0033160","count":5},{"id":"GO:0006935","count":5},{"id":"GO:0006006","count":5},{"id":"GO:0042220","count":5}]},{"hash":"278425892675565691","title":"Plant terpenoid biosynthesis and gibberellin signaling","description":"This cluster centers on terpenoid metabolism (geranyl diphosphate metabolism; monoterpene, sesquiterpene, and camphor biosynthesis) and gibberellin biosynthesis/signaling, with an additional signal for herbivore response, pointing to a plant module that links growth regulation with production of defensive terpenoids.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046944","count":1},{"id":"GO:0080027","count":1},{"id":"GO:0009740","count":1},{"id":"GO:0009686","count":1},{"id":"GO:0051762","count":1}]},{"hash":"1626205118257754518","title":"Central Metabolism and Redox/Xenobiotic Response","description":"The cluster centers on core energy pathways\u2014glycolysis and the TCA cycle\u2014along with related NADH/oxidation-reduction processes and fatty acid biosynthesis, plus responses to hydrogen peroxide and xenobiotic stimuli. This suggests a cohesive set of proteins tied to central carbon metabolism with redox balance and detox/defense signaling. Hence the name reflects the dominant themes without overreaching beyond the data.","confidence":"High","size":15,"edges":103,"triangles":429,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0006096","count":7},{"id":"GO:0042493","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0042759","count":3}]},{"hash":"428970327933356058","title":"Cell Cycle and Synaptic Trafficking","description":"The cluster links mitotic processes (mitotic cell cycle, cell division) with neural trafficking functions such as presynaptic assembly, receptor recycling, and endosome size regulation, plus signaling modules like GTPase activity and Ran-mediated transport. Visual perception and pheromone response terms hint at neuronal contexts, suggesting this group covers both cell-cycle regulation and vesicle trafficking/synaptic organization.","confidence":"Medium","size":15,"edges":95,"triangles":345,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0007601","count":6},{"id":"GO:1905490","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0043547","count":5}]},{"hash":"1907090218150017172","title":"Developmental Regulation and Cell-Cycle Signaling","description":"The top GO terms cluster around transcriptional regulation, developmental processes (heart, Schwann cell, visual perception), and G2/M cell-cycle control, plus signaling modulation, indicating a group of regulatory proteins that coordinate development with proliferation. Some terms (like abscisic acid signaling) may reflect cross-species annotations or broader signaling roles, but the core theme is regulatory factors in development and cell cycle.","confidence":"Medium","size":15,"edges":9,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045944","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0000086","count":6},{"id":"GO:0014044","count":6},{"id":"GO:0009738","count":6}]},{"hash":"355324750429571326","title":"Neuronal synaptic vesicle exocytosis and plasticity","description":"Top GO terms strongly point to neuronal signaling and vesicle trafficking (regulation of synaptic vesicle exocytosis, short-term potentiation, brain development, calcium-regulated lysosome exocytosis), with Rho signaling supporting cytoskeletal dynamics; additional terms like ribophagy and insulin secretion regulation may reflect ancillary metabolic connections in neurons. Overall, the cluster centers on synaptic activity and neuronal development.","confidence":"High","size":15,"edges":65,"triangles":106,"max_degree":13,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0010796","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0031384","count":5},{"id":"GO:0034517","count":5}]},{"hash":"1415387126456211336","title":"Unknown","description":"The top GO terms span disparate processes (cardiac signaling, immune signaling, reproductive development, and general signaling) with no unifying function, so there isn't a clear shared role for this protein set. ","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071872","count":10},{"id":"GO:0051591","count":10},{"id":"GO:0001824","count":10},{"id":"GO:0000742","count":10},{"id":"GO:0098907","count":9}]},{"hash":"2192496506775391075","title":"Phospholipid biosynthesis in development","description":"This cluster centers on phospholipid biosynthetic processes (phosphatidylethanolamine and phosphatidylserine) and lipids-related responses, with several developmental terms such as angiogenesis, layer formation in the cerebral cortex, cartilage condensation, and synapse assembly. The common thread appears to be lipid metabolism and signaling guiding tissue morphogenesis and neural development, with some ancillary terms (apoptotic clearance, cell-cycle regulation) reflecting broader developmental remodeling.","confidence":"High","size":15,"edges":27,"triangles":2,"max_degree":8,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006646","count":5},{"id":"GO:0043277","count":5},{"id":"GO:0051965","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0021819","count":5}]},{"hash":"163583017462092494","title":"Calcium signaling and ion transport in neuromuscular systems","description":"The top GO terms cluster around calcium and other metal ion transport (mitochondrial calcium homeostasis and transmembrane transport), along with regulation of skeletal and cardiac muscle contraction and synaptic plasticity (LTP/LTD). This suggests a cohesive theme of calcium-driven signaling that coordinates neuromuscular communication and contraction.","confidence":"High","size":15,"edges":23,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":6},{"id":"GO:0098703","count":6},{"id":"GO:0007154","count":5},{"id":"GO:0060292","count":5},{"id":"GO:0051560","count":5}]},{"hash":"1073496230965796654","title":"Nucleotide and Mitochondrial Energy Metabolism","description":"This cluster is dominated by terms tied to nucleotide metabolism (CDP/dCDP interconversion and biosynthesis) and mitochondrial energy processes (mitochondrial DNA replication, proton motive force-driven ATP synthesis, vacuolar acidification). These point to a shared theme of cellular energy production and nucleotide biosynthesis. A few terms (renal system process, caudal fin development, and p53-regulated apoptosis) are more peripheral, likely reflecting broader functional annotations of included proteins. Confidence: Medium.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"renal system process","top_go_terms":[{"id":"GO:0015949","count":3},{"id":"GO:0046704","count":3},{"id":"GO:0006240","count":3},{"id":"GO:0006264","count":3},{"id":"GO:0055114","count":3}]},{"hash":"1288225715448079967","title":"Plant light sensing and photoprotection","description":"The proteins cluster around light-related processes: photosynthesis and light harvesting, responses to red/far-red and UV-A light, responses to light intensity, and nonphotochemical quenching, with phytol/chlorophyll-related biosynthesis links. This indicates a cohesive role in plant light perception and protection of the photosynthetic apparatus.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904964","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0009768","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0010114","count":2}]},{"hash":"554628015010224137","title":"Ribosome biogenesis and translation machinery","description":"This cluster is dominated by ribosome-related terms: translation (GO:0006412), cytoplasmic translation (GO:0002181), and ribosome biogenesis (GO:0042254), plus ribosomal large subunit export from nucleus (GO:0000055). The presence of cell division and cell septum assembly terms (GO:0051301, GO:0090529) suggests coordination between ribosome assembly and the cell cycle. A few entries relate to antibiotic response or amino acid starvation, but these are secondary. ","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":6},{"id":"GO:0002181","count":5},{"id":"GO:0046677","count":3},{"id":"GO:1903833","count":3}]},{"hash":"236797292394125915","title":"Plant chloroplast function and vesicle trafficking","description":"This cluster is dominated by terms tied to photosynthesis and chloroplast-related processes (photosynthesis, proton transmembrane transport), alongside endomembrane system activities (multivesicular body disassembly, vacuolar protein processing) and plant-relevant signaling/response terms (UV-B response, G protein-coupled glutamate receptor signaling). The combination suggests a plant-centric theme where chloroplast function intersects with vesicle trafficking and light/membrane signaling. Confidence: Medium","confidence":"","size":15,"edges":83,"triangles":233,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0015979","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0034727","count":1},{"id":"GO:0030245","count":1}]},{"hash":"671713455657750210","title":"P450-driven xenobiotic detoxification","description":"The proteins appear to be involved in diverse catabolic and detoxification processes, including oxidation-reduction and detoxification of xenobiotics, as reflected by GO terms such as epoxygenase P450 pathway, cellular oxidant detoxification, and multiple xenobiotic catabolic processes (e.g., 1,2-dichloroethane, 3-phenylpropionate, glucuronoside, uracil). The presence of strigolactone biosynthesis suggests plant-related P450 activity. Although the edges are absent (potentially representing dispersed enzymes), the shared theme is metabolism and detoxification via P450- and related pathways. Confidence: High","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019380","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0009086","count":5},{"id":"GO:0009636","count":4},{"id":"GO:0006212","count":4}]},{"hash":"832974130204893585","title":"Mitochondrial inner-membrane energy metabolism","description":"This cluster\u2019s top GO terms center on mitochondria-related inner-membrane functions: proton motive force-driven ATP synthesis, cristae formation, and monoatomic cation transport, with heme biosynthesis also tied to mitochondrial pathways. These together point to energy production and structural organization of the mitochondrial inner membrane, with some nucleotide metabolism terms that can be linked to mitochondrial processes via broader metabolic roles. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":1},{"id":"GO:0035786","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0009220","count":1}]},{"hash":"810699024736888539","title":"Ribosome biogenesis and translation","description":"Reasoning: Core signals are translation and cytoplasmic translation, plus ribosome biogenesis, pointing to components of the protein synthesis machinery; cell-cycle and cell division terms suggest coordination with growth. An obsolete mitochondrion morphogenesis term appears incidental.","confidence":"High","size":15,"edges":41,"triangles":57,"max_degree":12,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0002181","count":4},{"id":"GO:0070584","count":3},{"id":"GO:1903833","count":3},{"id":"GO:0042254","count":3}]},{"hash":"1297895590926923868","title":"Unknown","description":"The most frequent terms cover disparate areas (cellulose catabolic process, antibiotic biosynthetic process, embryonic development, megakaryocyte differentiation, cold response) with no single dominant pathway. The lack of edges and the presence of an obsolete term further prevent a cohesive functional theme, so no reliable label can be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0030245","count":6},{"id":"GO:0098869","count":4},{"id":"GO:0009409","count":4},{"id":"GO:0001701","count":4}]},{"hash":"1203937671609680448","title":"Unknown","description":"This cluster links to diverse processes: innate immune response and lipopolysaccharide metabolism (immune-related), glycogen metabolism and carbohydrate phosphorylation (metabolic), box C/D snoRNP assembly and histone dephosphorylation (RNA/chromatin-related), cell division, protein heterooligomerization, atrial septum development, and UV-A response. The wide functional spread and only a single edge make it unclear what cohesive function or theme unites these proteins, so a specific label isn't justifiable.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0046835","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0016576","count":2},{"id":"GO:0000492","count":2}]},{"hash":"843401539054871775","title":"Unknown","description":"The GO terms span transcription, stress sensing (hypoxia, visible light), immune regulation, chlorophyll-related processes, metabolism, protein folding, and development, with no single shared function or pathway across the proteins, and zero edges, so there is no coherent theme to bind the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0070483","count":5},{"id":"GO:1903660","count":5},{"id":"GO:0010271","count":5},{"id":"GO:0017006","count":5}]},{"hash":"1640468597573486128","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0048701","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0043044","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0034476","count":3}]},{"hash":"1863229515851138714","title":"Patterning and organ development","description":"This cluster centers on developmental patterning and organogenesis across tissues, highlighted by terms like compartment pattern specification, leg segmentation from imaginal discs, ovarian follicle development, intestinal epithelial development, and Notch signaling regulation. While a few terms are more peripheral (e.g., B cell differentiation, obsolete glycan biosynthesis), the dominant theme is developmental patterning and tissue formation via signaling pathways such as Notch.","confidence":"Medium","size":15,"edges":15,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032092","count":4},{"id":"GO:0001541","count":4},{"id":"GO:0045747","count":4},{"id":"GO:0002315","count":4},{"id":"GO:0007386","count":4}]},{"hash":"1030287988183221775","title":"Mesodermal differentiation and organ morphogenesis","description":"The top GO terms cluster around differentiation and morphogenesis of mesoderm-derived tissues and organs (paraxial mesoderm, skeletal muscle, metanephric mesenchyme/kidney, heart/vessel morphogenesis, and related neuroendocrine tissues such as carotid body and lung neuroendocrine cells). This suggests a cohesive theme of developmental differentiation across multiple organ systems, with some additional metabolism-linked terms (SREBP signaling) that may modulate tissue development. Overall, the dominant signal is developmental differentiation and organ formation.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0032933","count":12},{"id":"GO:0043503","count":12},{"id":"GO:0061103","count":12},{"id":"GO:0048666","count":12},{"id":"GO:0061100","count":12}]},{"hash":"1407571005599168563","title":"Mesodermal and Neuroendocrine Differentiation","description":"Based on the top GO terms, the cluster is enriched for developmental processes across mesodermal derivatives (paraxial mesoderm, skeletal muscle, heart, aorta) and for differentiation of neuroendocrine tissues (carotid body glomus cells, lung neuroendocrine cells). There is also transcriptional regulation and signaling linked to differentiation, suggesting these proteins function in coordinating multi-tissue development and lineage specification.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":13},{"id":"GO:0032933","count":12},{"id":"GO:0043503","count":12},{"id":"GO:0061103","count":12},{"id":"GO:0048666","count":12}]},{"hash":"502018155487157418","title":"Plant membrane transport and glycosylation","description":"The cluster\u2019s GO terms are dominated by membrane transport activities (UDP-glucose, triose phosphate, and amino acid export/transmembrane transport) and glycosylation processes (O-linked fucosylation and N-glycan fucosylation), with additional plant-specific hints from defense against oomycetes and lateral root development. This pattern suggests a plant-focused set of proteins involved in transport and protein/glycan modification rather than a single tightly connected function. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0034635","count":1},{"id":"GO:0002229","count":1},{"id":"GO:0015786","count":1}]},{"hash":"1254123358040267546","title":"Unknown","description":"The GO terms span diverse areas including plant hormone signaling (cytokinin, gibberellin), lignin and flavonol biosynthesis, chromatin/telomere regulation, meiosis, and DNA repair, with several obsolete terms; there is no clear shared function or interaction pattern linking these proteins, so a specific functional label is not evident.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0009739","count":5},{"id":"GO:1901430","count":5},{"id":"GO:1905839","count":5},{"id":"GO:0010520","count":5}]},{"hash":"1975649618815609433","title":"Plant hormone signaling and phenylpropanoid biosynthesis","description":"The top GO terms are dominated by plant hormone signaling (cytokinin-activated signaling pathway; response to gibberellin) and phenylpropanoid metabolism (positive regulation of syringal lignin biosynthetic process; positive regulation of flavonol biosynthetic process). This suggests the cluster reflects proteins that integrate growth signaling with lignin and flavonoid biosynthesis, common in plant development and secondary metabolism. Some terms related to chromatin/DNA repair are present but less representative of the main theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0009739","count":5},{"id":"GO:1901430","count":5},{"id":"GO:1905839","count":5},{"id":"GO:0010520","count":5}]},{"hash":"167553660317735111","title":"Plant Hormone Signaling and Cell Wall Biogenesis","description":"This cluster is dominated by GO terms tied to plant hormone responses (gibberellin, salicylic acid, cytokinin signaling) and transcriptional regulation, plus specific terms for secondary cell wall formation and lignin biosynthesis. The convergence of hormone signaling with regulation of DNA-templated transcription suggests a cohesive module controlling growth and cell wall development in plants.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009739","count":4},{"id":"GO:0009751","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0006355","count":3}]},{"hash":"998335938870480171","title":"Plant cell wall biosynthesis and root hair development","description":"The top GO terms emphasize plant cell wall processes, including cell wall organization and rhamnogalacturonan II biosynthesis, along with root hair cell development, pointing to a cohesive theme around plant cell wall assembly and epidermal root growth. Some DNA repair/recombination annotations may be incidental or reflect shared domains, but the central signal is plant cell wall formation and root hair development.","confidence":"Medium","size":15,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0006281","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0010306","count":3},{"id":"GO:0016311","count":2}]},{"hash":"1950155482209124086","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:0031426","count":3},{"id":"GO:0000961","count":2},{"id":"GO:0010019","count":2},{"id":"GO:1905639","count":2}]},{"hash":"2114296692678691735","title":"Plant cell wall biosynthesis and abiotic stress response","description":"These proteins appear linked to plant cell wall construction and remodeling (xylan biosynthesis, secondary cell wall biogenesis, wall modification) and to secretory trafficking from ER to Golgi, which would support wall component delivery. The presence of abiotic stress signals (response to freezing, oxidative stress\u2013related signaling) suggests a module coordinating wall dynamics with stress adaptation. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0015031","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0002037","count":2},{"id":"GO:0008631","count":2}]},{"hash":"1545459156288731177","title":"Proteostasis and Stress Response","description":"This cluster centers on protein quality control and cellular stress pathways, with terms for heat response, unfolded protein response, ubiquitin/ERAD, and redox homeostasis, plus some transcription-related processes that reflect stress-induced transcriptional changes. Overall, it suggests a cohesive proteostasis/stress regulation module, though the DNA replication/transcription terms introduce some ambiguity.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009408","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0071260","count":3}]},{"hash":"469256130734106089","title":"Neuronal Vesicle Trafficking and Synaptic Signaling","description":"The top GO terms point to regulation of synaptic vesicle exocytosis, neurotransmitter secretion, and vesicle budding, along with brain development and small GTPase signaling, indicating a cohesive theme of presynaptic vesicle trafficking and neuronal signaling. Some apoptosis-related terms appear but are less representative of the core function; overall, the cluster seems centered on neuronal vesicle dynamics and development.","confidence":"Medium","size":15,"edges":48,"triangles":35,"max_degree":10,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0010796","count":8},{"id":"GO:2000300","count":8},{"id":"GO:0007420","count":8},{"id":"GO:0031384","count":8},{"id":"GO:0007269","count":6}]},{"hash":"725960709980483478","title":"Ubiquitin-dependent proteolysis","description":"This cluster is best labeled Ubiquitin-dependent proteolysis because the strongest GO terms point to ubiquitin-mediated protein degradation, including autoubiquitination and K48-linked ubiquitination, with related receptor downregulation (Wnt receptor catabolic process). A few other terms (e.g., dosage compensation and peroxisomal import) appear as peripheral associations.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0060816","count":5},{"id":"GO:0051865","count":5},{"id":"GO:1900095","count":5},{"id":"GO:0030433","count":5}]},{"hash":"1562629390948025534","title":"Plant floral organ and meristem specification regulators","description":"This cluster is dominated by transcription-related GO terms (DNA-templated transcription and regulation of transcription) and plant developmental processes such as flower development, meristem development, axis specification, abaxial cell fate, fruit dehiscence, somatic embryogenesis, and hormone/auxin signaling, pointing to transcription factors that coordinate floral organ formation and meristem identity in plants.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0010047","count":4},{"id":"GO:0009734","count":3},{"id":"GO:0010262","count":3}]},{"hash":"160999821533028917","title":"LSU rRNA Maturation","description":"The top GO terms in this cluster are strongly tied to maturation of LSU rRNA from a tricistronic transcript, pointing toward a ribosome biogenesis/ RNA processing theme. A number of other terms (lipid and metabolite biosynthesis, various post-translational modifications, stress response) appear only once and do not form a cohesive secondary theme, making the primary signal rRNA maturation less definitive. Overall, the strongest shared function is LSU rRNA maturation, but the sparse supporting terms reduce confidence.","confidence":"Low","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0001576","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0051999","count":1}]},{"hash":"224869473815473297","title":"Ubiquitin-Dependent Proteostasis and Peroxisomal Import","description":"The top GO terms are dominated by ubiquitin-related proteolysis (ubiquitin-dependent protein catabolic process, ERAD) and peroxisomal matrix protein import, with added ubiquitin-related regulation (autoubiquitination). This suggests a core theme of ubiquitin-mediated protein turnover and peroxisome targeting, with a few broader signaling terms that may be secondary. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0016558","count":6},{"id":"GO:0042981","count":5},{"id":"GO:0060816","count":5}]},{"hash":"439389576730132656","title":"Plant ubiquinone and tocopherol biosynthesis","description":"This cluster centers on biosynthetic processes for quinones (ubiquinone) and related lipid metabolism, highlighted by ubiquinone biosynthesis, regulation of ubiquinone biosynthetic process, and tocopherol cyclase activity. The presence of lipid homeostasis terms supports a broader plant lipid metabolism theme. Some terms (rRNA methylation, arginine hydroxylation, Purkinje cell layer morphogenesis) appear peripheral or cross-annotated, but do not outweigh the quinone/lipid biosynthesis signal. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":3},{"id":"GO:1901006","count":2},{"id":"GO:0010795","count":2},{"id":"GO:0055088","count":2},{"id":"GO:0021692","count":2}]},{"hash":"1714852508159985321","title":"Cell Polarity and Development Signaling","description":"The GO terms center on mitotic spindle orientation, centrosome positioning, and apical growth (polarity-related processes) with additional neural development terms, indicating a general theme of cellular polarity guiding development and membrane-associated signaling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":3},{"id":"GO:0016198","count":2},{"id":"GO:0070493","count":2},{"id":"GO:0001778","count":2},{"id":"GO:0021678","count":2}]},{"hash":"1648380634525703905","title":"Golgi\u2013ER vesicle trafficking","description":"This cluster\u2019s terms cluster around vesicle transport within the endomembrane system, especially Golgi\u2013ER retrograde and anterograde transport, Golgi organization, and Golgi-to-vacuole pathways, pointing to a core role in Golgi-ER trafficking and Golgi maintenance. The CvT pathway and endosome-to-Golgi retrograde transport support a broader vesicle-traffic theme in the Golgi network, with a few outliers likely representing related processes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0032258","count":2},{"id":"GO:0009860","count":2},{"id":"GO:0007030","count":2}]},{"hash":"1686305263877656156","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning lipid and nucleotide catabolism (triglyceride, uracil, glucuronoside), plant-specific metabolism (strigolactone, phytol), development (fat pad development), immune regulation, and even obsolete biosynthetic processes, with no clear single function tying the proteins together. The lack of edges reinforces the absence of a cohesive functional theme.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:0009086","count":1},{"id":"GO:0070236","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0033306","count":1}]},{"hash":"1136171625710233686","title":"Neuromuscular signaling and metabolic regulation","description":"This cluster is dominated by GO terms related to neurotransmitter secretion and neuromuscular process, including negative regulation of synaptic assembly at NMJ and collateral sprouting, suggesting a focus on signaling at neuromuscular junctions. Additional terms point to cellular metabolism and organelle dynamics (lipid droplet organization, mitochondrial membrane potential, peroxisome inheritance), implying coordinated metabolic regulation in neuromuscular contexts. The mix indicates a cohesive theme around nerve-muscle communication with metabolic support, rather than a single isolated function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007269","count":3},{"id":"GO:0045033","count":3},{"id":"GO:0060612","count":3},{"id":"GO:0030514","count":3},{"id":"GO:0009838","count":3}]},{"hash":"1839927990528147753","title":"Plant hormone biosynthesis and fruit ripening","description":"The top GO terms center on plant-specific processes: gibberellin biosynthesis and catabolism, ethylene biosynthesis, and fruit ripening, with proanthocyanidin biosynthesis also tying to plant secondary metabolism. These together suggest a cluster focused on plant hormone production and fruit maturation, despite a couple of outlier terms like spinal cord development. Overall, the prevailing theme is plant hormone-related biosynthesis and ripening, hence this label. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001247","count":2},{"id":"GO:2001246","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0010421","count":1},{"id":"GO:0010023","count":1}]},{"hash":"618339798133374548","title":"Neuronal synaptic signaling and plasticity","description":"The majority of GO terms relate to neuronal communication and plasticity, including GABA secretion, regulation of long-term potentiation and synaptic plasticity, and observational learning, suggesting these proteins cluster around neuronal signaling. A few terms (DNA-templated transcription, plant-type secondary cell wall biogenesis, polyamine biosynthesis) are broader or less specific but do not override the dominant neuronal theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045762","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0006596","count":2},{"id":"GO:0048715","count":2}]},{"hash":"345888495486218535","title":"Plant stress-response transcription regulators","description":"This cluster is dominated by DNA-templated transcription and its regulation, suggesting transcription factors or transcription regulators. The presence of plant hormone signaling terms (abscisic acid-activated and ethylene-activated pathways), along with responses to calcium, chitin, and defense-related regulation, points to stress-responsive signaling. Additional terms related to multicellular development and cutin biosynthesis align with plant epidermal development and cuticle formation, indicating a function in coordinating stress responses with growth. Overall, it seems to comprise plant transcription regulators involved in stress signaling and development.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0051592","count":2},{"id":"GO:0030199","count":2},{"id":"GO:0009738","count":2}]},{"hash":"1721238367957432589","title":"Ubiquitin-regulated innate immune signaling","description":"The GO terms converge on ubiquitination-related processes (ubiquitin-dependent proteolysis, autoubiquitination, K6-linked ubiquitination) and immune signaling (innate immune response, canonical NF-kappaB, TNF signaling). This suggests a cluster of proteins coordinating protein turnover with activation of innate immune pathways, with some chromatin/stress-related terms that support, but do not override, this theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0090141","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0051865","count":3},{"id":"GO:1903265","count":3}]},{"hash":"1729124407328348120","title":"Vesicle trafficking and exocytosis regulation","description":"The top GO terms point to secretory pathway activities and lipid handling\u2014ceramide transport and sterol biosynthesis\u2014together with exocytosis-related processes (acrosome reaction, synaptic vesicle priming) and regulation of signaling pathways (Rho/Ras) that modulate vesicle secretion. This combination suggests a cohesive theme around vesicle trafficking and exocytosis with lipid transport involvement, rather than disparate functions. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0044128","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0035621","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1088138898493685089","title":"Nucleotide Metabolism and RNA Editing","description":"Most terms cluster around nucleotide metabolism (cytosine, deoxycytidine, uridine biosynthesis/salvage, cytidine deamination) and RNA modification (tRNA wobble A-to-I editing). A riboflavin biosynthetic term appears but does not define the core function, and a single antibiotic response term is present, likely incidental. Overall, the cluster seems centered on nucleotide biosynthesis and RNA processing activities.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019858","count":2},{"id":"GO:0006217","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0046109","count":2},{"id":"GO:0009972","count":2}]},{"hash":"2122545981036864136","title":"Ion and Metabolite Transmembrane Transporters","description":"Top GO terms reveal diverse transmembrane transport of ions and small molecules, including nitrate, phosphate, potassium, sodium, arabinose, galactose, and xenobiotics, suggesting a cluster of membrane transport proteins.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":9},{"id":"GO:0042128","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0035435","count":3},{"id":"GO:0015751","count":3}]},{"hash":"1494116673786066135","title":"RNA and protein methylation with cofactor biosynthesis","description":"The top GO terms are dominated by RNA methylation (tRNA and rRNA methylation) and peptide methylation, indicating a core role in methylation-based modification. Additionally, several biosynthetic processes for cofactors and lipids (ubiquinone, sterols, vitamin E, cobalamin) suggest a metabolic, biosynthesis-focused cluster. Some xenobiotic response and aging terms appear less central but do not override the main methylation/cofactor theme.","confidence":"High","size":14,"edges":70,"triangles":185,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":11},{"id":"GO:0009236","count":11},{"id":"GO:0030961","count":7},{"id":"GO:0006744","count":7},{"id":"GO:0001300","count":7}]},{"hash":"250232298590771707","title":"Unknown","description":"The top GO terms mix ubiquitination/ERAD-related regulation with diverse metabolic processes (xylitol, galactose, furaldehyde, pyruvate fermentation), plus signaling aspects (prostaglandin metabolism, blood pressure) and post-translational modification (nitrosylation). There isn\u2019t a single coherent biological function linking these terms, suggesting the cluster does not reflect a unified theme. ","confidence":"","size":14,"edges":10,"triangles":3,"max_degree":4,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0051160","count":5},{"id":"GO:0033498","count":5},{"id":"GO:0033859","count":5}]},{"hash":"136793580391332821","title":"Immune and developmental signaling with cell cycle control","description":"Proteins cluster around signaling in immune cells (T cell receptor signaling; NK differentiation) and development (melanocyte and myoblast differentiation), plus cell-cycle regulation (spindle assembly, G2 checkpoint) and JUN phosphorylation. The common thread is signal transduction linking immune responses, development, and cell division; no single dominant function emerges, just broad signaling roles.","confidence":"Medium","size":14,"edges":68,"triangles":162,"max_degree":12,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":14},{"id":"GO:0097324","count":14},{"id":"GO:0009636","count":14},{"id":"GO:1990801","count":14},{"id":"GO:0014835","count":14}]},{"hash":"1152331264296388185","title":"Cellular Stress Response and Protein Homeostasis","description":"The top GO terms point to cellular responses to damaging or stressful conditions (gamma radiation, UV-A, hydrogen peroxide) and to protein quality control (deubiquitination, amyloid fibril formation regulation), complemented by transport modulation and tissue-specific contexts (lens morphogenesis, axonal transport, muscle contraction). This suggests a cohesive theme of how cells sense, respond to, and manage stress through signaling, protein turnover, and transport, across different tissues.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":8},{"id":"GO:0016579","count":7},{"id":"GO:0032355","count":7},{"id":"GO:0032387","count":7},{"id":"GO:0070141","count":7}]},{"hash":"423450310300971255","title":"Muscle T-tubule Ca2+ Handling and Ion Transport","description":"The cluster centers on calcium ion transport and intracellular calcium homeostasis, along with maintenance of membrane potential and T-tubule organization, all hallmarks of muscle membrane physiology and excitation-contraction coupling. Additional terms for proton and potassium transport and membrane lipid movement support a broader role in membrane ion regulation and signaling at specialized membrane domains.","confidence":"High","size":14,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1903515","count":1},{"id":"GO:0010248","count":1},{"id":"GO:0006874","count":1},{"id":"GO:0019373","count":1},{"id":"GO:1990573","count":1}]},{"hash":"570832335710336057","title":"Xenobiotic and nutrient transmembrane transporters","description":"The cluster is dominated by transmembrane transport GO terms, especially xenobiotic transmembrane transport, with supporting substrate-specific transport terms (phosphate, arabinose, nitrate, vitamins, selenite). This suggests a group of membrane transporter proteins that mediate uptake/export of diverse xenobiotics and nutrients across the plasma membrane.","confidence":"High","size":14,"edges":33,"triangles":21,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":14},{"id":"GO:0042891","count":14},{"id":"GO:0035461","count":14},{"id":"GO:0071332","count":7},{"id":"GO:0035435","count":7}]},{"hash":"752146491319313752","title":"Unknown","description":"The GO terms are highly diverse and do not point to a single cohesive function: sugar metabolism, transcriptional regulation, host-symbiont interaction, and even development terms are all present with no clear common pathway. With zero edges among proteins and a scattered term set, there isn\u2019t a unifying biological theme to name a specific cluster function. ","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046718","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0006012","count":2}]},{"hash":"352592544821409221","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":42,"triangles":52,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0010019","count":2}]},{"hash":"1648801412274508737","title":"Mitochondrial metabolite transport and energy homeostasis","description":"The top GO terms cluster around transmembrane transport of key cofactors and nutrients into mitochondria (phosphate, coenzyme A, thiamine pyrophosphate, pyrimidine nucleotides, manganese ions) and metabolic regulation signals (adaptive thermogenesis, fatty acid response, insulin secretion modulation, amino acid starvation response, liver regeneration). This combination suggests a functional theme of mitochondrial nutrient transport supporting energy metabolism and metabolic regulation.","confidence":"High","size":14,"edges":11,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":9},{"id":"GO:0034198","count":9},{"id":"GO:1990845","count":9},{"id":"GO:0061179","count":9},{"id":"GO:1990519","count":9}]},{"hash":"2025423942830252676","title":"Amino acid catabolism and metabolite biosynthesis","description":"This cluster is driven by amino acid catabolic processes (L-alanine, L-lysine, kynurenine) and multiple biosynthetic pathways (protoporphyrinogen IX, oxaloacetate, biotin, sphingomyelin), pointing to a metabolic theme centered on breaking down and producing key metabolites. Notch signaling and DNA-templated transcription appear less central to the dominant pattern, but do not override the metabolic signals. Therefore, the label captures the primary functional context with moderate confidence.","confidence":"Medium","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":7},{"id":"GO:0033512","count":7},{"id":"GO:0006782","count":7},{"id":"GO:0007219","count":7},{"id":"GO:0019878","count":7}]},{"hash":"2171531117330375799","title":"Unknown","description":"Top GO terms are highly heterogeneous: redox process, mitochondrial targeting (obsolete), and several biosynthetic processes (tropane alkaloid, mycolic acid, retinal metabolism, estrogen, testosterone, melanin) plus developmental/response terms (lung development, response to methotrexate). The diversity and presence of obsolete terms indicate no single cohesive function tying these proteins. Without a clear common biological theme, assign Unknown.","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0009710","count":1},{"id":"GO:0071768","count":1},{"id":"GO:0031427","count":1}]},{"hash":"540526580581053546","title":"APP-Linked Neuronal Signaling and Amyloid Biology","description":"The top GO terms cluster around amyloid precursor protein catabolic regulation and amyloid fibril formation, along with neuronal action potential propagation and axon regeneration, pointing to neural/amyloid biology. Some terms appear as outliers (cell division, heart morphogenesis, insulin regulation), indicating mixed or broader annotations, but the recurring neural/amyloid themes support this label.","confidence":"Medium","size":14,"edges":22,"triangles":5,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1902991","count":3},{"id":"GO:1990000","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0055010","count":3},{"id":"GO:0061179","count":3}]},{"hash":"1294760265496747834","title":"Neural development and sensory plasticity","description":"The cluster includes terms tied to sensory system development (compound eye photoreceptor development, chaeta development) and learning/habituation, as well as regulation of synaptic structure and receptor trafficking, pointing to neural development and plasticity. It also contains RNA granule and mRNA decay processes, suggesting activity-related gene regulation in neurons. Overall, a neural-development/sensory-plasticity theme best fits these terms.","confidence":"Medium","size":14,"edges":10,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0022416","count":3},{"id":"GO:0046959","count":3},{"id":"GO:0060340","count":3},{"id":"GO:0034063","count":3},{"id":"GO:0010603","count":3}]},{"hash":"975025951435321561","title":"Nuclear RNA processing and chromatin regulation","description":"This cluster is dominated by terms tied to RNA processing in the nucleus (transcription termination, spliceosome assembly, mRNA splicing, deadenylation-dependent decapping, histone mRNA metabolism) along with chromatin-related processes (pericentric heterochromatin formation). The co-occurrence of splicing and RNA decay with chromatin maintenance suggests proteins functioning at the intersection of RNA processing and chromatin regulation, rather than disparate roles. Confidence that this label captures the core function is High.","confidence":"","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":9},{"id":"GO:0070317","count":9},{"id":"GO:1990141","count":9},{"id":"GO:0000387","count":9},{"id":"GO:0042633","count":9}]},{"hash":"1852161655077489876","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0034247","count":4},{"id":"GO:0006364","count":4},{"id":"GO:0034414","count":4},{"id":"GO:0031126","count":4}]},{"hash":"1345531486980956042","title":"Calcium-regulated secretion and vesicle trafficking","description":"The top GO terms cluster around exocytosis, Golgi-to-plasma membrane transport, and exocyst localization, all pointing to a vesicle trafficking/secretion pathway. Calcium-related terms (calcium import into mitochondrion and regulation of mitochondrial calcium concentration) suggest Ca2+-dependent exocytosis, which aligns with processes like insulin secretion. Some terms (plastoquinone biosynthesis, ozone response) may reflect plant-specific context or annotations that are less directly tied to secretion, but the dominant signal is Ca2+-driven vesicle trafficking and secretion. ","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0036444","count":1},{"id":"GO:0032024","count":1},{"id":"GO:0051561","count":1},{"id":"GO:0035786","count":1},{"id":"GO:0010193","count":1}]},{"hash":"978196544100497619","title":"TLR signaling, autophagy, and cytoskeletal regulation","description":"This cluster centers on innate immune signaling via Toll-like receptors (including MyD88-dependent pathways) and autophagy, with concurrent hints of cytoskeletal remodeling (actin filament severing) and negative regulation of protein kinase activity, suggesting a theme of signaling modulation linked to autophagy and cytoskeleton dynamics. A few transport-related terms appear but are likely incidental to the main immune/autophagy theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0016239","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0034130","count":2},{"id":"GO:0002755","count":2}]},{"hash":"34693472938963970","title":"Chloroplast Light Harvesting and Photosynthesis","description":"Most terms cluster around photosynthesis and light responses in chloroplasts: photosynthesis, light harvesting in photosystem I, responses to red/far-red and UV-A light, and general light-intensity responses. This points to proteins involved in chloroplast energy capture and light signaling. Anomalous mitochondrial matrix import term is likely misannotation relative to the dominant chloroplast-focused theme.","confidence":"High","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":4},{"id":"GO:1904964","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0009768","count":2},{"id":"GO:0010218","count":2}]},{"hash":"85313098790974397","title":"Plant Hormone Signaling and Defense","description":"This cluster is dominated by GO terms tied to plant hormone signaling (gibberellin, salicylic acid, ethylene precursor ACC) alongside defense-related responses (chitin response, antifungal innate immune regulation) and developmental processes (sclerenchyma and atrichoblast differentiation). Despite one outlier term (thymic T cell selection), the common theme is plant growth regulation intertwined with immune and stress responses, suggesting a cohesive plant hormone\u2013defense cluster.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009739","count":8},{"id":"GO:0009751","count":8},{"id":"GO:0080169","count":7},{"id":"GO:0010200","count":7},{"id":"GO:0010055","count":7}]},{"hash":"1217057699334003632","title":"Neural development and cell proliferation","description":"The cluster is enriched for neural development terms (forebrain development, neural tube closure) and cell proliferation processes (mitotic cell cycle, cell division). Additional terms point to active transcription and ribosome biogenesis, suggesting these proteins participate in gene expression and growth during neural development. Some unrelated terms (metal transport, stress responses) may reflect annotation noise, but the neural-development plus proliferation signal is clear enough to warrant this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0015689","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0070059","count":3}]},{"hash":"470394606785622717","title":"Embryonic craniofacial and neural development","description":"The proteins cluster around embryonic morphogenesis across multiple head/face and neural tissues (roof of mouth, forebrain, oculomotor nerve, pituitary), plus digestive tract morphogenesis. The inclusion of regulation of transcription suggests these proteins function in developmental gene networks shaping these tissues; together they imply a shared role in embryonic craniofacial and neural development.","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060021","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0021983","count":4},{"id":"GO:0048557","count":3},{"id":"GO:0003168","count":3}]},{"hash":"809787222194277877","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":13},{"id":"GO:0030433","count":13},{"id":"GO:0045454","count":13},{"id":"GO:0006260","count":13},{"id":"GO:0006986","count":13}]},{"hash":"1975049884222623344","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms for ubiquitin-mediated proteolysis and various ubiquitination linkages (K48, K6, K63), autoubiquitination, and related protein catabolic processes, with ancillary links to TNF signaling and necroptosis regulation. This points to a cohesive theme of ubiquitin-dependent protein degradation.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:1903265","count":6},{"id":"GO:0051865","count":5},{"id":"GO:0036205","count":5},{"id":"GO:0070936","count":5}]},{"hash":"742936217844016387","title":"Unknown","description":"The top terms are a mix of very different processes (muscle function, development, transcription regulation, metabolism, glycan processing, fungal cell wall biosynthesis) and several obsolete terms, with no clear shared function or pathway. Edges are absent, indicating little or no functional connectivity among these proteins. This makes it impossible to assign a cohesive label beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0050884","count":3},{"id":"GO:0006491","count":3},{"id":"GO:0003007","count":3}]},{"hash":"1028436377289785486","title":"Unknown","description":"The top GO terms are a mix of plant-specific processes (gibberellic acid signaling, floral organ morphogenesis, cellulose catabolic) and animal neural development (neuroblast differentiation), aging, and transcription regulation, including obsolete terms. There is no unifying function or pathway across all members, so a single coherent label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010259","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0009740","count":1},{"id":"GO:0051384","count":1},{"id":"GO:0001507","count":1}]},{"hash":"1328782761082743826","title":"TOR signaling and translational control under stress","description":"The cluster\u2019s top GO terms center on TOR signaling and regulation of protein synthesis, including translational initiation and elongation, particularly in response to stress. Additional terms touch on apoptotic regulation and various developmental processes, suggesting a broader role in growth and development, but the strongest cohesive signal is TOR-mediated translation control under stress.","confidence":"Medium","size":14,"edges":44,"triangles":34,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":2},{"id":"GO:0043524","count":2},{"id":"GO:0045429","count":2},{"id":"GO:0031929","count":2},{"id":"GO:0043066","count":2}]},{"hash":"2053446587690728294","title":"Cellular stress response and transcriptional regulation","description":"This cluster is dominated by GO terms related to how cells respond to stress and regulate gene expression, such as cellular response to xenobiotic stimulus, detection of hypoxia, and negative regulation of transcription by RNA polymerase II, along with associated processes like proteolysis and regulation of catalytic activity. The presence of phytochelatin biosynthesis hints at detox-related roles in some members, but overall the common theme is regulatory and stress-response functions rather than a single biochemical pathway. Confidence: Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":3},{"id":"GO:0043085","count":3},{"id":"GO:1904715","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0006351","count":2}]},{"hash":"722369419036127922","title":"Peptidoglycan and LPS biosynthesis","description":"The top GO terms cluster around bacterial cell envelope biosynthesis: peptidoglycan, lipopolysaccharide and lipid A biosynthesis, and related precursor production (UDP-N-acetylglucosamine, GDP-mannose) along with cell wall organization and envelope-related antibiotic responses. This strongly signals a cohesive theme of cell wall/envelope biosynthesis rather than unrelated pathways.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006048","count":4},{"id":"GO:0009252","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0009298","count":4},{"id":"GO:0009245","count":4}]},{"hash":"318281394038757507","title":"Embryonic Development and Organogenesis","description":"The top GO terms cluster around vertebrate embryonic development and morphogenesis\u2014trophoblast giant cell differentiation, EMT in endocardial cushion formation, left-right patterning, cartilage morphogenesis, and endocrine/pancreatic development\u2014indicating a theme of developmental differentiation and organogenesis. A couple of plant-specific terms appear as outliers, but the dominant signal supports a developmental role for these proteins.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0060972","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0060536","count":2}]},{"hash":"915195237852299422","title":"Translational initiation and regulation","description":"Most GO terms cluster around protein synthesis: translation (GO:0006412) with 4 proteins, cap-dependent translational initiation (GO:0002191), and negative regulation of translation (GO:0017148). This suggests a core theme of translation initiation and its control. The other terms (sensory perception of sound, lung development, behavioral fear response, cell cycle transitions, germ-line development, dexamethasone response) are sporadic and likely annotation noise or pleiotropy rather than a shared module. With no edges connecting the proteins, the dominant signal is translation-related.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0007605","count":2},{"id":"GO:0030324","count":1},{"id":"GO:0000082","count":1},{"id":"GO:0007060","count":1}]},{"hash":"1134764029467080113","title":"Redox-responsive transcription regulators","description":"The top GO terms point to transcription regulation and DNA binding (positive/negative regulation of transcription, DNA-templated transcription), indicating that the proteins are linked to transcriptional control. Concurrently, several redox- and oxidative stress\u2013related terms (cellular response to oxidative stress, cellular oxidant detoxification, redox homeostasis, deglutathionylation) and a prolyl hydroxylation/repair motif suggest redox-sensitive regulation and protein maintenance. Together, these imply a cluster of transcription regulators whose activity is modulated by redox state and oxidative stress.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043388","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0018401","count":5},{"id":"GO:0030091","count":5},{"id":"GO:0034599","count":5}]},{"hash":"42378069038602699","title":"Ribosome biogenesis and translation initiation","description":"This cluster is driven by GO terms for translation (GO:0006412) and the formation of translation preinitiation complex (GO:0001731), plus a 90S preribosome assembly term, all pointing to ribosome assembly and protein synthesis. A few terms related to skeletal/ear development appear but are likely incidental annotations; the core function suggested is ribosome biogenesis and translation initiation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0001501","count":1},{"id":"GO:0007605","count":1},{"id":"GO:0048318","count":1}]},{"hash":"261110646282888244","title":"Innate antiviral defense and apoptosis regulation","description":"The top GO terms point strongly to antiviral and innate immune activities (defense response to virus, innate immune response), with supporting signals from protein ubiquitination and regulation of apoptosis, suggesting a cluster of immune signaling proteins involved in antiviral defense and cell fate decisions. Some terms are labeled obsolete, but the core theme remains antiviral defense and immune regulation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051607","count":7},{"id":"GO:0045087","count":6},{"id":"GO:0051865","count":5},{"id":"GO:1903762","count":5},{"id":"GO:0090073","count":5}]},{"hash":"914379224067023874","title":"Nuclear transcription and chromatin regulation","description":"The top GO terms point to nuclear processes: regulation of transcription by RNA polymerase II, CENP-A\u2013containing chromatin assembly, and regulation of DNA methylation, all of which reflect transcriptional control and chromatin dynamics. Additional terms like response to steroid hormone and cellular senescence suggest downstream gene-expression changes tied to hormonal signaling and aging, reinforcing a common theme of nuclear regulation of gene expression and chromatin state rather than cytoplasmic metabolic activities. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033601","count":2},{"id":"GO:0048545","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0010039","count":1}]},{"hash":"97216883849584029","title":"Neuronal vesicle trafficking and exocytosis","description":"The GO terms cluster around vesicle transport and exocytosis, especially synaptic vesicle cycling (ER-Golgi transport, Golgi to vacuole transport, regulation of synaptic vesicle exocytosis) and brain development/synaptic plasticity (long-term potentiation). The presence of acrosome reaction reflects shared exocytotic machinery, supporting a cohesive vesicle-secretion theme in neural contexts.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007340","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0006886","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0006888","count":4}]},{"hash":"2147157266411617006","title":"Plant autophagy and vacuolar trafficking","description":"Based on the GO terms, the strongest signal centers on autophagy-related processes (piecemeal microautophagy of the nucleus), vacuolar protein processing, and endosomal/vesicle dynamics (multivesicular body disassembly), with accompanying stress-response signals (UV-B, salicylic acid). While there are also lipid metabolism and cellulose-related terms, the recurring theme is intracellular membrane remodeling and autophagy/vacuolar trafficking in plant cells, making this label representative of the cluster.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034727","count":6},{"id":"GO:0030245","count":6},{"id":"GO:0042136","count":6},{"id":"GO:0006624","count":6},{"id":"GO:0071493","count":6}]},{"hash":"1262691921832757119","title":"Plant Photomorphogenesis and Transcriptional Regulation","description":"The top GO terms point to transcriptional regulation (regulation of DNA-templated transcription, DNA-templated transcription) coupled with light-responsive and hormone-related development processes (photomorphogenesis regulation, blue light response, auxin-activated signaling, primary root development, somatic embryogenesis). This suggests a cohesive theme of plant proteins that control gene expression during light- and hormone-driven development. Negative regulation terms may reflect modulatory checks within these pathways, but the core signal is transcriptional control tied to photomorphogenesis and growth.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0051245","count":1},{"id":"GO:1901001","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0080022","count":1}]},{"hash":"502020603950899879","title":"Actin Remodeling and Cell Migration","description":"The top GO terms cluster around lamellipodium assembly, actin filament bundle assembly, and regulation of Rho signaling, all core to actin cytoskeleton remodeling that drives cell movement. Neuron projection morphogenesis and cell migration further support a theme of actin-driven motility and process outgrowth, while insulin and B cell receptor signaling terms hint at broader signaling crosstalk with cytoskeletal dynamics. Overall, these proteins appear tied to actin-mediated remodeling and motility rather than a single, narrow pathway.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0031666","count":2},{"id":"GO:0048812","count":2},{"id":"GO:0051017","count":2}]},{"hash":"313559600775991101","title":"Ubiquitin-Dependent Degradation and Immune Signaling","description":"This cluster is dominated by GO terms for ubiquitin-mediated protein catabolism (ubiquitin-dependent degradation and autoubiquitination), and includes immune signaling pathways such as NF-\u03baB activation and TNF signaling, along with apoptosis regulation and V(D)J recombination. The recurring theme is ubiquitin-dependent protein turnover linked to immune response regulation, with some related but obsolete terms hinting at broader ubiquitin/ERAD roles. Overall, the proteins appear to function together in ubiquitin-proteasome processes that modulate immune signaling.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0051865","count":6},{"id":"GO:1903762","count":6},{"id":"GO:1901253","count":6},{"id":"GO:0042981","count":5}]},{"hash":"858661705448504822","title":"Plant Cell Wall Biosynthesis and Seed Lipid Storage","description":"The top GO terms cluster around plant cell wall construction (xyloglucan biosynthesis, plant-type secondary cell wall biogenesis, cell wall organization) alongside seed lipid-related processes (lipid storage, seed oilbody biogenesis), with supporting terms related to pollen hydration and salicylic acid signaling, suggesting a cohesive theme of plant structural biosynthesis and seed/ reproductive biology.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009969","count":3},{"id":"GO:0071555","count":2},{"id":"GO:0050826","count":2},{"id":"GO:0019915","count":2},{"id":"GO:0010344","count":2}]},{"hash":"466153357417038483","title":"ERK and p38 MAPK signaling in immune responses","description":"The cluster features two well-known MAPK cascades (ERK1/ERK2 and p38MAPK) and several immune-related processes (T cell receptor signaling, GM-CSF response, melanocyte migration) plus apoptosis and transcriptional regulation. This suggests a coherent module centered on MAPK-driven signaling that governs immune/stress responses and transcriptional changes.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:2000641","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0070371","count":2}]},{"hash":"363620507366341152","title":"ER Stress and Ubiquitin-Dependent Degradation","description":"Top GO terms emphasize ER stress\u2013driven apoptosis, ERAD, and ubiquitin-related protein turnover, with interferon signaling and innate immune responses also represented. Additional hints of cytoskeletal remodeling and signaling pathways suggest broader stress-response coordination. This cluster appears to center on ER quality-control and ubiquitin-mediated proteostasis coupled with immune signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0050830","count":2},{"id":"GO:0035458","count":2},{"id":"GO:0035523","count":2}]},{"hash":"548515807276700578","title":"Nuclear gene expression and cell cycle","description":"The top GO terms point to transcriptional regulation and RNA processing (DNA-templated transcription, mRNA processing) as well as cell cycle events (centrosome duplication, meiotic cell cycle), suggesting a cluster of proteins involved in gene expression control and cell division. While there are additional terms related to development and signaling, the dominant theme appears to be nuclear gene expression and cell cycle processes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051298","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1581809266747112972","title":"Unknown","description":"The top GO terms cover immune defense, lipid transport, protease regulation, nociception, Golgi organization, lung development, heat response, nuclear import, protein oligomerization, and Rho signaling, with no clear single function tying them together, so there is no coherent theme to label this cluster.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":3},{"id":"GO:0006869","count":3},{"id":"GO:0010951","count":3},{"id":"GO:0050966","count":2},{"id":"GO:0007030","count":1}]},{"hash":"2259482692464093086","title":"Mesodermal and Neural Crest Development","description":"This cluster centers on differentiation and morphogenesis of mesoderm-derived tissues (paraxial mesoderm differentiation, skeletal muscle adaptation, heart rate regulation, ascending aorta morphogenesis) as well as neural crest\u2013related lineages (neuron development, lung neuroendocrine cells, carotid body glomus cells). The combined signal points to a developmental program spanning muscle, cardiovascular structures, and neuroendocrine/neural crest\u2013derived tissues. Some terms like protein methylation and cobalamin biosynthesis are present but less central to the main theme.","confidence":"Medium","size":13,"edges":64,"triangles":168,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006479","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0032933","count":3},{"id":"GO:0043503","count":3},{"id":"GO:0061103","count":3}]},{"hash":"1965399153795973021","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0006351","count":2},{"id":"GO:0006015","count":2},{"id":"GO:0046651","count":2},{"id":"GO:0006189","count":2}]},{"hash":"173535665981724466","title":"Immune and retinal signaling","description":"The proteins in this cluster are enriched for immune-related signaling terms (T cell receptor signaling, NK cell differentiation, mast cell cytokine production, STAT phosphorylation, ERK cascade) and neural/retinal development terms (retinal ganglion cell axon guidance, retina vasculature development, neurotrophin signaling). This suggests a shared involvement in receptor- and growth factor\u2013mediated signaling that influences both immune function and retinal/neuronal development, indicating a broad signaling network rather than a single pathway. ","confidence":"Medium","size":13,"edges":48,"triangles":88,"max_degree":12,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":13},{"id":"GO:0097324","count":13},{"id":"GO:0001779","count":13},{"id":"GO:0042503","count":13},{"id":"GO:0070374","count":13}]},{"hash":"883901293247916204","title":"Unknown","description":"The cluster includes a mix of GO terms spanning DNA damage response and transcription regulation (e.g., p53-mediated arrest, DNA-templated transcription), immune signaling (T cell receptor pathway), cell migration (melanocyte migration), development and differentiation (myoblast differentiation), and mitotic/spindle checkpoint processes. The terms do not converge on a single coherent function or pathway, making it unclear how these proteins collectively function as a unit. ","confidence":"","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006977","count":8},{"id":"GO:0006351","count":7},{"id":"GO:0050852","count":6},{"id":"GO:0097324","count":6},{"id":"GO:0009636","count":6}]},{"hash":"2157313632962082870","title":"Pollen development and exine formation","description":"This cluster is anchored by GO terms specific to pollen biology, notably anther dehiscence and pollen exine formation, which strongly point to pollen development and pollen wall biosynthesis as the core function. The other terms reflect general cellular metabolism and growth but do not outweigh the pollen-specific signals.","confidence":"High","size":13,"edges":38,"triangles":44,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071405","count":3},{"id":"GO:0046032","count":3},{"id":"GO:0009901","count":3},{"id":"GO:0046706","count":3},{"id":"GO:0010584","count":3}]},{"hash":"1213729473990045690","title":"Embryonic and Neural Development","description":"This cluster is dominated by GO terms related to development, especially vertebrate neurodevelopment (multicellular organism development, forebrain development, neural tube closure) and growth-related processes (mitotic cell cycle, transcription). While there are a few stress/immune terms present, the core signal points to embryonic/neural organogenesis and related proliferation, making this an interpretable developmental cluster.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":10},{"id":"GO:0000278","count":9},{"id":"GO:0001843","count":7},{"id":"GO:0070059","count":7},{"id":"GO:0006351","count":7}]},{"hash":"880661332190029282","title":"Epigenetic regulation and translation in development","description":"This cluster centers on chromatin modifications (histone acetylation/methylation) and translation-related processes, with proteasomal degradation and developmental signaling (TGF-beta, seminiferous tubule development) suggesting coordinated regulation of gene expression during development.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0008283","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0071560","count":4}]},{"hash":"979826701574423692","title":"Transcription Regulation & mRNA Splicing","description":"Based on the top GO terms, the strongest signals are DNA-templated transcription and alternative mRNA splicing via spliceosome, indicating a core focus on transcriptional regulation and RNA processing. Other terms like cerebral cortex development, blood-nerve barrier establishment, viral process, and sperm capacitation appear less central or may reflect broader, incidental associations. Overall, the cluster seems to represent transcription control and mRNA splicing activity.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0048240","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0000380","count":2}]},{"hash":"1872444101617861387","title":"Ribosome biogenesis and translation","description":"The strongest signals are translation and ribosome biogenesis: translation, preribosome large subunit assembly, and positive regulation of ribosome biogenesis. Minor terms involve ribosome-associated modifications and mitochondrial metabolism, but the core theme is ribosome production and protein synthesis.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0070584","count":2},{"id":"GO:0090070","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0001887","count":1}]},{"hash":"901590002905354409","title":"Ribosome biogenesis and translation machinery","description":"Dominant signals are translation (GO:0006412) and ribosome biogenesis/assembly (GO:0042254, GO:0000027), plus related subunit export and tRNA modification, pointing to proteins that form and operate the ribosome and associated translation machinery.","confidence":"High","size":13,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000055","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0046677","count":2}]},{"hash":"337880860868122577","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0006986","count":6}]},{"hash":"328597883176946896","title":"Cell Cycle and Growth Regulation","description":"The cluster centers on control of cell fate and proliferation: regulation of apoptosis, cell cycle, DNA replication, and modulation of signaling pathways like Wnt. Additional terms point to migratory and developmental processes, plus metabolic (cholesterol biosynthesis) and stress-responsive (ethanol) aspects, suggesting a broad growth- and survival-regulation module rather than a single pathway.","confidence":"Medium","size":13,"edges":22,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043065","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0008285","count":5},{"id":"GO:0006695","count":4}]},{"hash":"1739685477895694766","title":"Ribosome biogenesis and transcription","description":"The top terms cluster around ribosome biogenesis and translation initiation, plus RNA Pol II\u2013dependent transcription, suggesting these proteins participate in core gene-expression machinery. A few outliers (cilium assembly, histone methylation) are less coherent. Overall, the cluster reflects components of RNA/protein synthesis and transcription rather than a single pathway.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0001731","count":3},{"id":"GO:0060271","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0034729","count":3}]},{"hash":"796392589791451154","title":"Mitochondrial energy metabolism and insulin signaling","description":"Top GO terms point to mitochondrial functions (membrane fission, mitochondrial nucleotide and CoA transport, phosphate transport) and energy-related processes (adaptive thermogenesis), with several terms tied to insulin response and glucose-stimulated regulation. This suggests a cohesive theme around mitochondrial energy metabolism coupled with insulin signaling.","confidence":"High","size":13,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":6},{"id":"GO:0000002","count":5},{"id":"GO:0090149","count":5},{"id":"GO:0051260","count":4},{"id":"GO:0035435","count":3}]},{"hash":"1749241012437078959","title":"Catecholamine Biosynthesis and Stress Response","description":"This cluster\u2019s top GO terms center on norepinephrine and related tyrosine-derived neurotransmitter biosynthesis, with supporting signals of broader stress responses (response to toxic substance, immobilization stress). While other terms touch development or remodeling, the strongest, coherent theme is catecholamine production coupled with stress-response processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006571","count":1},{"id":"GO:0060749","count":1},{"id":"GO:0035902","count":1}]},{"hash":"1388445805931663256","title":"Bacterial carbohydrate biosynthesis and thiol biosynthesis","description":"This cluster centers on carbohydrate metabolism (starch, glycogen, glucose, sucrose) and the biosynthesis of low-molecular-weight thiols (bacillithiol, mycothiol) used for redox balance in bacteria. The co-occurrence of these GO terms suggests enzymes involved in sugar biosynthesis/metabolism alongside thiol-based protective systems, common in Gram-positive bacteria. Some terms like \"response to flooding\" or \"feeding behavior\" may be incidental annotations, but the dominant theme is carbohydrate metabolism with thiol biosynthesis.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019252","count":6},{"id":"GO:0071793","count":6},{"id":"GO:0009413","count":6},{"id":"GO:0005978","count":6},{"id":"GO:0097502","count":6}]},{"hash":"2254371104042803086","title":"Diverse cellular processes","description":"The top GO terms span ER-Golgi transport, translation initiation, calcium signaling, mitotic regulation, NFAT signaling, DNA repair, mesoderm development, EMT, kinetochore-microtubule attachment, and metal ion response, indicating a mix of core cellular activities rather than a single cohesive function. This suggests a cluster of proteins involved in multiple essential processes, rather than a focused pathway, hence a broad label. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0099566","count":2},{"id":"GO:1905213","count":2},{"id":"GO:0051531","count":2}]},{"hash":"1535437126637472817","title":"Ribosome biogenesis and cytoplasmic translation","description":"The top GO terms are dominated by ribosome biogenesis and related processes (ribosome and small/large subunit biogenesis, ribosomal export) and cytoplasmic translation, indicating a core theme around ribosome assembly and protein synthesis. Some cell division-related terms appear, suggesting coordination with the cell cycle, but the central signal is ribosome production and translation machinery.","confidence":"High","size":13,"edges":69,"triangles":205,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0042274","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1326902427008830580","title":"Unknown","description":"The GO terms cover a wide range of distinct cellular processes (protein oligomerization, ER-Golgi transport, cell division and microtubule dynamics, CENP-A chromatin assembly, cytokinesis-related septum digestion, ERAD, peroxisome import, SREBP signaling, and ubiquitination regulation) with no clear unifying function or pathway connecting them. Therefore there is no concise, representative label that captures all terms in this cluster.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0051013","count":4},{"id":"GO:0061641","count":4}]},{"hash":"1218618494948327380","title":"Unknown","description":"The cluster shows a mix of DNA maintenance terms (DNA replication, nucleotide-excision repair), protein regulation and quality control (protein sumoylation, ERAD-associated ubiquitin-dependent degradation), and several unrelated terms (lipid A biosynthesis, cell morphogenesis, transcription regulation, innate immune signaling). The presence of a bacterial lipid A biosynthesis term and an innate immune signaling term, along with obsolete GO terms, makes it hard to identify a single cohesive functional theme. While some elements hint at cellular stress responses and protein homeostasis, the overall combination does not converge on a clear, shared function.","confidence":"","size":13,"edges":12,"triangles":3,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0016925","count":3},{"id":"GO:0009245","count":3},{"id":"GO:0000902","count":3}]},{"hash":"867057031296511167","title":"Cell Cycle and Genome Maintenance","description":"This cluster\u2019s top GO terms cluster around genome integrity and cell division\u2014centrosome cycle, DNA replication, regulation of helicase activity, and regulation of telomere maintenance via telomerase\u2014suggesting a core theme of cell-cycle control and genome maintenance. While there are some development-related terms present, the central connection appears to be processes governing replication, telomere maintenance, and centrosome dynamics, which often co-occur in proliferative contexts.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032211","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0060444","count":2},{"id":"GO:0048538","count":2}]},{"hash":"1990280838513141780","title":"Unknown","description":"The top terms span plant defense (response to wounding, jasmonic acid signaling) and animal brain-related processes (cerebellar development, glutamate response, calcium transport), plus apoptosis regulation, with no shared pathway linking all proteins and no edges connecting them. This heterogeneity suggests no coherent single function for the cluster, likely reflecting annotation noise or multi-function proteins. ","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009611","count":1},{"id":"GO:2000022","count":1},{"id":"GO:0009753","count":1},{"id":"GO:1900067","count":1},{"id":"GO:1902042","count":1}]},{"hash":"890323879519713311","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:1905323","count":2},{"id":"GO:0033260","count":1},{"id":"GO:0006398","count":1},{"id":"GO:0016032","count":1}]},{"hash":"874686992834325174","title":"Ribosome biogenesis and rRNA processing","description":"The terms are dominated by ribosome biogenesis and rRNA maturation, including maturation of SSU- and LSU-rRNA and ribosomal subunit biogenesis, with related TORC1 signaling and regulation of GTPase activity. This points to a cluster of proteins involved in ribosome assembly and RNA processing, influenced by nutrient signaling.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0070262","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0038202","count":6},{"id":"GO:0042254","count":6}]},{"hash":"402252442898212793","title":"Unknown","description":"The terms are highly diverse, spanning brain development, stress response, cell division, symbiont dormancy, and lipid signaling pathways, with only a couple touching sphingolipid metabolism. There is no clear, cohesive biological theme uniting these proteins, and the lack of edges supports ambiguity in function. Hence no specific label can be confidently assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0085014","count":3},{"id":"GO:0006950","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006648","count":2}]},{"hash":"2266175649981373161","title":"Strigolactone metabolism and detoxification","description":"The cluster\u2019s top GO terms center on strigolactone biosynthesis and cellular response to strigolactone, indicating a shared function in strigolactone signaling. Additional catabolic and detoxification terms (oxidation-reduction, cellular oxidant detoxification, response to toxic substance) suggest a broader metabolic/detoxification theme feeding into or accompanying hormone signaling in plants. This combination points to a cohesive role in strigolactone metabolism with related detoxification processes.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0001889","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006212","count":2}]},{"hash":"1712074579061624798","title":"Plant nucleotide metabolism and cell wall dynamics","description":"This cluster is dominated by nucleotide metabolism signals (nucleotide metabolic process, inosine salvage, nicotinamide riboside biosynthesis) and plant-specific cell wall processes (root hair development, plasmodesma organization, cell wall cellulose biosynthesis/modification). A couple non-plant terms appear but are low-frequency noise relative to the main themes. So, a combined label highlighting both nucleotide metabolism and plant cell wall remodeling best describes the cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009117","count":2},{"id":"GO:0071592","count":2},{"id":"GO:0071590","count":2},{"id":"GO:0006190","count":2},{"id":"GO:0080147","count":2}]},{"hash":"384320922393772781","title":"Plant cell wall polysaccharide biosynthesis and glycosylation","description":"The top GO terms point to plant cell wall composition and assembly, including mucilage biosynthesis, homogalacturonan and glucuronoxylan (xylan) biosynthesis, plant-type secondary cell wall biogenesis, and general cell wall organization. The presence of protein O-linked glycosylation terms (via GalNAc and mannose) aligns with modification of wall-associated proteins. While a couple of terms (skeletal muscle regeneration, glycogen biosynthesis) are less related, the dominant signal supports a plant cell wall biosynthesis and glycosylation theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010192","count":10},{"id":"GO:0006012","count":6},{"id":"GO:0010289","count":6},{"id":"GO:0009834","count":6},{"id":"GO:0071555","count":6}]},{"hash":"1781450186618367000","title":"TLR-Driven Antiviral Innate Immunity","description":"The group's GO terms cluster around innate immune recognition of viral components and downstream signaling via Toll-like receptors (TLR4 and TLR10) with MyD88-dependent pathways, dsRNA responses, interferon-beta production, and activation of macrophages and dendritic cells. This pattern points to a cohesive role in antiviral innate immunity driven by TLR signaling.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051607","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0034166","count":4},{"id":"GO:0042116","count":4},{"id":"GO:0043330","count":4}]},{"hash":"1788852884481039515","title":"Unknown","description":"The terms include ER-Golgi transport, ubiquitin-proteasome degradation, ER-associated degradation, translation initiation, lipid biosynthesis, and various signaling pathways, with outliers in actin capping and angiogenesis regulation. There is no coherent single function linking these terms, so a clear cluster name cannot be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051016","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0031146","count":2}]},{"hash":"1100201158174193044","title":"Unknown","description":"The top GO terms are a mixed bag, spanning mammalian innate immunity (innate immune response, NOD2 signaling, NF-kappaB regulation) and plant-specific processes (pectin/mucilage biosynthesis, cell wall modification, plant cell plate formation), plus unrelated terms like skeletal muscle regeneration and telomere localization, with no edges connecting proteins. This lack of a coherent, single functional theme among the cluster members suggests no clear shared function.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043403","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0048358","count":1}]},{"hash":"599686842964915921","title":"Membrane Transport and Ionic Homeostasis","description":"The top GO terms cluster around transport across membranes and ion balance: imports of amino acids across the plasma membrane (arginine, ornithine, lysine, etc.), transepithelial chloride transport, and intracellular chloride ion homeostasis, with chemical synaptic transmission also tying to membrane activity. Peripheral terms like pectin catabolic process and swim bladder inflation appear less central but do not override the core theme of membrane transport and ionic/osmotic regulation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":3},{"id":"GO:0045795","count":2},{"id":"GO:0030644","count":2},{"id":"GO:0097638","count":2},{"id":"GO:0030321","count":2}]},{"hash":"1194655411026082323","title":"Developmental Regulation and Stress Signaling","description":"The cluster shows enrichment in developmental processes across tissues (hair cycle regulation, labyrinthine layer morphogenesis, skeletal muscle differentiation, pancreatic cell development) alongside regulatory signaling and transcription (DNA-templated transcription, phosphorelay signaling, glucocorticoid pathway modulation) and stress/xenobiotic responses (oxidative stress-induced senescence, response to xenobiotic, drug response). This points to a set of proteins that coordinate development with hormonal and stress signaling rather than a single, narrow pathway. ","confidence":"Medium","size":12,"edges":18,"triangles":9,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000160","count":5},{"id":"GO:0042634","count":5},{"id":"GO:2000323","count":5},{"id":"GO:0090403","count":5}]},{"hash":"1618850359723068681","title":"Developmental pathways and myogenesis","description":"This cluster centers on developmental processes (multicellular development, neural tube closure) and muscle formation (myoblast fusion, response to muscle activity), with supporting roles from DNA replication and transcription (cell-cycle context) and apoptotic signaling (ER stress) indicating a broader developmental regulation and tissue remodeling program.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0070059","count":4}]},{"hash":"2224335080523607641","title":"Unknown","description":"The terms are highly heterogeneous, spanning bacterial cell-wall biosynthesis and eukaryotic cell-cycle and gene-expression processes, with no shared pathway or interactions among the proteins (Edges=0). This makes it unclear what unifies the cluster functionally, so Unknown is appropriate.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008360","count":4},{"id":"GO:0000902","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006397","count":3}]},{"hash":"1377455988311392680","title":"Skeletal muscle development and contractile apparatus","description":"Top terms emphasize skeletal muscle fiber development, thin filament assembly, and actomyosin contraction, with calcium signaling as a key regulatory input. The cluster also includes cell polarity and shape maintenance, which supports proper muscle fiber alignment and architecture. A couple of histone-related terms are obsolete, but the dominant signal is muscle formation and contractile function.","confidence":"High","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0043503","count":8},{"id":"GO:0071963","count":8},{"id":"GO:0051592","count":8},{"id":"GO:0000916","count":8},{"id":"GO:0030240","count":8}]},{"hash":"2273553348148586597","title":"Mammary gland epithelial development and proliferation","description":"The cluster shows strong signals for mammary gland\u2013specific processes: alveolus development and positive regulation of mammary gland epithelial cell proliferation, along with cell-cycle and transcriptional regulation terms. The presence of endoplasmic reticulum unfolded protein response fits the secretory nature of mammary epithelium. While some terms reflect broader epithelial differentiation (and a plant-specific term appears), the dominant theme is mammary epithelial development and proliferative regulation.","confidence":"Medium","size":12,"edges":13,"triangles":5,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030968","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0010444","count":5},{"id":"GO:0000411","count":5}]},{"hash":"585535867968291012","title":"Neuronal vesicle trafficking and protein turnover","description":"This cluster centers on intracellular transport and synaptic vesicle maturation (tubulin complex assembly, synaptic vesicle maturation, intracellular transport) with strong ties to ubiquitin-dependent protein degradation via the multivesicular body pathway, all within a neural/developmental context (brain development, cilium localization, neuronal transport). These together suggest a module dedicated to neuronal vesicle trafficking and targeted protein turnover. ","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0016188","count":2},{"id":"GO:0010796","count":2}]},{"hash":"54616167495387495","title":"T and NK lymphocyte signaling","description":"The top GO terms center on T cell receptor signaling and natural killer cell differentiation, with JUN phosphorylation supporting immune activation; other terms hint at broader cell cycle and differentiation roles, but the immune signaling themes predominate. It suggests a cluster annotated to lymphocyte activation rather than a single cohesive functional module, hence a label focusing on immune signaling is most representative.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":10},{"id":"GO:0097324","count":10},{"id":"GO:0009636","count":10},{"id":"GO:1990801","count":10},{"id":"GO:0014835","count":10}]},{"hash":"2254090774509304303","title":"Chromatin modification and RNA processing","description":"This cluster is driven by chromatin-related terms (histone H4 acetylation) along with DNA-templated transcription and mRNA splicing, pointing to a core theme of gene expression regulation and RNA processing. Peripheral terms about ER-Golgi transport and cell-wall\u2013related processes appear less central, suggesting some annotation noise or broader functional overlap but a primary link to nuclear gene regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043982","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1704844690962830931","title":"Plant innate immunity and hypersensitive response","description":"The cluster is dominated by plant-specific immune terms: innate immune signaling pathway, defense response to bacterium, and plant-type hypersensitive response, indicating a cohesive group of proteins involved in plant immune signaling and hypersensitive responses. Some broader terms about actin nucleation regulation and macrophage activation appear, but the plant defense theme is the strongest thread.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0034051","count":2},{"id":"GO:0010204","count":2},{"id":"GO:0009816","count":2},{"id":"GO:0009626","count":2}]},{"hash":"1398751361890343287","title":"Viral assembly and host translation","description":"The top GO terms show strong signals for translation and ribosome-related processes (translation, translational elongation, rRNA maturation) alongside viral lifecycle steps (viral capsid assembly, virion assembly, viral release). This suggests a cluster of proteins involved in viral replication/assembly and their reliance on host translation machinery, with some host-cell interactions indicated by terms like cell cycle and mitochondrial import. Overall, the cluster appears centered on viral assembly processes linked to translation.","confidence":"Medium","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006414","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0019069","count":2},{"id":"GO:0051085","count":2}]},{"hash":"221924432391522663","title":"Mitochondrial Translation Machinery","description":"This cluster is dominated by GO terms for general translation and, importantly, several mitochondria-specific tRNA aminoacylation activities (mitochondrial threonyl-, seryl-, and alanyl-tRNA charging) along with initiation, elongation, and termination of translation. These collectively point to proteins involved in mitochondrial protein synthesis. A couple of terms (embryonic development, ap4A biosynthesis) appear peripheral and do not disrupt the central theme of mitochondrial translation machinery.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0045901","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0070159","count":2}]},{"hash":"2171312073348096361","title":"Shikimate Pathway and Aromatic AA Biosynthesis","description":"This cluster is dominated by GO terms for the shikimate metabolic process and chorismate biosynthesis, which are the core steps in aromatic amino acid production (phenylalanine, tyrosine, tryptophan). Additional terms related to L-proline and L-alanine biosynthesis and one-carbon metabolism align with broader amino acid metabolism, while a translation term may reflect general housekeeping roles or annotation noise. Overall, the cohesive theme is aromatic amino acid biosynthesis via the shikimate pathway.","confidence":"High","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0009073","count":2},{"id":"GO:0019510","count":2},{"id":"GO:0055129","count":2}]},{"hash":"1455619680062025451","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":59,"triangles":161,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":5},{"id":"GO:0006006","count":5},{"id":"GO:0006096","count":5},{"id":"GO:0035606","count":5},{"id":"GO:0042823","count":5}]},{"hash":"448999115027260600","title":"Unknown","description":"The GO terms span diverse processes (lipid metabolism, bacterial-type flagellum assembly, vacuolar acidification, proteasome storage granule assembly, proton transport and mitochondrial ATP synthesis, angiogenesis and endothelial migration, transcription regulation, and histidine homeostasis) with no single shared function across the 12 proteins. This heterogeneity suggests there is no coherent cluster-level theme to label precisely.","confidence":"","size":12,"edges":12,"triangles":1,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006629","count":3},{"id":"GO:0044780","count":3},{"id":"GO:0007035","count":3},{"id":"GO:1902906","count":3},{"id":"GO:0015991","count":3}]},{"hash":"409375290312500506","title":"Diverse Metabolite Biosynthesis","description":"This cluster centers on a range of biosynthetic processes across different molecule classes\u2014lipids (mycolic acid, sphingolipid), pigments (melanin), hormones (estrogen, testosterone), plant alkaloids (tropane alkaloid), and retinal metabolism\u2014with one more general term about transcription regulation also present. The common thread is biosynthesis of diverse metabolites rather than a single unified pathway, hence a high-level label of Diverse Metabolite Biosynthesis. ","confidence":"Medium","size":12,"edges":19,"triangles":9,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":11},{"id":"GO:0009710","count":10},{"id":"GO:0071768","count":10},{"id":"GO:0031427","count":10},{"id":"GO:0042574","count":10}]},{"hash":"983737476154564216","title":"Cofactor and vitamin biosynthesis","description":"This cluster is enriched for multiple biosynthetic processes that produce vitamins and cofactors (thiamine, biotin, menaquinone, molybdopterin cofactor, protoporphyrinogen IX), plus related tRNA modification, indicating a unifying theme of small-molecule cofactor biosynthesis and metabolism.","confidence":"High","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0006782","count":4},{"id":"GO:0009102","count":4}]},{"hash":"1099982609241452544","title":"Ribosome Biogenesis and Shoot Meristem Regulation","description":"The cluster is dominated by GO terms for ribosome biogenesis and ribosomal small subunit assembly, pointing to a core role in ribosome production. The concurrent plant-development terms for axillary shoot meristem initiation and regulation of secondary shoot formation suggest an additional connection to shoot growth control in plants. Some annotations like telomerase assembly or hemidesmosome assembly may reflect multi-function proteins or cross-species annotation noise, but the strongest, coherent signal centers on ribosome assembly with plant development context.","confidence":"Medium","size":12,"edges":37,"triangles":36,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0000028","count":5},{"id":"GO:0090506","count":4},{"id":"GO:0034198","count":4},{"id":"GO:0006407","count":4}]},{"hash":"1570651886947963833","title":"Ribosome biogenesis and translation","description":"The top terms cluster around translation and ribosome assembly, including cytoplasmic and mitochondrial translation, ribosomal subunit assembly, and rRNA maturation, pointing to a cohesive role in ribosome production and protein synthesis across compartments.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0071353","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0070126","count":1},{"id":"GO:0006259","count":1}]},{"hash":"1897500678595077730","title":"Ribosome Biogenesis and Metal Homeostasis","description":"Top terms include ribosome biogenesis and translation, indicating protein synthesis activity, alongside multiple metal ion transport/detoxification processes (mercury, copper, zinc, iron) and metal homeostasis. Pantothenate biosynthesis and superoxide metabolism appear but do not dominate, suggesting a cluster where protein synthesis machinery coexists with metal handling and oxidative stress responses. Therefore, the label captures the main themes: ribosome-related function with metal ion management.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0033317","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0006801","count":1}]},{"hash":"1491959826973443152","title":"Unknown","description":"The GO terms are highly diverse, including nucleotide catabolic processes (ADP, GDP, UDP, CDP), protein N-linked glycosylation, pollen development (anther dehiscence, pollen exine formation), a methanol response, and nitrate transport. This mix does not reveal a single cohesive function or pathway across the 12 proteins, so a specific, representative label cannot be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071405","count":1},{"id":"GO:0046032","count":1},{"id":"GO:0009901","count":1},{"id":"GO:0046706","count":1},{"id":"GO:0010584","count":1}]},{"hash":"2205167604529285918","title":"Fruit Ripening Hormone and Polyphenol Biosynthesis","description":"The top terms cluster around ethylene and gibberellin biosynthesis, fruit ripening, and proanthocyanidin (polyphenol) biosynthesis, with hydrogen peroxide\u2013mediated PCD linking to senescence during fruit maturation. These collectively point to plant fruit development and hormone-regulated secondary metabolism, despite some outliers (e.g., LPS and histidine biosynthesis) likely reflecting annotation noise. ","confidence":"Medium","size":12,"edges":41,"triangles":66,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0009835","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0000105","count":4},{"id":"GO:0010421","count":4}]},{"hash":"507771678540229275","title":"Zinc Ion Homeostasis and Transport","description":"The top GO terms are dominated by zinc-related processes: response to zinc ion, intracellular zinc ion homeostasis, zinc ion transmembrane transport, and regulation of zinc ion import, with only peripheral mentions of other metals like iron and cadmium. This indicates a cohesive functional cluster centered on zinc handling and transport across membranes.","confidence":"High","size":12,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010043","count":5},{"id":"GO:0006882","count":4},{"id":"GO:0006877","count":4},{"id":"GO:0032119","count":4},{"id":"GO:0071584","count":4}]},{"hash":"1273362243425251917","title":"RNA modification and translation","description":"The cluster\u2019s top GO terms cluster around RNA methylation (RNA guanine-N7-methylation) and protein/post-translational modifications (N-terminal peptidyl-alanine trimethylation, peptidyl-arginine hydroxylation) as well as cytoplasmic translation, suggesting a shared theme of RNA-related processing and protein synthesis. Some biosynthetic and growth-related terms are present but are less tightly connected to the core signal, making a unifying label centered on RNA modification and translation most representative. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0001300","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0018012","count":4},{"id":"GO:0009102","count":4}]},{"hash":"2211816552384935371","title":"Biosynthesis of Vitamins and Secondary Metabolites","description":"The top GO terms cluster around the production of diverse small molecules, including vitamins (retinol, retinal, cobalamin) and secondary metabolites (antibiotics, tropane alkaloids, mycolic acids). Sporulation and antibiotic response appear as related stress/metabolic contexts, but the core theme is biosynthetic processes for vitamins and other metabolites. ","confidence":"Medium","size":12,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0030435","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0046677","count":3}]},{"hash":"2272618134926964116","title":"Ion Transport and Osmotic Regulation","description":"The top GO terms point to membrane transport activities across the plasma membrane, including sodium and potassium ion transport, amino acid import (L-arginine, D-alanine, D-serine), and cell volume homeostasis, with a notable osmotic stress response. While intracellular signal transduction is present, the transport and osmoregulatory terms are more representative of the cluster\u2019s shared function, suggesting these proteins collectively mediate ion gradients and osmotic balance rather than a single signaling pathway.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0021707","count":3},{"id":"GO:0035725","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0071805","count":2}]},{"hash":"530895218728938477","title":"RNA and protein methylation","description":"The Top Terms are dominated by methylation-related processes: tRNA methylation, RNA (guanine-N7)-methylation, peptidyl-glutamine dimethylation, peptidyl-lysine dimethylation, and mRNA capping, plus tRNA wobble uridine modification. These indicate a cohesive theme around RNA and protein modification by methylation, even though other biosynthetic terms appear (antibiotic, sterol, anthocyanin biosynthesis) and are less central. Confidence in the label is Medium.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0030488","count":4},{"id":"GO:0016126","count":3},{"id":"GO:0009718","count":3},{"id":"GO:0018364","count":3}]},{"hash":"375138166244606943","title":"Ubiquitin-Dependent Proteolysis in Antiviral Immunity","description":"The top terms cluster around ubiquitin-dependent protein catabolic processes and ERAD, including ubiquitin-dependent autoubiquitination, suggesting involvement of the ubiquitin-proteasome system. Concurrent terms for innate immune response and defense against virus support a role in antiviral immunity, where ubiquitination regulates stability of immune signaling proteins. Additional terms point to signaling pathways such as TNF-mediated signaling and receptor turnover (Wnt receptor catabolic process), consistent with ubiquitin-mediated regulation of immune and cell-surface signaling. Together these terms imply a functional cluster centered on ubiquitin-regulated protein turnover in immune defense.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0030433","count":6},{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0050999","count":5}]},{"hash":"311484025364379724","title":"Developmental differentiation and organogenesis","description":"The top GO terms point to tissue-specific differentiation and morphogenesis across multiple lineages (paraxial mesoderm, heart, skeletal muscle, kidney/metanephros, lung neuroendocrine, carotid body), plus neuron development and transcriptional regulation by RNA polymerase II. This suggests a cluster of genes involved in broad developmental programs spanning several organs, rather than a single pathway.","confidence":"Medium","size":12,"edges":61,"triangles":177,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":11},{"id":"GO:0032933","count":7},{"id":"GO:0043503","count":7},{"id":"GO:0061103","count":7},{"id":"GO:0048666","count":7}]},{"hash":"2252916799660324434","title":"Unknown","description":"The GO terms are highly diverse, spanning sensory detection (hypoxia, visible light), immune regulation, development, metabolism, protein folding, phosphorylation, and chemotaxis, with no dominant shared function or pathway tying the proteins together into a cohesive cluster.","confidence":"","size":12,"edges":14,"triangles":3,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0070483","count":5},{"id":"GO:1903660","count":5},{"id":"GO:0017006","count":5},{"id":"GO:0046777","count":5},{"id":"GO:0009584","count":5}]},{"hash":"49514947871148281","title":"Unknown","description":"The top terms span mitosis (spindle checkpoint, microtubule localization), ubiquitination, metal ion transport, signaling (TNF, Wnt), chromatin modification, and immune interactions, with no clear shared function linking all proteins. The lack of cohesive biology and zero edges suggests this cluster is a mix of unrelated annotations rather than a single module, so Unknown is appropriate.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035372","count":2},{"id":"GO:0060816","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0044810","count":2},{"id":"GO:0033572","count":2}]},{"hash":"1453381718515896045","title":"Intracellular Metabolite and Cofactor Transport","description":"GO terms indicate transport across membranes of metabolites and cofactors (phosphate, CoA, thiamine pyrophosphate, pyrimidine nucleotides) and intracellular vesicle transport, with metabolic regulation contexts, pointing to a cohesive theme of intracellular metabolite and cofactor transport.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0006886","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0034198","count":2},{"id":"GO:1990845","count":2}]},{"hash":"1149005793816920629","title":"Regulated Signaling and Proliferation","description":"The dominant GO terms describe upregulation of signaling components (kinase and GTPase activity), transcription, and cell cycle progression, coupled with processes like mRNA transport and calcium signaling, plus stress and immune signaling hints (hypoxia response, Fc-epsilon receptor signaling). This pattern suggests a broad cluster centered on positive regulation of signaling pathways that drive proliferation or activation, rather than a single specific pathway.","confidence":"Medium","size":12,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008284","count":9},{"id":"GO:0031954","count":9},{"id":"GO:0051028","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0043547","count":9}]},{"hash":"707100159288756849","title":"Kinetochore and spindle checkpoint regulators","description":"The top GO terms strongly point to mitosis and spindle assembly control, including protein localization to the kinetochore, mitotic G2 DNA damage checkpoint signaling, and regulation of protein import during the spindle checkpoint. While there are a few terms related to signaling and differentiation, the dominant theme ties to mitotic regulation and kinetochore function.","confidence":"Medium","size":12,"edges":50,"triangles":111,"max_degree":10,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0034501","count":12},{"id":"GO:0045736","count":12},{"id":"GO:0050852","count":10},{"id":"GO:0097324","count":10},{"id":"GO:0009636","count":10}]},{"hash":"54748924336964517","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by translation and ribosome-related processes (translation, translational elongation, ribosomal large subunit biogenesis, ribosomal large subunit assembly), pointing to proteins involved in ribosome assembly and protein synthesis. Retina/optic nerve development and cell cycle terms appear only peripherally and do not override the ribosome-centric signature. Therefore, the cluster is best labeled as ribosome biogenesis and translation machinery.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006414","count":2},{"id":"GO:0032781","count":1},{"id":"GO:0021554","count":1},{"id":"GO:0060041","count":1}]},{"hash":"1466628575293702167","title":"mRNA processing and translation initiation","description":"This cluster centers on RNA processing and regulation of translation, including mRNA splicing, polyadenylation regulation, and formation of translation preinitiation complexes, as well as IRES-driven and viral translation initiation/reinitiation. The shared themes point to coordinated control of mRNA maturation and the start of protein synthesis.","confidence":"High","size":12,"edges":11,"triangles":1,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":8},{"id":"GO:0002188","count":8},{"id":"GO:1901407","count":8},{"id":"GO:0001731","count":8},{"id":"GO:0006446","count":8}]},{"hash":"1519635190484798814","title":"Neural vesicle trafficking and axon guidance","description":"This cluster is dominated by GO terms related to neural development and vesicle trafficking, including regulation of synaptic vesicle exocytosis, Golgi vesicle docking, axon guidance, and brain development. While some terms appear unrelated (mitotic spindle, mitochondrial membrane permeabilization, plant hormone signaling, immune signaling), the central pattern centers on neural vesicle traffic and guidance, suggesting a coherent neuronal function theme for the proteins.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010796","count":4},{"id":"GO:2000300","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0031384","count":4},{"id":"GO:0090307","count":3}]},{"hash":"605352797583248652","title":"Regulatory Signaling and Transcription","description":"The GO terms show a common theme of signaling pathway regulation (NF-kappaB signaling, insulin receptor signaling, Rho signal transduction) alongside control of gene expression (DNA-templated transcription and its regulation). Additional terms touch on cytoskeletal organization (lamellipodium assembly) and basic cellular processes like cell division and mitochondrial protein import, suggesting a cluster of regulatory proteins that influence signaling and transcription, with some ancillary roles in other cellular processes. The lack of observed interactions in the network does not undermine the thematic clustering around signaling and transcription regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0045041","count":2},{"id":"GO:0051131","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0035023","count":2}]},{"hash":"1171381507732228990","title":"Bacterial cell wall biosynthesis and division","description":"The cluster\u2019s top GO terms cluster around cell division (GO:0051301), cell cycle, and cell wall-related processes (peptidoglycan biosynthesis/turnover, cell wall organization), pointing to bacterial growth and envelope biogenesis. There are additional broad processes like DNA-templated transcription, and a few outliers (gastrulation, cellulose catabolic process) that likely reflect annotation noise rather than a core function. Overall, the dominant theme is cell growth, division, and cell wall construction, hence this label. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0009254","count":1}]},{"hash":"259379807263012198","title":"Plant development, hormone biosynthesis, and nitrate response","description":"The cluster centers on plant growth and development (gibberellin biosynthesis, fruit ripening), alongside secondary metabolism (proanthocyanidin biosynthesis) and nutrient/ROS signaling (nitrate response/transport, hydrogen peroxide-mediated PCD), with a note on post-translational modification regulation. This mix points to a cohesive theme of developmental progression coordinated with hormone synthesis and nutrient/stress signaling.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1901874","count":2},{"id":"GO:0032364","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0010167","count":1}]},{"hash":"581924384799992564","title":"Bacterial transcription regulation and chemotaxis","description":"The cluster shows strong links to DNA-templated transcription and its regulation, coupled with chemotaxis and flagellum-dependent motility, plus signaling components like phosphorelay systems and nitro\u00adgen utilization regulation. These together point to a bacterial-style regulatory network that coordinates gene expression with environmental cues, including movement toward stimuli. The presence of plant cytokinin signaling is likely a cross-annotation artifact rather than core to this cluster. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006935","count":2},{"id":"GO:0051606","count":2},{"id":"GO:0042173","count":2},{"id":"GO:0009736","count":2}]},{"hash":"801093976678070479","title":"Cadmium Stress and Ubiquitin Regulation","description":"The GO terms show cellular response to cadmium ion, protein autoubiquitination regulation, and innate immune/wound responses, pointing to a metal-stress response with ubiquitin-mediated regulation as the core theme; several other terms (development, cell cycle, histone dephosphorylation) are less coherent or obsolete, indicating some noise but not overriding the main signal. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0006730","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0045842","count":2},{"id":"GO:1902499","count":2}]},{"hash":"374347073546132938","title":"Mitotic progression and ubiquitin-mediated proteolysis","description":"Top GO terms point to mitosis regulation (G2/M transition, exit from mitosis, chromosome segregation) and ubiquitin-dependent proteolysis (SCF, K11-linked). This suggests a module coordinating mitotic progression via targeted degradation. Other terms like NER, viral process, and embryonic development are broader contexts but don't override the central mitotic-ubiquitin theme.","confidence":"High","size":12,"edges":43,"triangles":59,"max_degree":11,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0000086","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0010458","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0007059","count":5}]},{"hash":"2062863652142927557","title":"Mitochondrial transport and energy metabolism","description":"Top GO terms suggest a cohesive role for transporting metabolites and ions across mitochondrial membranes (pyrimidine nucleotides, CoA, TPP, manganese, phosphate) together with energy/homeostasis processes (adaptive thermogenesis, insulin/glucose response, amino acid starvation). This points to a functional cluster of mitochondrial transporters linked to energy regulation. ","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":4},{"id":"GO:0035435","count":3},{"id":"GO:0034198","count":3},{"id":"GO:1990845","count":3},{"id":"GO:0061179","count":3}]},{"hash":"244405780517364378","title":"Plant stress signaling and cell wall remodeling","description":"This cluster features GO terms for cAMP/cGMP signaling and receptor guanylyl cyclase pathways, plus ion transport across the plasma membrane and oxidative stress response, with plant-type cell wall organization and lignin catabolic processes hinting at cell wall remodeling. Together these terms suggest a plant stress-response module linking signaling to cell wall modification, though a term like aerotaxis introduces some inconsistency.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0010754","count":3},{"id":"GO:0097623","count":3}]},{"hash":"1440494239179367850","title":"ER-Golgi Trafficking and ERAD","description":"The top GO terms are dominated by intracellular protein transport between the ER and Golgi, including ER-to-Golgi and Golgi-to-ER retrograde transport, as well as the ubiquitin-dependent ERAD pathway, pointing to a cohesive theme of ER-Golgi vesicle trafficking and quality control. Other terms like mRNA transport and transcription appear less central, likely reflecting broader cellular functions in this cluster. Overall, the strongest signal is for ER-Golgi trafficking and ER-associated degradation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1580077586864020627","title":"Transcriptional Regulation in Development and Regeneration","description":"The cluster is strongly characterized by transcription regulation by RNA polymerase II (DNA-templated transcription, positive/negative regulation of transcription by Pol II) and links to cell cycle control (G1/S transition). Developmental and regenerative terms such as liver regeneration, forebrain development, and trophoblast differentiation suggest these proteins coordinately regulate gene expression during development and tissue repair, while metabolic terms like gluconeogenesis and amino acid transport may reflect broader growth-related regulation. ","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:2000134","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0097421","count":2}]},{"hash":"151579094662693617","title":"TLR signaling and antiviral innate immunity","description":"GO terms show a cohesive pattern around Toll-like receptor signaling (TLR8/10, Toll pathway), antiviral defense (defense response to virus, response to dsRNA, interferon production), and macrophage activation, suggesting the proteins participate in innate immune sensing and antiviral responses. Some non-immune terms related to floral development appear as noise, but do not obscure the primary immune-related signal.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006963","count":12},{"id":"GO:0045078","count":12},{"id":"GO:0034158","count":12},{"id":"GO:0034166","count":12},{"id":"GO:0048833","count":12}]},{"hash":"1769767015489319253","title":"Unknown","description":"The terms span DNA metabolism (transcription, repair, replication) and metabolism/differentiation signals (cholesterol biosynthesis, T cell signaling, melanocyte migration, myoblast differentiation) with no clear shared function, so no coherent cluster label can be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006281","count":9},{"id":"GO:0000435","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0006695","count":9}]},{"hash":"562148003739659001","title":"Unknown","description":"The GO terms are highly diverse, including cell division, cell cycle, potassium transport, visual perception, nitrate assimilation, and fatty acid biosynthesis, with no dominant shared function or pathway. The lack of edges and zero triangles suggests no tight functional module. Therefore a single meaningful label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0042128","count":2}]},{"hash":"2036553375000661429","title":"Ubiquitin-Proteasome Mediated Cell Cycle Regulation","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes and ubiquitination, including SCF-dependent proteasomal degradation, indicating a core role in targeted protein turnover. Related terms for spindle assembly and G1/S transcription regulation suggest involvement in cell cycle control, while circadian regulation and growth hint broader regulatory roles. The plant-specific brassinosteroid signaling and wybutosine biosynthesis appear as peripheral associations. Overall, the central theme is ubiquitin-mediated proteolysis coordinating cell cycle progression.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0042752","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0031146","count":2}]},{"hash":"1522601320587955701","title":"Plant nucleobase transporters","description":"The cluster is characterized by multiple GO terms pointing to import/transport of nucleobases (uracil, adenine, guanine) and related metabolites (urate, xanthine), indicating a shared function as nucleobase transporters. The presence of plant-specific terms such as defense against fungus and sexual reproduction suggests these transporters operate in a plant context, potentially linking nutrient transport to development and defense. However, the mix of terms beyond pure transport makes the signal less than perfect, hence a Medium confidence.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0006949","count":2},{"id":"GO:0009828","count":2},{"id":"GO:0019953","count":2},{"id":"GO:0098721","count":1}]},{"hash":"2190661478116149557","title":"Meiosis and DNA replication regulation","description":"The top GO terms are dominated by DNA replication, centrosome cycle, and meiotic regulation (e.g., positive regulation of nuclear DNA replication, meiotic double-strand break formation, centrosome cycle), pointing to cell-cycle/meiotic control. Other terms reflect growth signaling and stress responses (TORC1 signaling, amino acid starvation) and some development or signaling processes (sperm capacitation, embryonic skeleton morphogenesis, T cell receptor pathway). Overall, the cluster appears to center on meiosis and DNA replication control with supporting regulatory and stress-response roles.","confidence":"Medium","size":11,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0006260","count":6},{"id":"GO:1903343","count":6},{"id":"GO:0034198","count":6}]},{"hash":"1213386182002710137","title":"Mitotic progression and spindle checkpoint signaling","description":"Most terms point to cell division: mitotic cycle, DNA replication, spindle checkpoint, and related phosphorylation. A few signaling/differentiation terms may reflect broader regulatory connections, but the mitosis-focused terms dominate the cluster.","confidence":"Medium","size":11,"edges":12,"triangles":3,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":11},{"id":"GO:0006260","count":11},{"id":"GO:0050852","count":10},{"id":"GO:0097324","count":10},{"id":"GO:0009636","count":10}]},{"hash":"155256281084020659","title":"Bacterial cell wall biosynthesis and division","description":"Several top terms point to peptidoglycan and other cell wall biosynthetic processes, along with cell division and regulation of cell shape. This pattern suggests a cluster of proteins involved in cell envelope biogenesis and the coordination of cell division in bacteria.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0009252","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0055114","count":2}]},{"hash":"872404315300008111","title":"Unknown","description":"The top GO terms span a wide, disjoint set of processes (serine biosynthesis, LPS biosynthesis, copper and cadmium transport, calcium homeostasis, P450 epoxygenase pathway, stilbene catabolism, and various dephosphorylation/phospholipid dephosphorylation activities), including bacterial, plant, and eukaryotic pathways. There isn\u2019t a clear unified function tying these proteins together, so a concise, representative label isn\u2019t discernible beyond Unknown.","confidence":"","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":5},{"id":"GO:0009103","count":5},{"id":"GO:0006825","count":4},{"id":"GO:0006874","count":4},{"id":"GO:0019373","count":4}]},{"hash":"1891305671763173846","title":"Mitotic spindle and microtubule organization","description":"The top GO terms point strongly to microtubule dynamics and mitotic machinery (mitotic spindle midzone assembly, spindle pole body duplication, cytoplasmic microtubule organization, and cell division, plus cytokinesis), indicating proteins involved in spindle formation and chromosome segregation. A few terms about mechanosensation and IL-4 signaling are present but appear secondary to the core cytoskeletal/mitotic theme. ","confidence":"High","size":11,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071353","count":6},{"id":"GO:0030182","count":5},{"id":"GO:0090529","count":5},{"id":"GO:0051256","count":5},{"id":"GO:0031122","count":5}]},{"hash":"1074649082104626871","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms related to ribosome function and production, including translation, ribosome biogenesis, small subunit assembly, and rRNA maturation/processing (SSU/LSU), with supportive terms like snoRNP assembly. The hub of ribosome biosynthesis and protein synthesis machinery suggests a coherent functional theme around making and using ribosomes. ","confidence":"High","size":11,"edges":52,"triangles":141,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0042254","count":5},{"id":"GO:0006407","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0000462","count":2}]},{"hash":"938207822440604893","title":"Urmylation and tRNA wobble thiolation","description":"The top GO terms include tRNA wobble position uridine thiolation and protein urmylation, indicating a cluster centered on Urm1/Urmylation and tRNA modification pathways. Other terms (redox homeostasis, molybdopterin cofactor biosynthesis) may reflect broader metabolic context, while development and mitotic terms appear peripheral. Overall, the strongest signal is Urm1-mediated tRNA modification and urmylation.","confidence":"Medium","size":11,"edges":23,"triangles":24,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":1},{"id":"GO:0018192","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0030855","count":1}]},{"hash":"2116275344680935135","title":"Bacterial biosynthesis and stress response","description":"The top terms show biosynthetic pathways (terpenoid/isoprenoid via MEP/mevalonate-independent routes, LPS precursor ADP-L-glycero-beta-D-manno-heptose, trehalose biosynthesis) and stress-related processes (cellular response to heat, dephosphorylation, redox). This mixture points to bacterial metabolism with adaptation to stress, rather than a single animal-specific function. An outlier term about axon localization likely reflects annotation noise. ","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0051484","count":2},{"id":"GO:0051483","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0070413","count":2}]},{"hash":"1338233241163485762","title":"Unknown","description":"Top terms span tRNA modification, cAMP signaling, detoxification, hematopoietic and pituitary development, energy metabolism (lipoate, 2-oxoglutarate, glycolysis), and epigenetic regulation. The diversity indicates no single dominant function linking all proteins, so a unified label cannot be confidently assigned.","confidence":"","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":5},{"id":"GO:0071320","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0051068","count":4}]},{"hash":"1225994105092860171","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":16,"triangles":1,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006986","count":4}]},{"hash":"393984870545341409","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for translation, cytoplasmic translation, ribosome biogenesis, and cytosolic ribosome assembly, with SSU-rRNA maturation supporting a ribosome-focused group; a few transcription/DNA damage\u2013related terms are present but not central. ","confidence":"High","size":11,"edges":41,"triangles":77,"max_degree":10,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0002181","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0000462","count":1},{"id":"GO:0031564","count":1}]},{"hash":"1783732790391534317","title":"Steroid Hormone Metabolism","description":"This cluster is dominated by GO terms for steroid hormones, including testosterone biosynthetic process, androgen metabolic process, progesterone metabolic process, and aldosterone-regulated blood volume, pointing to a core theme of steroid hormone biosynthesis and metabolism. The presence of related xenobiotic and retinoic acid catabolic processes suggests additional metabolic or detoxification roles, but the strongest signal remains steroid hormone pathways. ","confidence":"High","size":11,"edges":16,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0061370","count":8},{"id":"GO:0008209","count":8},{"id":"GO:0010193","count":7},{"id":"GO:0034653","count":7},{"id":"GO:0035865","count":7}]},{"hash":"1688783183006578982","title":"mRNA Splicing and Processing Regulation","description":"The cluster is dominated by GO terms tied to post-transcriptional control: spliceosome-mediated mRNA splicing, splice site recognition, mRNA modification and polyadenylation regulation, as well as ncRNA-mediated gene silencing and stress-related mRNA stability. Together these point to a cohesive function in mRNA maturation, processing, and turnover, rather than transcriptional control. ","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":8},{"id":"GO:0031047","count":8},{"id":"GO:1901407","count":7},{"id":"GO:0006376","count":5},{"id":"GO:1900363","count":5}]},{"hash":"163892149682644681","title":"Redox-regulated transcription under ER stress","description":"The cluster features several redox-related terms (cell redox homeostasis, protein deglutathionylation, oxidation\u2013reduction processes) coupled with transcriptional regulation (DNA-templated transcription, regulation of DNA binding, positive/negative regulation of DNA binding) and a clear link to ER stress response. This suggests a theme where redox state influences transcriptional control via ER stress signaling, with some post-translational modification aspects (e.g., proline hydroxylation) that can affect protein function. Confidence: Medium","confidence":"","size":11,"edges":8,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0034976","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0080058","count":2}]},{"hash":"2299164672753761418","title":"Chromatin Remodeling and Epigenetic Regulation","description":"The cluster is dominated by GO terms tied to chromatin dynamics and epigenetic control, including DNA replication-dependent chromatin assembly, transcription initiation-coupled chromatin remodeling, rDNA heterochromatin formation, and histone modification regulation. While a few terms reference development (spermatogenesis, midbrain morphogenesis) or other processes, the common thread appears to be chromatin organization and its role in transcriptional regulation and genome stability.","confidence":"High","size":11,"edges":52,"triangles":141,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":10},{"id":"GO:0045815","count":10},{"id":"GO:0051290","count":10},{"id":"GO:0000183","count":10},{"id":"GO:0002227","count":9}]},{"hash":"938546757267481151","title":"Chromatin remodeling and transcriptional regulation in development","description":"The top terms center on chromatin remodeling and transcriptional control (chromatin remodeling; negative regulation of transcription by RNA Pol II; rDNA heterochromatin formation), suggesting a nuclear regulatory module. The presence of multiple developmental GO terms (brain development, embryonic digestive tract morphogenesis, ureteric bud morphogenesis, single fertilization) indicates these regulators function in embryogenesis and organogenesis. Some plant-specific hormone and defense responses appear among the list, but do not obscure the core chromatin-regulatory theme. Overall, this cluster likely comprises chromatin remodelers and transcriptional regulators influencing developmental processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0009739","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0009751","count":3}]},{"hash":"477451323899580821","title":"Unknown","description":"The GO terms are diverse and cover DNA recombination, RNA hydrolysis, signaling responses to cAMP and peptide hormones, lipid signaling via phosphatidylinositol dephosphorylation, metabolism, redox homeostasis, and even hemolysis; with no clear common function linking all 11 proteins, there is no coherent label to assign.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":5},{"id":"GO:0090502","count":5},{"id":"GO:2000327","count":4},{"id":"GO:0071320","count":4},{"id":"GO:0046856","count":4}]},{"hash":"1047125215436764845","title":"Protein quality control: ERAD and autophagy regulation","description":"The top terms center on ubiquitin-dependent degradation pathways (ERAD), autoubiquitination, and autophagy-related processes (aggrephagy), with related hints from mitochondrial fusion regulation and calcium signaling; together they point to a cohesive theme of cellular protein quality control and turnover. Some terms are peripheral or obsolete, but the core signal is ubiquitin-mediated degradation and autophagy.","confidence":"Medium","size":11,"edges":48,"triangles":118,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1904049","count":8},{"id":"GO:1902283","count":8},{"id":"GO:1904378","count":8},{"id":"GO:1903071","count":8},{"id":"GO:0051865","count":8}]},{"hash":"1438646669269485118","title":"Ubiquitin-Proteasome Regulation in Meiosis","description":"The cluster is dominated by ubiquitin-dependent proteolysis terms (SCF-dependent proteasomal degradation, protein polyubiquitination) and meiosis-related processes (oocyte maturation, spindle assembly in female meiosis I, microtubule polymerization), suggesting a cohesive theme of regulated protein turnover supporting meiotic spindle dynamics. Some circadian/development terms appear but do not override the core ubiquitin\u2013proteasome\u2013meiosis connection.","confidence":"High","size":11,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0042787","count":6},{"id":"GO:0042752","count":6},{"id":"GO:0000209","count":6}]},{"hash":"1193312124020613060","title":"Redox Detoxification and Cofactor Metabolism","description":"Top GO terms are dominated by cellular oxidant detoxification and redox homeostasis, with supporting metabolism terms like NAD+ and thiamine biosynthesis and anaerobic respiration. This suggests the proteins function together to maintain redox balance and supply essential cofactors, with a potential incidental cortical development annotation likely not reflective of the core function.","confidence":"High","size":11,"edges":12,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0046653","count":3},{"id":"GO:0009061","count":3}]},{"hash":"1224326683686283846","title":"Chromatin remodeling and transcription regulation","description":"This cluster includes terms tied to chromatin assembly, histone modification, and transcription initiation/regulation by RNA polymerase II (including preinitiation complex assembly and rDNA heterochromatin formation), with an additional link to photomorphogenesis-related transcription, pointing to a cohesive chromatin-based control module.","confidence":"High","size":11,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":5},{"id":"GO:0006335","count":4},{"id":"GO:0045815","count":4},{"id":"GO:2000306","count":4},{"id":"GO:0045898","count":4}]},{"hash":"999084782184887126","title":"mRNA processing and translation machinery","description":"The GO terms are dominated by translation-related processes (translation, cytoplasmic translation, translation preinitiation complex) and RNA processing (mRNA splicing via spliceosome, polyadenylation), indicating a cluster of proteins involved in RNA metabolism and protein synthesis; a few terms about cell cycle or development are present but much less represented, so the label reflects the core shared function.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2}]},{"hash":"2063408889837819707","title":"JNK Signaling and Cell Cycle Regulation","description":"These proteins appear to participate in phosphorylation-driven signaling that spans immune differentiation (T cell receptor signaling, NK differentiation) and development (myoblast differentiation, melanocyte migration), as well as cell-cycle control (mitotic G2 checkpoint signaling, spindle assembly-related processes, nuclear import regulation) and JUN phosphorylation. The repeated emphasis on phosphorylation events and checkpoint signaling points to a module centered on MAPK/JNK-like signaling that modulates both immune differentiation cues and mitosis. Thus, a concise label is JNK Signaling and Cell Cycle Regulation.","confidence":"Medium","size":11,"edges":12,"triangles":6,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":11},{"id":"GO:0097324","count":11},{"id":"GO:0009636","count":11},{"id":"GO:1990801","count":11},{"id":"GO:0014835","count":11}]},{"hash":"147765163380637308","title":"Plant Hormone Signaling and Seed/Cuticle Development","description":"These terms point to plant-specific hormone signaling (ABA and ethylene) driving transcriptional regulation tied to development, including seed formation and outer surface (cuticle and wax) biosynthesis, with links to defense responses. The cluster seems to group proteins involved in hormone signaling pathways that influence seed and cuticle development, rather than a single narrow function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0007275","count":2}]},{"hash":"903601860703460236","title":"mRNA Processing and Splicing Regulation","description":"Top terms indicate strong enrichment for mRNA processing and RNA splicing, including mRNA splicing and regulation of alternative splicing via the spliceosome. Additional hints of polyadenylation regulation, ER stress\u2013related pathways, and deubiquitination suggest regulatory layers around RNA maturation, but the dominant theme is RNA processing/splicing machinery.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":4},{"id":"GO:0035523","count":2},{"id":"GO:0035329","count":2},{"id":"GO:1904378","count":2},{"id":"GO:1900363","count":2}]},{"hash":"1687432967525681381","title":"Mitochondrial Metabolite Transporters","description":"The proteins in this cluster are tied to transmembrane transport of various metabolites and cofactors into mitochondria (phosphate, CoA, thiamine pyrophosphate, pyrimidine nucleotides, Mn2+), with broader links to energy metabolism and metabolic regulation (thermogenesis, insulin/glucose signaling, liver metabolism), suggesting a cohesive theme around mitochondrial metabolite transport.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":2},{"id":"GO:0034198","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0061179","count":2},{"id":"GO:1990519","count":2}]},{"hash":"1865882770078563729","title":"ER-Golgi vesicle trafficking and lysosome targeting","description":"The cluster is dominated by GO terms for ER-Golgi and retrograde vesicle transport, as well as protein targeting to lysosome, with supporting notes of GTPase activity regulation and TORC1 signaling. A few cell-cycle\u2013related terms appear, but the strongest cohesive theme is intracellular trafficking between the ER, Golgi, and lysosome, suggesting a vesicle transport module. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006622","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0051028","count":4}]},{"hash":"20860017645362627","title":"Nuclear DNA Transcription, Replication, and Repair","description":"The cluster shows strong representation of DNA-templated transcription, DNA replication, and DNA repair, pointing to a core theme of nuclear DNA metabolism. Supporting terms include regulation of nuclear export and various signaling or developmental processes (cadmium response, parathyroid hormone stimulus, mesoderm formation, and focal adhesion regulation), which may reflect pleiotropy or annotation breadth. Overall, the dominant function appears to be DNA maintenance and transcription in the nucleus, with secondary regulatory or signaling associations.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0046826","count":4},{"id":"GO:0071374","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0051893","count":3}]},{"hash":"1146128390660782252","title":"Electrical signaling in excitable tissues (heart and nerves)","description":"The terms cluster around electrical activity and signaling in excitable tissues: regulation of cardiac action potentials (SA node, atrial repolarization), potassium ion transport, GABA secretion, mechanosensation, and pain perception. While there are general processes like transcription and development also listed, the strongest theme is excitability and neurotransmission in heart and neural contexts, suggesting proteins involved in electrical signaling rather than housekeeping functions.","confidence":"High","size":11,"edges":23,"triangles":5,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0050976","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0098914","count":4}]},{"hash":"1800353215842545738","title":"Plant secondary metabolite biosynthesis","description":"This cluster is characterized by GO terms spanning biosynthetic pathways for plant-derived compounds (sporopollenin, flavonoids, chalcones, resorcinol, cytokinin; plus fatty acid and long-chain fatty-acyl-CoA metabolism and cell wall layer assembly). Despite one term about postsynaptic calcium regulation, the dominant signal is metabolic biosynthesis in plants, especially secondary metabolism and lipid synthesis, suggesting a cohesive biosynthesis-focused cluster.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080110","count":1},{"id":"GO:0009813","count":1},{"id":"GO:0019505","count":1},{"id":"GO:0071770","count":1},{"id":"GO:0031148","count":1}]},{"hash":"706910258301325881","title":"Mitotic spindle and chromosome segregation","description":"The top GO terms are dominated by mitosis-related processes: spindle assembly, sister chromatid segregation, APC-dependent catabolic processes, and mitotic DNA replication/Okazaki fragment processing, plus cell division and some nuclear pore involvement. While there are a few outliers (actin depolymerization and lens fiber differentiation), the overall signature points to a cohesive mitotic machinery and chromosome segregation function cluster.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030042","count":6},{"id":"GO:0070306","count":6},{"id":"GO:0040020","count":6},{"id":"GO:1904263","count":6},{"id":"GO:0051301","count":6}]},{"hash":"1329054657052841418","title":"Golgi-ER vesicle trafficking","description":"This cluster is dominated by GO terms related to the Golgi apparatus, ER-Golgi vesicle transport, and intra-Golgi and retrograde trafficking (e.g., Golgi ribbon formation, vesicle fusion with Golgi/ER, endosome-to-Golgi transport), indicating a cohesive role in Golgi- and ER-associated vesicle trafficking.","confidence":"High","size":11,"edges":46,"triangles":113,"max_degree":10,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0090161","count":6},{"id":"GO:0048280","count":5},{"id":"GO:0042147","count":4},{"id":"GO:0006896","count":4},{"id":"GO:0006891","count":4}]},{"hash":"2003890234289094094","title":"Xylan biosynthesis and plant cell wall biogenesis","description":"The strongest signals are about xylan production and secondary cell wall formation (xylan biosynthesis, plant-type secondary cell wall biogenesis, xylan acetylation), which points to a protein cluster involved in plant cell wall synthesis and modification. Additional terms related to cell wall organization and regulation of cell shape support this theme, with gibberellin response suggesting growth-related remodeling. A few outlier terms (peptidoglycan biosynthesis, pyrrolysine biosynthesis) may reflect annotation noise or distant homology rather than core function. Overall, the cluster appears to center on plant cell wall biosynthesis and xylan processing, with possible trafficking components (ER export regulation) linked to cell wall protein delivery.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045492","count":2},{"id":"GO:0009834","count":2},{"id":"GO:1990937","count":2},{"id":"GO:0070863","count":2},{"id":"GO:0009252","count":1}]},{"hash":"486277704287326116","title":"Metal and xenobiotic transporters","description":"The GO terms show a clear emphasis on transporter activities for metals (cobalt, molybdate) and xenobiotics (daunorubicin, bacteriocin, xenobiotic transmembrane transport), with related processes like cytochrome complex assembly and SOS response suggesting linked detoxification and stress responses. Some odd terms (nodulation, sorocarp morphogenesis) may be annotation noise, but the dominant signal points to metal and toxin transport functions.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":3},{"id":"GO:0006824","count":2},{"id":"GO:0031288","count":2},{"id":"GO:0055099","count":2},{"id":"GO:0009432","count":2}]},{"hash":"201789282990274021","title":"Small-molecule metabolism and drug response","description":"Top GO terms include metabolism of xylitol, furaldehyde, prostaglandin, and pyruvate/ethanol pathways, plus a drug-response term and redox signaling; together they point to a cluster centered on metabolism of diverse small molecules with associated signaling and pharmacologic response. Confidence in this label is Medium.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0051160","count":10},{"id":"GO:0033859","count":10},{"id":"GO:0045777","count":10},{"id":"GO:0097327","count":10},{"id":"GO:0006693","count":10}]},{"hash":"1251999736308345952","title":"Sugar metabolism and redox processes","description":"The cluster is dominated by terms related to carbohydrate catabolism (xylitol, galactose, pyruvate fermentation) and a general oxidation-reduction theme, with additional signals from prostaglandin metabolism and a nitrosylation event. This suggests a group of proteins involved in energy metabolism and redox balance, rather than a single, narrow pathway. Confidence: Medium","confidence":"","size":10,"edges":10,"triangles":2,"max_degree":8,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0051160","count":5},{"id":"GO:0033498","count":5},{"id":"GO:0033859","count":5},{"id":"GO:0045777","count":5}]},{"hash":"144808080452352562","title":"Post-transcriptional mRNA processing and translation","description":"This cluster centers on post-transcriptional gene expression steps: ribosome biogenesis and translation, plus multiple mRNA processing events (splicing, polyadenylation, tail regulation, and stability). The dominance of translation- and ribosome-related terms, alongside several mRNA maturation terms, indicates a cohesive group of proteins involved in RNA processing and translation.","confidence":"High","size":10,"edges":14,"triangles":10,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":4},{"id":"GO:1901407","count":3},{"id":"GO:0006376","count":2},{"id":"GO:1900363","count":2}]},{"hash":"605719555267716902","title":"Immune cell signaling and differentiation","description":"The cluster is dominated by immune-related terms such as T cell receptor signaling and natural killer cell differentiation, with JUN phosphorylation pointing to shared signaling pathways. While there are also differentiation terms for other lineages (myoblast, melanocyte) and some cell-cycle\u2013related processes (spindle assembly, mitotic checkpoint), the strongest signal centers on immune signaling and differentiation. This supports a label focused on immune signaling with broader differentiation context.","confidence":"Medium","size":10,"edges":33,"triangles":52,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":10},{"id":"GO:0097324","count":10},{"id":"GO:0009636","count":10},{"id":"GO:1990801","count":10},{"id":"GO:0014835","count":10}]},{"hash":"560919695905578428","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000466","count":6},{"id":"GO:0042273","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0000480","count":5},{"id":"GO:0000462","count":5}]},{"hash":"745770132251881597","title":"Immune activation and differentiation signaling","description":"Top GO terms include T cell receptor signaling pathway and natural killer cell differentiation, pointing to immune activation. Other terms point to differentiation processes (myoblast differentiation in skeletal muscle regeneration, melanocyte migration) and signaling events (JUN phosphorylation, mitotic checkpoints). The collection seems to reflect general signaling networks that coordinate immune responses and developmental differentiation rather than a single cohesive pathway, so this label emphasizes both immune activation and differentiation signaling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046827","count":8},{"id":"GO:0009636","count":8},{"id":"GO:0050852","count":7},{"id":"GO:0097324","count":7},{"id":"GO:1990801","count":7}]},{"hash":"2301992282342839683","title":"Extracellular Matrix Remodeling and Morphogenesis","description":"Go terms point to extracellular matrix remodeling and tissue development: basement membrane disassembly, bone resorption, decidualization, and morphogenetic processes like lung branching, with ancillary proteolysis and hormone/immune regulation. The shared extracellular context (Wnt localization to extracellular region) reinforces this theme. Some terms touch on immune/hormone signaling, but the core connection is remodeling of extracellular matrices during development and tissue remodeling.","confidence":"Medium","size":10,"edges":25,"triangles":23,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035593","count":7},{"id":"GO:0097067","count":7},{"id":"GO:0045453","count":7},{"id":"GO:0010815","count":7},{"id":"GO:0046697","count":7}]},{"hash":"751108276966162536","title":"DNA damage response and protein turnover","description":"Top GO terms include nucleotide-excision repair and transcription-coupled repair, along with negative regulation of G2/M transition, ubiquitin-dependent protein catabolic process, and translation-related processes such as translation reinitiation and deneddylation regulation. With no edges connecting the proteins, there isn\u2019t a single tight interaction module, but the recurring themes center on genome maintenance and proteostasis rather than a narrow function; some developmental terms appear but do not define the cluster\u2019s core. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030182","count":2},{"id":"GO:0010972","count":2},{"id":"GO:0000715","count":2},{"id":"GO:0048142","count":2},{"id":"GO:0008283","count":2}]},{"hash":"2023834519473394152","title":"Jasmonate-responsive calcium signaling and ion transport","description":"Top GO terms show a mix of jasmonic acid response and multiple membrane/ion transport processes (calcium ion transport to ER, calcium homeostasis, proton and potassium transmembrane transport, electrochemical gradient maintenance) plus membrane organization (T-tubule). This points to a theme of hormone-triggered signaling that coordinates calcium signaling and ion transport, with some accompanying transcriptional regulation reflected by the spliceosome terms. Together, these features suggest a module focused on jasmonate-linked signaling and ion homeostasis rather than a single isolated process. ","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009753","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0000380","count":2},{"id":"GO:1903515","count":1},{"id":"GO:0010248","count":1}]},{"hash":"1664689324387614117","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0048568","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000480","count":4}]},{"hash":"1802848255482640793","title":"Mitochondrial metabolism, dynamics, and apoptosis","description":"The GO terms cluster around mitochondrial functions: regulation of pyruvate decarboxylation to acetyl-CoA, mitochondrial membrane fission, apoptotic process, and mitochondrial translation/transcription, with related mitochondrial genome maintenance and stress responses to xenobiotics and aluminum. This points to a cohesive mitochondria-centered cluster involving energy metabolism, organelle dynamics, and cell death.","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010510","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0000002","count":2}]},{"hash":"1880956574969208500","title":"MAPK Signaling and RNA Processing","description":"Top terms indicate a core emphasis on MAPK signaling cascades (ERK1/ERK2, p38) with immune-related signaling (GM-CSF stimulus, T cell receptor signaling), complemented by RNA processing processes (mRNA capping, RNA splicing) and cell morphogenesis/migration. This combination points to a cluster defined by MAPK-driven signaling that influences gene expression and cell behavior, hence the proposed label. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0033120","count":2}]},{"hash":"1117136064462524218","title":"Neuronal development and synaptic signaling","description":"The dominant GO terms cluster around nervous system development, dendrite morphogenesis, axon extension, and excitatory postsynaptic potentials, pointing to roles in neuron differentiation and synaptic maturation; ERK and Wnt pathway regulation also support neural signaling. A few terms (mitotic cell cycle, T cell receptor signaling) may reflect annotation noise or shared modules but do not override the neural theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0050852","count":5},{"id":"GO:0070374","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0007399","count":5}]},{"hash":"2085216539478142740","title":"Ribosome Biogenesis and RNA Processing","description":"The dominant GO terms are rRNA processing and 90S preribosome assembly, pointing to ribosome biogenesis in the nucleolus. Complementary terms about RNA-templated transcription and RNA Pol II\u2013driven transcription initiation suggest broader nuclear RNA metabolism and transcription regulation. A few outlier terms (photosynthesis, pancreatic cell apoptosis regulation) likely reflect annotation noise rather than core cluster function.","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0001172","count":2},{"id":"GO:0097394","count":2},{"id":"GO:0006367","count":2}]},{"hash":"653699841495013686","title":"Mitochondrial Metabolite Transporters","description":"Most of the top GO terms point to transmembrane transport of metabolites and ions into mitochondria (phosphate, CoA, thiamine pyrophosphate, pyrimidine nucleotides, manganese) and related energy metabolism processes (adaptive thermogenesis, response to fatty acids, glucose signaling). While some terms touch on broader cellular processes like cell division and amino acid starvation, the strongest theme is mitochondrial metabolite/ion import, suggesting a cluster of mitochondrial transporter proteins.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0034198","count":2},{"id":"GO:1990845","count":2},{"id":"GO:0061179","count":2}]},{"hash":"1728954733848727538","title":"mRNA Splicing and Post-Transcriptional Regulation","description":"The proteins map to spliceosome activity, mRNA polyadenylation regulation, mRNA modification, and stress-related mRNA stability, with links to ncRNA-mediated silencing and translation reinitiation, indicating a focus on RNA processing and post-transcriptional control.","confidence":"High","size":10,"edges":39,"triangles":80,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0006376","count":4},{"id":"GO:1900363","count":4},{"id":"GO:0060211","count":4}]},{"hash":"1177550118721600384","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":16,"triangles":10,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0034476","count":4},{"id":"GO:1990417","count":4},{"id":"GO:0009432","count":4}]},{"hash":"84764268861821457","title":"Amino Acid Biosynthesis & Metabolism","description":"The dominant GO terms are biosynthetic processes for several amino acids (tryptophan, arginine, citrulline, glutamine) and related precursors (carbamoyl phosphate), indicating the cluster centers on amino acid production and metabolism. Some additional terms about responses to stimuli (dexamethasone, ethanol, food) may reflect regulatory contexts rather than core function, but the amino acid biosynthesis theme is clear.","confidence":"High","size":10,"edges":22,"triangles":17,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000162","count":2},{"id":"GO:0006526","count":2},{"id":"GO:0071548","count":2},{"id":"GO:0019240","count":2},{"id":"GO:0071320","count":2}]},{"hash":"1343395541525027361","title":"Transcription and Translation Machinery with Ribosome Biogenesis","description":"The top GO terms cluster around core gene expression processes: transcription (DNA-templated transcription, transcription termination, negative regulation of transcription by RNA Pol II) and translation (translation, translational elongation, negative regulation of translation) plus ribosome assembly. The co-occurrence of these core expression processes, with some stress-response regulation, supports a theme of transcription-translation coordination and ribosome biogenesis, justifying the chosen name.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006351","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0006414","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1604382882985519301","title":"Mitochondrial metabolism and translation","description":"The cluster is enriched for mitochondrial fatty acid catabolism, TCA cycle, and mitochondrial translation (glutaminyl-tRNAGln biosynthesis via transamidation), pointing to core mitochondrial energy production and protein synthesis. ER organization and nutrient/hypoxia response terms suggest broader metabolic coordination, though a single nylon catabolic term may be noise. Overall, the cluster aligns with mitochondrial metabolism and translation.","confidence":"Medium","size":10,"edges":15,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009062","count":5},{"id":"GO:0032543","count":5},{"id":"GO:0070681","count":5},{"id":"GO:0019876","count":5},{"id":"GO:0007029","count":5}]},{"hash":"2059184047627819315","title":"Peptidoglycan synthesis and cell division","description":"This cluster is enriched for peptidoglycan biosynthesis/turnover and cell wall organization, together with cell division and cell-cycle terms. The dominant theme is bacterial cell envelope synthesis and division, with a few redox/metabolic notes likely reflecting broader growth context.","confidence":"High","size":10,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009254","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0071555","count":1}]},{"hash":"431784437139041125","title":"Protein quality control and turnover","description":"The cluster includes terms tied to protein handling and degradation: mitochondrial protein import (intermembrane space and matrix), protein processing, proteasome regulatory particle assembly, and late endosomal microautophagy, along with oxidation-dependent protein catabolic processes. While a few terms relate to broader cellular processes (cell division, dense core vesicle transport, nonfunctional rRNA decay, carbohydrate phosphorylation), the dominant theme is proteostasis and turnover across organelles, justifying a label focused on protein quality control and turnover.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:1990048","count":1},{"id":"GO:0070407","count":1},{"id":"GO:0070651","count":1},{"id":"GO:0051301","count":1}]},{"hash":"1344807312253783173","title":"DNA-Templated Transcription","description":"The top GO term across the cluster is DNA-templated transcription (GO:0006351) with 3 occurrences, suggesting these proteins are linked to transcription-related functions. The other terms are a mix of transcription-related and unrelated or obsolete annotations, and there are no reported edges, indicating a dispersed set of proteins rather than a single cohesive complex. Given the transcription signal amid heterogeneity, this label captures the most coherent shared theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070207","count":3},{"id":"GO:0043497","count":3},{"id":"GO:1900427","count":3},{"id":"GO:0060136","count":3}]},{"hash":"1489577398373609000","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":8},{"id":"GO:0034476","count":7},{"id":"GO:1990417","count":7},{"id":"GO:0009432","count":7},{"id":"GO:0042273","count":7}]},{"hash":"1152003521787690964","title":"Embryonic Development and Hormone Signaling","description":"The cluster centers on embryonic development processes (head involution, heart development, hemocyte development) and is linked to signaling pathways (Hippo). It also includes responses to steroid hormones (estradiol, glucocorticoid) and oxidative stress (hydrogen peroxide), plus protein processing, suggesting a coordinated role in development with hormonal and stress-response regulation.","confidence":"Medium","size":10,"edges":32,"triangles":43,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":3},{"id":"GO:0042542","count":3},{"id":"GO:0030220","count":3},{"id":"GO:0007516","count":2},{"id":"GO:0035329","count":2}]},{"hash":"1322415876558294524","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":2},{"id":"GO:0010719","count":2},{"id":"GO:0033317","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0019482","count":1}]},{"hash":"1222365776649886418","title":"Unknown","description":"The top GO terms span several unrelated biological areas (plant hormone signaling, transcription, hypoxia sensing, chlorophyll turnover, light detection, protein autophosphorylation, placental development, immune regulation, and metabolism) with no single prevailing theme tying most proteins together. This dispersion suggests no coherent functional cluster beyond general, heterogeneous annotations.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0006351","count":3},{"id":"GO:0070483","count":3},{"id":"GO:1903660","count":3},{"id":"GO:0010271","count":3}]},{"hash":"955288809449344017","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":33,"triangles":51,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000462","count":3}]},{"hash":"408016034625749620","title":"Unknown","description":"Top terms span neuron development, metabolism, differentiation across skin and germ cells, and nucleotide biosynthesis, with no single unifying function. No network connectivity to tie them together, so a confident, representative label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0071398","count":2},{"id":"GO:0046777","count":2},{"id":"GO:0030819","count":2}]},{"hash":"1377404210751459253","title":"Mitotic Chromosome Assembly and Segregation","description":"These terms point to cell division, especially mitosis, chromatin assembly at centromeres (CENP-A), and microtubule-related processes, consistent with a cluster of proteins involved in chromosome segregation during mitosis. Ancillary terms like ER-Golgi transport and transcription may reflect broader roles or annotation noise but do not override the dominant mitotic/chromatin signal.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0061087","count":4},{"id":"GO:0033314","count":3},{"id":"GO:0051260","count":3}]},{"hash":"727340668544307527","title":"Developmental Gene Regulation and Morphogenesis","description":"The top GO terms cluster around developmental processes and transcriptional control, including multicellular organism development, left/right pattern formation, roof of mouth development, EMT in endocardial cushion formation, trophoblast giant cell differentiation, and neuron maturation, along with DNA-templated transcription regulation. Although ubiquinone and abscisic acid biosynthesis are less obviously connected, the dominant theme is development coupled with gene regulation, suggesting this cluster reflects developmental gene expression programs. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0009688","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0042551","count":2},{"id":"GO:0006351","count":2}]},{"hash":"23240825723158584","title":"Transcription and ribosome biogenesis with proliferation signaling","description":"This cluster centers on DNA-templated transcription and maturation of rRNA (ribosome biogenesis), complemented by mRNA transport and signals for cell proliferation and cytoskeletal remodeling. The presence of transcription and rRNA maturation terms suggests a gene-expression/ribosome-assembly module, while cell growth and actin-nucleation terms hint at coordinated cytoskeletal dynamics during proliferation. Confidence: Medium","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1496135105901945197","title":"Ubiquitin-mediated immune signaling and cell cycle control","description":"The terms cluster around ubiquitination processes (autoubiquitination; K63- and K11-linked ubiquitination; ubiquitin-dependent ERAD) and connect to both innate immunity (innate immune response, defense against virus, response to chitin) and cell cycle regulation (cell division, mitotic cell cycle), suggesting a theme of ubiquitin-driven control of immune defense and cell-cycle progression. Confidence: High","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0010200","count":2},{"id":"GO:0009938","count":2}]},{"hash":"642820040975503647","title":"mRNA Splicing and Polyadenylation Regulation","description":"The cluster is enriched for splicing-related terms (mRNA splicing via spliceosome, splice site recognition) and polyadenylation regulation (poly(A) tail shortening, regulation of mRNA polyadenylation), along with transcription termination by RNA Pol II. This points to a cohesive post-transcriptional RNA processing module with regulatory control over mRNA maturation, supported by translation reinitiation and ncRNA-mediated gene silencing terms.","confidence":"High","size":10,"edges":35,"triangles":55,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0045292","count":4},{"id":"GO:0006378","count":4}]},{"hash":"1483451327588393792","title":"Translation Initiation and Ubiquitin-Proteasome Regulation","description":"This cluster centers on translation initiation and the ubiquitin-proteasome system. GO terms include formation of translation preinitiation complexes and translation itself, alongside autoubiquitination, K63-linked ubiquitination, and SCF-dependent proteasomal degradation, suggesting tight coupling of protein synthesis and targeted protein turnover. Some terms also point to stress signaling (NF-kappaB) and cell proliferation, likely reflecting regulatory connections to proteostasis.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0001732","count":2},{"id":"GO:0000715","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070534","count":2}]},{"hash":"1702138370296042880","title":"Ribosome biogenesis and cell growth","description":"The top GO terms are ribosome biogenesis and ribosomal large subunit biogenesis (4 hits each), which together point to assembly of the protein-synthesis machinery; additional terms related to cell division and proliferation support a link to cellular growth processes.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0032933","count":3},{"id":"GO:1902525","count":3}]},{"hash":"1263794272883906595","title":"Plant Hormone Signaling and Seed Cuticle Development","description":"Top GO terms are dominated by plant hormone signaling (abscisic acid-activated and ethylene-activated pathways), seed development, and regulation of wax and cutin biosynthesis, with supporting terms for transcription regulation and defense response. This points to a cohesive cluster centered on plant hormonal control of seed and cuticle-related developmental processes and associated defense mechanisms.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009738","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009873","count":3},{"id":"GO:0010200","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1245615762526519578","title":"Proteostasis and Stress Signaling","description":"This cluster centers on proteostasis-related processes: negative regulation of proteasomal ubiquitin-dependent protein catabolic process, misfolded protein transport, post-translational targeting to membranes, and protein autophosphorylation, pointing to regulation of protein quality control and kinase signaling under stress. Additional hints like cellular response to ATP and detection of hypoxia suggest energy and oxygen-responsive regulation linked to these proteostasis pathways. Some terms (otolith tethering, protein-tetrapyrrole linkage) are less clearly connected, but the dominant theme remains proteostasis and stress signaling.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0031204","count":2},{"id":"GO:0070483","count":1},{"id":"GO:1903660","count":1}]},{"hash":"77198377085940957","title":"Diverse solute transmembrane transporters","description":"The top GO terms are all transmembrane transport processes for a wide range of substrates (phosphate, vitamins, sugars, nitrate, sialic acid, potassium, xenobiotics), suggesting a cluster of membrane transporter proteins with broad substrate specificity rather than a single substrate pathway.","confidence":"High","size":10,"edges":28,"triangles":33,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0015751","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0042891","count":3}]},{"hash":"104861191142607192","title":"Plant Cell Wall Biogenesis and Pollen Germination","description":"This cluster is dominated by GO terms related to plant cell wall biosynthesis and organization (primary and secondary cell wall biogenesis, cell wall organization, and cell plate assembly), plus polysaccharide metabolism (rhamnogalacturonan I side chains). The inclusion of pollen germination points to a plant-reproductive context that often hinges on cell wall remodeling. Overall, the common theme appears to be plant cell wall construction and related processes, with pollen-related aspects reflecting functional specialization.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010400","count":2},{"id":"GO:0042248","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0009833","count":2},{"id":"GO:0000919","count":2}]},{"hash":"1059749819829493742","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045071","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0042535","count":3},{"id":"GO:0070935","count":3},{"id":"GO:0071222","count":3}]},{"hash":"205651865500690177","title":"Virus Particle Assembly and RIG-I Suppression","description":"The top GO terms are dominated by viral processes: viral capsid/virion assembly and viral release, indicating particle formation and egress. Coupled with negative regulation of the RIG-I signaling pathway, this points to viral strategies to assemble particles while dampening host innate immunity. Some other terms (cell cycle, mitochondrial protein import) are less prominent and may reflect secondary host interactions, but the strongest signal centers on virus assembly and immune evasion.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039536","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0060548","count":2},{"id":"GO:0019069","count":1},{"id":"GO:0051085","count":1}]},{"hash":"1336654866572662622","title":"Neural development and cell cycle regulation","description":"Most of the top GO terms cluster around neural development (forebrain development, neural tube closure) and general developmental processes (multicellular organism development). Additional terms point to cell cycle control (mitotic cell cycle) and transcriptional regulation (DNA-templated transcription), suggesting a cohesive theme of development-associated proliferation and differentiation. A few items reference stress or immune responses (ER stress\u2013related apoptosis, cadmium response, defense against Gram-positive bacteria), which may reflect ancillary cellular stress pathways but do not dominate the cluster\u2019s theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1984612343995330718","title":"Jasmonate-oxylipin signaling in plant defense and development","description":"The top terms cluster around oxylipin and jasmonic acid biosynthesis, plus responses to ozone and toxic substances, and stamen development, suggesting a lipid-signaling module that coordinates stress defense with developmental processes in plants. Some peripheral terms are present, but the dominant theme is jasmonate/oxylipin\u2013mediated signaling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":2},{"id":"GO:0033543","count":2},{"id":"GO:0031408","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0048443","count":2}]},{"hash":"1929876777706288180","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000447","count":3}]},{"hash":"1905668273450228885","title":"Transcription and mitotic cell-cycle regulation","description":"The proteins are enriched for DNA-templated transcription, mitotic cell cycle, and cytokinesis-related processes, along with TORC1 signaling, ribosome biogenesis, and mRNA transport. This pattern points to coordination between gene expression, protein synthesis machinery, and cell-division controls, rather than a single specialized function. Forebrain development is present but likely not central to the cluster\u2019s core theme. Overall, the label reflects a theme of nuclear gene expression coupled to growth and division.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0032466","count":3}]},{"hash":"823180010748347017","title":"Unknown","description":"The GO terms are highly diverse (insulin signaling, foam cell and thrombocyte differentiation, histone acetylation, chromatin remodeling, multiple developmental processes) with no clear shared function. There are no edges or coherent theme tying the terms together, so a specific representative label cannot be assigned. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":1},{"id":"GO:0010742","count":1},{"id":"GO:0002574","count":1},{"id":"GO:0018076","count":1},{"id":"GO:0045815","count":1}]},{"hash":"841402647795998381","title":"Membrane Transport and Vesicle Trafficking","description":"The top GO terms cluster around transmembrane transport of small molecules (thiamine, cytosine, uracil, amino acids) and vesicle-related processes (COPII vesicle coating) with autophagy also involving vesicles, suggesting a cohesive theme of membrane transport and vesicle trafficking, despite a few outlier terms like pigmentation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015888","count":1},{"id":"GO:0006209","count":1},{"id":"GO:0015856","count":1},{"id":"GO:1903088","count":1},{"id":"GO:1903791","count":1}]},{"hash":"2057304771065925153","title":"DNA Replication and Mitosis","description":"The top GO terms are dominated by DNA replication and cell cycle processes (DNA replication, cell cycle, mitotic sister chromatid separation, and mitotic DNA replication initiation), indicating proteins in this cluster participate in S-phase and mitosis. Some adjacent terms involve DNA repair during replication, supporting a replication-associated network; a few unrelated terms appear as annotation noise. Overall, the cluster centers on nuclear DNA replication and mitotic progression.","confidence":"High","size":9,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0051306","count":4},{"id":"GO:1990048","count":3},{"id":"GO:0000727","count":3}]},{"hash":"1540228231936897674","title":"Immune-vascular signaling and muscle regeneration","description":"Based on the top GO terms, the proteins appear involved in blood vessel formation (angiogenesis), immune signaling (T cell receptor signaling, defense against Gram-positive bacteria), and tissue remodeling (myoblast differentiation for muscle regeneration). The presence of glucose stimulus response and melanocyte migration suggests broader metabolic and migratory activation common in wound healing and inflammation. Taken together, the cluster likely represents coordinated immune-vascular signaling linked to tissue regeneration, not a single narrow function.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0045766","count":9},{"id":"GO:0071333","count":9},{"id":"GO:0014068","count":9},{"id":"GO:0050830","count":9},{"id":"GO:0050852","count":8}]},{"hash":"411376821246475091","title":"Sterol and lipid biosynthesis with metabolic stress","description":"The strongest signals are cholesterol and ergosterol biosynthesis, plus fatty acid oxidation, indicating a lipid/metabolic core. Additional terms point to broader stress and signaling responses (to toxic substances, hormones, and immune signaling), suggesting a lipid-centric metabolic cluster with ancillary signaling roles.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0006695","count":3},{"id":"GO:0071372","count":3}]},{"hash":"1457043857472063987","title":"Metal and xenobiotic transporters","description":"The top GO terms are dominated by transport activities, especially metal ion transport (molybdate, cobalt, chloride) and xenobiotic-associated transport (xenobiotic, daunorubicin, bacteriocin). While a couple of terms refer to stress response or respiration, the prevailing signal is membrane transport of metal ions and xenobiotics, suggesting a cohesive transporter-focused cluster.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015689","count":2},{"id":"GO:1902476","count":1},{"id":"GO:0006824","count":1},{"id":"GO:0009432","count":1},{"id":"GO:0043215","count":1}]},{"hash":"986520750886441140","title":"Developmental cell proliferation and morphogenesis","description":"This cluster centers on developmental processes (embryonic cranial skeleton morphogenesis) and cell-cycle-related activities (DNA replication, centrosome cycle, microtubule localization) with supporting roles in cell migration and signaling regulation (Wnt pathway). While innate immune response appears among terms, the stronger signal is toward development and cell-cycle/migration control, justifying the label. ","confidence":"Medium","size":9,"edges":15,"triangles":9,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043065","count":8},{"id":"GO:0016477","count":8},{"id":"GO:0090090","count":8},{"id":"GO:0008285","count":8},{"id":"GO:0007098","count":7}]},{"hash":"1483428796023542290","title":"Ion Transport and Salt Stress Response","description":"The top GO terms cluster around ion transport across membranes (sodium and potassium import/export), vacuolar acidification, and cell volume homeostasis, all tied to salt/osmotic stress responses. Additional terms point to stress signaling pathways (e.g., methylglyoxal response) and membrane-associated regulation, supporting a cohesive theme of maintaining ion balance and osmotic stability under stress. Some outliers (e.g., signaling pathways not directly tied to transport) exist, but the dominant pattern is clear.","confidence":"High","size":9,"edges":29,"triangles":48,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0009651","count":3},{"id":"GO:0006884","count":3},{"id":"GO:0007035","count":3},{"id":"GO:1903281","count":3},{"id":"GO:0031547","count":3}]},{"hash":"205686677460041896","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0070935","count":2},{"id":"GO:0033129","count":2}]},{"hash":"240308650143037147","title":"Negative regulation of MAPK and T cell signaling","description":"This cluster is dominated by GO terms that describe negative regulation of kinase signaling, notably the ERK/MAPK cascade and T cell receptor signaling, as well as processes involving tyrosine dephosphorylation. The presence of terms like peptidyl-tyrosine dephosphorylation and inactivation of protein kinase activity supports a phosphatase-mediated dampening of signaling. Some developmental terms appear, but the core theme points to suppression of phosphorylation-driven signaling pathways.","confidence":"Medium","size":9,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070373","count":5},{"id":"GO:0050860","count":5},{"id":"GO:0000200","count":5},{"id":"GO:0008286","count":4},{"id":"GO:0050852","count":4}]},{"hash":"1322766797962522718","title":"Unknown","description":"These nine proteins appear associated with a broad, heterogeneous set of GO terms, spanning signaling (cellular response to cAMP), transcription and translation, metabolism (galactose, mercury detoxification, pinoresinol catabolism), and various development processes (neural projection development and cerebral cortex development). The terms do not point to a single cohesive function or pathway, so a specific, representative cluster label cannot be confidently assigned.","confidence":"","size":9,"edges":11,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":2},{"id":"GO:0045648","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006012","count":1},{"id":"GO:0006351","count":1}]},{"hash":"697724280595515479","title":"Chloroplast pigment and quinone biosynthesis","description":"The cluster is dominated by GO terms for chlorophyll biosynthesis and various quinone biosynthetic processes (phylloquinone, plastoquinone, menaquinone, ubiquinone), all essential to chloroplast function and photosynthesis. This cohesive theme suggests proteins participate in pigment and quinone biosynthesis within plastids, with minor amino acid biosynthesis terms likely incidental. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0048034","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0010236","count":2}]},{"hash":"1929806198343360308","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006189","count":2},{"id":"GO:0006015","count":1},{"id":"GO:0046651","count":1},{"id":"GO:0046101","count":1}]},{"hash":"18935075155614221","title":"RNA Processing and Translation Initiation","description":"The top GO terms point to RNA maturation and regulation of translation: splicing via the spliceosome and small-subunit processome assembly, mRNA polyadenylation and tail regulation, mRNA modification, and translation initiation/reinitiation, with some stress-related mRNA stability regulation. These collectively suggest a cluster centered on RNA processing and the initiation of translation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0006376","count":6},{"id":"GO:1900363","count":5},{"id":"GO:0060211","count":5}]},{"hash":"1325686133146459164","title":"Mitochondrial Electron Transport and Apoptosis","description":"The cluster is dominated by GO terms tied to mitochondrial respiration (ubiquinol-to-cytochrome c and cytochrome c-to-oxygen steps) and cytochrome c\u2013related apoptosis signaling, along with oxidative stress regulation (hydrogen peroxide metabolism and negative regulation of H2O2 biosynthesis) and cytochrome c\u2013heme chemistry. These collectively point to proteins involved in mitochondrial energy production and programmed cell death, with related post-translational regulation; some terms like photosynthesis appear as peripheral stress-related associations. ","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006122","count":9},{"id":"GO:0015979","count":5},{"id":"GO:0042743","count":5},{"id":"GO:0006123","count":5},{"id":"GO:0006915","count":5}]},{"hash":"1368421720664949764","title":"Unknown","description":"The top terms span chromatin modification, RNA processing (snoRNP assembly), cell division, and immune/dsRNA responses, including obsolete GO terms, with no edges connecting proteins. There isn\u2019t a clear, single theme tying these functions together, so a specific, confident label isn\u2019t supported.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0016576","count":6},{"id":"GO:0000492","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0051291","count":6},{"id":"GO:1903071","count":6}]},{"hash":"648319915896266766","title":"Proteostasis and misfolded protein handling","description":"This cluster centers on protein quality control and turnover, with terms for misfolded-protein response, proteasome assembly, autophagic degradation, mitochondrial import related to protein processing, and inclusion-body formation, all pointing to cellular proteostasis.","confidence":"High","size":9,"edges":8,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0070407","count":4},{"id":"GO:0070651","count":4},{"id":"GO:0061738","count":4},{"id":"GO:0016485","count":4}]},{"hash":"1910616474623786366","title":"Mitotic spindle assembly and microtubule dynamics","description":"The top GO terms cluster around microtubule-based processes: spindle elongation, kinetochore attachment, spindle assembly, microtubule polarity, and nuclear migration along microtubules, all pointing to mitotic spindle function and microtubule organization. A couple terms about transcription and neuron projection maintenance are less central but may reflect broader cytoskeletal roles; overall, the core theme is microtubule dynamics during cell division.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1990535","count":2},{"id":"GO:0001560","count":2},{"id":"GO:0072092","count":2},{"id":"GO:0031534","count":2}]},{"hash":"621242283293151195","title":"DNA replication and cofactor biosynthesis","description":"The Top GO terms show a mix of nucleic acid metabolism (DNA replication, viral genome replication, RNA polymerase I transcription termination, DNA recombination) and biosynthesis of cofactors and related components (ADP-L-glycero-heptose, CoA, FAD, FMN, teichoic acid). This points to broad biosynthetic/metabolic functions rather than a single, cohesive protein complex, though nucleic-acid related and cofactor biosynthesis processes are the strongest signals. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0006363","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0097171","count":2}]},{"hash":"2001346853450108954","title":"Unknown","description":"The GO terms span a wide range of unrelated processes (antibiotic response, cytoplasmic translation, various metabolic pathways, transcription regulation, development, and pollen-related biosynthesis), with no clear unifying function across the cluster. This suggests the annotations reflect mixed or cross-species signals rather than a cohesive protein module.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0006012","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0001081","count":1}]},{"hash":"738622521166551861","title":"Redox-Regulated Signaling","description":"The cluster is dominated by GO terms for cellular oxidant detoxification and redox homeostasis, with additional signals related to nitric oxide storage and general toxic substance response. The presence of terms involving estradiol response, calcium-release\u2013driven muscle contraction, ERK/MAPK cascade regulation, leukocyte proliferation, and germ cell proliferation suggests a network that maintains redox balance while modulating diverse signaling pathways across tissues.","confidence":"Medium","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":6},{"id":"GO:0045454","count":6},{"id":"GO:2000255","count":5},{"id":"GO:0035732","count":4},{"id":"GO:1902476","count":4}]},{"hash":"898617880970544404","title":"DNA replication and mitotic cell cycle","description":"This cluster is dominated by GO terms for DNA replication, DNA-templated transcription, DNA repair, and mitotic cell cycle processes (including spindle assembly checkpoint). These strongly suggest a group of proteins involved in genome maintenance and cell division, with a few outlier terms likely due to annotation breadth. ","confidence":"High","size":9,"edges":23,"triangles":25,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0006281","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0050852","count":7}]},{"hash":"1656664367430701572","title":"Plant cell wall biosynthesis and organization","description":"The top GO terms cluster around plant cell wall construction and remodeling\u2014cellulose biosynthesis, RG I side chain metabolism, primary and secondary cell wall biogenesis, and cell wall organization, with related carbohydrate metabolism and pollen germination\u2014indicating a cohesive theme of wall biosynthesis in plants. A couple of outliers (DNA-templated transcription, animal organ regeneration) are peripheral and do not alter the main interpretation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010400","count":3},{"id":"GO:0000919","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0009833","count":3}]},{"hash":"987508774767793915","title":"Nitrogen metabolism and fixation regulation","description":"The top GO terms are dominated by nitrogen-related processes: cellular response to nitrogen starvation, nitrogen fixation, and nitrogen catabolite repression of transcription, indicating a cohesive theme around nitrogen status sensing and metabolic regulation in microbes. Some other terms appear unrelated (e.g., synaptic transmission, insulin secretion) and may be annotation noise, but the core pattern points to nitrogen metabolism and regulatory responses. ","confidence":"Medium","size":9,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0006995","count":4},{"id":"GO:0051968","count":4},{"id":"GO:0010756","count":4},{"id":"GO:0006542","count":4}]},{"hash":"139466472167235184","title":"Ubiquitin-Proteasome Regulation of Development and Cell Cycle","description":"This cluster is dominated by ubiquitin-dependent proteolysis terms (including SCF-dependent proteasomal ubiquitinylation) and cell cycle terms (mitotic and meiotic), with supporting developmental (nervous system development, cell differentiation) and antiviral defense terms. The unifying theme is proteasome-mediated protein turnover governed by ubiquitination, coordinating cell cycle progression and developmental processes, with links to innate immune responses.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0031146","count":5},{"id":"GO:0007399","count":4},{"id":"GO:0030154","count":4},{"id":"GO:0045087","count":4}]},{"hash":"492468616787405017","title":"Neuronal development and Golgi organization","description":"This cluster is dominated by neural-development terms (cerebral cortex development, neuron migration, substantia nigra development) and Golgi apparatus processes (Golgi reassembly, establishment of Golgi localization), with additional hints of protein complex formation (protein heterooligomerization). Together, they point to proteins involved in neuronal development that coordinate Golgi structure and trafficking, despite a few non-neural terms that are less central to the cluster\u2019s primary signal.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":8},{"id":"GO:0021987","count":7},{"id":"GO:0090168","count":7},{"id":"GO:0001764","count":7},{"id":"GO:0010482","count":7}]},{"hash":"1361955748047909133","title":"Mitochondrial protein import","description":"Proteins in this cluster show enrichment for GO terms tied to importing proteins into mitochondrial compartments (inner membrane and matrix) and mitochondrial genome maintenance, with additional links to energy metabolism and nutrient-response processes. The strongest signals are mitochondrial import terms, suggesting a core theme around mitochondrial protein trafficking and its regulation, with some cross-talk to energy balance pathways that can reflect the broader metabolic context. The presence of a chloroplast stroma import term may reflect dual-targeting annotations or broader organelle import capabilities, but the predominant pattern supports mitochondrial import machinery as the cluster\u2019s central function.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":3},{"id":"GO:0045039","count":2},{"id":"GO:0045037","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0032094","count":2}]},{"hash":"72728572684079590","title":"Photoreceptor cilium and outer segment localization","description":"The cluster shows strong enrichment for GO terms related to photoreceptor outer segment localization and non-motile cilium assembly, pointing to photoreceptor-specific ciliary trafficking and structure. Other terms are more miscellaneous, but the core theme centers on ciliary localization in photoreceptors.","confidence":"Medium","size":9,"edges":10,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903546","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0090526","count":4},{"id":"GO:1905515","count":4},{"id":"GO:0009938","count":4}]},{"hash":"988624948905669665","title":"Meiosis and oocyte maturation regulation","description":"The cluster is dominated by meiotic processes in female gametogenesis (meiotic cell cycle regulation, spindle elongation, female meiotic nuclear division, oocyte maturation) and general cell division, with supporting terms on nuclear transport and transcription regulation that may accompany meiotic programs.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0006275","count":3},{"id":"GO:0051306","count":3},{"id":"GO:0051232","count":3}]},{"hash":"1241116813941842335","title":"Membrane Protein Targeting and Folding Quality Control","description":"Proteins in this group cluster around SRP-dependent cotranslational and post-translational targeting to membranes, along with unfolded protein response and chaperone-assisted refolding, suggesting a shared role in membrane protein biogenesis and proteostasis. While other terms like iron-sulfur cluster assembly and DNA replication appear, the dominant theme is targeting nascent polypeptides to membranes and maintaining proper protein folding.","confidence":"Medium","size":9,"edges":10,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0006616","count":3},{"id":"GO:0016226","count":3},{"id":"GO:0090084","count":3}]},{"hash":"189097418438934703","title":"Proteostasis and stress response regulators","description":"The GO terms center on proteostasis and stress signaling, with unfolded protein response, ubiquitin-dependent ERAD, and redox homeostasis pointing to protein quality control, plus negative regulation of kinase activity and heat-response pathways suggesting broader signaling modulation. A few terms tied to gene expression (nuclear export regulation, translational frameshifting) appear secondary, and DNA replication/iron-sulfur cluster maturation may reflect multifunctional proteins or annotation noise. Overall, the cluster seems to group regulators of proteostasis and cellular stress responses.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:1901621","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1480306292368115248","title":"Mitochondrial dynamics and endocytosis","description":"The cluster centers on mitochondrial processes (regulation of cytochrome c release, mitochondrial membrane fission, intracellular distribution) with some links to mitochondrial genome maintenance, paired with endocytic activities (pinocytosis, receptor internalization) and an innate immune signal (response to type I interferon). This suggests a functional module where mitochondrial signaling interfaces with membrane trafficking and antiviral responses.","confidence":"Medium","size":9,"edges":14,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090199","count":2},{"id":"GO:0070584","count":2},{"id":"GO:0034340","count":2},{"id":"GO:0006907","count":2},{"id":"GO:0048312","count":2}]},{"hash":"462134466928456884","title":"Unknown","description":"The Top Terms include both plant-specific developmental processes (petal development, organ boundary specification in meristem) and a range of general cellular and immune processes (centrosome cycle, mRNA processing, apoptosis, autophagy regulation, immune tolerance, histone modification). There is no single coherent biological function tying these terms together, suggesting a heterogeneous cluster or annotation noise.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048441","count":3},{"id":"GO:0010199","count":3},{"id":"GO:0007098","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1351570651348387677","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098721","count":2},{"id":"GO:1903825","count":2},{"id":"GO:0015747","count":2},{"id":"GO:0042906","count":2},{"id":"GO:0098710","count":2}]},{"hash":"1133806675346015399","title":"Nucleotide metabolism and NAD biosynthesis","description":"The proteins cluster around nucleotide metabolic processes (nucleotide metabolic process, inosine salvage) and NAD-related biosynthesis (nicotinamide riboside and nicotinic acid riboside biosynthesis). This suggests a shared role in nucleotide turnover and NAD precursor production. The presence of a cytoplasmic translation term hints at general protein synthesis activity in the same set, while some tissue- or condition-specific terms (T cell differentiation, salivary gland development, estradiol response) may reflect broader pleiotropy or context-specific expression rather than a single cohesive function. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0046632","count":3},{"id":"GO:0071590","count":3},{"id":"GO:0006190","count":3},{"id":"GO:0009117","count":3}]},{"hash":"2187933617101433314","title":"Ribosome biogenesis and translation; cell cycle","description":"This cluster is dominated by GO terms for ribosome biogenesis, cytoplasmic translation, tRNA modification, and nuclear export of the ribosomal large subunit, with accompanying cell division and cell cycle terms. The shared theme across these functions points to a module coordinating ribosome assembly and protein synthesis with progression through the cell cycle or division, making this label representative of the cluster\u2019s biology.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0006400","count":4},{"id":"GO:1903833","count":3},{"id":"GO:0042254","count":3}]},{"hash":"512889176898589367","title":"Unknown","description":"The top GO terms span hormonal and environmental stress responses (estradiol, UV-A, gamma radiation, hydrogen peroxide), intracellular transport regulation and axonal transport, plus several unrelated processes (lens morphogenesis, muscle contraction, amyloid fibril regulation, aging), with no single cohesive function uniting all terms. Therefore there isn\u2019t a clear, representative label for this cluster.","confidence":"","size":9,"edges":29,"triangles":46,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":5},{"id":"GO:0032387","count":5},{"id":"GO:0070141","count":5},{"id":"GO:0071480","count":5},{"id":"GO:1905907","count":5}]},{"hash":"914141426048289440","title":"Placental development and proteostasis","description":"The GO terms point to placenta-related developmental programs (spongiotrophoblast and labyrinthine layer development, multicellular organism development) alongside proteostasis regulation (SCF-dependent ubiquitin-proteasomal degradation and protein deneddylation) and cell-cycle-related processes (endoreduplication, kinetochore assembly). This combination suggests a cluster of proteins involved in placental development with coordinated protein turnover and cell-cycle control. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0070294","count":2},{"id":"GO:0032875","count":1},{"id":"GO:0060712","count":1}]},{"hash":"2276482365769329233","title":"Ubiquitin-Mediated Protein Degradation & NF-kappaB Signaling","description":"Dominant GO terms center on ubiquitin-dependent protein catabolic processes (autoubiquitination, K6-linked ubiquitination) and related histone turnover, suggesting a core role in tagging proteins for degradation. Coherent signaling terms such as activation of NF-kappaB-inducing kinase and positive regulation of TNF-mediated signaling indicate regulation of apoptosis and cell survival through ubiquitin pathways. While a couple terms touch on chromatin or immune recombination, the strongest and most representative theme is ubiquitin-driven proteolysis coupled with NF-kappaB signaling.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0036205","count":6},{"id":"GO:0085020","count":6},{"id":"GO:1903265","count":6}]},{"hash":"1996775423053505108","title":"Broad Substrate Transmembrane Transporters","description":"Most of the top GO terms describe transmembrane transport of diverse substrates (phosphate, vitamins, sugars, nitrate, fucose, xenobiotics, etc.), pointing to a family of membrane transporter proteins. The viral replication complex formation term appears only twice and likely does not define the cluster's core function. Thus, the cluster is best labeled as broad substrate transmembrane transporters.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046786","count":2},{"id":"GO:0035435","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0008643","count":1}]},{"hash":"1139453325559391367","title":"Unknown","description":"The GO terms span chromatin assembly, plant stress signaling (abscisic acid pathway, salinity response), lipid/inositol biosynthesis, metabolism, and an immune regulation term, with no clear cohesive functional theme across the cluster. Therefore there isn't a reliable single-label function to assign. ","confidence":"","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0009738","count":1},{"id":"GO:0046854","count":1},{"id":"GO:0006661","count":1},{"id":"GO:0000103","count":1}]},{"hash":"439648535337101758","title":"Ubiquitin-Dependent NF-\u03baB/TNF Regulation","description":"Top GO terms point to ubiquitin-dependent proteolysis and multiple forms of ubiquitination (K63-linked, linear), including autoubiquitination, as well as processes tied to NF-\u03baB signaling and TNF-mediated pathways. The cluster also touches on immune regulation (T cell homeostasis) and stress-related responses (unfolded protein response, histone turnover), suggesting a cohesive theme around ubiquitin-mediated control of inflammatory signaling and related cellular processes.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0043029","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0060546","count":3},{"id":"GO:0097039","count":3}]},{"hash":"2272362493133654022","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0072752","count":1},{"id":"GO:0034414","count":1}]},{"hash":"530825931757250483","title":"Chromatin remodeling and nucleosome dynamics","description":"The top GO terms are dominated by nucleosome assembly/disassembly and histone acetylation regulation, indicating a chromatin-level theme; other terms touch on DNA decondensation and cell division contexts, but the strongest consistent signal is chromatin structure regulation, justifying a chromatin remodeling/nucleosome dynamics label.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000617","count":1},{"id":"GO:0071442","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0007117","count":1}]},{"hash":"1418160755448685763","title":"Chloroplast Light Response and Photoprotection","description":"The cluster is dominated by GO terms related to photosynthesis, light harvesting, and responses to various light wavelengths (red, far-red, UV, high/low light), along with nonphotochemical quenching, indicating a cohesive role in chloroplast light sensing and photoprotection during photosynthesis.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904964","count":1},{"id":"GO:0018298","count":1},{"id":"GO:0009768","count":1},{"id":"GO:0010218","count":1},{"id":"GO:0010114","count":1}]},{"hash":"656139620674395614","title":"Ubiquitin-Dependent NF-\u03baB and Apoptosis Regulators","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes and autoubiquitination, combined with regulation of apoptosis and NF-\u03baB\u2013related signaling (including I-kappaB phosphorylation and TNF-mediated pathways). While a couple of terms are obsolete or less directly connected (e.g., V(D)J recombination), the shared theme is ubiquitin-driven control of protein turnover and immune/survival signaling, especially NF-\u03baB, making this a coherent group of regulators of cell fate and immune response.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0042981","count":5},{"id":"GO:0051865","count":5},{"id":"GO:1903762","count":5},{"id":"GO:0007250","count":5}]},{"hash":"1752520325123860166","title":"Oocyte meiosis and spindle-assembly with ubiquitin regulation","description":"The cluster is dominated by GO terms related to oocyte maturation, spindle assembly in female meiosis I, microtubule polymerization, and ubiquitin-proteasome\u2013dependent protein degradation, all pointing to meiosis-specific cell-cycle control and spindle dynamics in oocytes. Some brain development terms appear, but the core theme remains meiosis/spindle regulation.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":9},{"id":"GO:0021678","count":9},{"id":"GO:0051436","count":9},{"id":"GO:0046785","count":9},{"id":"GO:0007057","count":9}]},{"hash":"103846826307937388","title":"Unknown","description":"The Top GO terms are diverse (muscle/neural development, heart morphogenesis, glycan processing, metabolism, vacuolar processes, fungal cell wall biosynthesis, host symbiosis, and respiration) with no single unifying function, so there is no coherent theme to label. ","confidence":"","size":9,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050884","count":2},{"id":"GO:0006491","count":2},{"id":"GO:0003007","count":2},{"id":"GO:0043181","count":2},{"id":"GO:0000023","count":2}]},{"hash":"1004080009795731854","title":"DNA replication and mitotic chromosome segregation","description":"The GO terms cluster around DNA replication, chromatin assembly during replication, and mitosis-related processes (nuclear membrane reassembly, sister chromatid cohesion and separation), suggesting a coherent theme of cell-cycle progression and chromosome handling. A few terms (viral process, extrinsic apoptotic signaling) may reflect broader or misannotated associations, but the dominant signals point to replication and chromosome segregation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0006335","count":1},{"id":"GO:0070262","count":1},{"id":"GO:0006275","count":1},{"id":"GO:0007084","count":1}]},{"hash":"1627309195199440956","title":"Protein quality control and ribosome biogenesis","description":"The top GO terms cluster around ER-assisted protein folding, autophagy-related processes (ribophagy and autophagosome assembly), protein ubiquitination and endocytosis, and nucleocytoplasmic transport of ribosomal components (ribosomal subunit export, rRNA and tRNA export). Together they point to maintenance of proteome homeostasis and ribosome production/turnover, with a few unrelated signaling terms likely representing noise. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":1},{"id":"GO:0000045","count":1},{"id":"GO:0050847","count":1},{"id":"GO:2000203","count":1},{"id":"GO:0034517","count":1}]},{"hash":"522676274775138332","title":"Unknown","description":"The terms are scattered across membrane transport, organelle organization, nuclear import, signaling, and extracellular processes, with some obsolete annotations, offering no clear common function. Therefore a precise label cannot be assigned; Unknown with None.","confidence":"","size":8,"edges":20,"triangles":22,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0015991","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007007","count":2}]},{"hash":"2113704670547218070","title":"Membrane lipid metabolism and metal ion transport","description":"The cluster's top GO terms span lipid-related processes (lipopolysaccharide biosynthesis, epoxygenase P450 pathway, phospholipid dephosphorylation, L-serine biosynthesis) and metal ion transport (cadmium, zinc, copper transmembrane transport) with calcium homeostasis, suggesting a membrane-associated emphasis on lipid remodeling alongside metal transport and handling. This combination implies a cohesive theme around membrane lipid metabolism coupled with metal ion transport rather than a single narrow function.","confidence":"Medium","size":8,"edges":13,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:0006874","count":4},{"id":"GO:0019373","count":4},{"id":"GO:0046272","count":4},{"id":"GO:0097755","count":4}]},{"hash":"1150713500990335783","title":"Nuclear transcription regulation and apoptosis","description":"The clustering shows a strong emphasis on DNA-templated transcription and its regulation (e.g., DNA-templated transcription and regulation of transcription) together with apoptotic and senescence-related terms, suggesting a theme around nuclear gene expression control and cell fate decisions. While a few terms (cochlea morphogenesis, protein localization to synapse) appear peripheral, the core signals point toward transcriptional control influencing apoptosis and stress responses.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0046827","count":2},{"id":"GO:0090103","count":2},{"id":"GO:0046886","count":2}]},{"hash":"2121859918025955519","title":"Golgi vesicle trafficking","description":"The top GO terms converge on Golgi-related processes: vesicle docking, multivesicular body sorting, and establishment of Golgi localization, plus localization to phagophore assembly sites (autophagy-related). This suggests a cohesive cluster centered on Golgi-associated vesicle trafficking and sorting, with other terms likely reflecting broader vesicle transport or signaling connections. ","confidence":"High","size":8,"edges":12,"triangles":6,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":6},{"id":"GO:0007411","count":6},{"id":"GO:0048211","count":6},{"id":"GO:0071985","count":6},{"id":"GO:0033688","count":6}]},{"hash":"192404986863998056","title":"Neuronal development and synaptic signaling","description":"The cluster is enriched with nervous system development, dendrite morphogenesis, axon extension, and excitatory postsynaptic potential terms, along with regulation of ERK and Wnt signaling and focal adhesion dynamics, all pointing to neural growth and synapse formation/function. A non-neuronal term (T cell receptor signaling) is present but does not override the dominant neuronal theme.","confidence":"High","size":8,"edges":19,"triangles":22,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":7},{"id":"GO:0070374","count":7},{"id":"GO:0090263","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0051893","count":7}]},{"hash":"2130904574448544554","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":4},{"id":"GO:0034476","count":3},{"id":"GO:0071051","count":3},{"id":"GO:0071035","count":3}]},{"hash":"330312594395181669","title":"ER protein folding and oxidative stress response","description":"The strongest shared theme among the top GO terms is protein folding in the endoplasmic reticulum, coupled with oxidative stress response and redox homeostasis, suggesting a cluster centered on ER-associated protein quality control under stress. Some terms (DNA replication/transcription, tRNA aminoacylation, photosystem I electron transport) appear less coherent with this theme and may reflect broad or misannotated associations, but the ER folding and redox-related terms dominate the cluster signal. Therefore, a concise label focusing on ER protein folding and oxidative stress is warranted.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":3},{"id":"GO:0034599","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070389","count":2}]},{"hash":"2138716465346885134","title":"Proteostasis and stress response","description":"The top terms point to protein quality control and turnover: ER unfolded protein response, protein processing, proteasome assembly, endosomal/autophagic pathways, and oxidative stress responses. Although there are hints of other processes (cell division, vesicle transport), the strongest cohesive theme is maintenance of proteome integrity and stress adaptation, i.e., proteostasis.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:1990048","count":3},{"id":"GO:0070651","count":3},{"id":"GO:0061738","count":3},{"id":"GO:0016485","count":3}]},{"hash":"1130693535050685964","title":"Unknown","description":"The top terms show a disparate mix: immune signaling (MyD88/TLR), protein sumoylation, and several unrelated metabolic/catabolic processes (retinoic acid, coumarin, camphor, progesterone), plus other diverse functions, with no clear shared theme linking the proteins. This makes a coherent, specific functional label unlikely.","confidence":"","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034126","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0010193","count":2},{"id":"GO:0034653","count":2},{"id":"GO:0035865","count":2}]},{"hash":"1358637352375270769","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms are centered on translation and ribosome biology, with GO:0006412 (translation) appearing most prominently, along with ribosomal subunit assembly/export and mitochondrial translational initiation. This pattern points to a cluster of proteins involved in the protein synthesis machinery and the assembly/export of ribosomes, spanning both cytosolic and mitochondrial translation. Some less central terms (e.g., RNA-templated transcription) may reflect broader gene-expression processes, but the core signal is clearly translation-related.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0071353","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0070124","count":2},{"id":"GO:0006407","count":2}]},{"hash":"462221977858009737","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006458","count":3},{"id":"GO:1902991","count":2},{"id":"GO:1990000","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0055010","count":2}]},{"hash":"2173758975399610832","title":"Insulin-responsive energy metabolism","description":"The GO terms show core energy pathways (glycolytic process and TCA cycle) and a cellular response to insulin stimulus, pointing to metabolism regulation in response to insulin. While some terms cover broader metabolic processes (lipid biosynthesis and various amino acid catabolisms), the shared theme is central metabolism tied to insulin signaling, justifying a label focused on energy metabolism and regulation.","confidence":"Medium","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":3},{"id":"GO:0033512","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0006351","count":2}]},{"hash":"570492147172544614","title":"Mitochondrial protein import and inner membrane insertion","description":"The top GO terms cluster around importing proteins into the mitochondrial matrix and inserting them into the inner membrane, plus general intracellular transmembrane transport and Tat-dependent transport. This suggests the proteins share a common role in mitochondrial protein targeting/translocation. Some terms (e.g., stomatal opening, obsolete aging) seem unrelated noise. ","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0001302","count":1},{"id":"GO:0009306","count":1},{"id":"GO:0043953","count":1}]},{"hash":"1158761238730634465","title":"Bacterial Photosynthesis and Flagellar Motility","description":"This cluster centers on photosynthesis and bacterial flagellar functions (assembly and flagellum-dependent motility), suggesting a bacterial subset tied to energy capture and movement. The presence of translation and various metabolic/biosynthetic terms adds housekeeping context, but the strongest link is between photosynthesis and motility in bacteria, justifying the label.","confidence":"Medium","size":8,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0044780","count":1},{"id":"GO:0042426","count":1}]},{"hash":"846722950378779195","title":"Spliceosome and RNA processing","description":"The protein set is enriched for spliceosome components and RNA processing steps: spliceosomal snRNP and complex assembly, mRNA splicing via spliceosome, and mRNA decay pathways, plus maturation of SSU-rRNA and histone mRNA metabolism; these together indicate a core role in RNA maturation and processing, with a few auxiliary links to transcription termination and chromatin/cell cycle regulation.","confidence":"High","size":8,"edges":15,"triangles":8,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030490","count":4},{"id":"GO:0006369","count":3},{"id":"GO:0070317","count":3},{"id":"GO:1990141","count":3},{"id":"GO:0000387","count":3}]},{"hash":"267430493075546832","title":"Nucleotide metabolism and salvage","description":"This cluster is dominated by GO terms for nucleotide metabolism and salvage (AMP salvage, nucleoside monophosphate phosphorylation, ADP/CDP biosynthesis, purine ribonucleotide interconversion, ITP and GTP metabolism). These point to a coordinated role in maintaining nucleotide pools. While liver and brain development terms appear, they likely reflect broader annotations rather than driving the cluster's primary function.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":5},{"id":"GO:0046940","count":5},{"id":"GO:0006172","count":5},{"id":"GO:0046705","count":5},{"id":"GO:0001889","count":5}]},{"hash":"2233341879597661645","title":"Ribosome Biogenesis and Translation Regulation","description":"The cluster is dominated by GO terms related to ribosome biogenesis and translation, including translation, ribosome biogenesis, cytosolic ribosome assembly, ribosomal large subunit biogenesis, and positive regulation of translation. A few transcription-related terms appear, but the core signal points to proteins involved in producing ribosomes and controlling protein synthesis. This makes \"Ribosome Biogenesis and Translation Regulation\" a concise and representative label.","confidence":"High","size":8,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0031564","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0045727","count":1}]},{"hash":"1869915243102908227","title":"Ribosome biogenesis and translation","description":"The dominant GO terms point to ribosome assembly and protein synthesis, including translation initiation, translation, and ribosome biogenesis (large subunit biogenesis and rRNA/snRNA pseudouridine synthesis). Some outliers (tryptophan biosynthesis, growth hormone response, fertilization) are present but do not override the core ribosome/translation theme.","confidence":"High","size":8,"edges":25,"triangles":40,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000162","count":2},{"id":"GO:0060416","count":2},{"id":"GO:0007338","count":2}]},{"hash":"937317942966128006","title":"Bacterial cell wall and lipid biosynthesis","description":"This cluster centers on biosynthetic pathways for cell wall components and associated lipids, including teichoic/lipoteichoic acid production, fatty acid and lipid A biosynthesis, and cell wall organization. The presence of nonribosomal peptide biosynthetic activation and antibiotic biosynthetic process hints at coordination with secondary metabolite production, a theme common in bacteria that build complex cell envelopes. While some terms are deprecated, the overall pattern points to enzymes involved in assembling the bacterial cell envelope and related lipid/peptide products.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0019878","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0009258","count":4},{"id":"GO:0009245","count":4}]},{"hash":"1599345672588313620","title":"Deubiquitinases","description":"Based on the top GO terms, the cluster is dominated by deubiquitination-related activities (K29- and K33-linked deubiquitination, and ubiquitin-dependent protein catabolic process), suggesting the proteins function as deubiquitinases regulating ubiquitin signaling and proteolysis. Some heart-development terms and cell-cycle/RNA export terms appear as secondary associations, but the strongest recurring theme across members is deubiquitinating activity.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035523","count":1},{"id":"GO:0071947","count":1},{"id":"GO:0003283","count":1},{"id":"GO:0090526","count":1},{"id":"GO:0003203","count":1}]},{"hash":"474929939915361469","title":"Unknown","description":"The top GO terms are heterogeneous, spanning chromatin modification, RNA processing, metabolism, cell division, protein interactions, development, and stress responses, with some obsolete annotations. This lack of a cohesive shared function across the cluster makes a precise, descriptive label unlikely, so an Unknown label is most appropriate.","confidence":"","size":8,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016576","count":2},{"id":"GO:0000492","count":2},{"id":"GO:0008653","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0051291","count":2}]},{"hash":"1758872204796383456","title":"Mitochondrial metabolism and Fe-S assembly","description":"The strongest shared themes among the top GO terms are mitochondrial processes (mitochondrion organization) and iron-sulfur cluster assembly, with additional mentions of amino acid metabolism (leucine biosynthesis/catabolism) and nutrient response. While some terms (e.g., osteoblast differentiation, transcription regulation) are less clearly connected, the core signals point to mitochondrial metabolic functions, particularly Fe-S cluster biogenesis, as defining features of this cluster.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0001649","count":2}]},{"hash":"2217666357220280491","title":"Galactose- and isoprenoid lipid metabolism","description":"The GO terms cluster around carbohydrate processing (galactose metabolism, glycolytic process from galactose, carbohydrate phosphorylation) and lipid/isoprenoid biosynthesis (cholesterol biosynthetic process, farnesyl diphosphate biosynthesis via mevalonate, IPP biosynthesis via MEP). This points to a general metabolic theme linking sugar utilization to lipid/isoprenoid production, rather than a single specific function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0009086","count":1},{"id":"GO:0019402","count":1},{"id":"GO:0009092","count":1}]},{"hash":"1612306897259959057","title":"Diverse biosynthesis pathways","description":"Proteins in this cluster are associated with a range of biosynthetic processes, including heme/porphyrin biosynthesis, amino acid biosynthesis and catabolism, biotin biosynthesis, and sphingomyelin biosynthesis. The lack of edges suggests there is no single cohesive pathway, so the cluster likely represents multiple independent biosynthetic roles rather than one function. Therefore the label highlights the general theme of biosynthetic/metabolic activity across diverse substrates.","confidence":"Low","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006782","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006686","count":3},{"id":"GO:0006533","count":3}]},{"hash":"1031642060335311126","title":"Ubiquitin-mediated stress response and transcription","description":"The top GO terms point to ubiquitin-related processes (ubiquitin-dependent ERAD pathway, autoubiquitination, aggresome assembly) and cellular stress responses (DNA damage checkpoint signaling, gamma radiation response), with additional links to transcription regulation. This suggests a cohesive cluster centered on ubiquitin-driven protein quality control and stress signaling, with transcriptional regulation tied to these stress responses.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0032968","count":3},{"id":"GO:0070842","count":3},{"id":"GO:0071480","count":3},{"id":"GO:0006351","count":2}]},{"hash":"1817212621982712142","title":"Ubiquitin-Dependent Proteolysis and Solute Transport","description":"The top GO terms point to ubiquitin-mediated protein degradation (SCF-dependent proteasomal ubiquitin-dependent catabolic process, protein polyubiquitination) as a core function, while several transport-related terms (fructose/arabinose/sugar and xenobiotic transport, phosphate/selenite transport) and cadmium response suggest membrane transport and stress/metabolite handling as accompanying activities. This combination suggests a cluster centered on proteostasis with associated solute transport responses.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006004","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0016310","count":2}]},{"hash":"501592732211792534","title":"Unknown","description":"The top GO terms are highly diverse, spanning insulin response, protein transport, cofactor biosynthesis, RNA modification, dephosphorylation, redox balance, and various developmental processes, with no dominant shared function. The lack of network connections (edges/triangles) further supports the absence of a cohesive theme, so a meaningful, specific label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0006777","count":1},{"id":"GO:0018192","count":1},{"id":"GO:0035335","count":1}]},{"hash":"1076205798922497150","title":"Calcium-NFAT signaling in development","description":"The top GO terms emphasize calcium-regulated signaling and the calcineurin-NFAT axis, along with developmental processes such as mesoderm, epithelial-to-mesenchymal transition, skeletal muscle, and lung development. While there are also mitosis and DNA repair terms, the strongest common thread is calcium-dependent signaling guiding developmental differentiation, especially muscle-related development. Confidence: High","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0099566","count":7},{"id":"GO:1905213","count":7},{"id":"GO:0051531","count":7},{"id":"GO:0010791","count":7},{"id":"GO:0007498","count":7}]},{"hash":"1783229103047351467","title":"Unknown","description":"The top terms are highly diverse (metabolic biosynthesis, response to cAMP, development in pituitary, capsule biosynthesis) and include obsolete GO terms, with no clear shared function. The cluster also has no edges or shared connectivity, indicating a lack of a cohesive biological theme among these proteins.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0071320","count":4},{"id":"GO:0019483","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0006782","count":4}]},{"hash":"436143185306509542","title":"Cardiac mitochondrial dynamics and heart development","description":"This cluster centers on mitochondrial remodeling actions (mitochondrial fusion, regulation of cytochrome c release; some fission terms are noted as obsolete) and cardiovascular development signals (ephrin receptor signaling, coronary vasculature development, ventricular septum development), suggesting a theme of mitochondrial dynamics tied to heart formation and function. Some terms pertain to general muscle or stress responses and several entries are obsolete, but the core pattern supports a cardiac mitochondrial-development link.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0001300","count":7},{"id":"GO:0014873","count":6},{"id":"GO:0090199","count":6},{"id":"GO:0070584","count":6},{"id":"GO:0048013","count":6}]},{"hash":"1443587898858681032","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030420","count":3},{"id":"GO:0034414","count":2},{"id":"GO:0031126","count":2},{"id":"GO:0046381","count":2},{"id":"GO:0019700","count":2}]},{"hash":"889227400778561526","title":"Epigenetic Chromatin Regulation","description":"The top GO terms cluster around regulation of chromatin state and epigenetic marks (negative regulation of heterochromatin formation, histone modifications like H3K27 trimethylation and histone deacetylase activity, and DNA methylation-related regulation), implying a shared role in controlling gene expression through chromatin remodeling. Some terms are obsolete, but the dominant theme points to epigenetic control of transcription and, by extension, development and immune-related processes.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901097","count":3},{"id":"GO:0010216","count":3},{"id":"GO:0061188","count":3},{"id":"GO:0098532","count":2},{"id":"GO:0002458","count":2}]},{"hash":"988106725068378082","title":"ER-Golgi vesicle transport and SNARE dynamics","description":"Based on the GO terms, this cluster is dominated by vesicle trafficking between the ER, Golgi, and endosomes (ER to Golgi, Golgi to endosome, endosome to melanosome, retrograde Golgi-ER) and by SNARE complex disassembly, with supporting terms for ERAD and actin cytoskeleton polarity. These collectively point to a cohesive module of secretory pathway transport and SNARE regulation, justifying a label focused on ER-Golgi vesicle transport and SNARE dynamics. A few terms related to cell division or ion transport are less aligned and appear as minor outliers, but they do not override the main theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0030420","count":2},{"id":"GO:0035646","count":2},{"id":"GO:0006895","count":2}]},{"hash":"813106561117675900","title":"Mitotic spindle assembly and cell cycle control","description":"This cluster\u2019s top GO terms cluster around mitosis-related processes: DNA replication, kinetochore localization, spindle assembly checkpoint regulation, and CDK activity control, pointing to cell cycle progression and mitotic regulation. Some terms (T cell receptor signaling, melanocyte migration, differentiation) appear more peripheral or as multi-functional annotations, contributing noise rather than a core theme.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0034501","count":8},{"id":"GO:0045736","count":8},{"id":"GO:0050852","count":7},{"id":"GO:0097324","count":7}]},{"hash":"562960867964405486","title":"Regulators of developmental signaling","description":"This cluster contains multiple GO terms centered on regulation of signaling pathways involved in development and immune signaling (e.g., negative regulation of Smoothened in neural patterning, positive regulation of ERK/MAPK, positive regulation of Wnt signaling, and T cell receptor signaling), along with mesoderm formation. Although some terms are more general or non-signaling (DNA replication, metal ion response), the dominant theme is regulation of signaling across developmental and immune contexts.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0006469","count":5},{"id":"GO:0001707","count":5},{"id":"GO:0071374","count":5}]},{"hash":"774905483052220024","title":"Cardiac development and septation","description":"This cluster\u2019s top GO terms are dominated by heart morphogenesis concepts: atrial septum development, ventricular septum development, cardiac right ventricle formation, endocardial cushion morphogenesis, and secondary heart field specification, all pointing to cardiac development and septation processes. While a couple terms relate to neural synaptic activity, the strong, coherent pattern around heart formation suggests the proteins are functionally linked to cardiac morphogenesis. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071318","count":1},{"id":"GO:0098976","count":1},{"id":"GO:0003283","count":1},{"id":"GO:0003281","count":1},{"id":"GO:0003219","count":1}]},{"hash":"878397178890096855","title":"ER protein folding and membrane targeting","description":"The cluster is dominated by GO terms related to protein folding and targeting to membranes during translation, such as SRP-dependent cotranslational translocation and cellular response to unfolded protein, pointing to ER targeting and protein quality control. Some terms (iron-sulfur cluster assembly, DNA replication, hematopoietic differentiation) appear as outliers and do not fit the central theme, suggesting mixed functions but a core emphasis on protein processing and ER/membrane targeting.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":2},{"id":"GO:0006616","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0090084","count":2},{"id":"GO:1902037","count":2}]},{"hash":"136616781873256842","title":"Diverse Regulatory and Cytoskeletal Functions","description":"Top GO terms indicate regulation of transcription, apoptosis, and ubiquitination, along with protein localization to microtubules and septin-ring organization, suggesting broader regulatory and cytoskeletal roles. Some terms refer to context-specific processes (viral suppression, spleen development), but there is no single cohesive pathway dominating the cluster. Therefore a broad label reflecting regulatory and cytoskeletal functions is most appropriate.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:1902187","count":1},{"id":"GO:1903886","count":1},{"id":"GO:0032186","count":1},{"id":"GO:0035372","count":1}]},{"hash":"1367553481913398087","title":"Plant oxidative stress response and cell wall remodeling","description":"Based on the prevalence of GO terms related to oxidative stress (response to oxidative stress, hydrogen peroxide catabolic process, cellular oxidant detoxification) and cell wall/lignin-related processes (plant-type cell wall organization, lignin catabolic process), the proteins in this cluster appear to participate in detoxifying reactive oxygen species and remodeling the plant cell wall under stress. This pattern supports a cohesive theme of ROS management coupled with lignin-associated cell wall modification, rather than other unrelated processes. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009664","count":2},{"id":"GO:0046274","count":2},{"id":"GO:0006979","count":2},{"id":"GO:0042744","count":2}]},{"hash":"249414024872861284","title":"Ethylene-driven fruit ripening and hormone biosynthesis","description":"The top GO terms point to plant developmental processes tied to fruit ripening and hormone biosynthesis, notably ethylene and gibberellin pathways, with related stress and secondary metabolism signals (e.g., flavonoid biosynthesis). This pattern suggests a cluster of proteins involved in maturation and hormone-regulated metabolism in plants, rather than a single enzyme pathway. The presence of ripening-associated processes supports a cohesive functional theme centered on ethylene-driven development, with supporting gibberellin and other hormone-related terms.","confidence":"High","size":8,"edges":23,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0010421","count":8},{"id":"GO:0010023","count":8},{"id":"GO:0009686","count":8},{"id":"GO:0009835","count":8},{"id":"GO:0045487","count":8}]},{"hash":"562733592155864967","title":"Detoxification and Xenobiotic Catabolism","description":"This cluster centers on multiple catabolic and detoxification GO terms, including cellular oxidant detoxification, response to toxic substances, and various xenobiotic/secondary metabolite catabolisms (stilbene, glucuronoside, strigolactone). The common theme is metabolic breakdown and detox of xenobiotics and plant-derived compounds.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0006212","count":3},{"id":"GO:0019391","count":3},{"id":"GO:1901601","count":3}]},{"hash":"1101483203589117956","title":"Immune receptor signaling and defense","description":"Most Top Terms are immune-related: T cell receptor signaling, NK cell differentiation, TLR8 signaling, tyrosine phosphorylation of STAT, ERK1/2 cascade regulation, and defense response to Gram-negative bacteria. This points to proteins involved in immune signal transduction and host defense, with a few non-immune terms (floral meristem growth, developmental growth, retinal axon guidance) likely as annotation noise. There are no network edges to reinforce a single pathway, but the term pattern supports an immune-focused label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050852","count":8},{"id":"GO:0097324","count":8},{"id":"GO:0001779","count":8},{"id":"GO:0042503","count":8},{"id":"GO:0034158","count":8}]},{"hash":"442883112470263844","title":"TLR-driven innate immune signaling","description":"The top GO terms center on innate immune pathways: Toll-like receptor signaling (TLR8 and TLR10), detection of bacterial lipopeptides, cytokine-mediated signaling, interferon production, and antibacterial peptide biosynthesis. While a few terms seem unrelated (developmental processes and axon regeneration), the dominant theme is bacterial sensing and cytokine/antimicrobial responses, suggesting these proteins participate in innate immune signaling and antibacterial defense.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019221","count":2},{"id":"GO:0070340","count":2},{"id":"GO:0006963","count":2},{"id":"GO:0072287","count":2},{"id":"GO:0045078","count":2}]},{"hash":"573786591649961784","title":"Plant pollen tube growth and cell wall remodeling","description":"This cluster includes GO terms tied to plant cell wall biosynthesis and modification (mucilage pectin biosynthetic process, pectin catabolic process, cell wall modification) and pollen tube growth, plus vascular patterning and vesicle trafficking pathways relevant to plant development. The combination suggests a coordinated role in plant cell wall remodeling during pollen tube extension and tissue patterning, with some broader growth regulation signals. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010222","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0042545","count":1},{"id":"GO:0048358","count":1},{"id":"GO:0009860","count":1}]},{"hash":"355127310249037567","title":"Unknown","description":"This cluster's top GO terms are highly diverse: acetylcholine secretion and biosynthesis indicate neural signaling; cardiac signaling terms (Purkinje-to-ventricular signaling and SA node action potential) point to heart electrical activity; while other terms relate to mitotic spindle organization and plant sieve element differentiation. There is no single unifying function across all terms, so a precise, representative label could not be determined.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061526","count":1},{"id":"GO:0008292","count":1},{"id":"GO:0090603","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0060236","count":1}]},{"hash":"930213238644679041","title":"Bacterial cell division and DNA maintenance","description":"The dominant GO terms are about cell cycle and cell division (GO:0007049, GO:0051301) with a negative regulation of cell division term, pointing to a shared theme of proliferation control in a prokaryotic context. Supporting signals include plasmid partitioning and iron-sulfur cluster assembly, which relate to DNA maintenance and essential bacterial metabolism. A few terms (nitrogen fixation, photosynthesis dark reaction) reflect broader bacterial metabolism present in some organisms but do not overpower the division-focused signal. Overall, the cluster appears centered on bacterial cell division and DNA maintenance processes.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0002098","count":1},{"id":"GO:0051782","count":1},{"id":"GO:0045226","count":1}]},{"hash":"2180197710066076411","title":"Carbohydrate and small-molecule metabolism","description":"This cluster shows enrichment for multiple carbohydrate catabolic processes (xylitol, galactose via D-galactonate) and related small-molecule metabolism (pyruvate fermentation to ethanol, furaldehyde), plus prostaglandin metabolism, suggesting a theme of broad metabolism of simple carbon substrates and lipid-derived mediators. Some terms point to signaling or drug response, but the core pattern is diversified small-molecule metabolism rather than a single pathway.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0051160","count":4},{"id":"GO:0033498","count":4},{"id":"GO:0033859","count":4},{"id":"GO:0045777","count":4}]},{"hash":"1296441040075710905","title":"DNA Transcription Regulation","description":"Most frequent GO terms point to regulation of DNA-templated transcription and DNA-templated transcription activity, suggesting these proteins act in controlling gene expression at the transcriptional level. While a few terms touch on circadian rhythm or differentiation, the dominant signal is transcriptional regulation linked to DNA processes, justifying this label.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0030224","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0051106","count":1},{"id":"GO:0007623","count":1}]},{"hash":"1371324411732627905","title":"SRP-dependent cotranslational protein targeting to membrane","description":"These proteins show a tight clustering around SRP-mediated cotranslational targeting to membranes (including translocation and signal sequence recognition) as the dominant GO signal. While other terms appear, they are less central, making the SRP-targeting function the best unifying label for this cluster.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":1},{"id":"GO:0006617","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0044781","count":1},{"id":"GO:0006614","count":1}]},{"hash":"1776504311594484473","title":"DNA replication and cell cycle proteins","description":"This cluster is characterized by GO terms centered on DNA replication and cell division (GO:0006260, GO:0051301), suggesting components of replication machinery and cell cycle progression, possibly forming multimeric complexes (protein homooligomerization). The presence of ER-Golgi transport and nuclear export-related terms hints at broader cellular roles or annotation noise, but the strongest, recurrent signals point to DNA synthesis and mitosis-related functions.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0070389","count":2}]},{"hash":"1799089834577742307","title":"Amino acid catabolism and central metabolism","description":"The enriched GO terms predominantly map to amino acid catabolic/biosynthetic processes (branched-chain amino acids, L-proline, beta-alanine) and a key metabolic link (pyruvate decarboxylation to acetyl-CoA), suggesting a cluster focused on amino acid turnover feeding central metabolism. Some terms (e.g., cell wall organization, megakaryocyte differentiation) are less directly connected, but the core theme centers on metabolism and redox-associated processes.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0006810","count":1},{"id":"GO:0071320","count":1},{"id":"GO:0010510","count":1},{"id":"GO:0009083","count":1}]},{"hash":"148171359476060640","title":"Proteostasis and protein quality control","description":"The GO terms cluster around proteostasis: response to misfolded proteins, proteasome assembly, protein processing and degradation pathways (including autophagy-related processes and mitochondrial intermembrane space import), all pointing to maintaining protein homeostasis and quality control.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0070407","count":2},{"id":"GO:0070651","count":2},{"id":"GO:0061738","count":2},{"id":"GO:0016485","count":2}]},{"hash":"1288946348993631820","title":"Plant chloroplast carbohydrate metabolism and lipid mobilization","description":"This cluster centers on carbon metabolism in chloroplasts, with strong signals for glycolysis, gluconeogenesis, glyceraldehyde-3-phosphate biosynthesis, and the pentose phosphate pathway, alongside chloroplast organization. Lipid mobilization signals (triglyceride/glycerol catabolism) and plant growth context (root development) further support a plant-specific carbon metabolism program tied to chloroplast function.","confidence":"Medium","size":7,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0061621","count":6},{"id":"GO:0009658","count":4},{"id":"GO:0006642","count":4},{"id":"GO:0046166","count":4},{"id":"GO:0019563","count":4}]},{"hash":"1768309156855774863","title":"Unknown","description":"The GO terms span unrelated areas: catabolic processes (xanthine, phenylacetate), nitrogen fixation, energy metabolism (ferredoxin, ATP synthesis with electron transport), sodium ion transport, lactation, and several terms related to negative regulation of vascular development (vasculogenesis/VEGF signaling and endothelial differentiation). There is no single cohesive biological function tying these together, indicating a heterogeneous set of activities rather than a unified pathway. ","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009115","count":6},{"id":"GO:0010124","count":6},{"id":"GO:0009399","count":6},{"id":"GO:2001213","count":6},{"id":"GO:1900747","count":6}]},{"hash":"2223194153335292297","title":"Heavy metal ion transport and detoxification","description":"This cluster is dominated by GO terms linking transport and homeostasis of multiple metal ions (mercury, copper, zinc, iron, cadmium) and detoxification/response to mercury, plus related metal ion export and transmembrane transport. The repeated emphasis on metal ion handling and detox processes suggests a cohesive function in metal homeostasis and detoxification.","confidence":"High","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":1},{"id":"GO:0006801","count":1},{"id":"GO:0006878","count":1},{"id":"GO:0060003","count":1},{"id":"GO:0015694","count":1}]},{"hash":"1578279934818398067","title":"Unknown","description":"The cluster shows a mix of signaling, transcription, ubiquitination, protein quality control, DNA repair, muscle atrophy, and early embryonic cell cycle terms, with no clear shared function across all members. Some terms are obsolete; thus no cohesive theme to name a concise function cluster.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1904049","count":7},{"id":"GO:0045944","count":7},{"id":"GO:1902283","count":7},{"id":"GO:0034126","count":7},{"id":"GO:1904378","count":7}]},{"hash":"875320183766892600","title":"Organelle Protein Import and Membrane Transport","description":"The cluster centers on protein import into mitochondria and chloroplasts (matrix, stroma) and includes several transmembrane transport terms (phosphate, arabinose, selenite, xenobiotic), indicating a theme of targeting/import into organelles combined with membrane transport of nutrients/metabolites. This combination best captures the shared functions of the proteins in the set.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0032094","count":1}]},{"hash":"1273677163628392689","title":"Pollen wall (exine) biosynthesis","description":"This cluster is enriched for sporopollenin biosynthesis, flavonoid and chalcone biosynthetic processes, and cell wall layer assembly, all of which are central to pollen wall/exine formation in plants. The convergence on lipid-derived exine components (sporopollenin, long-chain fatty-acyl-CoA metabolism) and phenylpropanoid derivatives (flavonoids) strongly points to pollen development and pollen coat formation. Some terms appear unrelated (DIF-1 biosynthesis, neuron apoptotic process) and may reflect annotation cross-talk or broad GO term mapping, but they do not overshadow the dominant pollen-wall biology signal.","confidence":"High","size":7,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0080110","count":4},{"id":"GO:0009813","count":4},{"id":"GO:0071770","count":4},{"id":"GO:0031148","count":4},{"id":"GO:0006633","count":4}]},{"hash":"2037170405837486075","title":"Glycolysis and TCA metabolism with oxidative stress","description":"This cluster centers on core energy pathways\u2014glycolysis and the TCA cycle (oxaloacetate, malate, NADH)\u2014and redox-related processes (oxidation-reduction, hydrogen peroxide) with stress-responsive signaling (response to xenobiotic stimulus) and possible apoptosis regulation, suggesting a unified theme of metabolism coupled to oxidative stress response.","confidence":"High","size":7,"edges":11,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006107","count":6},{"id":"GO:0006096","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0042493","count":6},{"id":"GO:0006099","count":6}]},{"hash":"475798572313177723","title":"Cytoplasmic Translation and mRNA Turnover","description":"The top GO terms are dominated by translation across initiation, elongation, termination, and cytoplasmic translation, with additional signals for deadenylation-dependent mRNA decay and selenocysteine incorporation, all pointing to core components of protein synthesis and its cytoplasmic regulation. The presence of translational regulation terms (positive regulation of elongation and cytoplasmic translation) further supports a translation-focused cluster, while glial cell proliferation may reflect cellular context rather than core function. This suggests the cluster represents ribosome/translation machinery and associated mRNA processing.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000288","count":3},{"id":"GO:0014009","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0045901","count":3}]},{"hash":"2202488252594630487","title":"Carbohydrate metabolism with PPP/PRPP biosynthesis","description":"The terms are dominated by carbohydrate metabolism: alpha-glucan and glycogen catabolism, fructose and fructose-6-phosphate metabolism, and the pentose phosphate shunt. The 5-phosphoribose 1-diphosphate biosynthetic process ties to PRPP, a key nucleotide precursor, reinforcing a carbohydrate/nucleotide biosynthesis theme. A few terms like necroptotic process and chorismate biosynthesis appear as outliers, but the overall signal centers on sugar metabolism and associated precursor generation.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030980","count":1},{"id":"GO:0005980","count":1},{"id":"GO:0006015","count":1},{"id":"GO:0070266","count":1},{"id":"GO:0001300","count":1}]},{"hash":"155845086674709778","title":"Redox homeostasis and oxidative stress response","description":"The cluster shows strong enrichment for oxidative stress and redox-related processes (cellular response to oxidative stress, cell redox homeostasis, oxidant detoxification, and protein deglutathionylation), indicating a shared function in maintaining redox balance and antioxidant defense. A few terms (methylamine metabolism, nucleotide biosynthesis, and a neural crest\u2013related migration term) appear ancillary or annotation-specific, but the dominant redox-related terms support this labeling.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0045454","count":4},{"id":"GO:0030416","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0003147","count":3}]},{"hash":"1004082520154606405","title":"Ribosome Biogenesis and Translation Machinery","description":"The dominant GO terms describe translation and assembly of the translation apparatus (translation, initiation, preinitiation complex formation, termination) along with rRNA maturation and large subunit biogenesis, indicating a core theme of ribosome production and protein synthesis. An unrelated retina development term appears but is not representative of the cluster\u2019s main function; overall, the cluster reflects ribosome biogenesis and translation machinery.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0001731","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0000462","count":2}]},{"hash":"570718105841937001","title":"Steroid and retinoid metabolism","description":"The top GO terms cluster around retinoid (retinal, retinol) and steroid hormone (testosterone, androgen, estrogen) biosynthesis/metabolism, indicating proteins likely involved in processing fat-soluble vitamins and steroid hormones. Some incidental terms (tropane alkaloid, mycolic acid biosynthesis) suggest broader biosynthetic capabilities but are less central.","confidence":"High","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042574","count":5},{"id":"GO:0061370","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0008209","count":5},{"id":"GO:0042572","count":5}]},{"hash":"2220728337650323142","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms tied to protein synthesis and ribosome formation, notably translation (GO:0006412) and maturation of SSU-rRNA, which point to ribosome biogenesis and ribosomal assembly. Transcription antitermination further supports a link to transcription-translation coordination, common in bacterial systems. The other terms (e.g., RNA-templated DNA biosynthetic process, protein folding, stress responses) appear as peripheral or broad cellular processes, but do not override the central ribosome/translation theme.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0031564","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0034220","count":1},{"id":"GO:0009992","count":1}]},{"hash":"1666328284965148190","title":"Ribosome biogenesis and translation regulation","description":"The top terms are dominated by translation (GO:0006412) and ribosome assembly (GO:0042255), with transcription-related processes (DNA-templated transcription and termination) and RNA regulation also appearing, suggesting a core focus on protein synthesis and RNA metabolism. Secondary signals include antibiotic response and sugar transport, but the primary theme centers on ribosome/function and translation control.","confidence":"High","size":7,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0060702","count":2}]},{"hash":"632403421600774416","title":"General stress and metabolic responses","description":"Top GO terms indicate responses to a variety of stimuli (fatty acid, ozone, estradiol, insulin, light, and various toxins) rather than a single pathway, with aerobic respiration as a metabolic anchor. The presence of a protein tetramerization term adds a structural attribute but does not define a cohesive mechanistic function. Together, the cluster seems to reflect a general cellular readiness to respond to diverse environmental and hormonal cues, rather than a specific signaling route.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":4},{"id":"GO:0010193","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0032355","count":3}]},{"hash":"2198280967844752476","title":"Ribosome Biogenesis and Translation","description":"These proteins are enriched for core ribosome-related processes (translation, ribosome biogenesis, LSU rRNA maturation) and snoRNP assembly, indicating involvement in ribosome production and translation fidelity. The presence of translation, ribosome biogenesis, and rRNA processing terms supports a cohesive theme around ribosome assembly and protein synthesis rather than unrelated pathways.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0045903","count":2}]},{"hash":"1162337006898671845","title":"Unknown","description":"The terms span signaling (protein autophosphorylation), metabolism (UTP biosynthesis, glucose and fatty acid responses), and various differentiation processes (neuron projection development, keratinocyte differentiation, spermatid differentiation), with some obsolete GO terms. This dispersion suggests no single coherent biological theme for the cluster, so a generic label Unknown best captures the lack of a unifying function.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0071398","count":2},{"id":"GO:0046777","count":2},{"id":"GO:0030819","count":2}]},{"hash":"2045966129979543958","title":"Mitotic checkpoint and DNA replication signaling","description":"The cluster\u2019s terms cluster around mitosis and cell-cycle control: spindle assembly checkpoint, mitotic spindle assembly-related regulation, G2 DNA damage checkpoint signaling, and DNA replication. JUN phosphorylation and related signaling also align with cell-cycle\u2013related mitogenic pathways. While a few terms touch on immune differentiation, the dominant theme is mitotic regulation and DNA replication.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0050852","count":2},{"id":"GO:0097324","count":2},{"id":"GO:0009636","count":2}]},{"hash":"506326489634024988","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":2},{"id":"GO:0019878","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0006531","count":1},{"id":"GO:0009090","count":1}]},{"hash":"1668231029101050542","title":"Strigolactone biosynthesis and response","description":"The cluster centers on GO terms for strigolactone biosynthesis and cellular response to strigolactone, indicating a core focus on strigolactone metabolism and signaling; the additional detoxification and catabolic terms suggest a broader plant stress/metabolic context that accompanies this pathway.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046656","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0019391","count":2}]},{"hash":"1336780264052418132","title":"Plant xenobiotic detox and metabolite catabolism","description":"The GO terms point to diverse catabolic and detoxification processes across metabolites (lipids like triglycerides, nucleosides like uracil, glycosides like glucuronosides) and xenobiotics (1,2-dichloroethane), plus pathways tied to cytochrome P450 epoxygenases and detox (cellular oxidant detoxification). The inclusion of strigolactone biosynthesis and response suggests a plant-specific metabolism/hormone angle, reinforcing a general theme of metabolite breakdown and detoxification in plants.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":6},{"id":"GO:0009086","count":4},{"id":"GO:0009636","count":4},{"id":"GO:0006212","count":4},{"id":"GO:0019391","count":4}]},{"hash":"1906216671252056110","title":"Embryonic organogenesis and neural development","description":"Top terms indicate broad embryonic development and organogenesis across multiple tissues (digestive tract, pancreas, ureteric bud) and neural development (neural crest migration, forebrain-midbrain boundary formation), with accompanying transcriptional regulation. This suggests the cluster comprises proteins involved in developmental gene expression guiding embryonic organ formation and neural differentiation.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048557","count":4},{"id":"GO:0090190","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0006366","count":4},{"id":"GO:0001755","count":4}]},{"hash":"381147261376593487","title":"Mitochondrial metabolite transporters","description":"These proteins appear to function as mitochondrial carriers, transporting phosphate, nucleotides, and cofactors (CoA, thiamine pyrophosphate) into mitochondria, which supports energy metabolism and adaptive thermogenesis. The connections to fatty acid and glucose-responsive processes reinforce a mitochondrial metabolic role; an outlier term about ERAD is likely noise. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0030308","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0034198","count":2},{"id":"GO:1990845","count":2}]},{"hash":"1067075750279371026","title":"Copper and metal ion transport and detoxification","description":"The GO terms cluster around copper ion homeostasis and transport (copper ion export/transport), plus handling of other metals (zinc, iron) and mercury detoxification, along with superoxide metabolism. The connection to mitochondrial complex IV assembly (which requires copper) reinforces the metal-ion cofactor theme. Overall, the proteins appear to participate in metal ion transport and detoxification pathways rather than a single specific function.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":2},{"id":"GO:0033617","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0006801","count":1},{"id":"GO:0006878","count":1}]},{"hash":"1069245169227696948","title":"Plant sugar catabolism and storage","description":"The top GO terms are dominated by sucrose, raffinose, and inulin catabolic processes along with carbohydrate storage, pointing to plant carbohydrate metabolism and energy reserve turnover. Plant-specific signals (gibberellin and karrikin responses) and melatonin biosynthesis further support a plant context, with transport terms adding related metabolite movement. Hence a label focusing on plant sugar catabolism and storage.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":2},{"id":"GO:0071370","count":2},{"id":"GO:1902927","count":2},{"id":"GO:0052576","count":2},{"id":"GO:0005987","count":2}]},{"hash":"2112747463580506695","title":"Filamentous growth under nutrient limitation","description":"The top GO terms show a strong emphasis on filamentous growth and invasion in response to glucose limitation, which points to a fungus/yeast adapting its morphology under nutrient stress. Additional terms about transport and metabolism likely accompany this adaptation, but the growth-related terms provide the core theme for the cluster.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0006884","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0009245","count":1}]},{"hash":"595007225482106416","title":"mRNA processing and post-transcriptional regulation","description":"The GO terms emphasize mRNA splicing, polyadenylation regulation, tail processing, mRNA stability under stress, and post-transcriptional translation control, indicating a cohesive module of RNA processing and translational regulation.","confidence":"High","size":7,"edges":14,"triangles":11,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":4},{"id":"GO:1900363","count":4},{"id":"GO:0060211","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0002188","count":4}]},{"hash":"308493704783770877","title":"Terpenoid and sterol biosynthesis","description":"The top GO terms cluster around isoprenoid metabolism: multiple biosynthetic steps for geranylgeranyl, geranyl, and farnesyl diphosphates, monoterpenes, cholesterol/sterol-related pathways, and ubiquinone-related processes, with supportive terms like coenzyme A biosynthesis and protein processing. This points to a cohesive theme of terpenoid/isoprenoid and sterol biosynthesis, with a couple general protein-related terms that are likely ancillary. ","confidence":"High","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901663","count":2},{"id":"GO:0051290","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0033386","count":2},{"id":"GO:0033384","count":2}]},{"hash":"304616717904025095","title":"Plant hormone signaling and secondary metabolite biosynthesis","description":"The terms point to plant-specific processes such as gibberellin response and lignin/flavonol biosynthesis, suggesting a theme around plant growth signaling and secondary metabolism; other terms like DNA repair and chromatin regulation seem incidental.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0009739","count":1},{"id":"GO:1901430","count":1},{"id":"GO:1905839","count":1},{"id":"GO:0010520","count":1}]},{"hash":"1062152427712466262","title":"Xenobiotic and steroid metabolism","description":"The top GO terms cluster around catabolic processes for xenobiotics (retinoic acid, coumarin, camphor, alkaloids) and hormone metabolism (progesterone, aldosterone regulation), suggesting a shared role in detoxification and steroid processing, with some non-central terms like stress responses appearing as secondary associations.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":4},{"id":"GO:0034653","count":4},{"id":"GO:0035865","count":4},{"id":"GO:0046226","count":4},{"id":"GO:0042448","count":4}]},{"hash":"1167511624583356323","title":"Developmental differentiation and stress signaling","description":"The cluster\u2019s GO terms center on differentiation processes (fat cell, myotube, male gonad development, neural tube closure) while also spanning growth/survival signaling (PI3K/AKT activation, NF-\u03baB/I\u03baB phosphorylation), redox homeostasis, and ER-stress\u2013related apoptosis. This points to a theme of differentiation integrated with cellular stress and survival signaling rather than a single, narrow function. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0022417","count":2}]},{"hash":"1305106960849395479","title":"Unknown","description":"The top terms mix neural development (nervous system development, Schwann cell development) with cell-cycle and chromosome-related processes (DNA replication, G1/S transition, mitotic checkpoint signaling, kinetochore localization), plus immune and metal-stress signals (B cell receptor signaling, cellular response to cadmium). This scattered mix lacks a single cohesive function or pathway, so there isn\u2019t a clear representative label.","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007399","count":5},{"id":"GO:0031571","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0051436","count":5},{"id":"GO:0008285","count":5}]},{"hash":"2112340586996876674","title":"Plant defense signaling and cuticle biosynthesis","description":"The cluster centers on plant hormone signaling (ABA and ethylene), defense responses (chitin response) and regulation of cuticle components (cutin and wax biosynthesis), with accompanying transcriptional regulation and development terms, suggesting a cohesive plant stress signaling and cuticle formation module.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0009738","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0009873","count":1},{"id":"GO:0010200","count":1}]},{"hash":"2060209322702746246","title":"Wnt inhibition, apoptosis, and migration regulation","description":"The top GO terms cluster around suppression of the canonical Wnt pathway, promotion of apoptotic processes, and negative regulation of cell proliferation, with accompanying cell migration and a ubiquitin-related modification (K63-linked ubiquitination). Together these suggest a module that modulates growth and movement through Wnt signaling control and ubiquitin-mediated signaling; stress-related terms like response to ethanol or chitin may reflect broader context rather than core function.","confidence":"Medium","size":7,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071361","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0043065","count":4},{"id":"GO:0090090","count":4}]},{"hash":"805307211203315476","title":"Metal Ion Transport and Detoxification","description":"The GO terms cluster around detoxification of mercury ions, various metal ion transport (copper, zinc, cadmium, iron), copper homeostasis, and metal-related responses, plus a note on copper-dependent protein maturation. This points to a cohesive theme of handling, transporting, and detoxifying metal ions across cellular compartments, rather than a single specific pathway, making a Metal Ion Transport and Detoxification label appropriate and representative.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":2},{"id":"GO:0006801","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0060003","count":2},{"id":"GO:0015694","count":2}]},{"hash":"1288444599971777824","title":"Synaptic adhesion and vesicle clustering","description":"The cluster\u2019s strongest signals are in proteins involved in cell adhesion and synaptic organization, especially synaptic vesicle clustering and localization to the synapse, which together point to a neuronal synapse function. There are also terms like amyloid precursor protein metabolic process and positive regulation of protein localization to the synapse that support a neural context. The presence of a plant cytokinin biosynthetic term is an outlier that may reflect cross-annotation or broader regulatory roles rather than a core function of these proteins. Overall, the dominant theme appears to be synaptic adhesion and vesicle organization, with APP-related processing as a related neuronal process. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":2},{"id":"GO:0009691","count":2},{"id":"GO:2000809","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0045212","count":1}]},{"hash":"368739949599338610","title":"Chromatin remodeling and histone modification","description":"This cluster centers on chromatin dynamics: nucleosome assembly/disassembly and histone H3 acetylation regulation dominate the terms, signaling epigenetic regulation and chromatin accessibility. Additional related terms like sperm DNA decondensation and regulation of microtubule polymerization touch on chromatin state and cell cycle connections, but the core theme is chromatin remodeling.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000617","count":1},{"id":"GO:0071442","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0007117","count":1}]},{"hash":"409667197918905088","title":"Central carbon metabolism regulation","description":"The top GO terms cluster around central carbon flux control\u2014gluconeogenesis, regulation of glycolytic process, carbohydrate phosphorylation, and pentose-phosphate shunt regulation, plus serine biosynthesis. These indicate proteins that collectively regulate core glucose metabolism rather than a single pathway, with some unrelated terms (e.g., cobalt response, brain development) likely incidental. Overall, a coherent theme of metabolic regulation of carbon metabolism emerges, justifying this label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0071279","count":1},{"id":"GO:0043456","count":1},{"id":"GO:0045820","count":1}]},{"hash":"600885687811225493","title":"Auxin transport and signaling","description":"These proteins are associated with auxin movement and response, including polar transport, export across the plasma membrane, and auxin-activated signaling. Additional terms point to ER\u2013Golgi vesicle trafficking, supporting a role in membrane transport and trafficking that often accompanies hormone transport. A root development term appears as a downstream effect, but the core theme is auxin transport/signaling. Confidence: High","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0009734","count":1},{"id":"GO:0080162","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0010315","count":1}]},{"hash":"1994010276306983895","title":"O-fucosylated Notch signaling in development","description":"The cluster is enriched for fucose metabolism and O-linked fucosylation, especially related to Notch signaling, along with EMT regulation and mesoderm formation. This suggests a theme of Notch pathway activity modulated by O-fucosylation during embryonic development, with some peripheral notes on oxidative stress and post-translational modification regulation.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006004","count":3},{"id":"GO:0007219","count":3},{"id":"GO:0036066","count":3},{"id":"GO:0010717","count":3},{"id":"GO:0001707","count":3}]},{"hash":"2293828619911242221","title":"Melanosome trafficking and vesicle transport","description":"These proteins cluster around intracellular vesicle movement, especially between Golgi, ER, endosomes, and melanosomes, with pigmentation pointing to melanosome-related transport. The top GO terms converge on endomembrane trafficking and melanosome transport processes, suggesting a cohesive vesicle-transport module rather than unrelated functions. Therefore, the label reflects the central theme of vesicle trafficking with a pigment/melanosome connection.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":1},{"id":"GO:0036465","count":1},{"id":"GO:0035646","count":1},{"id":"GO:0008344","count":1},{"id":"GO:0016185","count":1}]},{"hash":"1361643433158843113","title":"Transsulfuration and sulfur amino acid metabolism","description":"The top GO terms cluster around serine and homocysteine catabolism and transsulfuration, pointing to sulfur amino acid metabolism and cysteine biosynthesis. While some terms touch glucose metabolism or show tissue/immune annotations (retina development, IL-4 response) these appear less central. Overall, the strongest shared signal is transsulfuration and related cysteine/methionine metabolism.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0045722","count":6},{"id":"GO:0051289","count":6},{"id":"GO:0046651","count":6},{"id":"GO:0006565","count":6},{"id":"GO:0043418","count":6}]},{"hash":"1778088208825827944","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051790","count":2},{"id":"GO:0051792","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0019367","count":2},{"id":"GO:0051402","count":2}]},{"hash":"2123101407514937745","title":"Mitochondrial Translation and Fatty Acid Catabolism","description":"The cluster highlights two top GO terms equally: mitochondrial translation and fatty acid catabolic process, suggesting the proteins are tied to mitochondrial protein synthesis and energy-yielding lipid breakdown. The presence of a transamidation step for glutaminyl-tRNAGln aligns with mitochondria-specific translation machinery, reinforcing a mitochondria-centered theme. While other terms like ER organization and various catabolic processes appear, the strongest signal is mitochondria-associated translation and metabolism.","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009062","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0019876","count":2},{"id":"GO:0070681","count":2},{"id":"GO:0007029","count":2}]},{"hash":"1008230213534954657","title":"Mitochondrial Metabolism and Apoptosis Regulation","description":"The cluster is enriched for mitochondrial energy metabolism terms (fatty acid beta-oxidation, ketone body biosynthetic process, and amino acid catabolic process) and for negative regulation of mitochondrial membrane permeability in apoptotic signaling, suggesting a mitochondria-centered metabolic module that also influences apoptotic control. The additional development-related terms (brain, adipose tissue, and metanephric tubule development) likely reflect tissue-specific roles of mitochondrial metabolism during development. Overall, the data point to a cohesive theme around mitochondrial metabolism intertwined with apoptosis regulation.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":6},{"id":"GO:0009725","count":4},{"id":"GO:1901029","count":4},{"id":"GO:0019619","count":4},{"id":"GO:0007420","count":4}]},{"hash":"2293836713344830975","title":"Calcium Homeostasis and Membrane Ion Transport","description":"These proteins are enriched for GO terms focused on calcium handling (calcium transport into ER, intracellular calcium homeostasis) and maintaining transmembrane electrochemical gradients that underpin membrane potential. Additional terms point to proton and general ion transport, and to T-tubule organization, consistent with roles in membrane excitability and calcium signaling in muscle or neuronal contexts. Epoxygenase P450 pathway and ionotropic glutamate receptor signaling appear as ancillary associations rather than core themes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903515","count":3},{"id":"GO:0010248","count":3},{"id":"GO:0006874","count":3},{"id":"GO:0019373","count":3},{"id":"GO:1990573","count":3}]},{"hash":"1992420014266868832","title":"Light-Responsive Transcription and Chlorophyll Metabolism","description":"The cluster shows GO terms for transcription regulation (regulation of DNA-templated transcription, DNA-templated transcription) alongside terms tied to light sensing and chlorophyll-related processes (detection of visible light, detection of hypoxia, regulation of chlorophyll catabolic process, protein-tetrapyrrole linkage) and a signaling activity (protein autophosphorylation). This combination suggests a module where light perception influences transcription and chlorophyll/tetrapyrrole metabolism, with a signaling component connecting perception to gene regulation. Some terms like sporulation and complement regulation appear as less coherent outliers, but the core theme appears to center on light-responsive transcription and chlorophyll-associated metabolism.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0030435","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0070483","count":2}]},{"hash":"535203007864469197","title":"Neural crest\u2013driven craniofacial development","description":"This cluster is enriched for terms related to neural crest derivatives, including embryonic cranial skeleton morphogenesis, neuron development, and melanocyte migration, indicating a developmental theme focused on craniofacial formation. Additional terms on transcriptional regulation and cell cycle components may reflect general proliferative/differentiation processes accompanying development, but the neural crest\u2013craniofacial signal is the strongest across the top terms.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0007098","count":4},{"id":"GO:0010571","count":4},{"id":"GO:0032435","count":4}]},{"hash":"1153461067204245091","title":"Cell Cycle and Proteostasis","description":"The cluster shows strong signals for DNA replication and cell division (DNA replication, DNA biosynthetic process, cell division) paired with protein quality control and turnover pathways (protein processing, proteasome regulatory particle assembly, protein import into mitochondrial intermembrane space, late endosomal microautophagy, oxidation-dependent protein catabolic process, nonfunctional rRNA decay). This pattern suggests a functional module where DNA replication/cell cycle activities are coordinated with proteostasis and degradation pathways. The label captures this dual focus in a concise way.","confidence":"Medium","size":6,"edges":12,"triangles":11,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0071897","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0070407","count":3},{"id":"GO:0070651","count":3}]},{"hash":"1891067654691056797","title":"Unknown","description":"The top GO terms span both nuclear processes (cell division, microtubule severing, CENP-A chromatin assembly, transcription) and endoplasmic reticulum\u2013related pathways (ERAD, ER-to-Golgi transport, ER-stress\u2013induced apoptosis), with no clear unifying function. This mixed signal makes a specific, coherent cluster label unreliable.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0051013","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0061641","count":4}]},{"hash":"267647689891633994","title":"Unknown","description":"The GO terms are highly diverse\u2014tRNA transcription/export and ubiquitination are present, but there is no single unifying function across the terms (neuronal differentiation and ERK signaling appear incidental), so a cohesive cluster function cannot be inferred.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":2},{"id":"GO:2000809","count":1},{"id":"GO:0070373","count":1},{"id":"GO:0051865","count":1},{"id":"GO:2000238","count":1}]},{"hash":"531372311086034689","title":"Unknown","description":"The GO terms are highly diverse, spanning hypoxia response, amyloid precursor protein processing and fibril formation, neural signaling, heart development, insulin regulation, and even metabolic (homoserine biosynthesis) and obsolete annotations. There isn\u2019t a clear, single functional theme tying these proteins together, suggesting the cluster may be heterogeneous or noisily annotated. ","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:1902991","count":2},{"id":"GO:1990000","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0055010","count":2}]},{"hash":"1592158673424886194","title":"Neuronal development and vesicle trafficking","description":"The top GO terms emphasize brain development and dendrite morphogenesis, pointing to neuronal differentiation and morphology. Added terms about COPII vesicle budding and Golgi-to-ER trafficking suggest active secretory pathways, which are crucial for neurite outgrowth and membrane remodeling in developing neurons. While there are broader cell cycle and ribosome biogenesis signals, the neuronal-specific terms dominate, justifying a label centered on neural development with vesicular trafficking.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035264","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0007420","count":4}]},{"hash":"1270760293796623944","title":"Mitochondrial membranes and lipid localization","description":"The terms cluster around inner mitochondrial membrane organization, SREBP signaling and lipid localization, and membrane-raft protein localization, which together point to mitochondrial membrane dynamics and lipid trafficking as the core theme; immune/ECM terms seem more incidental noise.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007007","count":6},{"id":"GO:0022617","count":6},{"id":"GO:0032623","count":6},{"id":"GO:0032933","count":6},{"id":"GO:0070584","count":6}]},{"hash":"605394593758855156","title":"Neural development and axon growth","description":"The terms are dominated by nervous system development, hippocampus development, dendrite morphogenesis, and positive regulation of axon extension, along with cellular response to dopamine, suggesting proteins involved in neural differentiation and connectivity. Some terms (T cell receptor signaling, JNK cascade, mitotic cell cycle) are less directly aligned and may reflect multifunctional annotations or noise. Overall, the cluster appears best described by neural development and axon/dendrite growth functions.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":3},{"id":"GO:0031647","count":3},{"id":"GO:1903351","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0021766","count":3}]},{"hash":"198989736434044055","title":"Carbohydrate and lipid metabolism","description":"The terms cluster around energy metabolism, with gluconeogenesis, glycolysis, and pyruvate metabolism supporting carbohydrate flow, plus lipid biosynthesis (long-chain fatty acids, malonyl-CoA). Leucine catabolism adds an amino-acid energy angle, and a couple terms hint at liver development and mitochondrial organization, but the dominant signal is metabolic energy production through carbohydrate and lipid pathways.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0006814","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0042594","count":2}]},{"hash":"1128744650061632762","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms tied to ribosome function and protein synthesis: translation (cytoplasmic and general), ribosome biogenesis, export of ribosomal subunits from the nucleus, and tRNA modification. These clearly point to ribosome assembly and the machinery of translation. The inclusion of cell division and cell septum assembly terms may reflect broader links between growth, protein synthesis capacity, and division, while a couple of stress-response terms appear more peripheral. Overall, the core theme is ribosome-related biogenesis and translation.","confidence":"High","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0090529","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000055","count":2}]},{"hash":"2164042338913551151","title":"Ribosome Biogenesis and Translation","description":"This cluster is centered on ribosome assembly, small subunit biogenesis/export, and translation, indicating a core protein synthesis machinery function. Some additional terms pertain to nucleotide metabolism and DNA-related processes, but the dominant signal is ribosome biogenesis and translation.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1905053","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0061481","count":1},{"id":"GO:0006407","count":1}]},{"hash":"597776396834488907","title":"Nucleotide biosynthesis and RNA processing","description":"The cluster\u2019s top GO terms center on nucleotide metabolism: pentose-phosphate shunt (non-oxidative) and D-ribose metabolic process, plus uridine biosynthetic process, which together supply ribose and nucleotides. The presence of box C/D snoRNP assembly further points to RNA processing/modification. Peripheral terms like protein heterooligomerization and regulation of gluconeogenesis are less central. This combination supports a cohesive theme around nucleotide biosynthesis and RNA maturation.","confidence":"Medium","size":6,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009052","count":1},{"id":"GO:0006098","count":1},{"id":"GO:0006014","count":1},{"id":"GO:0046109","count":1},{"id":"GO:0016576","count":1}]},{"hash":"484142172132883511","title":"Unknown","description":"The terms are spread across ribosome assembly, translation regulation, amyloid processing, amyloid fibril formation, cell division, cardiac tissue morphogenesis, insulin secretion in response to glucose, and other unrelated processes, with only sparse connectivity (2 edges, 0 triangles). This lack of a clear, cohesive function makes it impossible to assign a specific, representative label beyond Unknown.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042256","count":1},{"id":"GO:0006417","count":1},{"id":"GO:1902991","count":1},{"id":"GO:1990000","count":1},{"id":"GO:0051301","count":1}]},{"hash":"1720801932197555210","title":"Photosynthesis light harvesting and light-stress response","description":"The terms cluster around photosynthesis and light responsiveness (photosynthesis; PSI light harvesting; NPQ) plus responses to red/far-red, UV-A, and varying light intensities, indicating a coherent theme of light-driven energy capture and photoprotection in plants.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":2},{"id":"GO:1904964","count":1},{"id":"GO:0018298","count":1},{"id":"GO:0009768","count":1},{"id":"GO:0010218","count":1}]},{"hash":"310923780476001453","title":"Organellar protein import and intron splicing","description":"The top terms are dominated by protein import into mitochondria and chloroplasts, including mitochondrial matrix and inner membrane insertion as well as chloroplast stroma import, plus Group I/II intron splicing. Together these point to organelle-targeted protein trafficking and organellar RNA processing, suggesting a coherent theme despite a few unrelated terms that may reflect annotation noise.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0032094","count":1}]},{"hash":"2030491008099184089","title":"Proteostasis and mitochondrial protein handling","description":"The terms cluster around protein processing, proteasome assembly, and autophagy-related processes (late endosomal microautophagy), plus protein import into the mitochondrial intermembrane space, all pointing to protein quality control and turnover across compartments. A couple of terms (biotin biosynthesis, cell division) seem ancillary, but the dominant theme supports a proteostasis-focused label.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:0009086","count":2},{"id":"GO:1990048","count":1},{"id":"GO:0070407","count":1},{"id":"GO:0070651","count":1}]},{"hash":"2083685457519672875","title":"Nucleotide biosynthesis and salvage","description":"The GO terms cluster around nucleotide metabolism: NAD+ biosynthesis, coenzyme A biosynthesis, AMP salvage, ADP/CDP/ITP phosphorylation, and purine ribonucleotide interconversion, indicating a shared role in nucleotide and nucleotide-derived cofactor production and turnover. A liver development term appears incidental. ","confidence":"High","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009435","count":6},{"id":"GO:0015937","count":6},{"id":"GO:0044209","count":6},{"id":"GO:0046940","count":6},{"id":"GO:0046705","count":6}]},{"hash":"975042144766099616","title":"mRNA Maturation and Post-transcriptional Regulation","description":"Proteins show strong representation of mRNA processing terms: spliceosome-mediated splicing (mRNA splice site recognition, cis splicing), polyadenylation regulation and poly(A) tail dynamics, mRNA modification, and stress-related mRNA stability, plus translation reinitiation and miRNA-mediated translational silencing. Together these point to a coordinated role in mRNA maturation and post-transcriptional regulation of gene expression.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":4},{"id":"GO:1900363","count":4},{"id":"GO:0060211","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0002188","count":4}]},{"hash":"1597038922402351156","title":"Proteostasis and innate immune response","description":"This cluster is enriched for unfolded protein response (proteostasis) and innate immune/dsRNA\u2013related signaling, with one-term hits in metabolism and cell cycle that may reflect broader cellular stress or housekeeping roles. The dominant themes point to stress management of misfolded proteins and antiviral-like responses.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0016576","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0051291","count":1},{"id":"GO:1903071","count":1}]},{"hash":"1358583230437650605","title":"Sodium and Potassium Ion Transport and Homeostasis","description":"The cluster shows strong enrichment for Na+ import and K+ export across membranes, along with intracellular potassium homeostasis, potassium ion transport, and salt-stress response, plus vacuolar acidification and cell volume regulation. Together these terms point to a cohesive module of ion transporters and regulators maintaining ionic balance and cell turgor under salt stress. An outlier GO term related to BDNF receptor signaling is likely incidental. ","confidence":"High","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":5},{"id":"GO:0097623","count":5},{"id":"GO:0030007","count":4},{"id":"GO:0009651","count":3},{"id":"GO:0006884","count":3}]},{"hash":"554955945024766060","title":"Spinal motor neuron development and migration","description":"The cluster\u2019s GO terms center on ventral spinal cord neuron specification and lateral motor column neuron migration, with connected themes of seed morphogenesis, cell-cell junction remodeling, actin cytoskeleton changes, and post-transcriptional regulation by miRNAs, all characteristic of spinal motor neuron differentiation and migration during development, influenced by thyroid hormone signaling.","confidence":"High","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048317","count":4},{"id":"GO:0021521","count":4},{"id":"GO:0021520","count":4},{"id":"GO:0045216","count":4},{"id":"GO:0097067","count":4}]},{"hash":"1239081050947350045","title":"Unknown","description":"These six proteins show a mix of GO terms spanning signaling (cellular response to cAMP), hematopoietic differentiation (megakaryocyte and granulocyte differentiation), metabolism (protoporphyrinogen IX biosynthesis), chromatin modification (obsolete histone deacetylation), redox biology (obsolete oxidation-reduction), capsule biosynthesis, endocrine development (pituitary gland development), and neurotransmitter regulation (negative regulation of serotonin secretion). Several terms are obsolete and there is no clear, shared function or pathway linking them all, so a coherent cluster label cannot be assigned.","confidence":"","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":3},{"id":"GO:0045654","count":3},{"id":"GO:0006782","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0055114","count":3}]},{"hash":"838953719389111481","title":"Male reproductive development and steroid signaling","description":"The cluster contains multiple terms tied to male reproductive biology: male sex differentiation, prostate gland development, and steroid hormone receptor complex assembly, suggesting a shared role in male development and steroid signaling. Other enriched terms (cell cycle, amyloid processing, cardiac morphogenesis) appear as broader or ancillary processes, but do not override the central reproductive theme.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0061179","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0007049","count":2}]},{"hash":"2100683069428779867","title":"Mitochondrial Metabolite Transport","description":"The top GO terms indicate transmembrane transport of metabolites and cofactors, including phosphate ions, CoA, thiamine pyrophosphate, and manganese, with a specific mitochondrial import for pyrimidine nucleotides. This suggests a core theme of mitochondrial metabolite transport. The presence of energy-related terms like adaptive thermogenesis and glucose-triggered insulin secretion supports a broader link to cellular energy homeostasis.","confidence":"High","size":6,"edges":10,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":5},{"id":"GO:0034198","count":5},{"id":"GO:1990845","count":5},{"id":"GO:0061179","count":5},{"id":"GO:1990519","count":5}]},{"hash":"548927296905464392","title":"Sterol and lipid biosynthesis","description":"The GO terms cluster around lipid and sterol biosynthesis\u2014ergosterol and cholesterol biosynthetic processes, unsaturated fatty acid biosynthesis, and related sphingolipid metabolism (MIPC). This suggests a cohesive function in lipid/sterol pathway enzymes, with a few outliers that may reflect broader metabolism or annotation noise.","confidence":"Medium","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006809","count":6},{"id":"GO:0006636","count":6},{"id":"GO:0042128","count":6},{"id":"GO:0000001","count":6},{"id":"GO:0032286","count":6}]},{"hash":"1784557431889699712","title":"Xenobiotic and steroid metabolism","description":"Most of the top GO terms describe catabolic or metabolic processes for xenobiotics and steroid-related compounds (retinoic acid, coumarin, camphor, progesterone, alkaloids, and aldosterone). This suggests a detoxification/metabolic theme focused on diverse foreign and hormonal molecules. A few terms relate to broader stress responses, which may be incidental. Overall, the cluster aligns with small-molecule metabolism and hormone processing, supporting this label.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":3},{"id":"GO:0034653","count":3},{"id":"GO:0035865","count":3},{"id":"GO:0046226","count":3},{"id":"GO:0042448","count":3}]},{"hash":"245494485712682761","title":"Embryonic and organ development","description":"The top GO terms cluster around developmental processes across diverse tissues, including placental differentiation and heart EMT, left\u2013right patterning, cartilage morphogenesis, and endocrine/pancreatic development, with a few plant development terms also present. This points to a broad theme of developmental biology and organogenesis rather than a single pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0060972","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0060536","count":2}]},{"hash":"206936043942887423","title":"Embryonic development and tissue differentiation","description":"This cluster\u2019s top GO terms cluster around various developmental and differentiation processes across multiple tissues (heart, forebrain, oculomotor nerve, Purkinje cells, keratinocytes, glial cells) and a related lipid biosynthetic process, suggesting a broad role in developmental regulation rather than a single pathway. The lack of edges supports a dispersed, multi-tissue function rather than a tightly connected module.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048557","count":2},{"id":"GO:0003168","count":2},{"id":"GO:0045617","count":2},{"id":"GO:0044708","count":2},{"id":"GO:0021905","count":2}]},{"hash":"1870821525350411352","title":"Plant hormone signaling and fungal defense","description":"The top GO terms point to responses to chitin and antifungal innate immunity, alongside hormone-related responses (salicylic acid, gibberellin, and ethylene precursor ACC) and regulation of GA signaling, plus some development/differentiation processes. This pattern suggests a functional theme where hormone signaling intersect with immune responses and growth/development in plants, rather than a single narrow task.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":4},{"id":"GO:0009739","count":3},{"id":"GO:0080169","count":3},{"id":"GO:0010055","count":3},{"id":"GO:1905034","count":3}]},{"hash":"1075270439747668729","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms related to ubiquitination and proteostasis, including ubiquitin-dependent ERAD and SMAD protein catabolic processes, various forms of ubiquitination (K63-linked), and autoubiquitination, indicating a role in tagging and degrading misfolded or regulatory proteins. Additional terms about chaperone-mediated assembly support a broader proteostasis function. Other terms like responses to chitin, ethanol, or glucocorticoids appear ancillary but do not override the central ubiquitination/degradation theme.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":6},{"id":"GO:0010200","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0070534","count":6},{"id":"GO:0090359","count":6}]},{"hash":"1882426207373243861","title":"Mitochondrial Electron Transport and Oxidative Phosphorylation","description":"The cluster is dominated by GO terms for oxidative phosphorylation, mitochondrial electron transport, proton transport, and aerobic respiration, indicating a shared function in energy production via the electron transport chain. Some plant-related terms appear, but the strongest signal centers on respiration/ETC, supporting a label of mitochondrial energy metabolism.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006119","count":1},{"id":"GO:0006123","count":1},{"id":"GO:0015990","count":1},{"id":"GO:0019411","count":1},{"id":"GO:0019646","count":1}]},{"hash":"560387399141325000","title":"Ubiquitin-Proteasome Regulation of Cell Cycle and Development","description":"The cluster is defined by ubiquitin-dependent proteolysis terms (K11-linked ubiquitination, SCF-dependent proteasomal degradation) tied to cell-cycle processes (mitotic cell cycle) and embryonic development (in utero development). While terms such as photomorphogenesis and synaptic plasticity appear, the dominant signal is ubiquitin-proteasome\u2013driven protein turnover regulating proliferation and development, making a coherent functional theme. ","confidence":"High","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008283","count":5},{"id":"GO:0009640","count":4},{"id":"GO:0031915","count":4},{"id":"GO:0070979","count":4},{"id":"GO:0042787","count":4}]},{"hash":"903132950771650175","title":"Ubiquitination-Regulated NF-kappaB Signaling","description":"The top GO terms cluster around ubiquitin-related processes (autoubiquitination, K48- and K63-linked ubiquitination, ubiquitin-dependent proteolysis) and the positive regulation of canonical NF-kappaB signaling and TNF-mediated pathways, with links to transcriptional activity. This suggests proteins here mainly modulate NF-kB\u2013related transcription and proteasomal turnover via ubiquitination. The gibberellin response term seems incidental.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0060546","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1408829205382356112","title":"Unknown","description":"The top GO terms mix meiosis-related DNA break formation, immune receptor signaling (Fc-epsilon and TCR), cell-cycle exit, DNA damage tolerance, protein ubiquitination, and unrelated processes like fungal cell wall organization and dipeptide transport. The absence of a clear, shared functional theme makes it hard to assign a specific, representative label with confidence.","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042138","count":6},{"id":"GO:0038095","count":6},{"id":"GO:0050852","count":6},{"id":"GO:0010458","count":6},{"id":"GO:0043951","count":6}]},{"hash":"217647758384799221","title":"Ubiquitin-mediated mitotic control","description":"This cluster is dominated by ubiquitin-dependent degradation terms (SCF and APC/C), mitotic processes (G2/M transition, exit from mitosis, chromosome segregation, anaphase-promoting complex\u2013dependent catabolic processes) and related modifications (neddylation), pointing to a shared function in proteolytic regulation of mitosis and chromosome dynamics; a DNA repair term likely reflects checkpoint coupling rather than a distinct function. ","confidence":"High","size":6,"edges":12,"triangles":10,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070911","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0016032","count":6},{"id":"GO:0010458","count":5},{"id":"GO:0000086","count":5}]},{"hash":"181686735407721433","title":"Xenobiotic and Hormone Metabolism","description":"The GO terms mostly describe catabolic metabolism of diverse xenobiotics (retinoic acid, coumarin, camphor, alkaloids) and hormones (progesterone), indicating a group of proteins involved in biotransformation rather than signaling; some stress-response terms appear but are less representative.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":3},{"id":"GO:0034653","count":3},{"id":"GO:0035865","count":3},{"id":"GO:0046226","count":3},{"id":"GO:0042448","count":3}]},{"hash":"955383999610211665","title":"Chromatin-modifying transcription regulators","description":"These proteins are enriched for transcription-related GO terms (DNA-templated transcription, regulation of transcription, mRNA processing) and cell cycle, with additional chromatin-modification signals (histone demethylation). This pattern points to regulators that control gene expression through transcriptional control and chromatin state, linking transcription to the cell cycle.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0034720","count":1}]},{"hash":"862157897304156750","title":"Plant barrier biosynthesis and symbiont immune modulation","description":"The cluster\u2019s top GO terms center on suberin and cutin biosynthesis, which are plant barrier components, along with defense responses to fungi and terms describing symbiont-mediated modulation of host immunity. This points to a shared theme of building protective barriers while regulating immune signaling during plant\u2013symbiont interactions, despite some cross-species terms (e.g., MHC II) that may reflect annotation noise. ","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010345","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0039648","count":1},{"id":"GO:0002495","count":1},{"id":"GO:0039504","count":1}]},{"hash":"1694290024313981718","title":"Unknown","description":"The GO terms span signaling, protein folding, DNA repair, host antiviral responses, miRNA silencing, membrane repair, microtubule localization, and light signaling, with plant- and animal-specific terms alike. There is no single cohesive function tying these proteins together, making a concise, representative label unreliable.","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000160","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0006298","count":2},{"id":"GO:1902187","count":1},{"id":"GO:2000637","count":1}]},{"hash":"231243605770199628","title":"Calcium-Dependent Developmental Signaling","description":"The cluster is dominated by GO terms tied to calcium signaling, including regulation of postsynaptic cytosolic calcium and calcineurin-NFAT signaling, which are key calcium-dependent pathways. Coupled with terms for mesoderm, skeletal muscle, and lung development, as well as EMT, the set points to a shared theme of calcium-regulated developmental signaling. Some mitosis and DNA repair terms are present as multifunctional annotations of the proteins, but the strongest coherent thread is calcium-driven developmental signaling rather than a single distinct biochemical process.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099566","count":2},{"id":"GO:1905213","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0010791","count":2},{"id":"GO:0007498","count":2}]},{"hash":"2123955033992627761","title":"Fatty acid metabolism and acyl-CoA pathways","description":"The top GO terms cluster around fatty acid biosynthesis and fatty-acyl-CoA metabolism (palmitic, medium- and long-chain FA synthesis and catabolism), indicating a shared role in fatty acid production and breakdown. Some outlier terms (CAAX-box processing, enterobactin biosynthesis) exist but do not outweigh the overall FA metabolism signal, supporting a label of fatty acid metabolism with associated acyl-CoA processes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071586","count":2},{"id":"GO:0009239","count":1},{"id":"GO:1900535","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0051792","count":1}]},{"hash":"1285853009706916955","title":"Rho GTPase\u2013driven neuronal cytoskeleton remodeling","description":"The cluster centers on small GTPase\u2013mediated signaling and filopodium assembly/regulation, with a neuronal emphasis from GABAergic synaptic transmission. This points to actin cytoskeleton remodeling in neurons governed by Rho family pathways, driving filopodia/spine dynamics and related adhesion processes; ubiquitination and mitochondrial fission entries likely reflect broader regulatory layers rather than separate themes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0051489","count":2}]},{"hash":"559495447929491538","title":"ER stress response and vesicle trafficking","description":"The terms converge on endoplasmic reticulum functions: unfolded protein response, ER localization, and COPII vesicle budding, plus calcium homeostasis, indicating ER quality control and ER-to-Golgi transport. Some host-virus interaction terms appear but are secondary noise; overall, the cluster most strongly reflects ER stress response and trafficking processes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0070972","count":1},{"id":"GO:0044791","count":1},{"id":"GO:0090114","count":1}]},{"hash":"8030232445794579","title":"Neural development, neuron apoptosis, and synaptic plasticity","description":"This cluster is dominated by GO terms tied to brain development (forebrain development, brain development, neural tube closure), neuron/glial apoptosis (neuron apoptotic process, glial cell apoptotic process, ER stress\u2013induced apoptotic signaling), and modulation of synaptic plasticity (positive regulation of synaptic plasticity), with supporting processes like SCF-dependent ubiquitin-mediated degradation and protein homooligomerization. Together these indicate a neural development module featuring neuronal survival and synaptic remodeling, with one outlier term related to defense responses. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0030900","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0034349","count":3}]},{"hash":"1672162572911826789","title":"Ubiquitin-Dependent Degradation and NF-\u03baB/JNK Signaling","description":"Most terms point to ubiquitination and ubiquitin-dependent proteolysis (autoubiquitination, K6/K48 linkages) and protein catabolic processes, alongside signaling components (TNF, NF-\u03baB, JNK). This suggests a coherent function focused on ubiquitin-mediated protein turnover and its role in inflammatory signaling pathways.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0085020","count":4},{"id":"GO:1903265","count":4}]},{"hash":"928579191753624793","title":"Phytohormone signaling and epidermal differentiation","description":"These proteins cluster around plant development tied to hormone signaling and defense: several GO terms describe epidermal and sclerenchyma/endodermal differentiation, while others relate to gibberellin signaling, response to the ethylene precursor ACC, and salicylic acid signaling. Additional terms point to chitin-triggered defense and antifungal response regulation, suggesting a module linking tissue differentiation with hormonal control and innate immunity in plants.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":1},{"id":"GO:0009739","count":1},{"id":"GO:0080169","count":1},{"id":"GO:0010200","count":1},{"id":"GO:0010055","count":1}]},{"hash":"2088788849310823464","title":"Mitochondrial Metabolite and Cofactor Transport","description":"GO terms cluster around transmembrane transport of cofactors and nucleotides into mitochondria (CoA, thiamine pyrophosphate, pyrimidines) and metal ions (manganese), with a few more diffuse terms. This suggests a cohesive theme of mitochondrial metabolite/cofactor transport, despite some less-specific annotations.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080167","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0034198","count":1},{"id":"GO:1990845","count":1},{"id":"GO:0061179","count":1}]},{"hash":"2235638346571980762","title":"Glycolysis-Driven Energy Metabolism","description":"This cluster is dominated by terms tied to glycolysis, ATP and pyruvate biosynthesis, and glucose/nutrient signaling (insulin response), pointing to a cohesive energy-production and nutrient-sensing program; a few terms related to heat stress and seed maturation appear as broader contexts but do not redefine the core function.","confidence":"Medium","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006754","count":2},{"id":"GO:0042866","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0012501","count":1},{"id":"GO:0033198","count":1}]},{"hash":"965542251235008670","title":"Protein quality control and degradation","description":"Top terms indicate protein maturation/processing, mitochondrial import, and degradation pathways (proteasome assembly, oxidation-dependent proteolysis, nonfunctional rRNA decay), along with autophagy-related processes and stress/dormancy responses. This constellation suggests a cohesive theme of proteostasis and protein turnover under stress and host-associated dormancy conditions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0085014","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0070407","count":1},{"id":"GO:0070651","count":1}]},{"hash":"38496928836930681","title":"Sec-dependent protein secretion and membrane targeting","description":"The top GO terms cluster around secretion and membrane targeting, including SRP-dependent cotranslational targeting, Sec complex\u2013mediated transport, and post-translational membrane targeting, indicating a cohesive function in directing proteins to membranes and across them.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009306","count":3},{"id":"GO:0006616","count":3},{"id":"GO:0043952","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0006605","count":3}]},{"hash":"1261820163365353812","title":"Immune signaling and differentiation","description":"This cluster is dominated by immune-related terms (T cell receptor signaling, NK cell differentiation) but also includes differentiation processes (myoblast, melanocyte) and cell-cycle signaling (JUN phosphorylation, spindle check). The common thread appears to be signaling pathways governing immune activation and cellular differentiation, with some cell-cycle regulation context. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":5},{"id":"GO:0097324","count":5},{"id":"GO:0009636","count":5},{"id":"GO:1990801","count":5},{"id":"GO:0014835","count":5}]},{"hash":"1028432035623300821","title":"Bacterial secondary metabolism and catabolism","description":"The top GO terms include antibiotic biosynthesis and quinone biosynthesis (phylloquinone and menaquinone), along with several catabolic pathways (phenylacetate, fatty acid beta-oxidation, and L-valine catabolism). This suggests a cluster of proteins involved in broad bacterial metabolism, spanning both production of secondary metabolites and degradation of organic substrates, rather than a single narrow function.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0042372","count":5},{"id":"GO:0009234","count":5},{"id":"GO:0010124","count":5},{"id":"GO:0006635","count":5}]},{"hash":"1485763763221571082","title":"TGF-\u03b2/BMP signaling regulation","description":"This cluster centers on terms that regulate TGF-\u03b2/BMP signaling and SMAD activity (e.g., negative regulation of SMAD complex assembly, negative regulation of TGF-\u03b2 receptor signaling, BMP signaling, and cellular response to TGF-\u03b2). Additional terms about SMAD phosphorylation status and nuclear export fit with modulation of signaling outputs, supporting a cohesive theme of pathway regulation, even if a plant development term appears as an outlier.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010991","count":4},{"id":"GO:0042347","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0030514","count":4},{"id":"GO:0046827","count":4}]},{"hash":"1501567848068858638","title":"Membrane ion and phosphate transport","description":"The dominant GO terms point to transmembrane transport of ions (Na+, K+), arsenite transport, and regulation of phosphate transmembrane transport, with a general transmembrane transport term also present. A few lipid biosynthesis-related terms appear but are less central, suggesting the core function is membrane transport and ion homeostasis rather than biosynthesis. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015700","count":2},{"id":"GO:2000185","count":2},{"id":"GO:0055085","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0006814","count":2}]},{"hash":"1620046675280480219","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0016973","count":3},{"id":"GO:0034476","count":2}]},{"hash":"1964530390745438961","title":"RNA processing and ribosome biogenesis","description":"This cluster is dominated by GO terms for ribosome assembly and rRNA maturation (both SSU and LSU), and RNA processing via the spliceosome, suggesting a shared function in RNA maturation and ribosome biogenesis. While other terms (embryonic development, ubiquitination, peroxisome import, GTPase regulation) appear, they seem ancillary and do not strongly redefine the core RNA-focused theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0048568","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0000466","count":2}]},{"hash":"798023927097746245","title":"Nuclear DNA Repair and Transcription Regulation","description":"The cluster is dominated by nuclear functions: DNA repair (GO:0006281) and DNA-templated transcription (GO:0006351), complemented by terms on nucleocytoplasmic transport during cell cycle events (e.g., negative regulation of protein import into/export from the nucleus) and spindle assembly related processes. Although there are a few outlier terms related to viral processes, T cell receptor signaling, and melanocyte migration, the strongest, most frequent signals point to nuclear genome maintenance and cell-cycle\u2013related regulation. This supports labeling the cluster as Nuclear DNA Repair and Transcription Regulation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046826","count":3},{"id":"GO:0016032","count":2},{"id":"GO:0050852","count":2}]},{"hash":"1703958829359388331","title":"Vascular ECM Remodeling","description":"The top GO terms cluster around extracellular matrix disassembly, elastin catabolism, smooth muscle cell migration, and fibrinolysis, which together point to remodeling of the vascular extracellular matrix and regulation of arterial dynamics. A couple of terms about lysine/LPS biosynthesis seem out of place, suggesting some noise, but the vascular remodeling signal is the strongest theme.","confidence":"Medium","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":2},{"id":"GO:0019877","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0014909","count":1},{"id":"GO:0022617","count":1}]},{"hash":"1743016530992015544","title":"Neural development and brain energy metabolism","description":"The top GO terms mix metabolic pathways (glucose, glycolysis, glyoxylate, branched-chain amino acids) with neural development processes (pyramidal neuron development, cerebellar cortex development, olfactory bulb layer development, neuron migration). This suggests a coherent theme of proteins involved in energy metabolism within developing brain regions, potentially coordinating growth and maturation in circuits such as the olfactory bulb and cerebellum. Confidence is medium due to the blend of metabolic and development terms and the lack of interaction data.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006006","count":1},{"id":"GO:0046487","count":1},{"id":"GO:0021860","count":1},{"id":"GO:0022028","count":1},{"id":"GO:0021695","count":1}]},{"hash":"888094878716841642","title":"Proteostasis and ER stress response","description":"The GO terms cluster around protein quality control and stress responses: ubiquitin-dependent ERAD, unfolded protein response, regulation of protein export from the nucleus, redox homeostasis, and translation-related processes. Although a few terms like DNA replication appear, the dominant theme is maintenance of proteostasis under stress, especially ER-associated degradation and ER stress signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:1901621","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0006260","count":3}]},{"hash":"202277256529747403","title":"Unknown","description":"The GO terms are highly disparate, spanning retina development, selenium metabolism, post-translational modifications, respiration, quinone biosynthesis, stress response, and aging, with no clear shared function or interaction linking these proteins; the network has no edges, so there is no cohesive theme. Therefore, Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":2},{"id":"GO:0001887","count":1},{"id":"GO:0030961","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0006744","count":1}]},{"hash":"2277633993703706268","title":"Chloroplast photosynthesis and pigment biosynthesis","description":"This cluster centers on chloroplast/plastid functions related to light harvesting and pigment biosynthesis: nonphotochemical quenching, thylakoid/granum organization, chlorophyll/phytol biosynthesis, and components of the electron transport chain (heme biosynthesis). The terms converge on plastid membranes and pigment-related processes, with supporting signals from plant-specific pathways, making a cohesive chloroplast-focused theme.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":2},{"id":"GO:0006783","count":1},{"id":"GO:0070453","count":1},{"id":"GO:0071668","count":1},{"id":"GO:1902001","count":1}]},{"hash":"1862075827732377665","title":"Photosynthesis Light-Response and Photoprotection","description":"These proteins cluster around light-related photosynthesis activities: light harvesting in photosystem I, responses to red and far-red light, low and high light intensity, UV-A, and nonphotochemical quenching, along with phytol biosynthesis regulation. The common theme is light perception and management within photosynthesis, including photoprotective mechanisms. ","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904964","count":1},{"id":"GO:0018298","count":1},{"id":"GO:0009768","count":1},{"id":"GO:0010218","count":1},{"id":"GO:0010114","count":1}]},{"hash":"1043136914109470974","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006986","count":2}]},{"hash":"790088963856321218","title":"Chloroplast protein import and photosynthesis","description":"This cluster is dominated by GO terms tied to chloroplast function in plants, including photosynthesis, photosystem I assembly, chloroplast stroma protein import, and related leaf metabolism. While a few mitochondrial or unrelated terms appear, the strongest and most frequent signals point to chloroplast targeting/import and photosynthetic machinery. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0045039","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0000002","count":1}]},{"hash":"91435180336274034","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048254","count":3},{"id":"GO:0000494","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0006356","count":3},{"id":"GO:1990258","count":3}]},{"hash":"1100034188219789264","title":"Unknown","description":"The top GO terms are highly diverse, including Golgi calcium transport/homeostasis, photosystem II assembly, serotonin uptake regulation, neural plate elongation, Rho signaling, NOD2 signaling, and protein dephosphorylation, plus several obsolete terms. There is no clear, shared function uniting all five proteins, and only a few terms hint at unrelated cellular processes. Therefore a coherent, representative label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035751","count":1},{"id":"GO:0032472","count":1},{"id":"GO:0032468","count":1},{"id":"GO:0010270","count":1},{"id":"GO:0051612","count":1}]},{"hash":"1935469510633687487","title":"Unknown","description":"Top GO terms span disparate biosynthetic and metabolic processes (lipopolysaccharide biosynthesis, porphyrin biosynthesis, calcium homeostasis, P450 epoxygenase pathway, sialic acid biosynthesis, carbohydrate metabolism, stilbene and glycolate catabolism) with no clear common function. The cluster has no interactions (Edges 0) and the terms do not converge on a single theme, so a reliable, specific label cannot be inferred.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0006782","count":2},{"id":"GO:0006874","count":2},{"id":"GO:0019373","count":2},{"id":"GO:0046380","count":2}]},{"hash":"800778175543922304","title":"Glycolysis and fructose metabolism","description":"The proteins show strong representation for canonical glycolysis, fructose catabolic processes to DHAP and glyceraldehyde-3-phosphate, and fructose-1,6-bisphosphate metabolism, with gluconeogenesis also present, indicating a core role in central carbohydrate metabolism and energy production. Additional terms like V-type ATPase assembly and protein tetramerization may reflect supporting structural or regulatory aspects but do not outweigh the glycolytic theme.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032781","count":2},{"id":"GO:0070072","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0061624","count":2},{"id":"GO:0061621","count":2}]},{"hash":"1615948534901347050","title":"Unknown","description":"The top GO terms are highly diverse (nitrogen starvation/fixation and various unrelated processes like synaptic transmission, plasminogen activation, and host interaction), and the proteins show no interactions (edges/triangles both zero), suggesting no coherent, single function links the cluster. Therefore there isn\u2019t a clear, representative label to assign.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":1},{"id":"GO:0006995","count":1},{"id":"GO:0051968","count":1},{"id":"GO:0010756","count":1},{"id":"GO:0006542","count":1}]},{"hash":"1582786733427264525","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000463","count":2},{"id":"GO:0000465","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0000447","count":1}]},{"hash":"110820928261277465","title":"Plant Photosynthesis and Central Carbon Metabolism","description":"The cluster's GO terms are dominated by photosynthesis-related processes (photosynthesis, carbon fixation, C4 photosynthesis, oxaloacetate metabolic process, and TCA cycle), with nitrate response as a related metabolic cue. This points to plant energy metabolism and carbon assimilation as the core function of the proteins. A few terms seem unrelated or outliers, but they do not override the strong photosynthesis/central metabolism signal.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0010167","count":1},{"id":"GO:0006107","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0009760","count":1}]},{"hash":"1704616480291786160","title":"Translation Machinery and Regulation","description":"This cluster is dominated by GO terms tied to translation processes across multiple compartments (translational initiation, elongation, termination, mitochondrial translation) and to translational fidelity, including the diphthamide modification of histidine essential for translation. The presence of related mRNA decay terms also ties to translation regulation, while neural/glial and muscle differentiation terms suggest context-related translational control during development. Overall, the label Translation Machinery and Regulation captures the core function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":1},{"id":"GO:0014009","count":1},{"id":"GO:1990416","count":1},{"id":"GO:1990145","count":1},{"id":"GO:0032543","count":1}]},{"hash":"991679548746471180","title":"Amino acid and small-molecule biosynthesis","description":"Most of the top GO terms point to biosynthetic and catabolic processes for amino acids (lysine, proline, ornithine, alanine) and related cofactors/metabolites (biotin, protoporphyrinogen IX). There are also terms for antibiotic biosynthesis and GABA catabolism, suggesting a metabolic cluster focused on synthesis and processing of diverse small molecules rather than a single function. One term about cocaine-related behavior seems unrelated and may be an annotation artifact. Overall, the cluster is best described as amino acid and small-molecule biosynthesis/metabolism.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0055129","count":2},{"id":"GO:0009450","count":2},{"id":"GO:0006593","count":2}]},{"hash":"143477629000273857","title":"Glycan biosynthesis and carbohydrate metabolism","description":"The top GO terms are dominated by sugar biosynthesis and metabolism (UDP-N-acetylglucosamine, GDP-mannose, lipopolysaccharide, glycogen, glucose-1-phosphate), suggesting a cohesive role in carbohydrate biosynthesis and sugar turnover. An outlier term like gravity detection may be noise or misannotation. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006048","count":1},{"id":"GO:0009590","count":1},{"id":"GO:0019388","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0009298","count":1}]},{"hash":"764605547164481920","title":"Cell Division and Microtubule Organization","description":"The top GO terms are dominated by cell cycle and mitotic machinery: mitotic spindle midzone assembly, cytoplasmic microtubule organization, mitotic cytokinesis, and general cell division, with supporting signals from DNA replication/recombination. This suggests the proteins cluster around mitosis and cytoskeletal organization, while a few neural mechanosensation terms appear incidental or multifunctional annotations.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0030182","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0051256","count":1}]},{"hash":"1596720405393014950","title":"Membrane Transport and Secretion","description":"This cluster is driven by GO terms related to protein secretion and various membrane transport processes (Tat complex transport, transmembrane transport, metal/organic anion transport, and plasma membrane transport), suggesting a shared role in moving proteins or ions across membranes. Some terms like translation or kidney development are less directly connected and may reflect broader annotations, but the dominant theme is membrane-associated transport/secretion. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009306","count":1},{"id":"GO:0043953","count":1},{"id":"GO:0065002","count":1},{"id":"GO:1902458","count":1},{"id":"GO:0015699","count":1}]},{"hash":"562843427555241838","title":"Bacterial Biosynthesis and Metabolism","description":"Most terms point to diverse biosynthetic and metabolic processes (poly-hydroxybutyrate, folate/tetrahydrofolate, rhamnose, galactose, glutamine metabolism, methylation, phosphorylation). This suggests a cluster of proteins involved in various metabolic biosynthesis pathways rather than a single function. An outlier term like hair follicle development likely represents noise. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0032259","count":1},{"id":"GO:0046654","count":1},{"id":"GO:0016310","count":1}]},{"hash":"1329954433525162751","title":"Mitosis and DNA Replication Machinery","description":"Based on the GO terms, the cluster is enriched for cell division, DNA replication, mitotic DNA replication checkpoint signaling, microtubule severing, and CENP-A\u2013containing chromatin assembly, all pointing to chromosome segregation and replication during mitosis. While there are a few terms related to protein quality control and trafficking (ERAD, ER-to-Golgi transport), these do not dominate the set and likely reflect ancillary roles. Overall, the proteins appear to function together in mitosis and DNA replication processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0070370","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1372950663159107692","title":"DNA Repair and Homologous Recombination","description":"The GO terms cluster around DNA recombination and repair, especially homologous recombination for double-strand break repair, heteroduplex formation, meiotic recombination, interstrand cross-link repair, telomere maintenance via recombination, and overall DNA repair and replication, indicating a cohesive DNA damage response pathway.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0010569","count":3},{"id":"GO:0030491","count":3},{"id":"GO:1990918","count":3},{"id":"GO:0036297","count":3},{"id":"GO:0006310","count":3}]},{"hash":"578253988277530570","title":"Pollen exine biosynthesis and rhamnose/xylose pathways","description":"The cluster shows strong representation of sporopollenin biosynthetic process and nucleotide-sugar biosynthesis (UDP-rhamnose/xylose, dTDP-rhamnose), which are key components of pollen exine and cell-wall polysaccharides, suggesting a coherent theme around pollen-wall formation. Other GO terms (photosynthesis, transcription) appear less central. Therefore the label reflects the dominant function of this cluster.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0019684","count":2},{"id":"GO:0006012","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0001081","count":1}]},{"hash":"362885264709895777","title":"Amino acid and cofactor biosynthesis cluster","description":"These proteins show GO terms across multiple biosynthetic pathways\u2014thiamine biosynthesis, several amino acid biosyntheses (glutamate, phenylalanine, glutamine), and menaquinone biosynthesis\u2014along with a related central metabolism term (TCA). The common thread is production of essential metabolites, implying a cluster of biosynthetic enzymes and related modifiers rather than catabolic or signaling roles. Some terms are obsolete, so the connection is suggestive but not absolute.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0019552","count":1},{"id":"GO:0019551","count":1},{"id":"GO:0006537","count":1}]},{"hash":"1913875392933251653","title":"RNA processing and translation control","description":"These proteins cluster around RNA maturation and post-transcriptional regulation, including mRNA splicing (spliceosome), polyadenylation regulation and tail dynamics, mRNA modification, and stress-related mRNA stability. Additional terms mention translation reinitiation and miRNA-mediated translational silencing, reinforcing a shared theme of RNA processing and control of gene expression after transcription.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0060211","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0002188","count":2}]},{"hash":"101646038002308362","title":"Plant pollen wall and cuticle biosynthesis","description":"Your cluster is dominated by terms related to sporopollenin biosynthesis, wax biosynthetic processes, and nucleotide-sugar\u2013based building blocks (e.g., UDP-rhamnose, UDP-xylose, galactose) that are characteristic of plant pollen wall formation and cuticle biosynthesis. Additional metabolic terms (SAM, L-glutamine) fit into general biosynthetic activity, while the hair follicle development term appears as an outlier noise rather than a defining feature. This combination points to a cohesive theme around plant surface and pollen coat construction rather than a single isolated function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006012","count":2},{"id":"GO:0001942","count":2},{"id":"GO:0019305","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0006556","count":2}]},{"hash":"587690036906998445","title":"Solute transporters (sugars, ions, xenobiotics)","description":"This cluster is dominated by transmembrane transport GO terms, including sugar and ion transport as well as xenobiotic transport. The proteins are likely solute transporters at the plasma membrane, handling nutrients and xenobiotics.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071332","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0097080","count":1},{"id":"GO:0042908","count":1}]},{"hash":"1472050897171154424","title":"HDAC-mediated transcriptional repression","description":"This cluster centers on deacetylation and transcriptional control, highlighted by terms for peptidyl-lysine and histone H3 deacetylation, DNA-templated transcription, and negative regulation of transcription by RNA polymerase I. Additional terms reflect chromatin silencing and regulation of protein stability, suggesting a broader connection to chromatin remodeling and transcriptional repression; a few entries touch on mitophagy, but the dominant signal is histone deacetylation\u2013driven transcriptional regulation.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031939","count":5},{"id":"GO:0006351","count":5},{"id":"GO:1902894","count":5},{"id":"GO:0045820","count":5},{"id":"GO:0034983","count":5}]},{"hash":"2133263950796181714","title":"Ubiquitin-Regulated Signaling and Cell Cycle","description":"The top GO terms center on protein deubiquitination and regulation of ubiquitin ligase activity, plus signaling pathways (Wnt canonical/PCP, Fc-epsilon receptor, T cell receptor) and a note of G2/M cell cycle control. This points to a module where ubiquitin turnover modulates signal transduction and cell cycle progression, with additional hints of zinc response and amino acid metabolism as ancillary processes.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":5},{"id":"GO:0038095","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0010972","count":3},{"id":"GO:0051437","count":3}]},{"hash":"1517236380585111179","title":"Xylem development and secondary cell wall biogenesis","description":"The top GO terms cluster around vascular tissue differentiation in plants\u2014protoxylem development, xylem vessel member cell differentiation, and plant-type secondary cell wall biogenesis/its regulation\u2014along with transcriptional regulation. This suggests the proteins work together in xylem formation and cell-wall biosynthesis, with some regulatory control over gene expression during organ formation.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0006351","count":4},{"id":"GO:1904250","count":4},{"id":"GO:0090059","count":4},{"id":"GO:0009834","count":4}]},{"hash":"1111072497434591850","title":"Embryonic craniofacial and forebrain morphogenesis","description":"The top GO terms cluster around embryonic head development, especially cranial skeleton morphogenesis and forebrain formation, with related oculomotor nerve development; other terms reflect broader embryogenesis, but the strongest signal is head/brain morphogenesis in early development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048701","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0006265","count":2},{"id":"GO:0048557","count":1},{"id":"GO:0003168","count":1}]},{"hash":"774529546578367914","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0006986","count":1}]},{"hash":"1530565267003001986","title":"DNA Damage Response and Translesion Synthesis","description":"This cluster centers on DNA damage response activities, highlighted by translesion synthesis (both error-prone and high-fidelity), nucleotide excision/repair pathways, and UV-C response, with an additional note of replication-related activity. While some metabolic GO terms appear, the dominant theme is lesion bypass and repair in response to DNA damage.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":2},{"id":"GO:0009435","count":2},{"id":"GO:0046940","count":2},{"id":"GO:0015937","count":2},{"id":"GO:0046939","count":2}]},{"hash":"2185790733306171234","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":4},{"id":"GO:0070417","count":3},{"id":"GO:0006265","count":3},{"id":"GO:0034476","count":2},{"id":"GO:1990417","count":2}]},{"hash":"1540608060583756459","title":"Antibiotic and Xenobiotic Membrane Transporters","description":"The GO terms point to multiple membrane transport processes across substrates such as antibiotics (response to antibiotic, daunorubicin transport, xenobiotic transmembrane transport, bacteriocin transport) and metal ions (cobalt, molybdate), as well as lipid translocation activities. This pattern suggests a function group centered on transporting xenobiotic compounds and related stress-associated substrates across membranes, potentially linked to antibiotic response mechanisms (SOS response). Confidence: Medium","confidence":"","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006824","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0043215","count":3},{"id":"GO:0006855","count":3}]},{"hash":"641859471859205541","title":"Triglyceride and phospholipid catabolism","description":"The top GO terms are dominated by triglyceride catabolic processes (triglyceride catabolic process, triglyceride mobilization, positive regulation of triglyceride catabolic process) and phospholipid catabolic processes (phosphatidylethanolamine and phosphatidylcholine catabolism) with remodeling of triglyceride acyl chains. This points to a cohesive theme of lipid breakdown and lipid remodeling, potentially linked to energy production as suggested by ATP synthesis coupled electron transport, and supported by regulatory signals such as negative regulation of PKA. Overall, the cluster appears to reflect lipid catabolism and remodeling in a metabolically coordinated context.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":3},{"id":"GO:0042773","count":2},{"id":"GO:0046338","count":2},{"id":"GO:0007114","count":2},{"id":"GO:0006642","count":2}]},{"hash":"1824335450080268412","title":"mRNA processing and translation regulation","description":"The proteins show enrichment for mRNA splicing, polyadenylation regulation/deadenylation, mRNA modification, and stress-related mRNA stability, plus translation reinitiation and miRNA-mediated silencing. Together these terms indicate a cohesive role in post-transcriptional mRNA maturation and control of translation, spanning spliceosome-related processes and tail dynamics. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":4},{"id":"GO:1900363","count":4},{"id":"GO:0060211","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0002188","count":4}]},{"hash":"1208665764336654243","title":"Golgi fucose transport and glycosylation","description":"Dominant GO terms center on transmembrane transport of sugar nucleotides into the Golgi lumen (GDP-fucose, UDP-glucose) and subsequent fucosylation steps (N- and O-linked glycosylation), indicating a glycosylation-focused transport cluster. Some terms related to general membrane transport appear as well, with a few unrelated developmental terms present as noise. Overall, the functions cohere around Golgi-based glycosylation processes.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901207","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0015786","count":1}]},{"hash":"1389628193284223316","title":"Ribosome Biogenesis and Translation","description":"Based on the top GO terms, the cluster centers on ribosome production and function: cytoplasmic translation, ribosomal subunit biogenesis, ribosome biogenesis, and export of the large subunit from the nucleus. Additional terms touch on cell division and septum assembly, but the dominant theme is ribosome assembly and protein synthesis machinery.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090529","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1903833","count":2}]},{"hash":"827348416626272675","title":"Heart development and NFAT signaling","description":"This cluster\u2019s top GO terms center on cardiac development and calcium/NFAT pathways, notably heart development (GO:0007507), ventricular cardiac muscle tissue morphogenesis (GO:0055010), and regulation of calcineurin-NFAT signaling cascade (GO:0051531), with a related calcium-regulated postsynaptic term (GO:0099566). These point to a cohesive theme around cardiac morphogenesis and calcium-dependent signaling. Some terms (e.g., karyogamy and vacuole fusion) appear unrelated to animal heart biology and may reflect broader or incidental annotations in a small cluster. Overall, the cardiac development/NFAT signaling theme justifies the name. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0042144","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0043065","count":3}]},{"hash":"589182848026035027","title":"RNA Modification and Processing","description":"This cluster's proteins are linked by RNA maturation activities, including tRNA/rRNA methylation, tRNA thio-modification, and mRNA splicing/poly(A) regulation, with thiamine biosynthesis terms appearing as noise; the dominant theme is RNA modification/processing.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0052837","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0009228","count":1}]},{"hash":"613539256224031073","title":"Unknown","description":"The top GO terms span vastly different processes (apoptotic signaling, nitric oxide synthesis, unsaturated fatty acid and ergosterol/sphingolipid metabolism, nitrate assimilation, mitochondrial inheritance, CNS myelin maintenance, sebaceous gland differentiation, and RNA polymerase III transcription). With no edges or cohesive functional theme, there is no clear unifying function for this cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097190","count":2},{"id":"GO:0006809","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0000001","count":2}]},{"hash":"764717319699251495","title":"Chloroplast Photosynthesis and Photoprotection","description":"Top GO terms show a strong emphasis on photosynthesis and photoprotection (photosynthesis, nonphotochemical quenching) and membrane energy translocation (proton transmembrane transport), suggesting chloroplast energy capture and light-stress protection as the shared function. The presence of several aromatic compound catabolic terms is inconsistent with this theme and may reflect annotation noise or mixed functions, but the dominant signal supports a photosynthesis-related cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0042203","count":2},{"id":"GO:0046232","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0046381","count":2}]},{"hash":"211703928737293800","title":"Cardiac contraction and calcium signaling regulation","description":"This cluster's top GO terms cluster around heart muscle function: regulation of cardiac muscle cell contraction, SA node cell action potential, ventricular cardiac muscle tissue morphogenesis, and calcium-related signaling (calcium transporter activity, postsynaptic calcium concentration) as well as calcineurin-NFAT\u2013mediated transcription. These point to proteins involved in excitation-contraction coupling and calcium-dependent signaling in cardiac tissue, with Rho signaling also linked to remodeling. A couple of terms (Fc-epsilon receptor signaling, pancreatic apoptotic process) seem less related and may reflect background noise. Overall the core theme is cardiac function and calcium signaling regulation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086004","count":3},{"id":"GO:1901896","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0098907","count":2},{"id":"GO:0099566","count":2}]},{"hash":"158189943409834917","title":"Plant light signaling and flowering regulation","description":"Top terms show cytokinin-activated signaling, far-red light signaling, regulation of flower development, and DNA-templated transcription, suggesting the cluster centers on plant light/hormone signaling driving transcriptional control and flowering processes. A few terms (chemotaxis, bacterial flagellum-dependent motility, sporulation regulation) may reflect annotation noise or cross-species homology, but the plant-related terms dominate, supporting a label focused on plant signaling and transcriptional regulation of development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0048579","count":1},{"id":"GO:0010018","count":1},{"id":"GO:0006935","count":1}]},{"hash":"2264015057691051593","title":"Membrane Transport of Xenobiotics and Metals","description":"The top terms are dominated by transmembrane transport activities for xenobiotics and metal ions (e.g., cobalt, molybdate), as well as lipid translocation, with related antimicrobial transport terms. While SOS response and transcription termination are present, the strongest common thread is membrane transport of xenobiotics and metals. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006353","count":2},{"id":"GO:0006824","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0043215","count":2},{"id":"GO:0006855","count":2}]},{"hash":"1069079687073683217","title":"Cell cycle regulation and mitosis","description":"The top GO terms cluster around DNA replication, mitotic checkpoints, spindle assembly, and related phosphorylation events, suggesting a shared role in cell division and mitotic progression. Although some terms touch on immune signaling and development, the dominant theme is cell cycle control, particularly G2/M checkpoint and spindle assembly processes, which supports labeling this cluster as cell cycle regulation and mitosis.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0050852","count":2},{"id":"GO:0097324","count":2},{"id":"GO:0009636","count":2}]},{"hash":"2273594377105318354","title":"Unknown","description":"The Top Terms are highly diverse, spanning lens development, various transport and metabolic processes, behavior, and virus budding, with no single cohesive function or pathway tying them together. The cluster lacks a clear shared biological theme, so assigning a specific, concise label is not feasible.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002088","count":1},{"id":"GO:0060905","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0080144","count":1},{"id":"GO:0015811","count":1}]},{"hash":"187131460808002556","title":"Skeletal muscle calcium handling and contraction","description":"The cluster's top GO terms are dominated by calcium ion transport into the sarcoplasmic/endoplasmic reticulum, regulation of SR Ca2+ concentration, and processes linked to contraction and relaxation in skeletal muscle (e.g., fast-twitch contraction, T-tubule organization). These collectively point to calcium signaling and excitation-contraction coupling specific to skeletal muscle, making this an intuitive label. Other ion transport terms (zinc, cadmium) are ancillary but do not override the central theme of Ca2+ homeostasis in muscle.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903515","count":3},{"id":"GO:0033292","count":3},{"id":"GO:1990036","count":3},{"id":"GO:0032470","count":3},{"id":"GO:0045299","count":3}]},{"hash":"1926845002784622058","title":"Retroviral life cycle and latency","description":"The top GO terms cluster around retroviral replication steps\u2014RNA-templated DNA biosynthesis (reverse transcription), virion assembly, uncoating, viral life cycle, and establishment of integrated proviral latency\u2014indicating a focus on retroviral processes rather than general cellular functions.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":2},{"id":"GO:0071492","count":2},{"id":"GO:0019058","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0010849","count":2}]},{"hash":"2099938653652879442","title":"Unknown","description":"The top GO terms cover immune signaling (T cell receptor signaling, natural killer cell differentiation), differentiation and migration (melanocyte migration, myoblast differentiation in skeletal muscle regeneration), and cell cycle/mitosis-related processes (mitotic spindle assembly, G2 DNA damage checkpoint signaling, JUN phosphorylation). This mix shows no single coherent biological function tying the proteins together, suggesting the cluster groups proteins from diverse pathways rather than a specific process. Therefore, there isn\u2019t a clear, representative label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0050852","count":5},{"id":"GO:0097324","count":5},{"id":"GO:0009636","count":5},{"id":"GO:1990801","count":5},{"id":"GO:0014835","count":5}]},{"hash":"1767629222037031763","title":"Unknown","description":"The GO terms span antibiotic biosynthesis, multiple lipid catabolic processes, regulation of endocannabinoid signaling, biosynthesis of vitamins/quinones, autophagy-related processes, cellulose breakdown, and neurotransmitter biosynthesis, a highly diverse set with no single cohesive function; there are no edges connecting proteins to reinforce a specific cluster function.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0019433","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0006660","count":2},{"id":"GO:0052651","count":2}]},{"hash":"509471096325691757","title":"Muscle and mesoderm development with calcium signaling","description":"This set mainly includes developmental terms tied to mesoderm- and muscle-derived tissues (mesoderm development, skeletal muscle fiber development, lung development) and epithelial-to-mesenchymal transition. Calcium-signaling terms (postsynaptic calcium regulation; calcineurin-NFAT signaling) fit with signaling controls in muscle and organ development. A few items like DNA repair and mitotic spindle attachment appear unrelated noise, but do not dominate the cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099566","count":1},{"id":"GO:1905213","count":1},{"id":"GO:0051531","count":1},{"id":"GO:0010791","count":1},{"id":"GO:0007498","count":1}]},{"hash":"2130470792152131601","title":"Yeast autophagy and CVT pathway","description":"Top terms indicate a core autophagy/vacuolar degradation theme in yeast, including macroautophagy, piecemeal microautophagy of the nucleus, and the cytoplasm-to-vacuole targeting (CVT) pathway. Additional terms about cell cycle regulation and pseudohyphal growth suggest a coordinated response linking metabolism, growth form, and proteostasis under nutrient stress. While sumoylation and thiamine biosynthesis appear ancillary, they can relate to broader regulatory and metabolic adjustments during autophagy. Overall, the cluster is best described as autophagy and vacuolar targeting in yeast, with related regulatory processes.","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0009228","count":3},{"id":"GO:0034727","count":3},{"id":"GO:0032258","count":3},{"id":"GO:2000220","count":3}]},{"hash":"792452032044237233","title":"Unknown","description":"The GO terms span translation and ribosome export, cell division, and various transport and stress-related processes (metal and xenobiotic), with no single cohesive function linking all five proteins; the lack of edges supports a heterogeneous cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090529","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0006824","count":1},{"id":"GO:0000055","count":1}]},{"hash":"686023729729708247","title":"Brain development and ER-stress\u2013induced apoptosis","description":"This cluster centers on neural development, with strong representation of forebrain development, neural tube closure, and overall brain development. It also includes apoptosis-related processes, including neuron and glial cell apoptosis and an intrinsic apoptotic signaling pathway in response to endoplasmic reticulum (ER) stress, suggesting a link between neural development and stress-induced cell death. DNA-templated transcription indicates regulatory programs driving these development and apoptotic processes. While a defense response term is present, the dominant theme is neural development coupled with apoptotic regulation, justifying the label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030900","count":5},{"id":"GO:0001843","count":5},{"id":"GO:0070059","count":5},{"id":"GO:0034349","count":5},{"id":"GO:0051260","count":5}]},{"hash":"1389212465039591555","title":"Unknown","description":"The GO terms show a highly diverse set of functions (RNA processing, ribosome biogenesis, ubiquitination regulation, signaling, and multiple developmental processes) with no single unifying theme or interaction pattern in this small cluster. The lack of edges and a cohesive functional cluster supports labeling as Unknown rather than forcing a misleading name.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0032933","count":1},{"id":"GO:1902525","count":1},{"id":"GO:0030900","count":1},{"id":"GO:0030042","count":1}]},{"hash":"1955135274131165001","title":"Unknown","description":"The two top GO terms (pollination and aluminum cation transport) describe disparate biological roles with no clear shared function or process, and the cluster shows minimal connectivity (one edge, no triangles). With such weak and conflicting functional signals, there isn't a coherent theme to name the cluster beyond Unknown.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009856","count":1},{"id":"GO:0015690","count":1}]},{"hash":"515104957137324480","title":"Starch and Trehalose Metabolism","description":"The GO terms cluster around carbohydrate metabolism with emphasis on starch biosynthesis (including amylopectin) and trehalose metabolism, plus linked sucrose and maltose pathways and even polysaccharide digestion. The cohesive set points to enzymes involved in synthesis and breakdown of starch-related carbohydrates, justifying the label.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019252","count":1},{"id":"GO:0005992","count":1},{"id":"GO:0005985","count":1},{"id":"GO:0010021","count":1},{"id":"GO:0005987","count":1}]},{"hash":"2160568346954062876","title":"Secretory vesicle trafficking (Golgi to membrane)","description":"The GO terms cluster around exocytosis and multiple Golgi-to-membrane/vacuole transport processes, with regulatory links to dense core granule transport, suggesting a cohesive theme of the secretory pathway and vesicle trafficking; some plant-specific biosynthesis terms appear as minor outliers, but the dominant signal is membrane trafficking and secretion.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048354","count":1},{"id":"GO:0080028","count":1},{"id":"GO:0010668","count":1},{"id":"GO:0090156","count":1},{"id":"GO:1904810","count":1}]},{"hash":"921213584067672872","title":"Plant light signaling and chlorophyll metabolism","description":"The cluster shows strong signals from light-related GO terms: red light signaling pathway, detection of visible light, and regulation of chlorophyll catabolic process, plus protein-tetrapyrrole linkage, all pointing to plant light perception and chlorophyll/tetrapyrrole metabolism. A few terms reflect general cellular processes or unrelated contexts (DNA-templated transcription, glucose metabolism, placenta development), which reduces coherence but the dominant pattern is plant light response and chlorophyll turnover. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0070483","count":1},{"id":"GO:1903660","count":1},{"id":"GO:0010161","count":1}]},{"hash":"988950081037089159","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0034476","count":2},{"id":"GO:1990417","count":2}]},{"hash":"1912835339850698929","title":"Unknown","description":"The cluster\u2019s top GO terms are a wide mix of unrelated processes (DNA transcription, hypoxia sensing, chlorophyll and light-related processes, placenta development, metabolism, protein folding, etc.) with no shared function or interaction pattern, and there are no edges, suggesting no cohesive biological theme. Unknown is therefore the appropriate label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0070483","count":1},{"id":"GO:1903660","count":1},{"id":"GO:0010271","count":1},{"id":"GO:0017006","count":1}]},{"hash":"227838499760915818","title":"Angiogenesis and Eye Vasculature Development","description":"This cluster is dominated by GO terms tied to blood vessel formation and vascular patterning, including angiogenesis (GO:0001525), retina vasculature development (GO:0061298), labyrinthine layer blood vessel development (GO:0060716), and positive regulation of endothelial cell migration (GO:0043536). These show a coherent theme of vascular development, especially in sensory organs like the retina and related inner ear structures, suggesting the proteins function together in angiogenesis and ocular/vestibular vascularization. Other terms (myoblast fusion, cell cycle transition) are broader developmental processes and likely represent secondary roles or cross-talk, but do not outweigh the central vascular signal.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":2},{"id":"GO:0060716","count":2},{"id":"GO:0061298","count":2},{"id":"GO:0043536","count":2},{"id":"GO:0043065","count":2}]},{"hash":"1035672156146239776","title":"Amino Acid Catabolism and Redox Balance","description":"Core signals point to serine/homocysteine catabolism and transsulfuration, and a cellular response to oxidative stress, suggesting a cluster focused on amino-acid derived metabolism and redox homeostasis. Some GO terms (blastocyst/retina development, gluconeogenesis, carbohydrate metabolism) are less directly related and may reflect broader metabolic context or annotation noise, but the dominant theme is amino acid breakdown coupled with redox regulation.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0045722","count":1},{"id":"GO:0051289","count":1},{"id":"GO:0046651","count":1}]},{"hash":"1707820737083298647","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034476","count":1},{"id":"GO:0009432","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0048701","count":1},{"id":"GO:0043486","count":1}]},{"hash":"1516668879050554418","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019236","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071044","count":2},{"id":"GO:0034476","count":2},{"id":"GO:1990417","count":2}]},{"hash":"2116492635384673462","title":"Neural development and brain growth","description":"This cluster's top GO terms cluster around neural development: spinal cord development and cerebellar Purkinje cell layer morphogenesis, plus growth-related processes like multicellular organism growth. These recurrent terms suggest proteins participate in nervous system development and brain morphogenesis. A few items reference broader metabolic/growth pathways (TORC1 signaling, ubiquinone biosynthesis), which may reflect shared roles in cellular growth rather than a brain-specific function. Overall, the dominant signal is neural development.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0019509","count":1}]},{"hash":"2086097366168316674","title":"Actin Cytoskeleton Dynamics and Vesicle Trafficking","description":"The cluster centers on positive regulation of actin polymerization, stress fiber and formin-nucleated actin cable assembly, and actin organization, with supporting signals of GTPase regulation\u2014pointing to actin cytoskeleton remodeling. The vesicle transport terms (ER-to-Golgi and exocytosis regulation) suggest coordinated regulation of membrane trafficking alongside actin dynamics, forming a cohesive actin- and trafficking-related module.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051496","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0090338","count":2},{"id":"GO:0030838","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2052205111304011581","title":"Arterial ECM Remodeling and Coagulation","description":"These proteins show GO terms centered on arterial extracellular matrix turnover (ECM disassembly, elastin catabolic process), smooth muscle cell migration, fibrinolysis, and coagulation (Factor XII activation), plus related leukocyte recruitment\u2014collectively pointing to vascular remodeling and coagulation/inflammatory signaling in arteries. This label captures the core theme of the cluster.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014909","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0060309","count":1},{"id":"GO:0003050","count":1},{"id":"GO:0051919","count":1}]},{"hash":"1478872144120907933","title":"Mitochondrial redox balance and antioxidant defense","description":"The cluster shows a strong emphasis on redox homeostasis and detoxification (cellular oxidant detoxification, redox homeostasis, hydrogen peroxide catabolic process, removal of superoxide radicals) with a mitochondrial connection indicated by cytochrome complex assembly, suggesting roles in mitochondrial redox regulation and antioxidant defense. A few terms about spermatogenesis and extracellular matrix organization are present but appear context-specific rather than defining the core function.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0017004","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0030198","count":3}]},{"hash":"2146250119731830449","title":"Nucleotide metabolism and cofactor biosynthesis","description":"This cluster is focused on nucleotide biosynthesis and interconversion, including AMP salvage, various nucleotide phosphorylations (ADP, CDP, nucleoside monophosphate), and cofactors like NAD+ and CoA biosynthesis. The presence of these GO terms suggests a common theme around nucleotide metabolism and related cofactor biosynthesis, with one outlier term (liver development) likely representing annotation noise rather than a core function.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009435","count":4},{"id":"GO:0015937","count":4},{"id":"GO:0044209","count":4},{"id":"GO:0046940","count":4},{"id":"GO:0046705","count":4}]},{"hash":"2244245823120277957","title":"Unknown","description":"The listed GO terms cover diverse processes: RNA localization to a Cajal body, pore complex assembly, mitochondrial intermembrane space protein import, virion assembly and host-cell translocation, and inflammatory/immunological regulation. The set spans nuclear transport, mitochondrial import, viral life cycle steps, and immune signaling without a single coherent, unifying function for all four proteins. Therefore, no clear, specific label can be confidently assigned.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090666","count":4},{"id":"GO:0046931","count":4},{"id":"GO:0071866","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0050729","count":4}]},{"hash":"2171078894303524041","title":"Redox Homeostasis and Glutathione Metabolism","description":"The GO terms show a clear emphasis on redox balance, oxidative stress response, detoxification, and glutathione biosynthesis, with related processes like cellular redox homeostasis and protein repair. This suggests the cluster centers on maintaining cellular redox state and detoxification pathways, rather than a specific signaling or transcription factor function. While a few terms are peripheral, the dominant theme is redox maintenance via glutathione-related metabolism.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0030091","count":1},{"id":"GO:0034599","count":1}]},{"hash":"1134362490871081933","title":"Plant light sensing and circadian leaf regulation","description":"The GO terms point to plant-specific light perception and circadian control affecting leaves and stomata (detection of visible light, photoprotection, photoreactive repair, circadian rhythm regulation, leaf morphogenesis, stomatal movement). Although there is a term about lateral root development, the dominant themes are photoreception and circadian regulation of leaf physiology. This makes a cohesive, specific cluster name appropriate.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901332","count":1},{"id":"GO:0010617","count":1},{"id":"GO:0010117","count":1},{"id":"GO:0009584","count":1},{"id":"GO:0000719","count":1}]},{"hash":"547518000863654206","title":"Developmental signaling and cytoskeletal regulation","description":"This cluster's top GO terms center on mesoderm development, epithelial to mesenchymal transition, skeletal muscle development, and signaling pathways like calcineurin-NFAT and beta-catenin, plus mitotic spindle attachments and chromosomal condensation. The shared theme is developmental signaling tied to cytoskeletal dynamics and cell cycle regulation, with some DNA repair and metal-response terms present as peripheral associations.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0099566","count":4},{"id":"GO:1905213","count":4},{"id":"GO:0051531","count":4},{"id":"GO:0010791","count":4},{"id":"GO:0007498","count":4}]},{"hash":"79120773455131538","title":"Unknown","description":"The GO terms show a scattered mix: a couple about photosynthesis, but many terms from animal development, yeast growth, RNA modification, and redox processes, with no clear shared function or pathway. Because there is no cohesive theme among the proteins, I cannot assign a meaningful label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0048564","count":2},{"id":"GO:0006777","count":1},{"id":"GO:0018192","count":1},{"id":"GO:0035335","count":1}]},{"hash":"2045677766272615062","title":"Unknown","description":"The top GO terms span redox/respiratory processes, bacterial denitrification, proton transport, and mitochondrial assembly, but also include immune regulation and viral replication and other unrelated processes. There is no single coherent function linking these terms, so a meaningful cluster label cannot be assigned. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0019333","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0070483","count":1}]},{"hash":"1105310895408295862","title":"Nuclear transport and RNA processing","description":"The cluster centers on intracellular transport and RNA localization: scaRNA localization to Cajal bodies and pore complex assembly suggest nuclear trafficking; protein import into mitochondrial intermembrane space and translocation of peptides into host cell cytoplasm indicate broader translocation roles. Some terms (cell division, inflammatory regulation, virion assembly) are more general or context-dependent, so the link is present but not tight.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090666","count":4},{"id":"GO:0046931","count":4},{"id":"GO:0071866","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0050729","count":4}]},{"hash":"375711166955352960","title":"Unknown","description":"This cluster shows a mix of GO terms from neurodevelopment, metabolism (thiamine and beta-alanine biosynthesis), epigenetic modification, immune differentiation, and signaling, with no clear single function tying the proteins together. Therefore there is no reliable cohesive label to assign.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0019383","count":2}]},{"hash":"889225812773551927","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055081","count":1},{"id":"GO:0070207","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0007494","count":1},{"id":"GO:0044205","count":1}]},{"hash":"1399631462032000619","title":"Cofactor biosynthesis and energy metabolism","description":"This cluster shows enrichment for biosynthetic processes such as biotin biosynthesis, protoporphyrinogen IX biosynthesis, lysine biosynthesis, ATP biosynthesis, and pyruvate biosynthesis, pointing to production of cofactors and key energy-related metabolites. A few other terms reflect stress or signaling responses, but the dominant theme is metabolic biosynthesis and energy substrate production, justifying this label.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0012501","count":1}]},{"hash":"250934823950970547","title":"Virus-host interaction and intracellular transport","description":"The cluster includes terms for nuclear pore complex assembly and scaRNA localization to Cajal bodies (nuclear transport/RNA processing), protein import into the mitochondrial intermembrane space, and translocation of peptides into host cell cytoplasm, plus virion assembly and inflammatory signaling such as TNF production. These together suggest a shared theme of intracellular trafficking and host response to infection, spanning transport between compartments and interactions with pathogens. Some terms (cell division, obsolete chaperone folding) are broader or less connected, but the prominent signals are transport-related and inflammation-related processes. Confidence in this label is Moderate.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090666","count":4},{"id":"GO:0046931","count":4},{"id":"GO:0071866","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0050729","count":4}]},{"hash":"2290075714591511442","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning antibiotic response, hormone biosynthesis, diverse biosynthetic pathways (tropane alkaloids, mycolic acids, retinal, melanin), and development, with no connecting edges among the proteins. There isn\u2019t a coherent shared function to justify a specific label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0009710","count":1},{"id":"GO:0071768","count":1},{"id":"GO:0031427","count":1},{"id":"GO:0042574","count":1}]},{"hash":"1437115977771402220","title":"Mesodermal Muscle Development and EMT","description":"The top GO terms point to mesoderm development, epithelial-to-mesenchymal transition, skeletal muscle fiber development, and lung development, suggesting a developmental program centered on mesoderm-derived tissues and muscle differentiation, with EMT linking these processes. Some terms related to calcium signaling and mitotic aspects are present but appear less central to the cluster\u2019s core theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0099566","count":4},{"id":"GO:1905213","count":4},{"id":"GO:0051531","count":4},{"id":"GO:0010791","count":4},{"id":"GO:0007498","count":4}]},{"hash":"2271477098506867584","title":"Amino acid and central carbon metabolism","description":"The proteins appear tied to various amino-acid pathways (glutamate/glutamine, phenylalanine, leucine, lysine) and core central-carbon processes (glycolysis, pyruvate decarboxylation to acetyl-CoA, TCA), suggesting a broad metabolic cluster focused on amino-acid turnover together with general carbon metabolism rather than a single specialized pathway.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019552","count":1},{"id":"GO:0019551","count":1},{"id":"GO:0006537","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0072350","count":1}]},{"hash":"769409499824392196","title":"Fatty acid metabolism and transport","description":"GO terms cluster around fatty acid metabolic processes, biosynthesis, and transport/import across membranes, plus related lipid biosynthesis like lipoteichoic acid and menaquinone. This points to a cohesive group of proteins involved in lipid processing and membrane-associated transport, with a few outliers likely due to annotation noise (e.g., seed coat development). ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019629","count":2},{"id":"GO:0036112","count":2},{"id":"GO:0070395","count":2},{"id":"GO:0015911","count":2},{"id":"GO:0010214","count":2}]},{"hash":"476756167586797038","title":"Chromatin Organization and Nucleosome Assembly","description":"These proteins cluster around chromatin-related processes: heterochromatin organization, nucleosome assembly, and histone modification marks. The terms also point to protein localization to chromatin and regulation of nucleus size, supporting a chromatin maintenance/module interpretation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070828","count":4},{"id":"GO:0098532","count":4},{"id":"GO:0071169","count":4},{"id":"GO:0097298","count":4},{"id":"GO:0080182","count":4}]},{"hash":"829694802123873405","title":"Unknown","description":"The GO terms are highly diverse and do not converge on a single coherent function or pathway (histone mRNA catabolism, mitochondrial translation, DNA repair, plastid transcription, brain development, etc.). With zero edges and only scattered one-off terms, there is no clear common theme to label this cluster a concise biological function. The annotation set also mentions \u201c20 proteins re-added by ReCIPE,\u201d suggesting potential noise rather than a true functional module.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071044","count":1},{"id":"GO:0001560","count":1},{"id":"GO:1905639","count":1},{"id":"GO:1904753","count":1},{"id":"GO:0070129","count":1}]},{"hash":"449374972690335746","title":"Chromatin regulation and transcription control","description":"This cluster is dominated by GO terms tied to controlling gene expression via chromatin state and transcription machinery: DNA-templated transcription, negative regulation of transcription by RNA polymerase I, and histone deacetylation-related terms, suggesting roles in chromatin modification and transcriptional regulation. While there are misc terms related to mitophagy and protein stability, the central theme appears to be transcriptional regulation through chromatin remodeling and histone modification. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031939","count":4},{"id":"GO:0006351","count":4},{"id":"GO:1902894","count":4},{"id":"GO:0045820","count":4},{"id":"GO:0034983","count":4}]},{"hash":"78160593817756074","title":"Unknown","description":"The top GO terms point to a broad mix of processes (dorsal closure, circadian rhythm, pigmentation, seed maturation, lactation, wound healing, liver regeneration, and histone modification regulation) with no obvious common function. With only two edges among four proteins, the cluster shows weak functional coherence, so a precise, representative label cannot be confidently assigned.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007391","count":2},{"id":"GO:0007623","count":2},{"id":"GO:0031063","count":2},{"id":"GO:0034198","count":2},{"id":"GO:2000693","count":2}]},{"hash":"509491749783382171","title":"Amino acid and polyamine acetylation","description":"The cluster is dominated by acetylation-related GO terms, including N-terminal, peptidyl-methionine, spermidine, and putrescine acetylation, plus propionylation. There are also several amino-acid and small-molecule biosynthesis terms (arginine, mycothiol, ectoine, melatonin), suggesting a broader theme around acetylation-regulated biosynthesis. Some terms (e.g., angiogenesis) may reflect annotation noise, but the core signal centers on acetylation processes and related biosynthetic pathways.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":2},{"id":"GO:0006526","count":2},{"id":"GO:0032918","count":2},{"id":"GO:0017196","count":2},{"id":"GO:0001525","count":2}]},{"hash":"2225060241040906016","title":"RNA processing and post-transcriptional regulation","description":"The GO terms center on mRNA splicing, polyadenylation regulation, mRNA tail processing, modification, and stability, as well as translation reinitiation and miRNA-mediated gene silencing, all of which point to post-transcriptional control of gene expression; a note on small-subunit processome assembly aligns with RNA processing in the same broader theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":3},{"id":"GO:1900363","count":3},{"id":"GO:0060211","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1971905383046842175","title":"Plant cell wall biosynthesis and plasmodesmata organization","description":"These GO terms point to plant-specific cell wall formation (oligosaccharide biosynthesis, cellulose biosynthetic regulation, wall modification) and intercellular connectivity (plasmodesma organization), with accompanying glycosylation processes that modify wall components. The cluster likely represents proteins involved in plant cell wall biosynthesis and plasmodesmatal regulation.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009312","count":2},{"id":"GO:0018279","count":2},{"id":"GO:2001009","count":1},{"id":"GO:0009831","count":1},{"id":"GO:0009663","count":1}]},{"hash":"1404777378305519442","title":"Osmoregulation and Osmotic Stress Response","description":"The top GO terms cluster around monoatomic ion transmembrane transport, intracellular water homeostasis, and cellular response to osmotic stress, all of which together indicate a common theme of osmoregulation and adapting to osmotic challenges. This label captures the shared function implied by these terms in a concise way.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034220","count":3},{"id":"GO:0009992","count":3},{"id":"GO:0071470","count":3}]},{"hash":"39272162754902896","title":"Mitochondrial Complex I and IV Assembly","description":"These proteins are tied to assembling mitochondrial respiratory chain complexes I and IV, suggesting a role in mitochondrial biogenesis/assembly rather than catalysis. The GO terms explicitly reference assembly of Complex I and Complex IV, indicating a common theme of respiratory chain biogenesis for this cluster.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032981","count":1},{"id":"GO:0033617","count":1}]},{"hash":"1381661716491614278","title":"Golgi-ER Secretory Trafficking","description":"The cluster shows strong enrichment for GO terms tied to the secretory pathway: protein localization to the Golgi, Golgi-to-plasma membrane transport, and protein secretion, plus endocytic recycling and ER stress response, all pointing to trafficking through the ER\u2013Golgi\u2013plasma membrane axis. Some terms like ribosome biogenesis and DNA-templated transcription are less directly related and may reflect broader roles or annotation noise, but the dominant theme is Golgi/ER\u2013mediated protein trafficking.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000042","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0034976","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0042254","count":2}]},{"hash":"585841498835182193","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006417","count":2},{"id":"GO:0046944","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0034965","count":1},{"id":"GO:1905267","count":1}]},{"hash":"1800636793167148478","title":"mRNA Splicing and Processing Regulation","description":"Most of the top GO terms relate to mRNA maturation and post-transcriptional control, especially mRNA splicing (splice site recognition, spliceosome-mediated splicing) and polyadenylation regulation, along with aspects of mRNA stability and translation regulation (including translation reinitiation and miRNA-mediated silencing). This suggests a cohesive cluster centered on mRNA processing and translational control rather than other functions, even though a stress-related stability term is also present. Confidence: High","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0060211","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0002188","count":2}]},{"hash":"972531786206754096","title":"Unknown","description":"This cluster shows a mix of GO terms centered on neuronal signaling (glutamatergic transmission, long-term potentiation, regulation of synaptic plasticity) but also includes muscle development (myoblast fusion), plant hormone signaling (abscisic acid-activated pathway), sphingolipid biosynthesis, and apoptosis regulation. With only four proteins and no clear, overarching function uniting these terms, there isn\u2019t a defensible single-label theme to assign.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001324","count":2},{"id":"GO:0060963","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0031914","count":2}]},{"hash":"2233648671977663908","title":"Xenobiotic catabolism","description":"The top GO terms point to catabolic and metabolic processing of various chemical compounds (retinoic acid, coumarin, camphor, alkaloids, progesterone) and associated detoxification or stress-related responses (ozone, immobilization stress). This pattern suggests a cluster of proteins involved in xenobiotic metabolism and detoxification rather than a single specific pathway. Confidence: Medium","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":2},{"id":"GO:0034653","count":2},{"id":"GO:0035865","count":2},{"id":"GO:0046226","count":2},{"id":"GO:0042448","count":2}]},{"hash":"1109305966917439508","title":"Cell wall polysaccharide metabolism","description":"The GO terms cluster around remodeling and synthesis of polysaccharides in cell walls (glucan/pectin/alginate) and general cell wall organization, spanning fungal and plant/algal contexts. This suggests a theme of cell wall polysaccharide metabolism rather than a specific, narrow function.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006076","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0042121","count":1},{"id":"GO:0009556","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1487731675964050137","title":"Viral life cycle and virion assembly","description":"The GO terms are centered on viral processes: virion assembly, uncoating, viral life cycle, and proviral latency, with supporting hints from lipid droplet organization and related host interactions. This suggests the cluster comprises proteins involved in viral replication/assembly and associated host factors, rather than a single host pathway. ","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":4},{"id":"GO:0006278","count":3},{"id":"GO:0071492","count":3},{"id":"GO:0019058","count":3},{"id":"GO:0006457","count":3}]},{"hash":"519689272982143524","title":"Plant stress signaling and hormone pathways","description":"The top GO terms center on abscisic acid biosynthesis and signaling, ethylene signaling, and responses to desiccation and high light, pointing to a plant stress-signaling module regulated by ABA and ethylene. There are also transcription-related terms, with a few ribosome-associated quality-control terms that may reflect general stress-related housekeeping rather than defining the cluster. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990116","count":1},{"id":"GO:0072344","count":1},{"id":"GO:0010116","count":1},{"id":"GO:0009644","count":1},{"id":"GO:0009269","count":1}]},{"hash":"135883018916299801","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006294","count":1},{"id":"GO:0006295","count":1},{"id":"GO:0006361","count":1},{"id":"GO:0070911","count":1},{"id":"GO:0006293","count":1}]},{"hash":"1442513785083730590","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045016","count":1},{"id":"GO:0006824","count":1},{"id":"GO:1903830","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0051083","count":1}]},{"hash":"954856600176002136","title":"Vacuolar autophagy pathways (Cvt and macroautophagy)","description":"The top GO terms are dominated by autophagy-related processes: cytoplasm to vacuole targeting by the Cvt pathway, macroautophagy, and piecemeal microautophagy of the nucleus, pointing to a cluster of proteins involved in vacuolar degradation and selective autophagy. Ubiquitination further supports involvement in protein turnover. Some terms (e.g., hippocampus development, thiamine biosynthesis) are likely ancillary annotations or noise, but the core signal supports autophagy/vesicular degradation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0032258","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0009228","count":1},{"id":"GO:0034727","count":1}]},{"hash":"2026009755049078904","title":"Unknown","description":"The GO terms span detoxification (epoxygenase P450), oxidative stress and toxin responses, cell-cycle and DNA replication regulation, microtubule dynamics, and development, with no clear shared function or interaction pattern among the four proteins. The absence of a cohesive theme or network connectivity suggests there isn\u2019t a single interpretable cluster beyond miscellaneous functions.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":2},{"id":"GO:1903378","count":1},{"id":"GO:0046685","count":1},{"id":"GO:0071406","count":1},{"id":"GO:0031571","count":1}]},{"hash":"1883351637053344953","title":"Nervous system development","description":"The cluster\u2019s GO terms cluster around neural development and glial differentiation (glial cell fate determination; CNS vasculogenesis), with additional connections to cell adhesion, cytoskeleton remodeling, and broader developmental processes. While some terms (root development, cuticle patterning) are non-neural outliers, the convergent signals point to a developmental, especially neural, theme. Confidence: Medium","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":4},{"id":"GO:1904793","count":3},{"id":"GO:0071562","count":3},{"id":"GO:0015991","count":3},{"id":"GO:0090138","count":3}]},{"hash":"363913056488635936","title":"Unknown","description":"Top terms are empty and there are no edges among the four proteins, so there is no detectable shared function or enrichment to name the cluster. Thus Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"138453023475138058","title":"SRP-dependent Cotranslational Targeting to Membrane","description":"Several of the top GO terms cluster around the SRP-dependent cotranslational targeting to the membrane, indicating these proteins are mainly involved in guiding nascent polypeptides to the membrane during translation. While there are some unrelated or obsolete annotations present, the strongest recurring function is membrane targeting via the signal recognition particle pathway, suggesting this cluster represents SRP-mediated protein targeting to membranes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044781","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0006351","count":1}]},{"hash":"91100273433587568","title":"Pentose phosphate pathway proteins","description":"GO terms cluster around pentose-phosphate shunt and pentose catabolic processes, indicating metabolism of pentose sugars via the pentose phosphate pathway, including the non-oxidative branch. This consistent theme supports a cohesive label for the cluster as PPP-related proteins.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009052","count":3},{"id":"GO:0019323","count":3},{"id":"GO:0044262","count":3},{"id":"GO:0006098","count":3}]},{"hash":"1989165121539437013","title":"Vacuolar Ion Transport and Acidification","description":"The GO terms cluster around vacuolar processes, including vacuolar acidification, vacuole organization, and protein targeting to the vacuole, plus ion transport such as sodium and proton transmembrane movement and copper homeostasis. This combination points to a module of proteins involved in maintaining vacuolar ion balance and acidification, potentially including vesicle trafficking to the vacuole and associated proton pumps or transporters.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0042777","count":2},{"id":"GO:0006626","count":2}]},{"hash":"1894174559154920832","title":"Mitotic spindle dynamics and microtubule organization","description":"The top GO terms are dominated by microtubule- and spindle-related processes, including spindle assembly and elongation, lateral attachment to kinetochores, minus-end directional sliding, nuclear migration along microtubules, and maintenance of microtubule polarity. A neuronal projection maintenance term suggests a broader microtubule framework governing neurite stability as well. This points to a coherent cluster of proteins tied to microtubule organization and spindle dynamics rather than signaling or metabolic roles.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990535","count":3},{"id":"GO:0001560","count":3},{"id":"GO:0072092","count":3},{"id":"GO:0031534","count":3},{"id":"GO:0000022","count":3}]},{"hash":"225447191923766859","title":"Developmental gene regulation and neural development","description":"This cluster is dominated by terms related to development and neural formation (forebrain development, neural tube closure, multicellular organism development, skeletal system development) and transcriptional control (DNA-templated transcription), suggesting proteins that jointly regulate gene expression during development and neural patterning. Additional items about ER-stress\u2013induced apoptosis and stress responses (cadmium, Gram-positive defense) may reflect cellular stress contexts these proteins participate in, or pleiotropic roles during development. Overall, the core theme is developmental transcriptional regulation with emphasis on neural and organogenesis processes.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001843","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0071276","count":2}]},{"hash":"2092637772151574231","title":"Unknown","description":"The top terms span immune signaling (T cell receptor signaling; natural killer cell differentiation), development (melanocyte migration; myoblast differentiation; budding cell apical bud growth), and cell cycle regulation (mitotic spindle assembly; DNA damage checkpoint signaling; JUN phosphorylation; protein import into nucleus). With only 3 proteins and no obvious shared pathway or function, there isn\u2019t a coherent theme to label a specific cluster function other than Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050852","count":1},{"id":"GO:0097324","count":1},{"id":"GO:0009636","count":1},{"id":"GO:1990801","count":1},{"id":"GO:0014835","count":1}]},{"hash":"1194803352633105699","title":"Unknown","description":"The top GO terms are a mix of antibiotic biosynthesis and purine/ureide catabolism along with several unrelated cellular processes (neuronal vesicle transport, autophagy, proteasome assembly), showing no single coherent function tying the proteins together. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:1901766","count":2},{"id":"GO:0010136","count":2},{"id":"GO:0006145","count":2},{"id":"GO:0000256","count":2}]},{"hash":"200726058058913669","title":"Metal Ion Transport and Mercury Detox","description":"This cluster centers on ion transport and metal detox processes, with GO terms covering calcium, copper, potassium, and proton transport, maintenance of electrochemical gradients, and detoxification/response to mercury. The presence of related terms like T-tubule organization suggests membrane-associated ion handling typical of muscle cells, but the unifying theme remains metal ion transport and detoxification.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046689","count":3},{"id":"GO:1903515","count":2},{"id":"GO:0010248","count":2},{"id":"GO:0050787","count":2},{"id":"GO:0006825","count":2}]},{"hash":"2097754137729446040","title":"Proteostasis and stress response","description":"This cluster's GO terms center on maintaining protein homeostasis and managing cellular stress: ER unfolded protein response, proteasome regulatory particle assembly, late endosomal microautophagy, protein processing and folding, and oxidative stress response. While there is a minor term about neuronal vesicle transport, the dominant themes point to proteostasis and cellular stress adaptation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990048","count":2},{"id":"GO:0070651","count":2},{"id":"GO:0061738","count":2},{"id":"GO:0016485","count":2},{"id":"GO:0070682","count":2}]},{"hash":"1716982618473749164","title":"Innate Immune Signaling Regulation and PI3K/AKT","description":"The top terms cluster around regulation of innate immune signaling (RIG-I/MDA-5 pathways, interferon production) and PI3K/AKT signaling, suggesting a core theme of immune signaling modulation coupled with PI3K pathway control. Additional terms touch ribosome assembly and mitochondrial translation, which may reflect housekeeping processes present in the same proteins but do not define the cluster\u2019s primary function. Overall, the clump most coherently maps to innate immune signaling regulation with PI3K/AKT involvement.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014065","count":1},{"id":"GO:0042256","count":1},{"id":"GO:2000510","count":1},{"id":"GO:0090023","count":1},{"id":"GO:0039534","count":1}]},{"hash":"526967509953860301","title":"Unknown","description":"The GO terms are highly diverse (epigenetic demethylation, hormone signaling, immune cytokine production, cartilage development, nitrogen metabolism, nucleotide biosynthesis), showing no single clear functional theme for the cluster. With only three proteins and scattered terms, a cohesive, specific label is not justifiable.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070988","count":1},{"id":"GO:0090031","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0060192","count":1},{"id":"GO:0003420","count":1}]},{"hash":"146808938920748174","title":"Detoxification and xenobiotic catabolism","description":"The top GO terms show detoxification (cellular oxidant detoxification, epoxygenase P450 pathway) and various catabolic processes for diverse molecules (stilbene, uracil, glucuronoside, strigolactone). This suggests the proteins function in metabolizing and clearing xenobiotics and secondary metabolites rather than a single, tight pathway, hence the label.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0006212","count":1},{"id":"GO:0019391","count":1},{"id":"GO:1901601","count":1}]},{"hash":"1890061012773572811","title":"Proteostasis and Protein Quality Control","description":"The GO terms collectively point to protein folding, processing, misfolded-protein response, and degradation pathways (including autophagy and proteasome-related processes), plus mitochondrial protein import and inclusion body dynamics. This pattern suggests the cluster centers on maintaining protein homeostasis rather than a single specific pathway. Therefore the label Proteostasis and Protein Quality Control is appropriate.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070407","count":1},{"id":"GO:0070651","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0061738","count":1},{"id":"GO:0016485","count":1}]},{"hash":"436514022474940963","title":"Aminoacyl-tRNA Synthetases","description":"The top GO terms are dominated by multiple aminoacyl-tRNA synthetases (valyl-, isoleucyl-, methionyl-, leucyl-) and general translation-related terms (translation, regulation of translational fidelity). This strongly indicates the cluster centers on aminoacylation of tRNAs and protein synthesis machinery, with a few outliers likely due to annotation noise (e.g., chitin response, ERAD). Therefore, a concise label focusing on aaRS and translation is most representative.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006438","count":1},{"id":"GO:0000372","count":1},{"id":"GO:0006428","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006431","count":1}]},{"hash":"318694917706254885","title":"Photosystem I and light-stress response","description":"The top GO terms center on photosystem I functions (photosynthesis, PSI electron transport, NADP+ reduction, PSI stabilization) with supporting terms for high-light and desiccation responses. This indicates a cluster of PSI-related components or assembly/stability factors that operate under light stress and drought conditions.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009780","count":1},{"id":"GO:0009773","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0042550","count":1},{"id":"GO:0010116","count":1}]},{"hash":"793518220691462576","title":"Proteostasis and stress response","description":"This cluster\u2019s GO terms point to protein homeostasis and cellular stress management, including ER unfolded protein response, protein processing and folding, proteasome assembly, and late endosomal microautophagy, along with oxidative stress response and metabolic regulation. Although a few terms are peripheral (e.g., rRNA decay, translesion synthesis), the dominant theme is proteostasis networks that maintain protein quality under stress.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1990048","count":3},{"id":"GO:0070651","count":3},{"id":"GO:0061738","count":3},{"id":"GO:0016485","count":3},{"id":"GO:0070682","count":3}]},{"hash":"1940968158495416874","title":"Nucleocytoplasmic Transport","description":"Based on the GO terms, the proteins are involved in importing NLS-bearing proteins into the nucleus, exporting tRNA from the nucleus, nuclear pore organization, and regulation of nuclear import, indicating a core function in nucleocytoplasmic transport and nuclear pore dynamics. Additional terms about nuclear inner membrane localization and mitotic nuclear membrane events support a shared theme around nuclear transport machinery.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":3},{"id":"GO:0006409","count":3},{"id":"GO:0010827","count":2},{"id":"GO:0006999","count":2},{"id":"GO:0070208","count":2}]},{"hash":"2227590215443536508","title":"Muscle metabolism and cytoskeletal remodeling","description":"The Top Terms include glycolysis and gluconeogenesis (energy metabolism) as well as processes tied to cytoskeleton organization, axon guidance, and skeletal muscle tissue regeneration. This suggests a theme where metabolic energy production supports structural remodeling in muscle and neural contexts, despite some unrelated or obsolete terms present. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903298","count":1},{"id":"GO:0032889","count":1},{"id":"GO:0061621","count":1},{"id":"GO:0043403","count":1},{"id":"GO:0009405","count":1}]},{"hash":"1663119373901187523","title":"Unknown","description":"The terms show a highly heterogeneous mix (DNA replication, translation initiation, GTPase regulation, plant/oligodendrocyte/ethylene-related processes, and amino acid metabolism), with several obsolete GO entries. There isn\u2019t a single coherent biological theme that distinctly characterizes the cluster, so a definite functional label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0019509","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0006446","count":1}]},{"hash":"1498889737199759524","title":"Unknown","description":"The top GO terms are a mix of viral-related processes (virion assembly, uncoating of virus, proviral latency, viral life cycle) with unrelated terms (carotene biosynthesis, UV-A response, lipid droplet organization, protein folding). There is no clear, cohesive functional theme linking the proteins, and the lack of edges/triangles supports a non-specific grouping. Therefore, this cluster cannot be confidently labeled with a single representative function.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016120","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0071492","count":1},{"id":"GO:0019058","count":1},{"id":"GO:0006457","count":1}]},{"hash":"192122175807699175","title":"Plant photosynthesis and metabolism","description":"The top GO terms cluster around the core photosynthetic processes: reductive pentose-phosphate cycle (Calvin cycle), photorespiration, photosynthesis, and carbon fixation, indicating proteins involved in plant energy capture and carbon metabolism. Additional terms point to plant-specific aspects like cell wall assembly and fatty acid transport, suggesting broader plant metabolism involvement. Overall, the cluster appears to represent plant photosynthetic function and related metabolic pathways.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019253","count":2},{"id":"GO:0009853","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0015977","count":2},{"id":"GO:0006783","count":1}]},{"hash":"2249456883186635070","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006543","count":1},{"id":"GO:0042823","count":1},{"id":"GO:0008614","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0000304","count":1}]},{"hash":"596989182308411539","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0035606","count":3},{"id":"GO:0042823","count":3}]},{"hash":"744217138511850627","title":"Metabolic and Redox Pathways","description":"The GO terms indicate diverse metabolic activities (xanthine catabolism, nitrate assimilation, folate metabolism) alongside energy production and redox processes (ATP synthesis coupled electron transport, ROS metabolism, ferredoxin metabolism), suggesting a cluster defined by general cellular metabolism and redox balance rather than a single specific pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009115","count":1},{"id":"GO:0042773","count":1},{"id":"GO:0006124","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0051881","count":1}]},{"hash":"1527883008751880918","title":"Mitochondrial dynamics and vesicle trafficking","description":"The top GO terms cluster around mitochondrial processes (distribution, fission, inheritance, membrane organization) and intracellular trafficking (Golgi to plasma membrane transport, endocytic recycling, protein targeting to vacuole), suggesting proteins involved in regulating mitochondrial morphology together with vesicle trafficking pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048013","count":2},{"id":"GO:0048312","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0000266","count":2}]},{"hash":"919283971894063256","title":"Vitamin biosynthesis and turnover","description":"The GO terms point to biosynthetic and catabolic processes for several vitamins (folic acid, thiamine, and PQQ), suggesting a cohesive theme of vitamin production and breakdown rather than other functions. Confidence: High","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009396","count":1},{"id":"GO:0035999","count":1},{"id":"GO:0015942","count":1},{"id":"GO:0046657","count":1},{"id":"GO:0009228","count":1}]},{"hash":"1614868553108607407","title":"Carbohydrate catabolism and nucleotide salvage","description":"This cluster is dominated by GO terms related to sugar metabolism and breakdown (lactose/tagatose-6-phosphate pathways, sucrose response, carbohydrate phosphorylation, tagatose-6-phosphate catabolic processes) and also includes nucleotide salvage/biosynthesis (adenosine/AMP salvage, dATP biosynthesis). While a couple of terms like hepatocyte differentiation appear, the sugar metabolism signals are the strongest common theme, justifying a carbohydrate-centered label with nucleotide salvage as a secondary facet.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032094","count":2},{"id":"GO:0070365","count":2},{"id":"GO:0019512","count":1},{"id":"GO:0097171","count":1},{"id":"GO:0006175","count":1}]},{"hash":"978577039131504549","title":"One-carbon metabolism and tetrapyrrole biosynthesis","description":"The GO terms cluster around methylation, methionine and homocysteine metabolism, and adenine biosynthesis, along with protein-tetrapyrrole linkage and chlorophyll-related processes. This points to a broader metabolism theme centered on one-carbon units and tetrapyrrole biosynthesis (which includes chlorophyll and heme-related cofactors), with a hint of plant-specific regulation (chlorophyll turnover, hypoxia sensing) and a general transcription/response context. While some terms are peripheral, the dominant signal is metabolic biosynthesis linked to one-carbon chemistry.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":2},{"id":"GO:0019280","count":2},{"id":"GO:0044416","count":2},{"id":"GO:0046084","count":2},{"id":"GO:0050667","count":2}]},{"hash":"990842759769393674","title":"RNA splicing and mRNA processing cluster","description":"The terms are dominated by spliceosome-related processes (snRNP and spliceosomal complex assembly) and mRNA processing (splicing, deadenylation-dependent decapping, histone mRNA metabolism, transcription termination), indicating a coherent RNA-processing/splicing function for this cluster, with a few peripheral terms.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":2},{"id":"GO:0070317","count":2},{"id":"GO:1990141","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0042633","count":2}]},{"hash":"2173020989449678099","title":"Mesodermal differentiation and organogenesis","description":"Most terms describe development and differentiation of mesoderm-derived tissues (paraxial mesoderm, skeletal muscle, heart/aorta, kidney mesenchyme). Additional terms touch on differentiation of other organs (lung neuroendocrine cells, carotid body) and muscle adaptation, indicating a core theme of mesodermal lineage specification and organ formation. Some terms are broader or metabolic in nature, but the dominant signal is mesodermal development.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":3},{"id":"GO:0043503","count":3},{"id":"GO:0061103","count":3},{"id":"GO:0048666","count":3},{"id":"GO:0061100","count":3}]},{"hash":"1610582719791194485","title":"DNA Damage Recognition and Transcriptional Regulation with Proteostasis","description":"This cluster shows strong signals for DNA damage recognition and transcriptional regulation, with additional hints of proteostasis and ubiquitin-related control (protein stabilization, neddylation regulation), suggesting a combined role in genome maintenance, transcription control, and protein quality management rather than a single pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000715","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0032092","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0050821","count":1}]},{"hash":"711204449677678397","title":"Multi-lineage differentiation","description":"The GO terms reflect differentiation across multiple lineages (immune, neural, hematopoietic, epithelial) and developmental processes, rather than a single pathway, so the proteins likely participate in general cell fate decisions. With no detected interactions among the proteins, the label captures a broad functional theme rather than a specific mechanism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045061","count":3},{"id":"GO:0090295","count":3},{"id":"GO:2000977","count":3},{"id":"GO:0060216","count":3},{"id":"GO:0035799","count":3}]},{"hash":"1965943473671770431","title":"Glycolysis and PPP Regulation","description":"Top GO terms converge on regulation of glucose utilization and carbohydrate metabolism, including glycolysis inhibition, PPP shunt regulation, and fructose 2,6-bisphosphate\u2013related metabolic steps. The brain development term and other notes appear incidental to the core metabolic theme. Thus, a label reflecting control of carbohydrate flux is appropriate.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071279","count":1},{"id":"GO:0043456","count":1},{"id":"GO:0045820","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0007420","count":1}]},{"hash":"1574934020569811691","title":"Selective organelle autophagy under nitrogen starvation","description":"The proteins here are linked to multiple autophagy-related processes, including mitophagy, pexophagy, glycophagy, nucleophagy, and autophagosome assembly, along with a cellular response to nitrogen starvation. This combination points to a cohesive theme of selective organelle turnover and autophagy activity during nutrient limitation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006995","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0030242","count":2},{"id":"GO:0061723","count":2}]},{"hash":"2273034268382308318","title":"RNA transcription machinery and ribosome biogenesis","description":"These terms center on RNA transcription by RNA polymerases I, II, and III (including tRNA transcription and transcription elongation/termination) and on ribosome biogenesis, suggesting the cluster comprises general transcription-related proteins linked to ribosome production.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0006386","count":1},{"id":"GO:0006385","count":1},{"id":"GO:0006360","count":1}]},{"hash":"1589710373660687286","title":"Unknown","description":"No coherent functional theme is detectable: there are no edges, no enriched GO terms, and no shared annotations to tie these proteins together. Without functional signals, a reliable label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1907158389402167569","title":"Xenobiotic and steroid catabolism","description":"This cluster is dominated by GO terms describing catabolic/metabolic processes for various small molecules and steroids (retinoic acid, coumarin, camphor, alkaloids, progesterone) and related hormone regulation; the strongest signal points to breakdown of xenobiotics and steroid compounds. A few terms relate to stress responses or regulation, but the core theme centers on chemical metabolism and catabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":2},{"id":"GO:0034653","count":2},{"id":"GO:0035865","count":2},{"id":"GO:0046226","count":2},{"id":"GO:0042448","count":2}]},{"hash":"1367620239840099421","title":"Male germ cell development and spermatogenesis","description":"The top GO terms are heavily focused on male gonad development and spermatogenesis, including a term for negative regulation of male germ cell proliferation, indicating a germline development/regulation theme. Other terms (DNA-templated transcription, oxidative stress response, prolyl hydroxylation, ECM organization) appear secondary or ancillary. Given the prominence of germline-related terms, this label best captures the core function of the cluster, though some annotations may reflect broader or multi-functional roles. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0030198","count":1},{"id":"GO:0018401","count":1}]},{"hash":"1160999490863716890","title":"Mitochondrial respiration and proton transport","description":"The Top Terms point to mitochondrial energy metabolism and electron transport (mitochondrial respiratory chain assembly, electron transport from ubiquinol to cytochrome c, aerobic respiration) and proton transmembrane transport, indicating a core theme of mitochondrial function. Some unrelated terms may reflect annotation noise but do not outweigh the mitochondrial signal. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034551","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0009060","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0048235","count":1}]},{"hash":"643906860860832040","title":"Unknown","description":"The GO terms span multiple disparate biological areas (cofactors biosynthesis, metabolism, development, immune differentiation, and signaling) with no clear shared function tying the cluster together. Because of this lack of a cohesive theme, I label it Unknown.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009435","count":1},{"id":"GO:0010269","count":1},{"id":"GO:0021987","count":1},{"id":"GO:0009228","count":1},{"id":"GO:0034720","count":1}]},{"hash":"1335957182380093983","title":"Plant peptide and nutrient transporters with hormone signaling","description":"This cluster is enriched for transmembrane transport of dipeptides/oligopeptides, nitrate, phosphate, and arabinose, plus hormone-related terms (auxin signaling and gibberellin homeostasis). The mix suggests a group of plant membrane transporters involved in nutrient uptake and coordinated hormonal responses.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":3},{"id":"GO:0042938","count":3},{"id":"GO:0010167","count":3},{"id":"GO:0080055","count":3},{"id":"GO:0009635","count":3}]},{"hash":"388195005688173041","title":"Diverse Solute Transmembrane Transporters","description":"The top GO terms are dominated by various transmembrane transport activities for different solutes (sulfate, aspartate, chloride, fructose, oxalate) and by regulation of membrane potential, suggesting a membrane transporter or transporter-associated function. A few terms like gastric acid secretion and sperm capacitation are also membrane-related but less central to a cohesive transport theme. Overall, the cluster appears to reflect diverse membrane transport capabilities across different substrates.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:1902358","count":1},{"id":"GO:0089712","count":1},{"id":"GO:1902476","count":1},{"id":"GO:0042391","count":1}]},{"hash":"187875252563502669","title":"Vacuolar amino acid transporters","description":"Top GO terms indicate transmembrane transport of several amino acids (asparagine, arginine, histidine, glutamate, proline) into or out of the vacuole, including import into and export from the vacuole. This suggests a cohesive function as vacuolar amino acid transporters. Some terms are obsolete or peripheral, but the dominant signal supports this transporter role.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006867","count":1},{"id":"GO:1990818","count":1},{"id":"GO:0090452","count":1},{"id":"GO:0089708","count":1},{"id":"GO:1901481","count":1}]},{"hash":"1283325405314873113","title":"Diverse Substrate Transmembrane Transporters","description":"This cluster is best described by transmembrane transport activity across a wide range of substrates (phosphate, arabinose, nitrate, vitamins, carbohydrates, xenobiotics, etc.), pointing to membrane transporter proteins with broad specificity rather than a single substrate. The varied GO terms cluster around transport rather than a single metabolic process, supporting a transporter-focused designation, even though the network is small.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0008643","count":1},{"id":"GO:1900754","count":1}]},{"hash":"1893836140153655552","title":"Plant Hormone Response and Phenylpropanoid Biosynthesis","description":"The top GO terms cluster around plant hormone responses (gibberellin and ethylene) and regulation of secondary metabolism pathways (lignin and flavonol biosynthesis), suggesting a theme of hormone signaling linked to phenylpropanoid metabolism. A few other terms (chromatin/meiotic processes) appear sparsely, likely noise, but the hormone-metabolism connection is the strongest signal.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009739","count":1},{"id":"GO:1901430","count":1},{"id":"GO:1905839","count":1},{"id":"GO:0010520","count":1},{"id":"GO:0035066","count":1}]},{"hash":"2206912006485810390","title":"DNA methylation\u2013mediated gene silencing in development","description":"The top GO terms center on DNA methylation and siRNA-directed gene silencing, with related chromatin modification annotations and a couple of development terms (antennal and eye photoreceptor development). This points to an epigenetic regulatory role in development, mainly via DNA methylation pathways. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010424","count":1},{"id":"GO:0080188","count":1},{"id":"GO:0071158","count":1},{"id":"GO:0090308","count":1},{"id":"GO:0010390","count":1}]},{"hash":"2204067182650715229","title":"Cellular stress responses and transport regulation","description":"The top GO terms cluster around responses to UV-A, gamma radiation, and hydrogen peroxide, plus estradiol signaling and negative regulation of intracellular transport, with transport-related terms (anterograde axonal protein transport) and some lens/aging related terms. Together they suggest a functional module where cellular stress signaling intersects with regulation of intracellular trafficking.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":2},{"id":"GO:0032387","count":2},{"id":"GO:0070141","count":2},{"id":"GO:0071480","count":2},{"id":"GO:1905907","count":2}]},{"hash":"438604884141490016","title":"Unknown","description":"The terms cover chromatin modification, protein assembly, ubiquitin-mediated regulation, metabolism, plant hormone signaling, metal stress response, immune signaling, and chlorophyll pathways, with no clear shared function. This makes an Unknown label the most appropriate.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016576","count":2},{"id":"GO:0051291","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0090526","count":2},{"id":"GO:1902325","count":2}]},{"hash":"749664557169547902","title":"Regulation of synaptic vesicle exocytosis","description":"The top GO terms center on vesicle release and synaptic function\u2014short-term synaptic potentiation, regulation of vesicle fusion and exocytosis, and calcium-regulated exocytosis\u2014together with neuronal development cues like dendrite extension. Although a few terms touch on non-neuronal exocytosis (e.g., insulin secretion), the dominant pattern is regulatory control of vesicle release at synapses, suggesting a neural communication theme.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990926","count":2},{"id":"GO:0032024","count":2},{"id":"GO:1990927","count":2},{"id":"GO:0035023","count":2},{"id":"GO:1901002","count":2}]},{"hash":"1344632722470987924","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071044","count":3},{"id":"GO:2000627","count":3},{"id":"GO:2000637","count":3},{"id":"GO:0042780","count":3},{"id":"GO:0034476","count":3}]},{"hash":"2179251785737748588","title":"Unknown","description":"The top terms are highly diverse and include obsolete chromatin-related regulation, vesicle and junction assembly, stress and developmental terms, and basic cellular processes with no clear shared function. With only three proteins and no edges, there is no cohesive biological theme tying these terms together, so the cluster appears functionally heterogeneous.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904793","count":2},{"id":"GO:0071562","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0015991","count":2}]},{"hash":"2218080662895066590","title":"Unknown","description":"There is no clear shared function among the proteins; the only annotated terms are pollination and aluminum cation transport, each with a single occurrence, and the cluster has no observed interactions (Edges 0, Max Degree 0). This prevents defining a concise, representative label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009856","count":1},{"id":"GO:0015690","count":1}]},{"hash":"544700069957237384","title":"Gluconeogenesis and Glycolysis Regulation","description":"This cluster centers on carbohydrate metabolism, with GO terms highlighting gluconeogenesis, regulation of glycolytic process, fructose-1,6-bisphosphate metabolism, and glycerol catabolic processes, plus related responses such as cellular reaction to glucose starvation. While a few terms touch on other processes, the dominant theme is control and flux through glucose metabolism pathways.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006111","count":1},{"id":"GO:0051289","count":1},{"id":"GO:0030308","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0045820","count":1}]},{"hash":"797734973327280274","title":"Unknown","description":"The cluster contains 3 proteins with no edges or shared GO terms provided, so there is no identifiable common function or pathway to name the group. Without overlapping annotations or interactions, the functional theme cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]}]