[{"hash":"794208000041736908","title":"Floral Meristem Identity Regulation","description":"The cluster shows strong enrichment for terms about maintenance of floral and inflorescence meristem identity, combined with DNA-templated transcription and plant reproductive processes (e.g., double fertilization forming zygote and endosperm). This pattern suggests a group of transcriptional regulators coordinating floral/inflorescence meristem identity and flowering-related development in plants.","confidence":"High","size":29,"edges":403,"triangles":3576,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0010076","count":11},{"id":"GO:0090009","count":11},{"id":"GO:0010077","count":11},{"id":"GO:2001016","count":11}]},{"hash":"1788996371538489257","title":"Drosophila egg chamber development and epithelial polarity","description":"The cluster shows strong representation of follicle cell adhesion and maintenance of polarity in the follicular epithelium, which are central to Drosophila egg chamber development. Chitin biosynthesis also fits with extracellular structures associated with the egg chamber and epithelial remodeling. Some defense- or salicylic-acid related terms may be noise or broader regulatory signals, but the dominant theme is oogenesis-related epithelial organization.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031347","count":2},{"id":"GO:0071446","count":2},{"id":"GO:2000031","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0006031","count":2}]},{"hash":"1767917985372228897","title":"Centromeric chromatin assembly and mitosis","description":"The top terms cluster around chromatin organization and centromere-specific assembly (CENP-A), including histone H3 acetylation and mitotic-related processes like cell division and microtubule severing, suggesting a chromatin-centric role in mitosis. Some terms (ER transport, development) seem peripheral or noisy, but the dominant signal is centromeric chromatin assembly linked to cell division.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0043966","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0006888","count":3}]},{"hash":"1647843861525594529","title":"Mitochondrial and plastid RNA processing in plants","description":"The top GO terms cluster around RNA maturation, editing, and transcription in plant organelles (mitochondria and chloroplasts/plastids), including mitochondrial mRNA processing/modification, cytidine-to-uridine editing, plastid transcription, and chloroplast RNA modification, as well as chloroplast-nucleus signaling. This pattern strongly suggests a set of proteins involved in organellar RNA processing and regulation in plants, with the seed dormancy term likely reflecting broader developmental context. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":7},{"id":"GO:0009451","count":7},{"id":"GO:0016554","count":7},{"id":"GO:0080156","count":7},{"id":"GO:1905639","count":7}]},{"hash":"1360949165993734970","title":"Diverse Transmembrane Transporters","description":"The cluster is dominated by GO terms for transport across membranes of a wide range of substrates (sialic acid, vitamins, urate, organic cations, galactose, 4-hydroxyphenylacetate, nitrate, potassium) and even neurotransmitter loading into synaptic vesicles, indicating a cohesive group of membrane transport proteins with broad substrate specificity rather than a single substrate.","confidence":"High","size":29,"edges":43,"triangles":13,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":13},{"id":"GO:0035461","count":13},{"id":"GO:0015747","count":13},{"id":"GO:0070715","count":13},{"id":"GO:0015757","count":13}]},{"hash":"652986550641097957","title":"Unknown","description":"The Top Terms reveal a highly diverse set of functions, including visual perception, angiogenesis, multicellular development, apoptosis regulation, plant photosynthetic electron transport, tRNA aminoacylation, and various stress responses, with several terms labeled obsolete. These terms span animal, plant, and broad cellular processes with little apparent overlap, making it hard to identify a single coherent biological theme for the cluster. Given this heterogeneity, there isn't a clear functional label beyond Unknown.","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0007275","count":2}]},{"hash":"586806624567218944","title":"Unknown","description":"The terms span development (neural tube closure, forebrain and skeletal system development) and basic cellular processes (cell division, mitotic cycle, transcription) alongside stress/immune-related responses (defense to Gram-positive bacteria, ER stress\u2013induced apoptosis, invasive growth under glucose limitation). The lack of a unifying biological theme and the absence of network structure (Edges 0, Triangles 0) suggest these proteins do not form a coherent functional cluster, so no specific label can be confidently assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050830","count":5},{"id":"GO:0001843","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0001403","count":4}]},{"hash":"2043502718890394412","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0090615","count":5},{"id":"GO:0009451","count":5},{"id":"GO:0016554","count":5},{"id":"GO:0090502","count":5},{"id":"GO:0070129","count":5}]},{"hash":"1735763066698849154","title":"RNA processing and translation initiation factors","description":"The Top Terms cluster around RNA metabolism and translation control\u2014notably IRES-dependent translational initiation, mRNA modification/stabilization, and helicase activity regulation\u2014suggesting a theme of RNA processing and regulation of protein synthesis. While a couple of terms (e.g., DNA integration, defense response) are broader or historical annotations, the dominant signal points to RNA maturation and initiation of translation. This supports labeling the cluster as RNA processing and translation initiation factors.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0051245","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0015074","count":2}]},{"hash":"1477446233541184675","title":"Plant transcriptional regulation and development","description":"This cluster is enriched for terms tied to regulation of transcription (GO:0006355, GO:0000122) and chromatin remodeling, alongside plant-specific developmental and hormone signaling processes (cytokinin-activated signaling, secondary cell wall biogenesis, seed growth, chlorophyll biosynthesis). The common theme appears to be transcriptional control combined with growth- and development-related signaling in plants, which likely coordinates cell-wall remodeling and chlorophyll-related processes during development.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0009736","count":5},{"id":"GO:0043044","count":4},{"id":"GO:1901348","count":4},{"id":"GO:0021983","count":3}]},{"hash":"1058312627216263779","title":"Unknown","description":"The GO terms span unrelated themes (antibacterial peptide regulation, proteolysis, antigen processing, systemic resistance, signaling, physiology, and plant-like xylan metabolism) with no clear shared process or strong connectivity, so there is no coherent functional label for this cluster. Therefore, Unknown is the most appropriate designation.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002803","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0070305","count":2},{"id":"GO:0002016","count":2},{"id":"GO:0042985","count":2}]},{"hash":"37343946453174840","title":"Unknown","description":"The Top Terms include regulation of transcription, general metabolic processes, DNA integration, neuron-specific localization, and several plant secondary metabolism terms (lignin, anthocyanin) alongside xenobiotic and antibiotic metabolism. This mix spans diverse biological areas with no clear unifying pathway or function, and the absence of edges within the cluster further suggests a lack of cohesive function. Therefore, a single, representative label cannot be confidently assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0006796","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0090502","count":2},{"id":"GO:0002175","count":2}]},{"hash":"1529869639180925572","title":"Auxin-regulated plant cell wall biosynthesis","description":"The cluster centers on auxin signaling/transport and biosynthetic processes for the plant cell wall, including lignin and cutin biosynthesis and secondary cell wall biogenesis, suggesting proteins linked to auxin-driven growth and wall remodeling. The DNA integration term is less aligned, but the dominant auxin and wall biosynthesis themes support this interpretation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0009834","count":2},{"id":"GO:0046620","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2}]},{"hash":"786174114627605733","title":"Glycolysis and Carbohydrate Metabolism","description":"Most frequent GO terms point to glycolytic processes and carbohydrate metabolism (canonical glycolysis; fructose-6-phosphate metabolism; glycogen catabolism; glycolysis from storage polysaccharides), indicating energy-yielding carbohydrate pathways as the cluster's core function. A few terms related to tRNA processing, methylation, cobalamin and daunorubicin biosynthesis are less representative.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":5},{"id":"GO:0009834","count":4},{"id":"GO:0006002","count":4},{"id":"GO:0061621","count":4},{"id":"GO:0005980","count":4}]},{"hash":"1339739700732551952","title":"Organelle RNA editing and processing","description":"The cluster is dominated by GO terms tied to RNA editing/modification and processing in mitochondria and chloroplasts/plastids (e.g., mitochondrial mRNA processing, RNA modification, cytidine-to-uridine editing, chloroplast RNA modification, plastid transcription). This points to a cohesive theme of organellar RNA maturation and gene expression, with chloroplast\u2013nucleus signaling as a related facet; the embryo dormancy term appears peripheral. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090615","count":21},{"id":"GO:0009451","count":21},{"id":"GO:0016554","count":21},{"id":"GO:0080156","count":21},{"id":"GO:1905639","count":21}]},{"hash":"1810304365077777125","title":"Immune activation and cytokine signaling","description":"The proteins show strong enrichment for immune-related processes: positive regulation of T cell proliferation, cytokine production (including IL-4), neutrophil clearance, and immune response regulation, along with Rho signaling and endothelial cell migration that link immune signaling to tissue remodeling. While there are a few ontologies touching development and microtubule localization (cartilage condensation, protein localization to microtubule), the dominant pattern points to immune activation and inflammatory signaling, with associated vascular remodeling. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":29},{"id":"GO:0001502","count":29},{"id":"GO:0097350","count":29},{"id":"GO:0035372","count":29},{"id":"GO:0043068","count":29}]},{"hash":"1210307302415126371","title":"DNA replication and mitosis machinery","description":"The cluster is dominated by GO terms for DNA replication and mitotic cell cycle, indicating core involvement in genome duplication and cell division. Additional terms point to cytoskeletal remodeling and signaling pathways (actin cytoskeleton reorganization, focal adhesion regulation, MAPK, ephrin signaling) that often coordinate mitotic progression with cytoskeletal dynamics and cell communication. Together, these terms suggest a cohesive group of proteins functioning in DNA synthesis and mitosis, with supporting regulation of cytoskeleton and adhesion.","confidence":"High","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":28},{"id":"GO:0000278","count":28},{"id":"GO:0031532","count":27},{"id":"GO:0045773","count":27},{"id":"GO:0051893","count":27}]},{"hash":"1983052562662634050","title":"Immune development and cytoskeletal signaling","description":"The terms show a strong presence of immune-related processes (T cell proliferation, cytokine production, neutrophil clearance) together with developmental events (cartilage condensation, visual perception) and cytoskeletal/microtubule localization and signaling (Rho pathway), indicating a cluster that ties immune regulation to development and cytoskeletal dynamics.","confidence":"Medium","size":29,"edges":383,"triangles":3077,"max_degree":28,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":29},{"id":"GO:0007601","count":29},{"id":"GO:0046641","count":27},{"id":"GO:0001502","count":27},{"id":"GO:0097350","count":27}]},{"hash":"1290184741628893719","title":"Glutathione metabolism and redox homeostasis","description":"The cluster is dominated by glutathione-related terms (glutathione metabolic process and glutathione derivative biosynthetic process) and redox homeostasis, plus detoxification-related processes, suggesting a cohesive role in antioxidant defense and detoxification. While other metabolic terms appear, the strong glutathione signal across all proteins makes this a representative label.","confidence":"High","size":29,"edges":388,"triangles":3215,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0014810","count":29},{"id":"GO:0045669","count":29},{"id":"GO:1901687","count":29},{"id":"GO:0043651","count":29},{"id":"GO:0045454","count":29}]},{"hash":"1096532801562547533","title":"Lignin, Cutin, and Flavonoid Biosynthesis","description":"The top GO terms are plant-specific biosynthetic pathways: lignin and cutin biosynthesis, positive regulation of flavonoid biosynthesis, and related hydroxycinnamate conjugates, pointing to plant secondary metabolism and cell-wall/cuticle formation as the cluster\u2019s main theme. Some general terms appear (transcription, response to substances) but do not overshadow the plant metabolite biosynthesis signal.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010252","count":9},{"id":"GO:0010143","count":9},{"id":"GO:0080088","count":9},{"id":"GO:0009809","count":9},{"id":"GO:0009963","count":9}]},{"hash":"802407733665362430","title":"Neural development and vesicle trafficking","description":"The cluster shows enrichment for brain development and neurotransmitter secretion, paired with terms related to intracellular transport, lysosome exocytosis, and autophagy, all of which point to neuronal maturation and the vesicle trafficking machinery essential for synaptic function. Lipid biosynthesis terms (PE and PC) support membrane production needed for vesicle formation and trafficking, aligning with a neural development/neuronal signaling role that hinges on vesicle cycling.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0060313","count":5},{"id":"GO:0006886","count":5},{"id":"GO:0006646","count":4},{"id":"GO:0046580","count":4}]},{"hash":"84764201146343722","title":"Plant innate immune signaling and defense","description":"This cluster is dominated by GO terms related to plant defense against bacteria and hypersensitive response, including positive and negative regulation of plant-type hypersensitive response and innate immune signaling pathways, suggesting a coherent theme of plant immune signaling and defense. Some peripheral terms (e.g., neurotransmitter secretion, morphogenesis) likely reflect broader, cross-species GO annotations, but the core cluster centers on plant defense and innate immunity.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034051","count":2},{"id":"GO:0009816","count":2},{"id":"GO:0009626","count":2},{"id":"GO:0010204","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1230031072502368107","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":7},{"id":"GO:0031408","count":7},{"id":"GO:0050427","count":5},{"id":"GO:0006068","count":5},{"id":"GO:0006044","count":5}]},{"hash":"115942017421068348","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0075522","count":3},{"id":"GO:0035278","count":3},{"id":"GO:0006378","count":3}]},{"hash":"288610849695908005","title":"Plant RNA processing and light-regulated transcription","description":"The cluster is enriched for RNA processing terms (RNA splicing, mRNA and tRNA processing, RNA-templated DNA biosynthesis) alongside light-responsive terms (far-red phototransduction, far-red signaling, circadian rhythm regulation), indicating plant proteins that link RNA metabolism to light-regulated transcription.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":2},{"id":"GO:0048235","count":2},{"id":"GO:0006314","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0006278","count":1}]},{"hash":"138212862166702960","title":"Organelle RNA processing and editing (mitochondria and chloroplasts)","description":"The terms cluster around RNA maturation in organelles, especially mitochondrial and chloroplast RNA processing and editing (including cytidine to uridine editing), plus plastid transcription and chloroplast-nucleus signaling. This points to a shared function in organellar gene expression and retrograde signaling in plants, with seed dormancy reflecting broader plant development context. ","confidence":"High","size":29,"edges":13,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":4},{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3}]},{"hash":"878920217473039805","title":"Unknown","description":"The terms mix transcription regulation with multiple catabolic metabolic processes (galactose, glycosphingolipid, proteoglycan, and polysaccharide catabolism) and developmental terms (pituitary gland and palate), and there are no edges connecting the proteins. This suggests no single coherent functional module, so a specific, representative label cannot be confidently assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006012","count":5},{"id":"GO:0019388","count":5},{"id":"GO:0042340","count":4}]},{"hash":"811220186521560473","title":"Steroid and lipid metabolism with hormone biosynthesis","description":"The top GO terms cluster around lipid- and hormone-derived pathways: prostaglandin biosynthesis, cortisol and testosterone biosynthesis, retinoic acid catabolism, and fatty acid omega-oxidation, plus xenobiotic catabolic processes tied to detoxification enzymes. These points suggest a cohesive theme of lipid/hormone biosynthesis and metabolism across tissues, with mammary gland development and endothelial adhesion likely reflecting downstream developmental and vascular effects of such signaling. Overall, a plausible, specific theme is lipid-derived hormone metabolism and related detox pathways.","confidence":"Medium","size":29,"edges":96,"triangles":83,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":27},{"id":"GO:0030879","count":24},{"id":"GO:0071603","count":24},{"id":"GO:0034651","count":24},{"id":"GO:0070989","count":24}]},{"hash":"1327981193778842963","title":"Ubiquitin-Proteasome System","description":"This cluster is dominated by ubiquitin-dependent protein catabolic processes, including SCF-mediated ubiquitination and K48-linked ubiquitination, indicating targeting of substrates for proteasomal degradation. The presence of autoubiquitination and multiple ubiquitin linkage types reinforces the core proteolytic turnover function. Some histone-related ubiquitination and acetylation terms appear, but the central theme remains protein degradation via the ubiquitin-proteasome system. Overall, the cluster reflects UPS-driven protein turnover and regulation. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031146","count":17},{"id":"GO:0042787","count":15},{"id":"GO:0070936","count":9},{"id":"GO:0051865","count":9},{"id":"GO:0085020","count":9}]},{"hash":"18484229580597186","title":"DNA-Templated Transcription Regulation and Ion Transport","description":"This cluster centers on DNA-templated transcription and its regulation, alongside notable ion transport activities (potassium and sodium transport) and nutrient-related signaling (nitrate assimilation, auxin signaling) as well as stress responses (glucose starvation). The combination suggests proteins that regulate transcription while linking to membrane transport and nutrient signaling, a pattern common in plant stress or developmental regulation. The presence of an outlier term like \u201cresponse to amphetamine\u201d may reflect annotation noise or broader signaling connections, but the dominant themes point to transcriptional control coupled with ion/nutrient handling.","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":3},{"id":"GO:0006355","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0001975","count":3},{"id":"GO:0042149","count":2}]},{"hash":"341186299546417848","title":"Xenobiotic and steroid metabolism","description":"The cluster is dominated by GO terms related to breakdown and processing of lipophilic compounds (carbazole and xenobiotic catabolic processes, omega-oxidation, oxidative demethylation, retinoic acid catabolic, vitamin D response) and by steroid hormone biosynthesis (cortisol, testosterone). This points to a common theme of xenobiotic and steroid metabolism, with tissue-specific aspects such as mammary gland development and endothelial adhesion perhaps reflecting broader physiological contexts. Overall, the set seems to represent metabolic processing of xenobiotics and hormones rather than a single signaling pathway.","confidence":"Medium","size":29,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":26},{"id":"GO:0030879","count":25},{"id":"GO:0071603","count":25},{"id":"GO:0034651","count":25},{"id":"GO:0070989","count":25}]},{"hash":"1398502116435086015","title":"Ubiquitin-Dependent Mitosis and Septin Organization","description":"The top GO terms point to ubiquitination and ubiquitin-dependent protein catabolic processes, paired with septin ring assembly/organization and mitotic spindle checkpoint signaling. Together they describe a cluster of proteins involved in ubiquitin-mediated regulation of mitosis and septin-driven cytokinesis, despite some broader terms like Wnt receptor and histone catabolism appearing as well.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0032186","count":5},{"id":"GO:0044810","count":4},{"id":"GO:1902364","count":4}]},{"hash":"2120773681153797904","title":"Plant secondary metabolite and polymer biosynthesis","description":"The top GO terms cluster around biosynthetic processes for plant polymers and specialized metabolites, including lignin and cutin biosynthesis, flavonoid biosynthesis, and related compound biosynthesis. While some terms are less plant-specific or obsolete, the recurring theme is synthesis of plant cell-wall components and secondary metabolites, suggesting proteins in this cluster participate in these biosynthetic pathways.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009809","count":4},{"id":"GO:0009636","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0009102","count":4}]},{"hash":"167964400983190098","title":"Chloroplast/mitochondrial gene expression and organelle biosynthesis","description":"This cluster shows a cohesive emphasis on plant organelle biology: mitochondrial transcription, Group II intron splicing, and chloroplast organization point to organelle gene expression and biogenesis, with supporting links to related biosynthetic pathways (folic acid, tetrahydrobiopterin). Some terms reflect broader cellular processes or plant development, but the dominant theme is plastid/mitochondrial gene expression and metabolism in plants.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0000373","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006729","count":2},{"id":"GO:0051291","count":2}]},{"hash":"503141260912457712","title":"Immune activation and cytokine signaling","description":"The top GO terms are dominated by immune-related processes: positive regulation of T cell proliferation, neutrophil clearance, and cytokine (including IL-4) production, indicating activation and regulation of the immune response. While other terms touch on development and cytoskeletal localization, the strongest signal across the cluster points to immune activation and cytokine signaling.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":29},{"id":"GO:0001502","count":29},{"id":"GO:0097350","count":29},{"id":"GO:0035372","count":29},{"id":"GO:0043068","count":29}]},{"hash":"1022644672414091374","title":"Plant Floral Development and Cuticle Biosynthesis Regulation","description":"The cluster shows strong signals for plant development (multicellular organism development, floral meristem growth, bract development) together with transcriptional regulation, hormone signaling (ethylene, ABA), and regulation of wax and cutin biosynthesis, suggesting coordination of floral development with cuticle formation and related signaling pathways.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0010451","count":3},{"id":"GO:0009873","count":3},{"id":"GO:0010432","count":3}]},{"hash":"1141555627472014003","title":"DNA repair and chromosome maintenance","description":"The dominant GO terms cluster around genome integrity: DNA repair, mitotic DNA replication, meiotic recombination, heteroduplex formation, and telomere maintenance involving telomerase and chromosome localization. A couple of outlier terms (photosynthesis, triglyceride biosynthesis) are likely annotation noise and do not redefine the main theme. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":4},{"id":"GO:0019432","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0015967","count":2},{"id":"GO:0007131","count":2}]},{"hash":"2166842075353734812","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0070129","count":2}]},{"hash":"2025054934980753754","title":"Ribosome Biogenesis and rRNA Maturation","description":"The dominant GO terms point to ribosome assembly and rRNA processing (maturation of SSU/LSU rRNA and ribosomal large subunit biogenesis), indicating proteins involved in ribosome biogenesis. While there are related terms for transcription regulation and development, the core signal is ribosome-related functions.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000463","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0006355","count":3}]},{"hash":"751143170345190533","title":"Ubiquitin-Proteasome Degradation","description":"The top GO terms are dominated by processes related to ubiquitination and proteasome-dependent protein catabolism (ubiquitin-dependent proteolysis, SCF-dependent degradation, and proteasome assembly), pointing to a cluster centered on ubiquitin-proteasome\u2013mediated protein turnover. Peripheral terms like response to vitamin D and thermoception exist but do not override the core degradation theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0033280","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0000083","count":3},{"id":"GO:0007155","count":3},{"id":"GO:0031146","count":2}]},{"hash":"1701487990224268598","title":"DNA metabolism and cell wall biosynthesis","description":"These GO terms cluster around core nucleic acid processes\u2014DNA replication, recombination, base-excision repair, and RNA-templated DNA synthesis\u2014alongside strong signals for cell wall biogenesis, including teichoic acid biosynthesis and plant-type secondary cell wall organization. This suggests proteins involved in both DNA metabolism and cell wall biosynthesis, typical of Gram-positive bacteria and related pathways, hence a dual-focused label. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":6},{"id":"GO:0071555","count":6},{"id":"GO:0006310","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0006284","count":4}]},{"hash":"799526015314665350","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2},{"id":"GO:0075713","count":2}]},{"hash":"264310289788141713","title":"Unknown","description":"The top GO terms span very different biological contexts (drug response, chemotaxis, meiotic cell cycle, nutrient-responsive growth, cell size regulation, DNA replication, Schwann cell development, kinetochore localization, and neuronal signaling) with no dominant shared function, so there is no coherent theme to label the cluster.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":5},{"id":"GO:0006935","count":4},{"id":"GO:0051321","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0045793","count":4}]},{"hash":"277322220267949688","title":"Transmembrane transporters for ions and nutrients","description":"Proteins in this cluster are enriched for a broad set of transmembrane transport activities, spanning ion transport (Na+, K+), sugar and vitamin transport, xenobiotic transport, and related substrate movement across membranes, as well as a role in loading neurotransmitters into synaptic vesicles. The common thread is membrane transporter function acting on diverse substrates, indicating a cohesive transporter-centric cluster.","confidence":"High","size":28,"edges":29,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":7},{"id":"GO:0015739","count":5},{"id":"GO:0035461","count":5},{"id":"GO:0015757","count":5},{"id":"GO:0042891","count":5}]},{"hash":"1190126882226324757","title":"Hormone-regulated development and transcription","description":"This cluster highlights hormone signaling (abscisic acid and related stimuli) paired with transcriptional and developmental processes (DNA-templated transcription, mesoderm formation, multicellular development, and regulation of kinase activity). The mix of plant- and animal-associated terms suggests cross-kingdom homologs annotated to similar developmental signaling roles, so a label capturing hormone-triggered development and gene expression best fits.","confidence":"Medium","size":28,"edges":33,"triangles":5,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009738","count":4},{"id":"GO:0009737","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:1901621","count":3}]},{"hash":"2126654693535708905","title":"Cell wall and ECM glycan biosynthesis","description":"This cluster's top GO terms center on building structural glycans and matrices: plant-type secondary cell wall biogenesis, mucilage biosynthesis in seed coats, and proteoglycan/glycan biosynthetic processes (chondroitin/heparan sulfate, poly-N-acetyllactosamine). Together they point to synthesis of cell wall and extracellular matrix components. A few terms related to stress or apoptosis are present but not dominant, so the core theme is ECM/glycan biosynthesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0042493","count":4},{"id":"GO:0050650","count":4},{"id":"GO:0015012","count":4},{"id":"GO:0009834","count":4}]},{"hash":"113721488480070841","title":"DNA replication, repair, and transcription regulation","description":"The top GO terms are dominated by core nuclear processes: transcription, replication, and DNA repair, with accompanying regulation of protein export from the nucleus. This points to a nuclear DNA metabolism and gene-expression\u2013regulatory program as the defining theme of the cluster, despite some peripheral terms like T-cell proliferation and ion transport. ","confidence":"High","size":28,"edges":23,"triangles":5,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":22},{"id":"GO:0009636","count":22},{"id":"GO:0006281","count":21},{"id":"GO:0046826","count":21},{"id":"GO:0006260","count":21}]},{"hash":"1066049105445582806","title":"Mitochondrial lipid metabolism and remodeling","description":"This cluster is dominated by GO terms related to lipid biosynthesis and remodeling (phosphatidylcholine, cardiolipin, triglycerides, CDP-diacylglycerol) and mitochondrial energy production (mitochondrial ATP synthesis coupled electron transport), suggesting a cohesive theme around lipid metabolism linked to mitochondrial function. Some terms appear unrelated (immune regulation, tissue morphogenesis, plant cutin biosynthesis), but the lipid/mitochondrial signals are strongest.","confidence":"Medium","size":28,"edges":113,"triangles":205,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0070236","count":19},{"id":"GO:2001246","count":19},{"id":"GO:0010143","count":19},{"id":"GO:0042775","count":19},{"id":"GO:0021587","count":19}]},{"hash":"631011313913730852","title":"Unknown","description":"The top terms are highly heterogeneous (RNA processing, various differentiation processes like fat cell and cartilage condensation, immune proliferation, telomere maintenance, and general cell migration) with no clear shared function or pathway linking the cluster. The presence of an obsolete GO term and zero edges/triangles further suggests a non-cohesive set of functions, making a specific, representative label inappropriate.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2001275","count":27},{"id":"GO:0006397","count":27},{"id":"GO:0035994","count":27},{"id":"GO:0032212","count":27},{"id":"GO:1904355","count":27}]},{"hash":"2256143735554048520","title":"Neuronal signaling and development","description":"This cluster shows a strong enrichment for neural-related terms: intracellular signal transduction, cerebellar granule cell differentiation, neuromuscular synaptic transmission, neuron apoptotic regulation, dopamine metabolism, ionotropic glutamate receptor signaling, and learning-related processes. While a couple terms (cell wall organization, imaginal disc morphogenesis) are non-neural, the dominant theme centers on neural signaling and development, suggesting these proteins function together in brain-related communication and maturation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0021707","count":3},{"id":"GO:0007274","count":2},{"id":"GO:0043523","count":2},{"id":"GO:0008542","count":2}]},{"hash":"825541274390243801","title":"Plant Growth and Secondary Cell Wall Regulation","description":"This cluster is enriched for plant-specific regulatory processes, notably cytokinin-activated signaling, regulation of secondary cell wall biogenesis and lignin biosynthesis, and growth-related functions such as seed and root meristem development, with additional notes on chlorophyll regulation and leaf senescence. The shared theme appears to be coordination of plant development and wood formation rather than a single enzymatic activity.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":9},{"id":"GO:0006334","count":9},{"id":"GO:1901348","count":9},{"id":"GO:0010380","count":8},{"id":"GO:0080113","count":8}]},{"hash":"551286687607634460","title":"Unknown","description":"The top GO terms span diverse biosynthetic and regulatory processes (antibiotic biosynthesis, sporulation, PHB biosynthesis, anthocyanin and testosterone biosynthesis, transcription regulation, vitamin D response). This spread across bacteria, plants, and animals suggests no single unifying function or pathway for the cluster. Therefore, I label it Unknown.","confidence":"","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0030435","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0008209","count":5},{"id":"GO:0042619","count":5}]},{"hash":"422930425849241488","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0006351","count":2}]},{"hash":"776243656870031427","title":"Cell wall and extracellular polysaccharide biosynthesis","description":"This cluster is enriched for cell wall organization and polysaccharide biosynthetic processes (cellulose, chitin, mycolate), as well as glycosylation pathways (O-linked GalNAc) and UDP-D-galactose metabolism.","confidence":"","size":28,"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:0071769","count":3},{"id":"GO:0070592","count":3},{"id":"GO:0030244","count":3}]},{"hash":"561775038097410717","title":"Drosophila development and morphogenesis","description":"The top GO terms point to developmental and morphogenetic processes typical of Drosophila, including imaginal disc-derived wing hair orientation, larval cuticle development, neural retina development, and heart/ventricular morphogenesis, along with DNA-templated transcription. The combination of insect-specific developmental terms with organogenesis supports a cohesive theme of Drosophila development and morphogenesis, making this label a good fit.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0001569","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0070588","count":2},{"id":"GO:0003407","count":2}]},{"hash":"1436653376984422796","title":"Ubiquitin-dependent proteolysis and meiosis/oocyte maturation","description":"The cluster is dominated by GO terms related to ubiquitin-dependent protein catabolic processes (SCF-dependent proteasomal degradation) and components of the meiotic machinery (spindle assembly in female meiosis I, oocyte maturation). This points to a coherent theme of proteostasis coupled to meiotic cell-cycle regulation in oocytes. Additional terms hint at broader developmental processes, but the strongest signals align with ubiquitin-mediated degradation during meiosis and oocyte maturation.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0042787","count":11},{"id":"GO:0046785","count":10},{"id":"GO:0007057","count":10},{"id":"GO:0021678","count":10}]},{"hash":"1953895072223854598","title":"Flavonoid and lignin biosynthesis","description":"The dominant GO terms cluster around phenylpropanoid and flavonoid pathways, including lignin metabolism and anthocyanin/cyanidin biosynthesis, with related glycosylation/glucuronidation processes. This points to a group of proteins involved in plant secondary metabolism, especially flavonoid and lignin precursor biosynthesis and modification. A few terms appear as artifacts (e.g., paranode localization), but the core signal supports this functional theme.","confidence":"High","size":28,"edges":35,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":27},{"id":"GO:0009808","count":27},{"id":"GO:0009718","count":27},{"id":"GO:0006711","count":27},{"id":"GO:0052697","count":27}]},{"hash":"1890913799404653811","title":"Plant nitrate and peptide transporter cluster","description":"This cluster is enriched for transmembrane transport GO terms, including nitrate transmembrane transport, nitrate assimilation, and dipeptide/oligopeptide transport, along with xenobiotic transmembrane transport and herbicide response. The pattern strongly points to membrane transporters involved in nutrient uptake and xenobiotic handling in plants, with nitrate and peptide transport as central themes (GA homeostasis as a potential ancillary link).","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010167","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0010336","count":3},{"id":"GO:0042128","count":3}]},{"hash":"282294228597897819","title":"RNA pseudouridine synthesis enzymes","description":"This cluster centers on GO terms for pseudouridine synthesis across multiple RNA types (tRNA, mRNA, snRNA, rRNA), indicating a set of RNA modification enzymes responsible for installing pseudouridine. While there are some unrelated terms (cell wall and glycosylation), the recurring RNA modification theme best represents the cluster\u2019s function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0005978","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0006011","count":2}]},{"hash":"1692651384301337218","title":"Fungal defense and signaling","description":"This cluster is dominated by defense response to fungus and intracellular signal transduction, suggesting proteins involved in fungal immune responses and signaling. Additional terms like cell migration and mRNA stability regulation imply dynamic cellular responses and gene expression control during defense. Lipid transport, vitamin D response, and proteasome assembly may reflect broader immune modulation and protein turnover accompanying defense signaling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":6},{"id":"GO:0007205","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0035556","count":3}]},{"hash":"1763345951126630960","title":"Phenylpropanoid and Sporopollenin Biosynthesis","description":"The top GO terms are dominated by anthocyanin biosynthesis, sporopollenin biosynthetic, and lignin metabolic processes, all stemming from the phenylpropanoid pathway and related plant secondary metabolism (pigments, cell wall components, pollen exine). Additional terms touch on detoxification and xenobiotic metabolism, which can be connected to broader metabolic capacity in these pathways. Although a single neuronal localization term appears unrelated, the central theme across most terms is plant-derived biosynthesis of phenylpropanoid compounds and related structural polymers. This makes the label a concise representation of the cluster\u2019s primary function.","confidence":"Medium","size":27,"edges":11,"triangles":6,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":10},{"id":"GO:0055114","count":9},{"id":"GO:0080110","count":8},{"id":"GO:0002175","count":7},{"id":"GO:0009808","count":7}]},{"hash":"101080114187843363","title":"RNA transcription and ribosome biogenesis","description":"Proteins in this cluster show enrichment for transcription-related GO terms (DNA-templated transcription, RNA polymerase II and III transcription, transcription termination) along with ribosome biogenesis and translational initiation, indicating a link between RNA synthesis and ribosome/translation machinery rather than a single specific function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0042797","count":2},{"id":"GO:0045947","count":2},{"id":"GO:1905618","count":2},{"id":"GO:0006413","count":2}]},{"hash":"1071960705102501162","title":"Developmental transcriptional regulation and signaling","description":"This cluster centers on regulation of gene expression during development (GO:0006355) and includes diverse morphogenetic and differentiation terms across tissues (shoot formation, spinal interneuron differentiation, aortic valve morphogenesis, megakaryocyte differentiation) along with signaling pathways such as Wnt and immune-responsive cues (interferon signaling). The common thread appears to be proteins that orchestrate developmental gene regulation through signaling inputs, rather than a single pathways-specific module.","confidence":"Medium","size":27,"edges":304,"triangles":2128,"max_degree":26,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:2000032","count":18},{"id":"GO:0006355","count":18},{"id":"GO:0061290","count":7},{"id":"GO:1902499","count":7},{"id":"GO:0021514","count":6}]},{"hash":"1820149974986231287","title":"Ribosome biogenesis and RNA processing","description":"The cluster is strongly enriched for ribosome biogenesis and translation initiation/processing terms (GO:0042254, GO:0001731, GO:0002188, GO:0042273) as well as mRNA splicing (GO:0000398) and rRNA processing (GO:0000447). The highest counts cluster around ribosome assembly and related RNA processing steps, indicating a core function in ribosome production and protein synthesis, with some development-related terms present as secondary associations. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":8},{"id":"GO:0042273","count":7},{"id":"GO:0000447","count":7},{"id":"GO:0042254","count":7},{"id":"GO:0002188","count":7}]},{"hash":"154538977193865733","title":"Ribosome Biogenesis and Translation with Apoptosis Signaling","description":"Explanation: Core GO terms show protein synthesis and ribosome assembly (translation, cytoplasmic translation, ribosome biogenesis) as the main theme. Additional terms for cell cycle, apoptosis/necroptosis, and interferon response suggest linked stress and immune signaling, but translation machinery remains the central link. Confidence is High.","confidence":"","size":27,"edges":17,"triangles":4,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0070266","count":5},{"id":"GO:0035455","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0002181","count":4}]},{"hash":"2055803986339000894","title":"Nuclear mRNA processing and maturation","description":"The top GO terms cluster around nuclear RNA processing activities: spliceosome-mediated splicing, 7-methylguanosine capping, and RNA guanine-N7 methylation, which collectively cover major stages of mRNA maturation. The presence of transcription-related tethering of RNA Pol II and regulatory processes suggests these proteins function in transcription-linked RNA processing and broader gene expression control during cell growth and development.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006370","count":3}]},{"hash":"962759018507136031","title":"Proteostasis and Stress Response","description":"The top terms center on ubiquitin-dependent ERAD, ER-associated degradation, and protein trafficking/retention, pointing to proteostasis and quality-control mechanisms that act under stress. Cadmium-related SCF disassembly and heat acclimation further support a stress-response angle, while energy metabolism terms may reflect cellular adaptation to stress as a secondary facet.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":15},{"id":"GO:0045053","count":13},{"id":"GO:0051301","count":13},{"id":"GO:1990171","count":12},{"id":"GO:0032979","count":12}]},{"hash":"2024535812405965741","title":"RNA processing and splicing factors","description":"Top terms are dominated by RNA metabolism: mRNA processing, miRNA processing, and alternative splicing via the spliceosome, suggesting these proteins function in RNA maturation and regulation. Other terms (ubiquitination, DNA repair, calcium signaling, and differentiation) are less cohesive with the main theme, so the label emphasizes RNA processing.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0051209","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0010018","count":2},{"id":"GO:0033280","count":2}]},{"hash":"623342611725388272","title":"Plant Developmental Transcription and RNA Processing","description":"This cluster centers on transcriptional regulation and RNA processing in the context of plant development, as reflected by GO terms for multicellular organism development, DNA-templated transcription, RNA polymerase II regulation, and spliceosomal snRNP assembly, with plant-specific development like phloem/xylem histogenesis. The presence of viral process terms and regulation of viral material transport suggests possible involvement in plant-virus interactions, but the dominant theme appears to be transcriptional and post-transcriptional control during development. The absence of edges indicates these proteins may function in regulatory networks rather than a single complex.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0042769","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1901253","count":2},{"id":"GO:0030433","count":2}]},{"hash":"465552194454216000","title":"Unknown","description":"The terms cover environmental stress responses, lipid biosynthesis, metal ion transport, and general regulation, with no clear single function tying all proteins together; the cluster appears heterogeneous rather than a cohesive pathway.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009409","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0070574","count":3},{"id":"GO:0071577","count":3},{"id":"GO:0006355","count":3}]},{"hash":"770559353199386506","title":"Flowering timing and floral development","description":"This cluster is dominated by plant reproductive timing and flowering-related processes (photoperiodism, inflorescence and flower development, and regulation of the vegetative-to-reproductive transition), indicating a cohesive role in flowering regulation. A few non-plant terms may reflect annotation noise.","confidence":"Medium","size":27,"edges":11,"triangles":0,"max_degree":5,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0048240","count":5},{"id":"GO:0010229","count":5},{"id":"GO:0048575","count":5},{"id":"GO:0042755","count":5},{"id":"GO:0009911","count":5}]},{"hash":"1581263663350788306","title":"Developmental transcriptional regulation","description":"The cluster\u2019s top GO terms emphasize transcriptional control during development: DNA-templated transcription and negative regulation of transcription by RNA polymerase II, alongside plant meristem identity and flower development terms, plus animal developmental terms like brain, primitive streak, and male gonad development. This suggests a shared theme of controlling developmental programs through transcriptional regulation, across species.","confidence":"Medium","size":27,"edges":274,"triangles":1394,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010076","count":9},{"id":"GO:0090009","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0071277","count":7},{"id":"GO:0010077","count":7}]},{"hash":"1327985736785394927","title":"Auxin Signaling and Plant Growth Regulation","description":"Dominant GO terms center on auxin-activated signaling, auxin transport, and responses to auxin, together with regulation of organ growth and transcription, pointing to a module involved in auxin-mediated plant development. A few terms reference animal contexts (placenta development, hair follicle maturation) that are likely annotation noise or cross-species overlap, but the overall signal is clearly plant hormone signaling and growth control.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2},{"id":"GO:0009733","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1365975589075320326","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":3},{"id":"GO:0016032","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2}]},{"hash":"1189936548860614524","title":"Proteasome-Mediated Protein Degradation (ERAD)","description":"This cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes, including ERAD and SCF- and K48-linked ubiquitination, indicating a shared function in tagging proteins for proteasomal degradation. A few terms about peroxisome matrix import and X chromosome dosage regulation appear as outliers, but the overall pattern centers on proteostasis through the ubiquitin-proteasome system.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":14},{"id":"GO:0042787","count":13},{"id":"GO:0051865","count":13},{"id":"GO:0038018","count":12},{"id":"GO:0070936","count":12}]},{"hash":"1521986449286610558","title":"Transcription regulation and chromatin assembly in development","description":"The cluster centers on regulation of transcription and nucleosome assembly, indicating transcriptional control and chromatin remodeling as core themes. Developmental terms, including multicellular organism development and plant secondary cell wall biogenesis, suggest a developmental regulatory role, with a few terms touching on signaling and protein quality control that can modulate these processes.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0006469","count":3},{"id":"GO:0006334","count":3},{"id":"GO:1901348","count":3},{"id":"GO:0006351","count":3}]},{"hash":"192725516597473002","title":"Developmental transcriptional regulation and differentiation","description":"This cluster is dominated by RNA polymerase II\u2013mediated transcription and extensive differentiation-related terms (mesenchyme, heart valve development, skeletal muscle and astrocyte differentiation, mast cell differentiation), plus regulation of the cell cycle and transcription factor activity, suggesting a cohesive role in transcriptional control during development and lineage specification.","confidence":"High","size":27,"edges":351,"triangles":2925,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":21},{"id":"GO:0048712","count":19},{"id":"GO:2001016","count":19},{"id":"GO:0043433","count":19},{"id":"GO:2001038","count":19}]},{"hash":"743635656306295979","title":"Anthocyanin and flavonoid biosynthesis","description":"The top GO terms point to anthocyanin-containing compound biosynthesis, cyanidin 3-O-glucoside biosynthesis, and flavonoid glucuronidation, with an additional lignin metabolic process term, indicating involvement in plant phenylpropanoid and pigment/lignin biosynthesis. Some terms appear tangential or noisy (e.g., axon localization, xenobiotic processes), but the flavonoid/anthocyanin signals dominate, supporting a flavonoid biosynthesis-focused cluster.","confidence":"Medium","size":27,"edges":28,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":20},{"id":"GO:0009808","count":20},{"id":"GO:0009718","count":20},{"id":"GO:0006711","count":20},{"id":"GO:0052697","count":20}]},{"hash":"1153366450001355360","title":"Golgi-ER Vesicle Transport and Endocytic Trafficking","description":"The top GO terms predominantly point to intracellular transport processes: ER-to-Golgi vesicle transport, Golgi localization, Golgi-to-vacuole transport, and regulation of endocytosis, plus endosome-related trafficking. A few terms touch on transcription or signaling, but the bulk of the signals describe vesicle trafficking within the secretory and endocytic pathways, suggesting this cluster mainly reflects membrane trafficking functions. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010018","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0016185","count":1},{"id":"GO:0035646","count":1}]},{"hash":"1541811370116822599","title":"Embryonic development and immune signaling","description":"The cluster centers on developmental processes (cranial skeleton morphogenesis, cartilage condensation) and cell proliferation (DNA replication) but also shows immune modulation (cytokine production, T cell proliferation) and cytoskeletal regulation (Rho signaling, microtubule localization), indicating a developmental program that integrates immune signaling rather than a single pathway.","confidence":"Medium","size":27,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":27},{"id":"GO:0048701","count":27},{"id":"GO:0046641","count":26},{"id":"GO:0001502","count":26},{"id":"GO:0097350","count":26}]},{"hash":"437769963739772185","title":"Vertebrate neural development and organogenesis","description":"The cluster is dominated by GO terms pointing to vertebrate development, especially neural development (forebrain development, neural tube closure) and organogenesis (multicellular organism development, skeletal system development). Although some terms reflect stress responses, the strong emphasis on neural and overall developmental processes suggests a coherent theme around neural development and tissue formation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001403","count":27},{"id":"GO:0050830","count":27},{"id":"GO:0007275","count":27},{"id":"GO:0030900","count":27},{"id":"GO:0006349","count":27}]},{"hash":"1370689455411157564","title":"Plant signaling and meristem regulation","description":"This cluster repeatedly shows terms about regulation of signaling pathways (BMP/TGF-beta, SMAD, NF-kappaB), MAPK cascades, and processes linked to development and stress responses, plus a plant-specific term for meristem identity maintenance. Taken together, the proteins appear to modulate signaling as a core function, with a focus on plant development and cellular response, rather than a single concrete enzyme or process. Confidence: Medium","confidence":"","size":27,"edges":315,"triangles":2372,"max_degree":25,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0080005","count":20},{"id":"GO:0000173","count":20},{"id":"GO:0046827","count":20},{"id":"GO:0071560","count":20},{"id":"GO:0010991","count":20}]},{"hash":"408766917825306001","title":"T cell activation and cytokine production","description":"Most of the top GO terms point to immune system activity, especially T cell proliferation, IL-4 production, and broader cytokine regulation. Additional terms involve neutrophil clearance, programmed cell death, and cytoskeletal/microtubule dynamics, suggesting immune cell activation and migration processes. While a cartilage condensation term appears, the dominant theme is immune activation and cytokine signaling, so the label reflects the cluster\u2019s core function.","confidence":"Medium","size":27,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":27},{"id":"GO:0001502","count":27},{"id":"GO:0097350","count":27},{"id":"GO:0035372","count":27},{"id":"GO:0043068","count":27}]},{"hash":"765102513325183831","title":"Axon guidance and synaptic signaling","description":"The top GO terms cluster around actin cytoskeleton remodeling, regulation of axon extension, focal adhesion dynamics, ephrin signaling, and synaptic activity (excitatory postsynaptic potential, dopamine response). This points to a coherent theme of neuronal growth cone navigation and downstream signaling processes that coordinate cytoskeletal changes with axon guidance and synaptic function.","confidence":"High","size":27,"edges":12,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031532","count":26},{"id":"GO:0045773","count":26},{"id":"GO:0051893","count":26},{"id":"GO:0043552","count":26},{"id":"GO:0043304","count":26}]},{"hash":"1259957294828783521","title":"T cell activation and cytokine production","description":"This cluster is dominated by GO terms related to immune cell activation and signaling, including positive regulation of alpha-beta T cell proliferation, cytokine production, and interleukin-4 production, as well as neutrophil clearance and endothelial cell migration, which together point to immune response modulation and leukocyte trafficking. Rho signaling and microtubule localization terms suggest cytoskeletal changes supporting immune cell movement and interactions. Although a few terms touch development or cell death, the overarching theme is immune activation and cytokine regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":27},{"id":"GO:0001502","count":27},{"id":"GO:0097350","count":27},{"id":"GO:0035372","count":27},{"id":"GO:0043068","count":27}]},{"hash":"1454037641907491075","title":"Developmental gene expression and RNA processing","description":"The prominent GO signals point to transcriptional control and RNA processing linked to multicellular development (DNA-templated transcription, mRNA processing, nuclear export) and accompanied by cell migration and telomere maintenance activities. A disparate pain perception term appears among the top terms but does not dominate the cluster; overall, this set reflects a developmental gene-expression module.","confidence":"Medium","size":27,"edges":96,"triangles":109,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":12},{"id":"GO:0007275","count":12},{"id":"GO:0046827","count":11},{"id":"GO:0006351","count":11},{"id":"GO:2001275","count":9}]},{"hash":"563999636667408719","title":"Transmembrane Transporters","description":"This cluster is dominated by GO terms for transport across membranes across a broad range of substrates (nitrate, potassium, sodium, galactose, sialic acid, vitamins, xenobiotics, and neurotransmitter loading into synaptic vesicles), indicating a cohesive function as membrane transporters with diverse substrate specificity.","confidence":"High","size":27,"edges":14,"triangles":2,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":10},{"id":"GO:0071805","count":10},{"id":"GO:0006855","count":10},{"id":"GO:0015739","count":9},{"id":"GO:0035461","count":9}]},{"hash":"1031730848501549559","title":"Plant lignan and anthocyanin biosynthesis","description":"The set includes GO terms for lignan biosynthesis (secoisolariciresinol, lariciresinol, pinoresinol) and for anthocyanin-containing compounds, indicating a common theme of plant phenylpropanoid-derived secondary metabolism. Additional terms reflect general carbohydrate metabolism (GDP-mannose) and amino acid metabolism (L-glutamine), which support these pathways; a few terms are broader or outliers, but the dominant signal is plant secondary metabolite biosynthesis.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0009244","count":3},{"id":"GO:1902135","count":3},{"id":"GO:1902131","count":3},{"id":"GO:0019673","count":3}]},{"hash":"1900082748576240584","title":"Plant Hormone Signaling and Nitrate Transport","description":"These proteins show a theme around plant growth regulation and nutrient handling: gibberellin homeostasis and auxin-activated signaling point to hormone signaling, while nitrate assimilation and nitrate/oligopeptide transport indicate nutrient uptake and processing. The presence of transcription and ubiquitination terms suggests regulatory control of these pathways. Overall, it fits a plant-growth signaling plus nutrient-transport cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010336","count":3},{"id":"GO:0035672","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0080055","count":3},{"id":"GO:0009635","count":3}]},{"hash":"264916443316734944","title":"Plant Hormone-Regulated Growth and Secondary Cell Wall Biosynthesis","description":"These proteins show enrichment in hormone signaling (cytokinin, gibberellin, salicylic acid) and development-related processes (seed growth, root meristem growth, leaf senescence) alongside regulation of secondary cell wall biogenesis and syringal lignin biosynthesis. This combination points to a coordinated plant program that links hormonal control with wood/lignin-forming cell wall regulation and broader growth outcomes, hence the chosen label.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1901348","count":9},{"id":"GO:0009736","count":9},{"id":"GO:0009751","count":8},{"id":"GO:0009739","count":8},{"id":"GO:0010380","count":7}]},{"hash":"1950760586511864121","title":"Neural development and synaptic regulation","description":"This cluster is enriched for neuronal development and synaptic function: neuroblast differentiation, synapse organization, learning, and regulation of cholinergic transmission, along with transcriptional control and membrane metabolism (cholesterol biosynthesis) and hormonal responses (glucocorticoid, folic acid). A few outlier terms like cellulose catabolic process may reflect annotation noise, but the dominant theme points to neuronal differentiation and synaptic activity.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0050808","count":8},{"id":"GO:0030245","count":8},{"id":"GO:0007612","count":8},{"id":"GO:0050783","count":8}]},{"hash":"186830574987449358","title":"Immune activation and cell adhesion","description":"The top GO terms cluster around immune-related processes (T cell activation; regulation of integrin-mediated cell-cell adhesion; cell adhesion; endothelial migration) along with leukocyte-associated activities (proteolysis, detoxification, cell proliferation). This combination points to immune activation and cell adhesion dynamics, particularly leukocyte trafficking and interaction with host tissues. A few terms (behavioral/psychomotor) appear unrelated or as noise, so the core signal is immune response and adhesion.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0042110","count":2},{"id":"GO:0033632","count":2},{"id":"GO:0001662","count":2}]},{"hash":"852157296633816141","title":"Oocyte maturation and meiotic spindle assembly","description":"The cluster is strongly enriched for processes tied to meiosis and oocyte development, including spindle assembly in female meiosis I, oocyte maturation, and ubiquitin-proteasome\u2013dependent protein degradation that regulates the cell cycle. While neural development terms are present, the predominant signals point to meiotic progression and oocyte maturation as the core function of this protein group.","confidence":"High","size":27,"edges":179,"triangles":525,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":26},{"id":"GO:0046785","count":24},{"id":"GO:0007057","count":24},{"id":"GO:0021678","count":24},{"id":"GO:0006516","count":24}]},{"hash":"879360817163852305","title":"Epigenetic Regulation: DNA Methylation & Histone Modifications","description":"The cluster is dominated by GO terms tied to DNA methylation (cytosine methylation), histone methylation (H3-K4 and H3-K9), and epigenetic programming of gene expression, indicating a coherent role in epigenetic control. There are also plant-specific terms (leaf pavement cell development, embryo sac cytokinesis) and a Ras signaling term, suggesting contextual modulation, but the core signal centers on epigenetic regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051571","count":4},{"id":"GO:0090116","count":3},{"id":"GO:0044030","count":3},{"id":"GO:0090309","count":3},{"id":"GO:0010216","count":3}]},{"hash":"525988883671648738","title":"Vesicle trafficking and exocytosis","description":"The top GO terms cluster around exocytosis, vesicle tethering, and Golgi-to-plasma membrane transport, with Rho-mediated signal transduction likely coordinating the cytoskeleton for vesicle movement. Although some terms touch neural development, the dominant signal is vesicle trafficking/exocytosis, supporting this label. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0006887","count":3},{"id":"GO:0006893","count":3},{"id":"GO:0090522","count":3},{"id":"GO:0001843","count":2}]},{"hash":"2290402536173864549","title":"Multicellular development and apoptosis","description":"GO terms show broad developmental processes across tissues (multicellular organism development, brain/forebrain development) and various apoptotic events (glial and cardiac muscle cell apoptosis), with additional development-related processes like salivary gland histolysis. While there are a few outliers (melanization, L-methionine cycle), the overall theme centers on development and programmed cell death across tissues.","confidence":"Medium","size":27,"edges":220,"triangles":914,"max_degree":23,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007275","count":14},{"id":"GO:0007420","count":13},{"id":"GO:0030900","count":12},{"id":"GO:0010659","count":12},{"id":"GO:0035006","count":12}]},{"hash":"114715759383084161","title":"Oocyte maturation and meiotic spindle assembly","description":"The strongest signals are oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, along with SCF-dependent ubiquitin-proteasome\u2013mediated protein degradation. These converge on meiosis/oocyte maturation and spindle dynamics with regulated proteolysis, forming the core theme of the cluster. Some neural development terms appear as secondary signals, but the primary pattern is meiosis-related. ","confidence":"High","size":27,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":21},{"id":"GO:0046785","count":17},{"id":"GO:0007057","count":17},{"id":"GO:0021678","count":17},{"id":"GO:0006516","count":17}]},{"hash":"275743322561009993","title":"Oocyte Meiosis, Spindle Assembly, and Proteasome Regulation","description":"Dominated by ubiquitin-dependent proteolysis and SCF-driven protein turnover, with strong signals for oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization. While neural development terms are present, the central theme is meiosis/cell-cycle control and spindle dynamics linked to proteasome regulation, justifying this label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0031146","count":9},{"id":"GO:0001556","count":7},{"id":"GO:0046785","count":7},{"id":"GO:0006516","count":7}]},{"hash":"1597391837803875727","title":"Stamen filament development and plant cell wall biosynthesis","description":"The cluster is dominated by GO terms related to plant cell wall biosynthesis and modification (xyloglucan metabolism, plant-type cell wall modification, cell wall biogenesis), with an additional term pointing to stamen filament development. This suggests a coherent theme around plant cell wall construction/remodeling, with a specific association to reproductive tissue development, making the label both specific and representative.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0080086","count":9},{"id":"GO:0032491","count":8},{"id":"GO:0031505","count":8},{"id":"GO:0010411","count":8},{"id":"GO:0042546","count":8}]},{"hash":"1065062966406220911","title":"Unknown","description":"The terms span amino-acid catabolism (tyrosine, phenylalanine, homogentisate), proteoglycan biosynthesis, neuronal differentiation, and immune/ER-stress regulation, with many obsolete GO entries and no edges connecting proteins; there is no single cohesive function tying the cluster together, so Unknown is appropriate.","confidence":"","size":27,"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:0015012","count":2},{"id":"GO:1902000","count":1},{"id":"GO:0006572","count":1}]},{"hash":"1530434041482750497","title":"Cell cycle control and chromatin modification","description":"The clustered terms point to processes governing cell division and chromosome regulation: cell division, cell cycle, spindle assembly, regulation of histone methylation, and protein ubiquitination. There are some outliers (cellulose catabolic process, hypoxia response) that may reflect annotation noise. Overall, the cluster seems to represent cell-cycle and chromatin-regulation activities.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0061087","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0016567","count":2}]},{"hash":"1558550000901985413","title":"Plant cell wall biosynthesis and organization","description":"Most terms cluster around plant cell wall construction and modification\u2014cell wall organization, plant-type secondary cell wall biogenesis, cellulose biosynthesis, and polysaccharide biosynthesis\u2014with supporting related processes like specific glycosylation. A couple of terms (immunoglobulin production, follicle cell adhesion) seem unrelated and may reflect noise, but the dominant signal clearly points to plant cell wall biosynthesis. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0016266","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0043086","count":2},{"id":"GO:1901599","count":2}]},{"hash":"1768559804208056521","title":"Exocytosis and Exocyst-Mediated Trafficking","description":"This cluster centers on vesicle transport from the Golgi to the plasma membrane, exocyst complex localization/assembly, vesicle tethering, and the exocytosis process, with supporting terms for protein transport, membrane repair, and Rho GTPase signaling. The strong representation of exocyst- and exocytosis-related GO terms suggests a cohesive membrane trafficking/exocytic function for these proteins.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006893","count":4},{"id":"GO:2000535","count":4},{"id":"GO:0043087","count":4},{"id":"GO:0001778","count":4},{"id":"GO:0051601","count":3}]},{"hash":"1200758655069710120","title":"Lipopolysaccharide and cell wall carbohydrate biosynthesis","description":"Based on the top GO terms, these proteins are enriched for sugar nucleotide biosynthesis (UDP-GlcNAc, UDP-Glc, GDP-Man), lipopolysaccharide biosynthesis, and cell wall\u2013related processes (mannoprotein biosynthesis, cell wall organization). This points to a cohesive role in assembling and modifying cell wall/envelope polysaccharides. Confidence in this label is High.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006048","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0009298","count":2},{"id":"GO:0071555","count":2}]},{"hash":"294782699815957122","title":"Mitochondrial protein import and energy metabolism","description":"This cluster centers on mitochondrial processes: protein import into the mitochondrial matrix, translation within mitochondria, ATP synthesis, and regulation of mitochondrial calcium, with additional links to calcium signaling and energy-demanding processes such as insulin secretion and cardiac muscle development. The presence of a photosynthesis term is likely incidental or cross-annotational, but the dominant pattern is mitochondrial function and energy production.","confidence":"High","size":26,"edges":325,"triangles":2600,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0036444","count":1},{"id":"GO:0032024","count":1}]},{"hash":"874024704287015201","title":"Cytoskeleton dynamics and developmental signaling","description":"This cluster centers on terms involving regulation of the cytoskeleton and small GTPase signaling (Rho, GTPase activity), with supporting ideas around mitotic processes, vesicle trafficking, and developmental events such as brain development, synaptic potentiation, and acrosome reaction. The shared theme appears to be modulation of cytoskeletal dynamics and signaling pathways that coordinate cell movement, division, and maturation across diverse contexts.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0006886","count":5},{"id":"GO:0090307","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0031384","count":4}]},{"hash":"528687123604846693","title":"Innate immunity and proteostasis","description":"This cluster is enriched for innate immune-related GO terms, including defense response to fungus, NOD2 signaling, and NF-kappaB regulation (including an obsolete sequestration term), as well as proteasome regulatory particle assembly and negative regulation of endopeptidase activity. These point to coordinated immune signaling and protein turnover. Other terms like mRNA processing, vitamin D response, thermoception, oligodendrocyte differentiation, and cell growth suggest broader regulatory roles, but the core theme appears to be innate immune signaling coupled with proteostasis.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":6},{"id":"GO:0010951","count":5},{"id":"GO:0006397","count":5},{"id":"GO:0033280","count":4},{"id":"GO:0050955","count":4}]},{"hash":"406621826093986441","title":"Developmental signaling and cell cycle regulation","description":"The cluster features enrichment for developmental processes (forebrain development, multicellular organism development) coupled with regulators of signaling and growth control (positive regulation of GTPase activity, cell cycle regulation, apoptotic process, and nuclear import). Together with protein homooligomerization, these terms point to a regulatory module coordinating development, nuclear transport, and cellular proliferation/differentiation.","confidence":"Medium","size":26,"edges":61,"triangles":96,"max_degree":13,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0051260","count":10},{"id":"GO:0043547","count":8},{"id":"GO:0015991","count":8},{"id":"GO:0007275","count":7},{"id":"GO:0006607","count":7}]},{"hash":"906326797754240441","title":"Unknown","description":"The top GO terms span broad, diverse processes including mitosis (metaphase alignment, spindle assembly, cytokinesis), nuclear migration, Rho signaling, development (hair follicle placode formation), and neural/structural organization (dendritic transport, cerebellar layer structures). There isn\u2019t a cohesive single function or pathway tying these terms together, suggesting heterogeneous roles or annotations, hence Unknown with None. ","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":3},{"id":"GO:0007080","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0007266","count":2},{"id":"GO:0071701","count":2}]},{"hash":"1860161139977077333","title":"Neural Development and Apoptotic Signaling","description":"Top terms cluster neural development (nervous system development, forebrain development, neural tube closure, dendrite morphogenesis) and apoptotic signaling (intrinsic apoptotic signaling pathway in response to ER stress, positive/negative regulation of apoptotic signaling), suggesting a neuronal differentiation program with apoptosis regulation.","confidence":"High","size":26,"edges":310,"triangles":2281,"max_degree":25,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0070059","count":16},{"id":"GO:0007399","count":14},{"id":"GO:0030154","count":14},{"id":"GO:0007275","count":14},{"id":"GO:0001843","count":13}]},{"hash":"514004376096254176","title":"Plant organelle RNA editing and processing","description":"TheGO terms cluster around RNA modification and processing in plant organelles, including mitochondrial mRNA processing/modification and cytidine-to-uridine editing, chloroplast RNA modification, and plastid transcription, plus chloroplast-nucleus signaling. This coherence points to a shared function in organellar RNA editing/processing in plants, with seed dormancy development appearing as a broader plant context. Confidence in this labeling is high.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":11},{"id":"GO:0009451","count":11},{"id":"GO:0016554","count":11},{"id":"GO:0080156","count":11},{"id":"GO:1905639","count":11}]},{"hash":"990468538099336007","title":"Plant growth and development regulation","description":"The top GO terms point to regulatory processes across plant growth and development, including cytokinin-activated signaling, chlorophyll biosynthesis regulation, seed and root meristem growth, and modulation of cell wall/lignin biosynthesis, with both positive and negative regulation evident. This suggests a cluster of proteins acting as regulators coordinating growth, metabolism, and tissue remodeling rather than a single enzymatic function.","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":8},{"id":"GO:0010380","count":6},{"id":"GO:0080113","count":6},{"id":"GO:1901430","count":6},{"id":"GO:1901347","count":6}]},{"hash":"2274562143833034085","title":"Mitochondrial Transporters and Metabolism","description":"GO terms emphasize transport of manganese, ATP, heme, thiosulfate, and coenzyme A across mitochondrial membranes, plus mitochondrial apoptotic changes and necroptosis regulation, with links to insulin/IGF-driven energy signaling. Together these points indicate a cluster of mitochondrial transporters linked to energy metabolism and apoptotic signaling.","confidence":"High","size":26,"edges":45,"triangles":32,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":10},{"id":"GO:0061179","count":10},{"id":"GO:1990544","count":10},{"id":"GO:0015886","count":10},{"id":"GO:0090152","count":10}]},{"hash":"991916353775146478","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":315,"triangles":2374,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1901006","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0009451","count":2}]},{"hash":"393824832691953422","title":"Cell Cycle Regulation and Gene Expression","description":"This cluster centers on controls of cell cycle progression and regulation of gene expression, including transcription and translation. Terms include regulation of cell cycle and cell cycle itself, negative regulation of transcription by RNA Pol II, DNA-templated transcription, translation and translational initiation, and ribosome biogenesis. The presence of negative regulation of apoptotic process also aligns with coordinating cell cycle and survival. Taken together, these proteins likely function as regulators connecting transcription, translation machinery, and cell cycle control.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1705293416841699516","title":"DNA-Templated Transcription and Embryogenesis","description":"The dominant GO term is DNA-templated transcription, supported by developmental terms like blastocyst development and embryonic processes, suggesting the proteins are associated with transcriptional regulation during early development. Other terms are scattered stress responses or obsolete processes, so the theme is best described as transcription-related factors linked to embryogenesis rather than a highly cohesive functional module.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0070207","count":3},{"id":"GO:0001824","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1364660677785630912","title":"Plant nuclear transcription regulation and stress signaling","description":"Top terms cluster around DNA-templated transcription, nucleosome assembly, and regulation of transcription, indicating chromatin-level control of gene expression. Additional plant-related signals (responses to salicylic acid and gibberellin), hypoxia detection, and DNA damage response/autophagy-related terms suggest integration of transcription regulation with growth, stress, and signaling pathways. This combination supports a coherent, though broad, theme of transcriptional control linked to plant stress and growth signaling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006334","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0018171","count":2},{"id":"GO:0070483","count":2}]},{"hash":"1128929148206362554","title":"DNA Damage Repair and Stress Response","description":"The cluster is enriched for multiple DNA repair pathways (base-excision, nucleotide-excision, alkylation repair) alongside DNA replication and recombination, plus stress-response terms ( xenobiotic stimulus, light, ethanol). This supports a cohesive role in DNA damage sensing/repair and genome maintenance under stress, with potential regulation of repair pathway choice (e.g., SSA).","confidence":"High","size":26,"edges":75,"triangles":73,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006284","count":8},{"id":"GO:0042493","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0006310","count":6},{"id":"GO:0007568","count":6}]},{"hash":"324333170982274263","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster is dominated by GO terms related to ribosome production and rRNA maturation (ribosome biogenesis, ribosomal subunit biogenesis, maturation of SSU-rRNA) and is complemented by DNA-templated transcription and mitotic cell cycle terms, suggesting a nucleolar ribosome assembly/function module tied to transcription during cell division.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0035948","count":2}]},{"hash":"1118660724531524125","title":"Plant developmental transcriptional regulation","description":"The dominant signals are transcriptional regulation and plant development (floral meristem growth, multicellular development) with ethylene and ABA signaling, suggesting a cluster of transcriptional regulators coordinating developmental programs in plants.","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0032979","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0009738","count":3}]},{"hash":"785819317435047570","title":"Calcium-regulated muscle differentiation regulators","description":"The cluster is driven by terms centered on muscle development (positive regulation of skeletal muscle cell differentiation) and calcium signaling (cellular response to calcium ion), with supporting transcriptional control terms (DNA-templated transcription, RNA polymerase II). This points to a set of proteins coordinating calcium-dependent gene expression during muscle differentiation, with additional developmental regulatory signals that may reflect broader transcriptional regulation contexts.","confidence":"Medium","size":26,"edges":320,"triangles":2485,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001016","count":13},{"id":"GO:0071277","count":12},{"id":"GO:0006351","count":10},{"id":"GO:0006366","count":10},{"id":"GO:0080155","count":8}]},{"hash":"2177782572149758977","title":"B and T Cell Receptor Signaling","description":"The cluster is enriched for immune signaling terms: B cell receptor signaling, T cell activation, IL-4 production, IL-7 response, integrin-mediated signaling, and JNK pathway regulation, with hints of actin cytoskeleton rearrangement and PLC activity. Together these point to lymphocyte activation and signaling processes, suggesting these proteins function in antigen receptor\u2013mediated activation and cytokine responses.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0046328","count":2},{"id":"GO:0002333","count":2},{"id":"GO:2000251","count":2},{"id":"GO:0050798","count":2}]},{"hash":"1573117677602765250","title":"Vascular Development and Hormone/Lipid Metabolism","description":"The cluster combines vascular-related GO terms (retina vasculature development, endothelial cell-cell adhesion) with multiple lipid and hormone metabolism processes (cortisol and testosterone biosynthesis, retinoic acid and vitamin D responses, omega-oxidation, xenobiotic and oxidative demethylation). This suggests a theme around vascular tissues modulated by lipid/hormone signaling and retinoid metabolism.","confidence":"Medium","size":26,"edges":170,"triangles":401,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0061298","count":6},{"id":"GO:0030879","count":5},{"id":"GO:0071603","count":5},{"id":"GO:0034651","count":5},{"id":"GO:0070989","count":5}]},{"hash":"2041114895067460686","title":"Steroid Hormone and Xenobiotic Metabolism","description":"This cluster is driven by GO terms for steroid biosynthesis (cortisol, testosterone), epoxygenase P450 pathways, and xenobiotic/retinoic acid catabolism, as well as vitamin D response, pointing to a shared theme of endogenous hormone production combined with metabolism of external compounds. While developmental and adhesion terms are present, the dominant signal reflects hormone and xenobiotic metabolic processes.","confidence":"High","size":26,"edges":27,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":4},{"id":"GO:0045292","count":3},{"id":"GO:0030879","count":3},{"id":"GO:0071603","count":3},{"id":"GO:0034651","count":3}]},{"hash":"1390811109234682044","title":"Developmental chromatin regulation","description":"This cluster is enriched for nucleosome assembly, heterochromatin formation, and histone modification terms, indicating involvement in chromatin remodeling and epigenetic control. Developmental contexts, such as brain and pituitary gland development, suggest these factors regulate gene expression during organismal development. Some plant hormone\u2013related terms appear, but the core signal is chromatin-based regulation of development.","confidence":"Medium","size":26,"edges":27,"triangles":3,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0021983","count":6},{"id":"GO:0009736","count":5},{"id":"GO:0009751","count":4},{"id":"GO:0009739","count":4}]},{"hash":"1909066614491667399","title":"Protein quality control and mitochondrial function","description":"The top GO terms emphasize protein quality control pathways (ubiquitin-dependent ERAD, proteasome assembly, chaperone-related refolding, general protein processing) and mitochondrial maintenance (inner-membrane protein insertion, mtDNA replication regulation, oxidative phosphorylation). Together these suggest a cluster of proteins dedicated to protein homeostasis across the ER and mitochondria, with ancillary links to Golgi retention and cell-cycle processes, but the strongest theme centers on protein quality control and mitochondrial function.","confidence":"High","size":26,"edges":27,"triangles":13,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":12},{"id":"GO:0051301","count":8},{"id":"GO:0032979","count":7},{"id":"GO:0045053","count":7},{"id":"GO:0070682","count":7}]},{"hash":"891710328804383044","title":"Neural development and glial apoptosis","description":"The cluster\u2019s top GO terms are strongly centered on nervous system development, especially forebrain development, and include a glial cell apoptotic process. This suggests that the proteins are primarily involved in neural development with related glial cell remodeling/death. Some other terms (e.g., L-methionine cycle, TGF-beta response, melanization) are broader or peripheral to neural fate, but the dominant signal points to neural development. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007399","count":25},{"id":"GO:0051260","count":25},{"id":"GO:0030900","count":24},{"id":"GO:0010659","count":24},{"id":"GO:0035006","count":24}]},{"hash":"1980789391970761151","title":"Plant Hormone Signaling and Defense","description":"The top GO terms point to plant-specific processes: responses to salicylic acid and gibberellin, auxin homeostasis, cutin biosynthesis, and defense regulation, with occasional peroxisomal import and viral process terms. This suggests a coherent theme around plant hormone signaling, epidermal barrier biosynthesis, and defense/stress responses, despite some term variability.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0090073","count":2},{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0016032","count":2}]},{"hash":"1187601160038645613","title":"Cell Division and Stress Response","description":"The cluster is dominated by terms related to the mitotic cell cycle and cell division (GO:0000278 and GO:0051301), indicating a core involvement in proliferation. Several accompanying terms point to environmental responses (nutrient, toxic substances, cadmium) and stress signaling (GO:0007584, GO:0071276, GO:9636), suggesting these proteins coordinately regulate growth under varying conditions. A few terms like placenta development or imprinting regulation may reflect broader or cross-species annotations, but do not override the central theme of cell division paired with stress/nutrient responses.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0007584","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0006349","count":3}]},{"hash":"199959957893839926","title":"Diverse Biosynthetic and Metabolic Pathways","description":"The top GO terms are dominated by various biosynthetic processes (antibiotic, biotin, LPS, PHB) and related metabolism, with additional lipid processing and protein modification terms. This pattern points to a cluster of proteins involved in broad metabolic biosynthesis rather than a single, cohesive pathway, so a wide, metabolism-focused label fits best.","confidence":"Medium","size":26,"edges":16,"triangles":5,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0017000","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0009413","count":3}]},{"hash":"699172031746014835","title":"Plant development and hormone signaling with wax biosynthesis","description":"This cluster is dominated by terms tied to plant development (floral meristem growth, bract development, multicellular organism development) and transcriptional regulation, plus hormone signaling (ethylene- and ABA-activated pathways) and epidermal wax biosynthesis. The overall theme suggests proteins involved in developmental programs coordinated by hormonal signals and epidermal differentiation, with a few outlier terms (equilibrioception, brush border) likely annotations from other contexts. ","confidence":"Medium","size":26,"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:0050957","count":2},{"id":"GO:1904970","count":2},{"id":"GO:0010451","count":2}]},{"hash":"12747726582353435","title":"mRNA processing and translation initiation","description":"Top GO terms emphasize mRNA maturation (polyadenylation, modification, stabilization, splicing) and translation initiation (IRES-dependent initiation, eIF4F complex assembly), suggesting a cohesive function in mRNA lifecycle and translation start.","confidence":"High","size":26,"edges":89,"triangles":212,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":7},{"id":"GO:0016556","count":6},{"id":"GO:0048255","count":6},{"id":"GO:0075522","count":6},{"id":"GO:1905663","count":6}]},{"hash":"1542367127730528653","title":"Diverse Solute Transporters","description":"This cluster is dominated by GO terms for transporting a wide range of solutes (nitrate, sialic acid, urate, galactose, vitamins, 4-hydroxyphenylacetate, sodium-dependent organic cations), indicating a core theme of membrane transport. The accompanying osmotic-stress response and DNA-templated transcription terms suggest regulatory and metabolic coordination around transport processes rather than a single substrate pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042128","count":6},{"id":"GO:0006970","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0015739","count":4},{"id":"GO:0035461","count":4}]},{"hash":"1736279177575640876","title":"Steroid and lipid metabolism","description":"This cluster is driven by GO terms related to lipid and steroid hormone biosynthesis and turnover (cortisol, testosterone, brassinosteroids), vitamin D response, retinoic acid catabolic processes, and fatty acid omega-oxidation, plus xenobiotic catabolic activity. Together these indicate a common theme of lipid- and steroid-hormone\u2013related metabolism and signaling, rather than a single, cohesive signaling pathway. Some tissue-level terms (mammary gland development, endothelial adhesion) may reflect broader roles of these metabolic processes or cross-species annotations, but the core signal is lipid/steroid metabolism. ","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":12},{"id":"GO:0030879","count":11},{"id":"GO:0071603","count":11},{"id":"GO:0034651","count":11},{"id":"GO:0070989","count":11}]},{"hash":"1189107859402615508","title":"Ubiquitin-Dependent Protein Degradation and Stress Response","description":"The cluster shows a clear enrichment for ubiquitin-mediated proteolysis, including ERAD and multivesicular body sorting pathways, plus oxidative and osmotic stress responses and apoptosis. This points to a core role in proteostasis and stress signaling, with some peripheral terms (cytokinin signaling, striatum development, viral process) likely reflecting broader annotation overlaps. Thus, the dominant theme is ubiquitin-dependent protein degradation coupled with cellular stress responses.","confidence":"High","size":26,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0009736","count":2}]},{"hash":"172525238967363647","title":"ER Protein Trafficking and Calcium Signaling","description":"The terms cluster around endoplasmic reticulum\u2013related processes, especially ER-to-Golgi transport, ER exit site localization, and general intracellular protein transport, paired with regulation of calcium (ER and mitochondrial) and calcium-mediated signaling. Appended terms related to ER calcium regulation, ER-associated ubiquitin-dependent turnover, and apoptotic signaling suggest ER stress\u2013linked pathways, with an additional note on osteoblast differentiation that can involve secretory ER functions. Together, these indicate a coherent theme of ER trafficking coupled with calcium signaling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":2},{"id":"GO:0051561","count":2},{"id":"GO:1904154","count":2},{"id":"GO:0035584","count":2},{"id":"GO:2001244","count":2}]},{"hash":"494411456732497349","title":"Ubiquitin-dependent proteolysis in meiosis and cell cycle","description":"The top GO terms cluster around ubiquitin-proteasome\u2013mediated protein degradation (SCF-dependent and ubiquitin-dependent catabolic processes) and cytoskeletal/spindle dynamics (microtubule polymerization, spindle assembly in female meiosis I, oocyte maturation). Although some developmental terms appear, the dominant signal is regulation of protein turnover and microtubule-associated processes during meiosis and cell-cycle progression, suggesting proteins in this cluster act to control meiosis/spindle function via ubiquitin-mediated proteolysis.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":16},{"id":"GO:0042787","count":13},{"id":"GO:0046785","count":12},{"id":"GO:0007057","count":12},{"id":"GO:0021678","count":12}]},{"hash":"1409115007446007729","title":"Immune Activation and Cell Migration","description":"This cluster is enriched for immune-related GO terms (positive regulation of cytokine production involved in immune response, T cell proliferation, neutrophil clearance) and for cell movement/cytoskeletal signaling (Rho pathway, microtubule localization, endothelial cell migration). While DNA replication appears, the dominant pattern points to immune signaling coupled with migratory/cytoskeletal processes, suggesting involvement in immune response and cell trafficking.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0046641","count":23},{"id":"GO:0001502","count":23},{"id":"GO:0097350","count":23},{"id":"GO:0035372","count":23}]},{"hash":"40839067105357602","title":"Plant membrane transporters for nitrate, peptides, and xenobiotics","description":"The GO terms point to multiple transmembrane transport activities (nitrate, dipeptide/oligopeptide, xenobiotic) along with herbicide response and hormone signaling (auxin, gibberellin), suggesting a cluster of plant transport proteins that mediate nutrient uptake and xenobiotic detoxification and interact with hormone pathways.","confidence":"High","size":26,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":5},{"id":"GO:0010336","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0010167","count":5},{"id":"GO:0042938","count":5}]},{"hash":"1201756106245056642","title":"Auxin-Driven Gene Expression Regulation","description":"This cluster is dominated by auxin-related GO terms (auxin-activated signaling pathway and response to auxin) alongside transcriptional regulation (DNA-templated transcription, regulation of transcription) and RNA processing/translation steps (splicing, translation initiation, translation reinitiation). Together, they suggest a coordinated plant hormone\u2013mediated program that modulates gene expression at multiple levels in response to auxin.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009734","count":4},{"id":"GO:0001731","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009733","count":3},{"id":"GO:0006355","count":3}]},{"hash":"530963249563587971","title":"Light-regulated transcription and circadian rhythm","description":"The top GO terms cluster around light-responsive transcription (DNA-templated transcription, phototransduction, far-red signaling) and circadian regulation, suggesting a common theme of light-driven gene expression; a few outlier terms (pectin catabolic process, viral process, ubiquitination, tarsal gland development) may reflect annotation noise or broader functions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0045490","count":2},{"id":"GO:0009585","count":2},{"id":"GO:0042753","count":2},{"id":"GO:0010018","count":2}]},{"hash":"1848857390912958283","title":"Plant lipid and cell wall catabolism","description":"The top GO terms point to catabolic processes across lipids (triglyceride, monoacylglycerol, phosphatidylserine, acylglycerol remodeling) and cell wall polysaccharides (cellulose, pectin), mostly within a plant context (aerenchyma formation, camalexin biosynthesis). This suggests a cluster of proteins involved in broad lipid and cell wall carbohydrate turnover/remodeling in plants.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":7},{"id":"GO:2000124","count":7},{"id":"GO:0006660","count":6},{"id":"GO:0052651","count":6},{"id":"GO:0030245","count":5}]},{"hash":"136168888162679985","title":"Xylem development and vascular differentiation","description":"This cluster is enriched for GO terms related to xylem and vascular development (protoxylem development, xylem vessel member cell differentiation) and secondary cell wall biosynthesis, along with transcriptional regulation of these processes (DNA-templated transcription and its regulation). Additional terms like callus formation and leaf senescence reflect broader developmental regulation in plants, but the strongest signal centers on vascular tissue formation and cell wall biosynthesis, justifying the label.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":6},{"id":"GO:1990110","count":5},{"id":"GO:1900057","count":5}]},{"hash":"1898351928513614930","title":"Nuclear DNA Repair and Antiviral Defense","description":"The cluster\u2019s top GO terms center on nuclear nucleotide-excision repair, PML body organization, innate immune and defense responses to virus, and ubiquitin-related regulation. This combination suggests a cohesive nuclear program coordinating genome maintenance with antiviral signaling, involving PML bodies and ubiquitination-mediated control. Despite some obsolete terms, the dominant theme links DNA damage response to innate immunity.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":2},{"id":"GO:0030578","count":2},{"id":"GO:1901253","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2}]},{"hash":"155538926058206531","title":"Oocyte maturation and meiotic spindle assembly","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, and proteasome/ubiquitin-dependent protein degradation, with microtubule polymerization also present. These together suggest a cohesive role in oocyte meiosis progression and spindle dynamics, despite a few unrelated developmental terms in the mix. ","confidence":"High","size":26,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0001556","count":10},{"id":"GO:0046785","count":10},{"id":"GO:0006516","count":10},{"id":"GO:0007057","count":10}]},{"hash":"156393238560838511","title":"Cytoskeletal and membrane remodeling during cytokinesis","description":"The cluster is dominated by terms tying actin-based structures and cytokinesis together (mitotic contractile ring actin filament bundle assembly, membrane addition at site of cytokinesis, regulation of actin organization), along with GTPase activity regulation and plasma membrane repair, pointing to a cohesive theme of cytoskeletal dynamics coupled to membrane remodeling during cell division and related processes. Transcription-related terms appear secondary and likely incidental.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0001778","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0006930","count":3},{"id":"GO:0043087","count":3}]},{"hash":"535854423092387426","title":"Neural development and glial apoptosis","description":"The top GO terms are heavily weighted toward nervous system and forebrain development (multicellular organism development, forebrain development, nervous system development) and glial cell apoptotic process, suggesting a neural development and cell death focus. While there are some outliers (e.g., L-methionine cycle, melanization defense), the dominant theme points to neural development with related apoptotic signaling, justifying the label. ","confidence":"Medium","size":26,"edges":26,"triangles":1,"max_degree":6,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007275","count":9},{"id":"GO:0030900","count":8},{"id":"GO:0010659","count":8},{"id":"GO:0035006","count":8},{"id":"GO:0033353","count":8}]},{"hash":"828032412003945301","title":"DNA-Templated Transcription and Neural Development","description":"The cluster is dominated by GO terms for DNA-templated transcription and its regulation, with additional signals of neural development (axonogenesis) and synaptic plasticity (long-term potentiation). This suggests a cohesive theme around transcriptional control linked to neural development and signaling. Some terms (DNA integration, proviral latency, symbiont-mediated host apoptosis, mitotic cell cycle) seem peripheral or context-specific, but do not overwhelm the central transcription/neural trend.","confidence":"Medium","size":26,"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:0009734","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0006469","count":2}]},{"hash":"134151415890688285","title":"Interferon-driven antiviral innate immunity","description":"The top GO terms center on innate antiviral responses, including cellular response to exogenous dsRNA, type I interferon signaling, and innate immune response, which together indicate a cluster focused on antiviral defense pathways. While some terms relate to hormones and cell cycle, the strongest and most consistent theme is interferon-mediated antiviral defense, making this the most representative label.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0050689","count":6},{"id":"GO:0045087","count":6},{"id":"GO:0071360","count":6},{"id":"GO:0071357","count":6}]},{"hash":"637604006097279920","title":"Auxin signaling and phenylpropanoid biosynthesis in plants","description":"This cluster's top GO terms cluster around plant growth regulation and secondary metabolite production: auxin-activated signaling, meristem development, and biosynthesis of lignin, cutin, and flavonoids (phenylpropanoid pathway). The presence of DNA-templated transcription indicates regulatory roles coordinating development and metabolic pathways. Some entries marked obsolete, but the core theme points to a plant developmental program combining hormone signaling with phenylpropanoid metabolism.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0010252","count":3},{"id":"GO:0010143","count":3},{"id":"GO:0080088","count":3},{"id":"GO:0009809","count":3}]},{"hash":"860607700018344009","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":5},{"id":"GO:2000344","count":5},{"id":"GO:0016042","count":5},{"id":"GO:0006979","count":3},{"id":"GO:0098869","count":3}]},{"hash":"1383879402467459601","title":"Mitochondria and chloroplast protein import","description":"This cluster's top GO terms mainly describe proteins being imported or inserted into organelle compartments, particularly the mitochondrial matrix/inner membrane and chloroplast stroma, indicating a cohesive theme of organelle protein import/localization. A few outlier terms (e.g., endosperm cellularization, neuron differentiation) are likely incidental or misannotations but do not override the dominant signal.","confidence":"High","size":25,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:0010342","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0000002","count":1}]},{"hash":"462167339789626906","title":"Neural development and apoptosis regulation","description":"This cluster is driven by neural development terms (neural tube closure, forebrain development) and apoptotic signaling/process terms (positive regulation of apoptotic signaling, regulation of apoptotic DNA fragmentation, glial cell apoptotic process), suggesting proteins involved in nervous system development with regulation of cell death. Other terms related to TGF-beta response, ubiquitin-dependent ERAD, and splicing support a broader developmental/regulatory context, but the core theme centers on neurodevelopment linked to apoptosis.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051260","count":9},{"id":"GO:0001843","count":8},{"id":"GO:0030433","count":8},{"id":"GO:2001235","count":8},{"id":"GO:0000398","count":8}]},{"hash":"1982656932838154824","title":"Plant organelle RNA editing and processing","description":"The top GO terms cluster around RNA modification and processing activities in plant organelles, especially chloroplasts (plastid transcription, chloroplast RNA processing, chloroplast RNA modification) and mitochondria (mitochondrial mRNA modification, editing). The presence of cytidine-to-uridine editing and polycistronic mRNA processing suggests coordinated RNA maturation in chloroplasts/mitochondria, with an additional plant-specific signal linking chloroplast function to nucleus signaling and seed development. This combination points to a coherent theme of organelle RNA editing/processing in plants.","confidence":"High","size":25,"edges":291,"triangles":2108,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0080156","count":4},{"id":"GO:1905639","count":4},{"id":"GO:0009793","count":4}]},{"hash":"1157223380112448981","title":"RNA processing and translation initiation","description":"The cluster\u2019s top GO terms cluster around RNA biology\u2014mRNA modification, stabilization, and alternative splicing\u2014along with components of translation initiation (eIF4F complex assembly, IRES-dependent translation). This suggests a cohesive group of proteins involved in transcript maturation and the initiation of translation, with a few developmental signals appearing peripherally. Confidence in this theme is high.","confidence":"High","size":25,"edges":62,"triangles":43,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:1903861","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1375751964570836253","title":"Glutamatergic Synaptic Transmission","description":"The top GO terms point strongly to neuronal signaling, especially glutamatergic synaptic transmission, excitatory postsynaptic potentials, and receptor clustering, along with sodium/potassium ion transport\u2014core features of synaptic function. Some terms (DNA replication, transcription, plant signaling) may reflect broader housekeeping annotations, but the dominant theme is synaptic activity in neurons. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035249","count":4},{"id":"GO:0009738","count":3},{"id":"GO:0008542","count":3},{"id":"GO:0043113","count":3}]},{"hash":"459066288837283527","title":"Nuclear RNA processing and chromatin regulation","description":"The cluster centers on nuclear-related activities: mRNA splicing, transcription termination, ribosomal RNA maturation, histone mRNA metabolism, and heterochromatin formation, with supporting terms like nuclear import and cell cycle-related regulation, indicating a cohesive theme of nuclear gene expression control. Some stress-response terms (abscisic acid, water deprivation) may reflect regulation of these nuclear processes under stress.","confidence":"Medium","size":25,"edges":211,"triangles":917,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":12},{"id":"GO:0006369","count":10},{"id":"GO:0051170","count":8},{"id":"GO:0008334","count":8},{"id":"GO:1990141","count":8}]},{"hash":"304226758437669365","title":"Organelle RNA Editing and Plastid mRNA Processing","description":"The top terms cluster around mitochondrial mRNA processing/modification and chloroplast/plastid RNA editing and transcription, including cytidine-to-uridine editing and polycistronic mRNA processing, plus chloroplast-nucleus signaling. This points to a module of organellar gene expression and inter-organellar communication, particularly in plants; the seed dormancy term likely reflects development contexts tied to plastid function. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":4},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0080156","count":4},{"id":"GO:1905639","count":4}]},{"hash":"876379142445170248","title":"ER Stress Response and Protein Quality Control","description":"The top GO terms strongly point to endoplasmic reticulum\u2013associated protein handling, including ubiquitin-dependent ERAD, misfolded protein transport, chaperone-assisted refolding, and ER-stress\u2013driven translation initiation, indicating a cohesive ER quality control module (despite a few unrelated terms). This makes a concise label focused on ER stress and protein quality control representative of the cluster.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:1901621","count":2},{"id":"GO:0051259","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0070389","count":2}]},{"hash":"587398204275141615","title":"Mitochondrial translation and intracellular transport","description":"The cluster is dominated by mitochondrial translation (GO:0032543) and also includes several terms related to intracellular trafficking and organelle quality control (nuclear import, mRNA export, ER organization, ERAD). The mix of metabolic-related terms (fatty acid catabolism, tRNA biosynthesis) suggests a broader, loosely connected set of functions rather than a single cohesive pathway. Therefore the label focuses on the most prominent theme\u2014translation within mitochondria and associated intracellular transport\u2014while acknowledging the weaker links to other processes. ","confidence":"Low","size":25,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0007029","count":5},{"id":"GO:0009062","count":5}]},{"hash":"378146133284459738","title":"Redox homeostasis and prostaglandin biosynthesis","description":"The top GO terms show strong enrichment for redox-related processes (cell redox homeostasis, glutathione metabolic and derivative biosynthesis, cellular oxidant detoxification) and prostaglandin biosynthesis, indicating a cluster centered on maintaining redox balance while producing lipid inflammatory mediators. Additional terms like platelet aggregation and calcium-regulated muscle contraction may reflect downstream signaling contexts, but the dominant themes are redox regulation and prostaglandin signaling.","confidence":"Medium","size":25,"edges":241,"triangles":1240,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":14},{"id":"GO:0001516","count":13},{"id":"GO:0006749","count":13},{"id":"GO:0098869","count":13},{"id":"GO:0070527","count":12}]},{"hash":"2030396994291884633","title":"Excitatory synapse plasticity and AMPA receptor clustering","description":"This cluster is driven by terms related to excitatory neurotransmission, synaptic plasticity, and AMPA receptor clustering, with supporting involvement of actin cytoskeleton dynamics that underlie spine remodeling. The presence of \u201cexcitatory chemical synaptic transmission,\u201d \u201cpositive regulation of synaptic plasticity,\u201d and \u201cpositive regulation of AMPA glutamate receptor clustering\u201d points to a coherent theme of excitatory synapse function and plasticity, despite a few unrelated or obsolete terms.","confidence":"High","size":25,"edges":14,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035214","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0006378","count":2},{"id":"GO:2001032","count":1},{"id":"GO:0010591","count":1}]},{"hash":"2295762553005085552","title":"Plant Hormone-Responsive Transcriptional Regulation","description":"Top terms indicate core transcriptional control (DNA-templated transcription, regulation of transcription) and RNA processing, together with multicellular development. The enrichment of abscisic acid\u2013activated signaling and salicylic acid\u2013mediated responses suggests hormone-regulated gene expression as a unifying theme in plant development, despite a few broader terms like cell migration and telomere maintenance. Overall, the cluster centers on transcriptional regulation in plant development and hormone signaling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0009738","count":3}]},{"hash":"1701951809133761213","title":"Innate Immune Signaling and Transcriptional Regulation","description":"GO terms strongly point to innate immunity (TLR8 signaling, response to fungus, regulation of cytokine production) combined with transcriptional control (DNA-templated transcription, regulation of transcription). While a few terms relate to development or other processes, the dominant signals align with immune signaling and transcriptional regulation, suggesting a cohesive cluster around immune response modulation and gene regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006469","count":10},{"id":"GO:0006351","count":8},{"id":"GO:0006355","count":8},{"id":"GO:0010596","count":8},{"id":"GO:0009620","count":8}]},{"hash":"806807249535241739","title":"RNA Splicing and Translation Initiation Complex","description":"The GO terms point to strong involvement in RNA processing (cis and alternative splicing, mRNA modification, stabilization, and polyadenylation) and in translation initiation (eIF4F complex assembly, IRES-dependent initiation), suggesting these proteins form a coordinated RNA maturation and translation initiation module.","confidence":"High","size":25,"edges":179,"triangles":690,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":13},{"id":"GO:0016556","count":12},{"id":"GO:0048255","count":12},{"id":"GO:0075522","count":12},{"id":"GO:1905663","count":12}]},{"hash":"297010564291469179","title":"Flower and Seed Development Transcription Regulators","description":"The cluster is dominated by terms for DNA-templated transcription and its regulation, with recurring associations to seed development, floral meristem growth, and bract development, indicating transcriptional regulators controlling plant development. Additional enrichment for ethylene- and ABA-activated signaling and wax biosynthetic regulation supports a role in hormone-mediated floral/seed development and related defense/wax pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0048316","count":5},{"id":"GO:0010451","count":4},{"id":"GO:0009873","count":4}]},{"hash":"1762342188216053005","title":"Organelle Protein Import","description":"The top GO terms point toward targeting and translocation of proteins into various organelles (chloroplast stroma, mitochondrial matrix/inner membrane, Golgi), indicating a cluster of proteins involved in organelle import and trafficking. While a few terms (e.g., microspike assembly, TLR signaling) appear less related, the dominant signal is protein import to organelles, suggesting a coherent function around intracellular protein targeting.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045037","count":3},{"id":"GO:0045053","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0032094","count":2}]},{"hash":"1910207107462195158","title":"Plant defense and cell wall remodeling","description":"This cluster\u2019s top GO terms are dominated by plant-specific processes, including oxidative stress response, cellular oxidant detoxification, lignin and hydrogen peroxide catabolic processes, and plant-type cell wall organization, with additional terms related to defense against fungi and pollen interactions. Together, these point to functions in plant immunity and dynamic cell wall remodeling, suggesting proteins involved in defense and cell wall modification rather than other broad categories. Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006979","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0046274","count":5},{"id":"GO:0042744","count":5}]},{"hash":"976658130949318086","title":"Mitotic spindle orientation and septin regulation","description":"The top GO terms converge on mitosis-related processes (sister chromatid biorientation, spindle orientation checkpoint signaling, chromosome localization) and septin ring organization/disassembly, indicating tight regulation of chromosome segregation and cytokinesis. Protein dephosphorylation and signal transduction support regulatory control of these events, while an outlier term (P granule assembly) does not override the overall cell-cycle focus.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090219","count":3},{"id":"GO:1903863","count":3},{"id":"GO:0007165","count":3},{"id":"GO:0031134","count":3},{"id":"GO:0031107","count":3}]},{"hash":"157300753455361871","title":"Ribosome biogenesis and nuclear transport","description":"The cluster shows enrichment for ribosome-related processes (maturation of 5.8S rRNA, ribosomal large subunit assembly) and nuclear import, suggesting a shared theme in ribosome assembly and nucleolar/nuclear trafficking; other scattered terms (metabolism, chemotaxis, developmental cues) may reflect broader regulatory roles or annotation noise.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045071","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0006006","count":2}]},{"hash":"1038212905597361363","title":"Ciliary Vision and Trafficking","description":"This cluster is dominated by GO terms for visual perception and cilium assembly, with many terms pointing to intracellular trafficking processes such as receptor recycling and regulation of endosome size. Together, these suggest a group of proteins involved in photoreceptor/ciliary function and the trafficking/signaling within cilia and neurons. While there are some cell cycle and growth-related terms present, the core theme centers on ciliary/visual biology and associated trafficking pathways.","confidence":"High","size":25,"edges":148,"triangles":482,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":23},{"id":"GO:0000278","count":23},{"id":"GO:0019236","count":20},{"id":"GO:0060271","count":20},{"id":"GO:0035330","count":20}]},{"hash":"1400227225391925970","title":"Neural Development and Angiogenesis","description":"The strongest terms point to neural development (forebrain development, neural tube closure, multicellular organism development) and associated vascular remodeling (positive regulation of angiogenesis), with proteolysis aiding tissue remodeling during development. Some other terms (immune defense, glucose response) are less central but can be related to development contexts. Overall, a cohesive theme of neural development with angiogenic processes.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006508","count":9},{"id":"GO:0050830","count":8},{"id":"GO:0007275","count":7},{"id":"GO:0045766","count":7},{"id":"GO:0014068","count":7}]},{"hash":"2275654493622438397","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001253","count":2},{"id":"GO:0031440","count":2},{"id":"GO:0042797","count":2},{"id":"GO:0045899","count":2},{"id":"GO:0006362","count":2}]},{"hash":"2011087798794028855","title":"RNA-based gene regulation","description":"The cluster\u2019s top terms are dominated by transcription (DNA-templated transcription) and RNA-level regulation (miRNA metabolic process and miRNA-mediated gene silencing), indicating a shared theme of controlling gene expression through transcriptional and post-transcriptional mechanisms. Other terms related to protein processing and immune signaling are present but appear secondary, so the core connection is RNA-mediated gene regulation. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1902187","count":2},{"id":"GO:0007014","count":2},{"id":"GO:0001519","count":2},{"id":"GO:0035278","count":2}]},{"hash":"515957316804655601","title":"ER-Golgi Vesicle Transport and Cell Division","description":"The top terms emphasize vesicle trafficking between the ER and Golgi (ER-Golgi and Golgi-ER transport) and mitosis-related processes (cell division, spindle orientation), suggesting the cluster centers on secretory pathway dynamics linked to cell-cycle events. While other terms (transcription, signaling) are present, the vesicle transport and division themes are most prominent.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070262","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0043547","count":2}]},{"hash":"2237367813127357775","title":"Immune Activation and Cytokine Regulation","description":"This cluster is dominated by GO terms tied to immune response activation and cytokine production, including positive regulation of T cell proliferation, interleukin-4 production, and positive regulation of cytokine production in immune responses, along with neutrophil clearance and endothelial migration. The presence of related processes like Rho signaling and cytoskeletal organization complements immune cell signaling and migration, supporting a cohesive theme of immune activation and cytokine regulation.","confidence":"High","size":25,"edges":73,"triangles":40,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":25},{"id":"GO:0001502","count":25},{"id":"GO:0097350","count":25},{"id":"GO:0035372","count":25},{"id":"GO:0043068","count":25}]},{"hash":"789040062134988114","title":"Plant Developmental Signaling Regulation","description":"The terms show a focus on regulation of signaling pathways (BMP/TGF-beta, SMAD, NF-kappaB, TGF-beta stimulus) and developmental processes (meristem identity), with supporting processes like phosphatase activity and vesicle/vacuole trafficking. Although some terms touch on photosystem adjustment, the cluster predominantly centers on modulation of signaling networks governing plant growth and development, justifying this label. ","confidence":"Medium","size":25,"edges":222,"triangles":1106,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0080005","count":24},{"id":"GO:0000173","count":24},{"id":"GO:0046827","count":24},{"id":"GO:0071560","count":24},{"id":"GO:0010991","count":24}]},{"hash":"2147496206037218749","title":"T Cell Activation and Cytokine Signaling","description":"The terms are dominated by immune system regulation: positive regulation of alpha-beta T cell proliferation, cytokine production including IL-4, neutrophil clearance, and immune response modulation. Additional terms about microtubule localization and Rho signaling reflect cytoskeletal changes during immune cell activation and migration; endothelial cell migration relates to vascular remodeling during inflammation. Collectively, these indicate a cluster centered on adaptive immune activation and inflammatory signaling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":24},{"id":"GO:0001502","count":24},{"id":"GO:0097350","count":24},{"id":"GO:0035372","count":24},{"id":"GO:0043068","count":24}]},{"hash":"1519388877528683209","title":"DNA-Templated Transcription Regulation","description":"The top GO terms are dominated by regulation of DNA-templated transcription and DNA-templated transcription, indicating the cluster is largely composed of transcriptional regulatory proteins. The other terms (ubiquitin-dependent protein catabolic process and various transport and metabolic processes) appear as secondary associations, suggesting either multifunctional proteins or incidental annotations. Overall, the dominant theme is transcriptional regulation.","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":5},{"id":"GO:0006351","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0015821","count":2},{"id":"GO:0010345","count":2}]},{"hash":"1156185096414921869","title":"Oocyte Meiosis, Spindle Assembly, and Proteolysis","description":"This cluster is dominated by GO terms for ubiquitin-dependent proteolysis (SCF-dependent proteasomal degradation) and general ubiquitin-mediated protein catabolism, along with microtubule polymerization and spindle assembly in female meiosis I, and oocyte maturation. The core theme appears to be proteolysis coordinating meiotic progression and spindle dynamics in oocytes, with a potential secondary signal from neural development terms that may reflect broader developmental regulation or annotation overlap. Overall, the cluster seems to represent a module of proteostasis linked to meiosis and oocyte maturation.","confidence":"Medium","size":25,"edges":16,"triangles":1,"max_degree":4,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0042787","count":10},{"id":"GO:0046785","count":9},{"id":"GO:0007057","count":9},{"id":"GO:0021678","count":9}]},{"hash":"1666555922737215012","title":"Diverse Membrane Transporters","description":"The top GO terms cluster around transmembrane transport of a wide range of substrates\u2014ions (sodium, potassium, phosphate), vitamins, sugars, xenobiotics, and other metabolites\u2014as well as neurotransmitter loading into synaptic vesicles. This pattern points to a family of membrane transport proteins with varied substrates, rather than a single specific substrate function.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:1900754","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0006855","count":3}]},{"hash":"1325096560572658794","title":"Biosynthesis and RNA Modification","description":"Top GO terms indicate a blend of biosynthetic processes (sterol, phosphatidylcholine, antibiotic biosynthesis) with RNA-centric activities (rRNA and tRNA methylation, ribosomal subunit export) and cell growth. This suggests proteins involved in metabolic biosynthesis alongside RNA modification/translation processes, rather than a single cohesive pathway. Therefore, the label emphasizes both biosynthesis and RNA modification as the cluster\u2019s core theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0016126","count":4},{"id":"GO:0046690","count":3},{"id":"GO:0090398","count":3}]},{"hash":"2297891468939394546","title":"Proteoglycan and Glycosaminoglycan Biosynthesis","description":"Derived from GO terms focused on chondroitin sulfate proteoglycan biosynthesis, UDP-D-xylose metabolism, and glycosylation, this cluster is centered on proteoglycan and GAG assembly, core ECM components, and related biosynthetic pathways. The presence of cell adhesion molecule production and leukocyte tethering/rolling terms suggests ECM-mediated cell interactions and mucosal immune environments, consistent with proteoglycan/ECM remodeling across tissues (including kidney and intestinal contexts). Overall, the common theme is proteoglycan and glycosaminoglycan biosynthesis and ECM-related processes.","confidence":"High","size":25,"edges":20,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":8},{"id":"GO:0042403","count":7},{"id":"GO:0060993","count":7},{"id":"GO:0033319","count":7},{"id":"GO:0002426","count":7}]},{"hash":"1112038914920773971","title":"Oocyte maturation and meiotic spindle assembly","description":"The top terms center on oocyte maturation and spindle assembly in female meiosis I, with associated ubiquitin-proteasome\u2013dependent protein turnover, suggesting a cohesive role in meiotic progression and oogenesis. While there are some broader developmental terms, the strongest, most specific signal is meiosis-related; thus the label aptly captures the cluster's core function.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":15},{"id":"GO:0001556","count":14},{"id":"GO:0046785","count":14},{"id":"GO:0006516","count":14},{"id":"GO:0007057","count":14}]},{"hash":"60193825744198775","title":"Floral development and hormone signaling in plants","description":"The top GO terms cluster around plant development and hormone-regulated processes, including auxin-activated signaling and polar transport, ethylene signaling, floral meristem growth, bract development, and multicellular organism development. Transcription-related terms (DNA-templated transcription and mRNA splicing) suggest regulatory proteins modulating gene expression during development. Together, these terms indicate a group of proteins coordinating floral structure formation through hormonal signaling and transcriptional regulation.","confidence":"High","size":25,"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:0000398","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2}]},{"hash":"2198453221983691854","title":"Transcription Regulation and Chromatin Remodeling","description":"The top GO terms center on DNA-templated transcription, transcription regulation by RNA polymerase II, nucleosome disassembly, and chromatin remodeling, indicating proteins involved in controlling transcription through chromatin dynamics. Some terms like neural retina development or triglyceride catabolic process appear peripheral, but the dominant signal is nuclear transcription regulation and chromatin remodeling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006337","count":2},{"id":"GO:2001165","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0043044","count":2}]},{"hash":"355575133944138024","title":"Oocyte meiosis and early neural development","description":"The cluster shows strong enrichment for processes tied to meiosis and oocyte maturation (spindle assembly in female meiosis I; oocyte maturation) and proteasome-ubiquitin\u2013mediated protein turnover (SCF-dependent ubiquitin ligase activity), plus microtubule polymerization. The presence of neural development terms (initiation of neural tube closure; third ventricle development) suggests additional involvement in early developmental events, but the dominant signal is meiosis/oocyte maturation with related cell-cycle regulation. ","confidence":"Medium","size":25,"edges":198,"triangles":677,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":22},{"id":"GO:0046785","count":20},{"id":"GO:0007057","count":20},{"id":"GO:0021678","count":20},{"id":"GO:0006516","count":20}]},{"hash":"1405365625370557297","title":"Ubiquitin-Proteasome Mediated Proteolysis","description":"The cluster is strongly enriched for ubiquitin-dependent protein catabolic processes, including SCF-dependent proteasomal degradation, K48- and K6-linked ubiquitination, and histone ubiquitination/autoubiquitination, pointing to a cohesive module centered on targeted protein degradation and histone turnover, with some links to TNF signaling pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0036205","count":8},{"id":"GO:0070936","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0085020","count":8}]},{"hash":"313103735006672188","title":"Interferon-Driven Innate Immunity","description":"This cluster is dominated by innate immune and antiviral signaling terms: cellular response to type I interferon, innate immune response, cellular response to exogenous dsRNA, and negative regulation of defense response to virus by host. The prominent IFN-related terms point to a core antiviral defense function, while the other terms (cell division and hormone-related development) may reflect incidental annotations or secondary roles.","confidence":"High","size":25,"edges":5,"triangles":0,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":11},{"id":"GO:0071357","count":11},{"id":"GO:0006463","count":10},{"id":"GO:0009938","count":10},{"id":"GO:0030850","count":10}]},{"hash":"1090677590466694634","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The cluster is dominated by GO terms for ubiquitination and proteolytic degradation, including ubiquitin-dependent protein catabolic processes, SCF-dependent ubiquitination, K48- and K6-linked ubiquitination, polyubiquitination, and autoubiquitination, with histone catabolic process also represented. This points to a cohesive theme of targeted protein turnover via the ubiquitin-proteasome system, possibly extending to signaling/cell stress responses linked to proteostasis. ","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:0031146","count":9},{"id":"GO:0036205","count":7},{"id":"GO:0070936","count":7},{"id":"GO:0051865","count":7}]},{"hash":"72313080669860769","title":"Plant Oxidative Stress Response and Cell Wall Remodeling","description":"The top GO terms cluster around oxidative stress response, detoxification of oxidants, hydrogen peroxide metabolism, and lignin/cell wall-related processes, with cytokinin signaling reinforcing a plant-growth response context. This suggests a cohesive theme of plant oxidative stress management coupled with cell wall remodeling, despite the absence of interactions in the network. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006979","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0046274","count":4},{"id":"GO:0042744","count":4}]},{"hash":"550223468906896262","title":"Plant pectin biosynthesis and cell wall remodeling","description":"This cluster is dominated by GO terms for pectin biosynthesis, pectin catabolic processes, and general cell wall modification, which together point to plant cell wall biosynthesis and remodeling. Additional signals of calcium ion detection and related regulatory processes suggest Ca2+-mediated signaling linked to cell wall dynamics. Some terms like skeletal muscle development appear less connected, but the strongest theme is plant cell wall/polysaccharide metabolism.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031573","count":4},{"id":"GO:0048741","count":4},{"id":"GO:0048358","count":3},{"id":"GO:0042545","count":3},{"id":"GO:0045490","count":3}]},{"hash":"562110219307610641","title":"Fungal beta-1,3-glucan synthesis and cell wall assembly","description":"This cluster is dominated by terms for fungal-type cell wall organization, (1->3)-beta-D-glucan biosynthesis and catabolism, and cell wall assembly, suggesting a cohesive role in fungal cell wall construction and remodeling (including septum-associated processes).","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031505","count":5},{"id":"GO:0006076","count":5},{"id":"GO:0000917","count":4},{"id":"GO:0071970","count":4},{"id":"GO:0071940","count":4}]},{"hash":"2095225916115834887","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090615","count":5},{"id":"GO:0016554","count":5},{"id":"GO:0080156","count":5},{"id":"GO:1905639","count":5},{"id":"GO:0009793","count":5}]},{"hash":"814693084114772245","title":"Chloroplast gene expression and photosynthesis","description":"Top terms point to chloroplast-related processes: translation (protein synthesis within plastids), DNA-templated transcription, Group II intron splicing (a hallmark of plastid RNA processing), and photosynthesis. Additional terms touch plastid metabolism (phenylalanine biosynthesis, tetrahydrobiopterin biosynthesis). Although some terms are obsolete or broad, the cluster most coherently represents plastid gene expression and photosynthetic function.","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0000373","count":2}]},{"hash":"740768859744866439","title":"RNA Polymerase II Transcription Regulation and Elongation","description":"This cluster\u2019s proteins are mainly annotated with RNA polymerase II\u2013dependent transcription terms, including elongation, initiation, and promoter clearance, with snRNA transcription by RNAP II also represented. The emphasis on transcription by RNAP II suggests these proteins function as regulators or components of transcription machinery; a few terms are obsolete but do not change the overall theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0043085","count":1},{"id":"GO:0080163","count":1}]},{"hash":"257510277974280793","title":"Neural development and cell cycle","description":"The cluster shows strong signals for DNA replication, mitosis, centrosome cycle, and DNA repair, indicating proliferative, cell-cycle\u2013active cells. It also includes neural-specific terms such as axonogenesis and Schwann cell development, suggesting neural lineage differentiation during embryogenesis. Therefore, a concise label capturing both proliferation and neural development is appropriate.","confidence":"Medium","size":24,"edges":40,"triangles":44,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":19},{"id":"GO:0048701","count":17},{"id":"GO:0006351","count":13},{"id":"GO:0000278","count":12},{"id":"GO:0007098","count":11}]},{"hash":"1747902473917658305","title":"Brain Development and Neural/Glial Apoptosis","description":"The GO terms cluster around forebrain and brain development, neural tube closure, and apoptosis in neurons and glia, with a TGF-beta signaling response, suggesting a developmental brain program involving programmed cell death. While there are some broader terms like aging and cardiac muscle cell apoptosis, the dominant signal is neural development coupled with apoptosis. ","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":6},{"id":"GO:0010659","count":6},{"id":"GO:0071560","count":6},{"id":"GO:0034349","count":6},{"id":"GO:0007568","count":6}]},{"hash":"1769167906291569783","title":"Diverse Regulatory Signaling and Differentiation","description":"The terms span regulation of gene expression (mRNA stability), signaling pathways (NOD2 signaling), kinase activity regulation, and various differentiation processes (oligodendrocyte differentiation, dendrite development), with additional sensory and hormonal response terms (thermoception, vitamin D response). This suggests a broad cluster centered on regulatory signaling and developmental regulation rather than a single cohesive function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":3},{"id":"GO:0033280","count":2},{"id":"GO:0050955","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0007253","count":2}]},{"hash":"1307959668637530623","title":"Virus-host interaction: virion assembly and release","description":"The presence of virion assembly and viral release terms points to a viral life-cycle theme, coupled with host vesicle trafficking (ER-Golgi) and protein turnover; more general processes like mRNA splicing and ribosome biogenesis suggest these proteins interact with core gene expression machinery during infection, producing a cluster centered on virus-host interplay.","confidence":"Low","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0007130","count":2}]},{"hash":"2107493742370273570","title":"Mercury detox and metal ion transport","description":"This cluster is enriched for mercury-related terms (mercury ion transport, detoxification, response) alongside broader metal ion transport and homeostasis terms (copper, zinc, cadmium transport; copper ion export; intracellular copper homeostasis). The shared theme is cellular handling of metal ions, particularly mercury, through transport and detox pathways, indicating a cohesive metal homeostasis/mercury detox function.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015694","count":3},{"id":"GO:0015680","count":3},{"id":"GO:0070574","count":3},{"id":"GO:0050787","count":3},{"id":"GO:0046689","count":3}]},{"hash":"640675214411677922","title":"Neural development and embryogenesis","description":"Based on the top GO terms, the cluster is enriched for neural and embryonic processes: spinal cord development, neural tube closure, neuron projection development, embryonic organ development. While there are a few general cellular processes (ribosome biogenesis, COPII vesicle budding), the predominant signal is neural development and embryogenesis, justifying a concise label.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0035264","count":5},{"id":"GO:0021510","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0001843","count":5}]},{"hash":"1750600127255238392","title":"Translation initiation and reinitiation control","description":"This cluster is dominated by GO terms related to translation initiation, preinitiation complex formation, and various reinitiation events (including IRES-dependent and viral termination-reinitiation), suggesting proteins functioning together to regulate translational initiation; other terms like splicing or ER-associated pathways appear as peripheral processes.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0075522","count":5},{"id":"GO:0075525","count":5},{"id":"GO:0006446","count":5}]},{"hash":"44981876369023019","title":"Plant Hormone Signaling and Chromatin Remodeling","description":"The top GO terms point to plant hormone responses (salicylic acid and gibberellin) and to transcriptional regulation through chromatin remodeling (including rDNA heterochromatin formation and regulation of DNA-templated transcription), along with development-related processes like seed growth and chlorophyll biosynthesis. This suggests a coherent theme of hormone-induced gene expression changes mediated by chromatin state, with some miscellaneous terms that are less central but do not override the main connection.","confidence":"Medium","size":24,"edges":5,"triangles":0,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009751","count":7},{"id":"GO:0009739","count":7},{"id":"GO:0043044","count":6},{"id":"GO:0000183","count":5},{"id":"GO:0006355","count":5}]},{"hash":"1079994541062244850","title":"DNA maintenance and proteostasis","description":"Most frequent terms center on nuclear DNA processes (DNA replication, DNA repair, DNA integration) and protein turnover (proteolysis, ubiquitin/ERAD pathway). This suggests a cluster focused on DNA maintenance coupled with proteostasis, with developmental or signaling terms appearing less central. Overall, the label reflects the dominant theme of DNA metabolism and proteolytic quality control.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0006281","count":2},{"id":"GO:1901621","count":2}]},{"hash":"1127979426261620556","title":"Plant Hormone Signaling Network","description":"This cluster is dominated by plant-specific hormone signaling terms: cytokinin-activated signaling, response to gibberellin, ACC (ethylene precursor) response, and salicylic acid response, plus atrichoblast differentiation and boron deprivation response, with supporting metabolism terms like cellulose catabolic and sterol biosynthesis. The convergence on multiple hormone signaling pathways and growth-related processes suggests proteins functioning in plant hormone signaling and growth regulation rather than a single metabolic pathway.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030245","count":5},{"id":"GO:0008286","count":4},{"id":"GO:0009736","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0016126","count":3}]},{"hash":"614595915172199171","title":"Plant Development and RNA Silencing","description":"This cluster is enriched for plant-development GO terms (auxin response/signaling, meristem development, vegetative phase change, wax biosynthesis, fruit dehiscence) and RNA silencing/epigenetic terms (ta-siRNA processing, RNAi antiviral response, siRNA-directed DNA methylation). The combination suggests a functional module where hormone-regulated development is coordinated by RNA silencing mechanisms and DNA methylation, pointing to a cohesive plant developmental program intertwined with gene-silencing regulation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009733","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0010267","count":1},{"id":"GO:0010025","count":1},{"id":"GO:0010050","count":1}]},{"hash":"1056877118582229198","title":"RNA processing and transcription regulation","description":"The top GO terms cluster around RNA biology and gene expression control: DNA-templated transcription, regulation of transcription, mRNA splicing, P-body assembly, mRNA decay via deadenylation, and translational initiation regulation. These indicate a cohesive theme of RNA processing and transcriptional/gene-expression regulation, with some additional transport-related terms that may reflect multifunctional roles of these proteins. ","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:0030433","count":2},{"id":"GO:0000132","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0035721","count":2}]},{"hash":"147798923354199033","title":"Embryonic neural patterning and heart morphogenesis","description":"The cluster combines terms tied to neural development (floor plate development; GABAergic interneuron differentiation; auditory receptor fate) with cardiac morphogenesis (heart valve development; outflow tract morphogenesis) and mesenchyme formation, suggesting a role in embryonic tissue patterning and organ formation. While some terms (e.g., transcription by RNA polymerase II) are broad, the convergent emphasis on neural and cardiac patterning supports a cohesive developmental theme.","confidence":"Medium","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":18},{"id":"GO:0031542","count":15},{"id":"GO:2000793","count":14},{"id":"GO:2000764","count":14},{"id":"GO:0060375","count":14}]},{"hash":"1243128749164000912","title":"Transcriptional Regulation in Stress and Development","description":"The cluster\u2019s top GO term is transcription by RNA polymerase II, and its members are linked to diverse regulatory and signaling processes (vitellogenesis, calcium signaling, IL-4 and TGF-\u03b2 related pathways, nitrosative stress\u2013related apoptosis, nutrient-responsive transcription, circadian locomotor rhythm, abscisic acid response). This pattern points to a group of proteins involved in regulating gene expression in response to developmental cues and environmental stresses, rather than a single core pathway, hence a label centered on transcriptional regulation across development and stress. ","confidence":"Medium","size":24,"edges":222,"triangles":1121,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":10},{"id":"GO:0007296","count":8},{"id":"GO:0071277","count":8},{"id":"GO:0045064","count":8},{"id":"GO:0009737","count":8}]},{"hash":"2101420185754463638","title":"Steroid and Prostaglandin Hormone Biosynthesis","description":"This cluster is enriched for prostaglandin biosynthesis and several steroid hormone biosynthesis terms (cortisol, testosterone) along with related lipid oxidation and xenobiotic metabolism processes, suggesting a cohesive module around lipid-derived hormone production and processing. Tissue-context terms like mammary gland development and endothelial cell-cell adhesion likely reflect physiological contexts rather than core function.","confidence":"Medium","size":24,"edges":237,"triangles":1334,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":20},{"id":"GO:0030879","count":14},{"id":"GO:0071603","count":14},{"id":"GO:0034651","count":14},{"id":"GO:0070989","count":14}]},{"hash":"1093032451804697039","title":"Neurodevelopmental apoptosis signaling","description":"The proteins are enriched for neural-development terms (neural tube closure, forebrain development) and various apoptotic processes (neuron and glial apoptotic processes, intrinsic ER-stress\u2013induced apoptosis, positive regulation of apoptotic signaling, regulation of apoptotic DNA fragmentation, and TGF-beta\u2013related signaling), indicating a cohesive theme of apoptosis regulation during neural development and related tissues.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007568","count":8},{"id":"GO:0001843","count":6},{"id":"GO:2001235","count":6},{"id":"GO:0030900","count":6},{"id":"GO:1902510","count":6}]},{"hash":"1508504009108115040","title":"Organelle RNA editing and processing in plants","description":"The cluster is dominated by GO terms tied to RNA metabolism in organelles, especially chloroplasts and mitochondria: plastid transcription, chloroplast RNA modification, mitochondrial mRNA processing and modification, RNA modification including cytidine-to-uridine editing, and polycistronic mRNA processing. These consistently point to organelle RNA editing/processing as the shared function of these proteins, with a potential minor contribution from seed dormancy development terms as incidental. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3}]},{"hash":"934024658098705737","title":"Organelle RNA Editing in mitochondria and chloroplasts","description":"The leading GO terms point to RNA processing and editing in organelles: mitochondrial mRNA processing and modification, chloroplast RNA modification, and cytidine-to-uridine RNA editing. This indicates a cohesive function in organellar RNA editing/modification, despite a few peripheral terms.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0090615","count":4},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4}]},{"hash":"1836991773490068332","title":"Neural development and synaptic signaling","description":"This cluster is enriched for nervous system\u2013related GO terms: visual perception, Schwann cell development, and excitatory postsynaptic potential, indicating neuronal development and synaptic signaling. Other terms (lipid transport, angiogenesis, defense response to fungus) are present but less central to the core theme.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010951","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0006869","count":3},{"id":"GO:0050832","count":3}]},{"hash":"1830855911848836909","title":"Neural development and transcription regulation","description":"Based on the terms, the cluster is enriched for neural-development related processes (brain development, spinal cord development, neural tube closure) and general gene-expression regulation (DNA-templated transcription). While there are some signals for protein ubiquitination and vesicular trafficking (polyubiquitination, COPII vesicle budding) and ribosome biogenesis, the prominent CNS development and transcription terms suggest the cluster centers on neural development coordinated with transcriptional control.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0035264","count":1},{"id":"GO:0021510","count":1}]},{"hash":"815403364490304004","title":"Chromatin and transcription regulation in plants","description":"Reasoning: The top GO terms cluster around nucleosome assembly, heterochromatin boundary formation, and regulation of DNA-templated transcription, suggesting a shared function in chromatin organization that controls gene expression. The presence of plant-development terms such as short-day photoperiodism and secondary cell wall biogenesis reinforces a role for chromatin- and transcription-level regulation in plant growth and response to developmental cues. A few viral-related terms and defense/salt-stress entries are less central but may reflect broader regulatory connections or annotation noise.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0033696","count":2},{"id":"GO:0051245","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0006351","count":2}]},{"hash":"88568948705925103","title":"Anthocyanin and lignin biosynthesis (phenylpropanoid pathway)","description":"The cluster is dominated by GO terms for anthocyanin biosynthesis and cyanidin-3-O-glucoside production, plus lignin metabolism, pointing to phenylpropanoid-derived secondary metabolism common to plant pigment and cell-wall biosynthesis. Additional terms reflect broader secondary metabolism and detoxification, which may reflect cross-species annotations or noise (e.g., xenobiotic processing, estrogen catabolism, paranode localization). Overall, the core theme ties to phenylpropanoid-derived pigment and lignin biosynthesis.","confidence":"Medium","size":24,"edges":218,"triangles":1034,"max_degree":22,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009718","count":9},{"id":"GO:0017000","count":8},{"id":"GO:0002175","count":7},{"id":"GO:0009808","count":7},{"id":"GO:0006711","count":7}]},{"hash":"372231893626883689","title":"Immune activation and cytokine production","description":"Based on the top GO terms, the cluster centers on immune system processes, including positive regulation of T cell proliferation, cytokine production, and interleukin-4 production, along with neutrophil clearance and inflammatory signaling. Additional terms about endothelial migration and Rho signaling suggest coordinated immune cell movement and activation. Taken together, these proteins appear to function in immune activation and cytokine-mediated immune responses.","confidence":"High","size":24,"edges":18,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":24},{"id":"GO:0001502","count":24},{"id":"GO:0097350","count":24},{"id":"GO:0035372","count":24},{"id":"GO:0043068","count":24}]},{"hash":"2228827046266520818","title":"Nuclear transcriptional regulation and immune signaling","description":"This cluster centers on nuclear processes like DNA-templated transcription and negative regulation of protein export from the nucleus, pointing to transcriptional regulation. It also includes immune-related signaling terms (B cell receptor signaling, positive regulation of cytokine production in immune response) and signaling/cytoskeletal terms (Rho signaling, microtubule localization, endothelial cell migration), suggesting a group of proteins that link transcriptional control with immune signaling and cell movement. The mix indicates a regulatory, signaling-oriented theme rather than a single metabolic function, hence this label. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046826","count":18},{"id":"GO:0006351","count":18},{"id":"GO:0009636","count":15},{"id":"GO:0001502","count":14},{"id":"GO:0035372","count":14}]},{"hash":"1444075998591282152","title":"Amino acid metabolism cluster","description":"The top GO terms are dominated by various amino acid biosynthesis and catabolic processes (alanine, tyrosine, histidine, aspartate, kynurenine) plus related pathways like protoporphyrinogen IX biosynthesis. There are also signaling-related terms (Notch, salicylic acid defense), but the strongest recurring theme across the cluster is amino acid metabolism and associated biosynthetic processes, suggesting a cohesive functional group focusing on amino acid turnover and related cofactors. ","confidence":"Medium","size":24,"edges":217,"triangles":1153,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":18},{"id":"GO:0006782","count":13},{"id":"GO:0097053","count":12},{"id":"GO:0006571","count":12},{"id":"GO:0000105","count":12}]},{"hash":"1349323554123083255","title":"Plant phenylpropanoid and cuticle biosynthesis","description":"This cluster is dominated by GO terms for lignin biosynthesis, cutin biosynthesis, and flavonoid biosynthesis, all pointing to phenylpropanoid metabolism and plant cell wall/cuticle formation. While there are a few general terms (cell cycle, nervous system development) that may reflect annotation noise or broader roles, the strongest signal is plant secondary metabolism related to lignin, cuticle, and flavonoids. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009809","count":5},{"id":"GO:0000082","count":4},{"id":"GO:0010252","count":4},{"id":"GO:0010143","count":4},{"id":"GO:0080088","count":4}]},{"hash":"512761833551533602","title":"Plant transcriptional regulation of vascular development","description":"The cluster combines transcription-related GO terms (DNA-templated transcription and its regulation) with plant-development processes such as protoxylem development, secondary cell wall biogenesis, and xylem vessel differentiation, plus related growth/differentiation events like callus formation, leaf senescence, and fruit dehiscence. This points to a cohesive theme of transcriptional control guiding vascular development and maturation in plants, making the label both specific and representative.","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0006355","count":8},{"id":"GO:0006378","count":4},{"id":"GO:1990110","count":4},{"id":"GO:1900057","count":4}]},{"hash":"9487105250202741","title":"Fruit ripening regulation and hormone biosynthesis","description":"The cluster is enriched for transcription-focused GO terms (regulation and DNA-templated transcription) alongside multiple hormone biosynthesis pathways tied to fruit ripening (ethylene, gibberellin, auxin catabolic, salicylic acid catabolic) and secondary metabolite production, suggesting a coherent module where transcriptional control modulates hormone synthesis to drive ripening. Some terms (e.g., penicillin biosynthesis) may reflect annotation noise, but the dominant theme centers on ripening-related transcription and hormone biology.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009835","count":2},{"id":"GO:0042318","count":2},{"id":"GO:0009686","count":2}]},{"hash":"64265664556496491","title":"Plant far-red light signaling and circadian regulation","description":"This cluster centers on plant light sensing (far-red signaling and phototransduction) and transcriptional control, with a clear emphasis on circadian rhythm regulation. The presence of related stress/defense signals (salicylic acid response, apoptosis) suggests downstream responses but does not overshadow the core theme of photoreceptor-driven transcriptional and circadian coordination. ","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010018","count":3},{"id":"GO:0009585","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0042753","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1890079943204085589","title":"Plant vacuolar amino acid transporters","description":"The cluster is characterized by GO terms focused on transmembrane transport of amino acids and related metabolites, including import into and export from the vacuole (e.g., tyrosine, arginine, histidine, asparagine), along with xenobiotic transport. While terms like photosynthesis and cellulose catabolic process appear, the strongest signal is membrane transport of amino acids into/from plant vacuoles, suggesting a transporter-focused group. ","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:0015979","count":4},{"id":"GO:0030245","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0003333","count":3}]},{"hash":"1005874606085828360","title":"Sporulation and Golgi glycosylation","description":"The top terms point to sporulation-related processes (ascospore-type prospore remodeling, regulation of sexual sporulation, filamentous growth) and Golgi-associated secretory functions (O-linked glycosylation via fucose, Golgi to plasma membrane transport). This suggests a theme around fungal sporulation with concurrent secretory pathway activity. Some terms (like pH response and placenta development) may reflect broader stress responses or annotation noise but do not override the core sporulation/Golgi link.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036066","count":2},{"id":"GO:0051452","count":1},{"id":"GO:0009268","count":1},{"id":"GO:0031322","count":1},{"id":"GO:0060548","count":1}]},{"hash":"1592946201196598577","title":"Transmembrane Transporters","description":"These proteins are linked to a broad set of membrane transport processes, including ion transport (Na+, K+), nutrient and vitamin translocation (galactose, sialic acid, vitamins), nitrate assimilation, xenobiotic, and even neurotransmitter loading into synaptic vesicles. The shared GO terms point to a cohesive theme of transmembrane transport functions, justifying a label focused on transporter activity.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0071805","count":5},{"id":"GO:0035725","count":5},{"id":"GO:0015739","count":4},{"id":"GO:0035461","count":4}]},{"hash":"434929142869197955","title":"GPI anchor biosynthesis and carbohydrate biosynthesis","description":"These terms cluster around biosynthetic processes for GPI anchors and various carbohydrate-related pathways (glycolipid, glucose, glycogen, sucrose, sorbitol biosynthesis), with GPI anchor biosynthesis providing a central theme. A few stress-response terms are present but appear secondary to the primary biosynthetic focus.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0010037","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0009247","count":2},{"id":"GO:0006006","count":2}]},{"hash":"223387690998576688","title":"Developmental transcriptional signaling and neural development","description":"The cluster is enriched for transcription and signaling processes (RNA Pol II transcription, SMAD/TGF-\u03b2 signaling, miRNA transcription, calcium response) and neural/developmental terms (olfactory bulb interneuron development, locomotor rhythm, skeletal muscle differentiation), suggesting a cohesive theme of gene regulation and signal transduction guiding development, including neural function, across tissues.","confidence":"Medium","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":18},{"id":"GO:0071277","count":12},{"id":"GO:2001016","count":11},{"id":"GO:0045475","count":10},{"id":"GO:0032915","count":10}]},{"hash":"2263516664290001606","title":"Chorismate-derived aromatic biosynthesis","description":"The cluster shows a strong signal around the chorismate metabolic pathway and its aromatic products: L-phenylalanine and L-tyrosine biosynthesis; salicylic acid biosynthesis via isochorismate; and pyochelin biosynthesis, all derived from chorismate. This coherent theme points to a shared function in producing aromatic metabolites. A few outlier terms (embryonic cleavage, pattern formation, primary miRNA processing, defense regulation by callose) likely reflect annotation noise or broader roles, but they do not override the dominant chorismate/aromatic biosynthesis pattern.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009094","count":2},{"id":"GO:0042864","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0009697","count":1},{"id":"GO:0046417","count":1}]},{"hash":"701881512601667632","title":"Light-driven plant growth and development","description":"The cluster\u2019s GO terms cluster around phytochrome-mediated light sensing (red/far-red phototransduction, far-red signaling) and circadian regulation, with hormone and developmental processes (gibberellin biosynthesis, fruit ripening) and secondary metabolism (proanthocyanidin biosynthesis) plus defense. This points to a cohesive theme of light signaling guiding plant growth and metabolism, with a few outliers likely due to annotation noise (e.g., penicillin biosynthetic process).","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009585","count":1},{"id":"GO:0042753","count":1},{"id":"GO:0010018","count":1},{"id":"GO:0006869","count":1},{"id":"GO:0050832","count":1}]},{"hash":"409701103773601369","title":"Plant nitrate and peptide transporters","description":"The cluster is enriched for membrane transport activities, notably nitrate assimilation and nitrate transmembrane transport, plus oligopeptide and dipeptide transport and other small-molecule transport, pointing to a cohesive theme of nutrient/peptide uptake. Hormone-related terms (gibberellin homeostasis and auxin signaling) suggest growth regulation linked to transport. Overall, the dominant function is plant nutrient and peptide transport, hence the name.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0010336","count":3},{"id":"GO:0035672","count":3},{"id":"GO:0080055","count":3},{"id":"GO:0009635","count":3}]},{"hash":"1378491532797176330","title":"Plant Development and Transcription Regulation","description":"This cluster centers on plant development and gene expression control, highlighted by GO terms for DNA-templated transcription and regulation of transcription, floral meristem growth, bract development, and ethylene-activated signaling, plus plant-type secondary cell wall biogenesis and multicellular organism development. Some DNA repair and spliceosome-related terms likely reflect shared basic cellular processes but are less specific to the plant development focus.","confidence":"High","size":24,"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:0006281","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0000387","count":1}]},{"hash":"846758783629954894","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"The top GO terms center on ubiquitin-proteasome\u2013mediated protein catabolism, particularly SCF-dependent ubiquitination, along with microtubule polymerization and spindle assembly in female meiosis I, and oocyte maturation. This suggests a coherent theme of regulated protein degradation coordinating meiotic spindle formation during oogenesis, with some broader neural development terms appearing less central but not contradicting the core function. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0046785","count":9},{"id":"GO:0007057","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0021678","count":9}]},{"hash":"179560605364826996","title":"Oocyte Meiosis, Spindle Assembly, and Proteasomal Degradation","description":"The cluster is dominated by GO terms for ubiquitin-dependent and SCF-mediated proteasomal degradation, microtubule polymerization, and spindle assembly in female meiosis I, plus oocyte maturation, which together point to a theme of meiosis/cell-cycle control in oocytes. A few neural development terms are present but do not override the primary meiotic/proteolytic signal.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0042787","count":10},{"id":"GO:0046785","count":6},{"id":"GO:0007057","count":6},{"id":"GO:0021678","count":6}]},{"hash":"953533765838863915","title":"SCF-Proteasome Regulation of Oocyte Meiosis and Spindle Assembly","description":"The top terms emphasize ubiquitin-dependent proteolysis, especially SCF-dependent proteasomal processes, which regulate protein turnover during the cell cycle. The recurrent meiotic terms (spindle assembly in female meiosis I and oocyte maturation) point to a role in meiosis entry and spindle dynamics in oocytes, while microtubule polymerization aligns with spindle function. Some neural development terms may reflect broader developmental roles, but the dominant signal is ubiquitin-mediated control of meiosis and spindle assembly in oocytes.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":14},{"id":"GO:0031146","count":13},{"id":"GO:0007057","count":9},{"id":"GO:0008285","count":9},{"id":"GO:0051436","count":9}]},{"hash":"1318832278920704916","title":"DNA Replication and Transcription Regulation with Calcium-NFAT Signaling","description":"This cluster centers on DNA replication and transcription regulation (DNA replication, transcription, regulation of transcription) with dephosphorylation and calcium/NFAT pathway involvement (detection of calcium, positive regulation of calcineurin-NFAT signaling, inflammatory response regulation). These terms together suggest a module where transcription and cell-cycle processes are coordinated through calcium-dependent signaling, particularly NFAT. Minor links to isoprenoid biosynthesis appear incidental rather than defining.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016311","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:2000002","count":3}]},{"hash":"1004720745609405608","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901348","count":2},{"id":"GO:0009856","count":1},{"id":"GO:0015690","count":1},{"id":"GO:0050427","count":1},{"id":"GO:0006068","count":1}]},{"hash":"1121874985951948300","title":"Plant Cell Wall Biogenesis and Catabolism","description":"The top GO terms emphasize cellulose catabolic process, plant-type secondary cell wall biogenesis, and detox/defense-related responses, with several plant-specific catabolic pathways (lipids, phenylpropionate, nicotine). Together these suggest a plant-focused cluster centered on cell wall construction/remodeling and related metabolic processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0098869","count":2}]},{"hash":"612481618735403086","title":"Diverse Metabolic and Detoxification Pathways","description":"The cluster centers on catabolic and detoxification processes across diverse compounds, including lipid catabolism (triglycerides, monoacylglycerols, phosphatidylserine), chlorophyll and alkaloid metabolism, biotin biosynthesis, and broader toxin response and secondary metabolite biosynthesis. This suggests a general metabolic theme focused on breakdown and neutralization rather than a single specific pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0009636","count":5},{"id":"GO:0015996","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0019433","count":5}]},{"hash":"713696528422265511","title":"Unknown","description":"The set of terms spans plant-specific stomatal morphogenesis, vacuolar protein degradation, alkaloid metabolism, various transport and processing processes, and several obsolete terms, with no clear single pathway linking all proteins. The lack of edges and triangles implies little interconnection among the proteins in this cluster, and the terms include unrelated processes (e.g., insulin processing, LDL receptor catabolic processes) that do not form a cohesive theme. Therefore a concise, representative label cannot be confidently assigned. ","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010103","count":3},{"id":"GO:0007039","count":3},{"id":"GO:0009820","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006813","count":2}]},{"hash":"1199542112291166159","title":"Flower development and cuticle biosynthesis regulation","description":"The GO terms point to plant developmental processes (floral meristem growth, bract development, multicellular development) coupled with transcriptional regulation and epidermal lipid biosynthesis (wax, cutin) modulated by plant hormones (ethylene, ABA). This suggests a cohesive module of transcriptional regulators coordinating floral/meristem development with cuticle formation and wax biosynthesis.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010432","count":2}]},{"hash":"1889072380565675908","title":"Rho GTPase Signaling and Cell Polarity Regulation","description":"The cluster is strongestly linked to regulation of Rho signaling, positive regulation of GTPase activity, and establishment of cell polarity, pointing to a module governing cytoskeletal dynamics and spatial organization. Additional terms cover poly-ADP-ribosylation, transcription, and cell cycle, which reflect broader regulatory roles but do not diminish the central theme of signaling pathways that control polarity and cytoskeletal behavior. Some terms (e.g., spinal cord development, plant hormone signaling) are broad cross-species annotations, but the core signal remains consistent.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0007584","count":3},{"id":"GO:2000114","count":3}]},{"hash":"2071509654621953469","title":"Organelle Gene Expression and RNA Processing","description":"The proteins are marked by RNA processing and transcription regulation terms, with a clear emphasis on organelle gene expression in chloroplasts and mitochondria (chloroplast organization; plastid rRNA transcription; mitochondrial transcription and its termination; mitochondrial ribosome assembly). Ubiquitin-dependent degradation terms may reflect turnover of organelle-targeted factors, supporting a cohesive theme of organelle gene expression and RNA processing.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0008380","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0009658","count":2}]},{"hash":"373231932973070728","title":"Fungal cell wall remodeling and polysaccharide catabolism","description":"The top GO terms cluster around fungal-type cell wall organization and degradation of plant-derived polysaccharides (beta-D-glucan, xylan, cellulose), suggesting enzymes that remodel or break down cell walls, with several biofilm formation terms indicating a capacity for single-species biofilms. Transcription-related terms imply coordinated regulation. Together, these point to a fungal-focused theme of cell wall remodeling and polysaccharide catabolism, sometimes linked to biofilm-associated lifestyle.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031505","count":3},{"id":"GO:0006076","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0045493","count":3},{"id":"GO:0030245","count":3}]},{"hash":"2174588858144721992","title":"Transcription Regulation and Apoptosis","description":"Top terms indicate a strong focus on DNA-templated transcription and its regulation, with additional association to apoptotic processes and general protein synthesis components. The presence of development-related GO terms (lateral root morphogenesis, seed development, hippocampus development) suggests the proteins are involved in broad regulatory programs across contexts, rather than a single dedicated pathway. Overall, the cluster centers on transcriptional control with secondary links to cell fate decisions, justifying the label, while acknowledging some heterogeneity in the terms.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0010102","count":2},{"id":"GO:0048316","count":2}]},{"hash":"1182123800546316813","title":"Glycosylation and cell-surface ECM in development","description":"The cluster centers on glycosylation-related processes (O-linked hydroxyproline glycosylation, arabinogalactan protein metabolism, poly-N-acetyllactosamine, Lewis a epitope biosynthesis) and development-associated cell-surface/epithelial functions (follicle epithelium adhesion and polarity). Although terms span plants and insects, the common theme is protein/glycan modifications that shape cell surfaces and tissue organization during development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007299","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0048354","count":3},{"id":"GO:0018258","count":3},{"id":"GO:0010493","count":3}]},{"hash":"920324299419199253","title":"Immune Activation and Cytokine Signaling","description":"These proteins are enriched for immune-related processes, such as positive regulation of T cell proliferation, IL-4 production, and overall positive regulation of cytokine production in immune responses. Neutrophil clearance and endothelial cell migration also reflect inflammatory signaling and immune cell trafficking. A few terms touch on development or cytoskeletal localization, but the dominant pattern centers on immune activation and cytokine regulation, suggesting the cluster reflects immune signaling pathways.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":24},{"id":"GO:0001502","count":24},{"id":"GO:0097350","count":24},{"id":"GO:0035372","count":24},{"id":"GO:0043068","count":24}]},{"hash":"1317727503027945830","title":"Ubiquitin Signaling and Transcription Regulation","description":"The cluster\u2019s top GO terms cluster around ubiquitin-related processes (protein ubiquitination and various deubiquitinations: K29, K63, K33) and transcriptional regulation of DNA-templated transcription, suggesting proteins involved in ubiquitin-mediated signaling that can influence transcription. Some entries (ERAD pathway) reinforce ubiquitin-dependent quality control, while a few terms (chloroplast mRNA modification, DNA damage response) may be less central. Overall, a cohesiveness around ubiquitin signaling with transcriptional control best fits the set.","confidence":"Medium","size":23,"edges":46,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035523","count":1},{"id":"GO:1900871","count":1}]},{"hash":"1823649386633852061","title":"Unknown","description":"The proteins map to a broad and disparate set of GO terms, including amino acid catabolism (L-alanine, L-lysine), kynurenine and GABA metabolic pathways, isoquinoline alkaloid and phytoalexin metabolism, plus Notch signaling, Leydig cell differentiation, cuticle pigmentation regulation, and intracellular pH changes. This diversity spans metabolic, signaling, and developmental processes across different kingdoms, with no single cohesive function tying them together. Therefore, there is no clear functional theme to assign a concise label beyond Unknown.","confidence":"","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097053","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0007219","count":7},{"id":"GO:0019878","count":7},{"id":"GO:0052314","count":7}]},{"hash":"198865657166574945","title":"RNA splicing and mRNA stability regulation","description":"These proteins cluster around post-transcriptional control of gene expression, dominated by mRNA splicing via the spliceosome, mRNA modification and stabilization, and regulatory ncRNA-mediated silencing, with links to translation initiation. The dominant themes are RNA processing and mRNA stability rather than transcriptional control, supporting a label focused on splicing and stability regulation.","confidence":"High","size":23,"edges":243,"triangles":1582,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":16},{"id":"GO:0031047","count":16},{"id":"GO:0006378","count":14},{"id":"GO:0045292","count":12},{"id":"GO:0010610","count":12}]},{"hash":"1264708213959658497","title":"Chitin-based cuticle development and molting","description":"The top GO terms are dominated by chitin catabolic process, chitin-based cuticle development, and ecdysis, pointing to a cohesive role in cuticle remodeling and molting in arthropods. While there are some additional terms related to immune signaling and cartilage development, the strongest and most representative cluster signal is centered on chitin-based cuticle formation/remodeling and molting processes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0006032","count":3},{"id":"GO:0040003","count":3},{"id":"GO:0071347","count":3}]},{"hash":"1988158855490561321","title":"Epigenetic Gene Regulation","description":"This cluster is dominated by GO terms about epigenetic control of gene expression, including histone methylation (H3-K4), DNA methylation, and epigenetic regulation of transcription. Although some terms are obsolete or tissue-specific, the common link is modulation of transcription via chromatin state and DNA methylation, suggesting proteins involved in chromatin modification and transcriptional regulation rather than a single unifying pathway.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051571","count":4},{"id":"GO:0032968","count":3},{"id":"GO:0010216","count":3},{"id":"GO:0010069","count":3},{"id":"GO:0061038","count":3}]},{"hash":"15417252279017943","title":"mRNA Splicing and Stability Regulation","description":"The top GO terms show a strong emphasis on mRNA processing and regulation: mRNA polyadenylation, spliceosome-mediated splicing and its positive regulation, mRNA modification, stabilization, and stress-related regulation of mRNA stability. Some terms also touch on IRES-dependent translation initiation, consistent with RNA-level control of gene expression. This combination indicates a cluster centered on RNA processing and post-transcriptional regulation rather than other cellular processes.","confidence":"High","size":23,"edges":245,"triangles":1615,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":13},{"id":"GO:0045292","count":13},{"id":"GO:0048026","count":13},{"id":"GO:0031047","count":13},{"id":"GO:0010610","count":12}]},{"hash":"1550108806539285313","title":"Transcriptional Regulation and Chromatin Remodeling in Development","description":"The strongest signals center on transcriptional control and chromatin dynamics (negative regulation of transcription by RNA Pol II, DNA-templated transcription, chromatin remodeling), suggesting a module of genes governing gene expression and genome accessibility. Development-related terms (epithelial differentiation, fin regeneration) point to roles in tissue formation, while ROS regulation and mitophagy imply integration with cellular stress responses during remodeling. Overall, a cohesive theme of transcriptional regulation during development with remodeling and stress-associated processes.","confidence":"Medium","size":23,"edges":24,"triangles":6,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:2000378","count":5},{"id":"GO:0043044","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0001662","count":4}]},{"hash":"1607584495478800944","title":"Pollen Wall Formation via Sporopollenin and Flavonoid Biosynthesis","description":"This cluster combines strong signals for sporopollenin biosynthesis (pollen exine), chalcone and flavonoid biosynthesis, and related lipid/phenylpropanoid pathways, all pointing to pollen wall formation and its associated metabolic processes rather than general metabolism.","confidence":"High","size":23,"edges":185,"triangles":741,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":9},{"id":"GO:0035336","count":9},{"id":"GO:0080110","count":8},{"id":"GO:0031148","count":8},{"id":"GO:0071770","count":8}]},{"hash":"1038403790843295913","title":"TLR-Mediated Innate Immune Signaling","description":"The top GO terms are dominated by innate immune responses and Toll-like receptor signaling, including MyD88-independent TLR signaling, TLR3 signaling, and defense against virus, pointing to a core theme of innate immune recognition and signaling. Some plant-related terms are present but appear secondary to the strong immune signaling signal. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045087","count":13},{"id":"GO:0009738","count":13},{"id":"GO:0060348","count":12},{"id":"GO:0007507","count":12},{"id":"GO:0009620","count":12}]},{"hash":"288627134738628510","title":"Chromatin Regulation and DNA Damage Response","description":"The cluster is enriched for histone-related processes (H4-K16 acetylation, H4-K20 methylation, histone catabolic process) and nucleotide-excision repair preincision complex assembly/stabilization, pointing to chromatin state control during DNA damage repair. Additional terms reference stress signaling pathways (JNK cascade regulation, NF-kappaB activation) and innate immune signaling (RIG-I), suggesting a broader link between chromatin dynamics and stress-response signaling. An outlier term about localization to bud neck may be an annotation artifact. Overall, the set centers on chromatin modification coupled with DNA repair and stress signaling.","confidence":"Medium","size":23,"edges":6,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097271","count":11},{"id":"GO:0043029","count":9},{"id":"GO:2000620","count":8},{"id":"GO:0039536","count":8},{"id":"GO:0006294","count":8}]},{"hash":"915874388522976656","title":"Meiosis I spindle assembly and oocyte maturation","description":"Most enriched terms point to meiosis and oocyte development (spindle assembly in female meiosis I, oocyte maturation, microtubule polymerization) and proteasome-mediated protein turnover (SCF-ubiquitin). A few neural-development terms appear but the core signal is meiotic cell cycle regulation and oocyte maturation.","confidence":"High","size":23,"edges":50,"triangles":46,"max_degree":11,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031146","count":19},{"id":"GO:0046785","count":15},{"id":"GO:0007057","count":15},{"id":"GO:0021678","count":15},{"id":"GO:0006516","count":15}]},{"hash":"887053593475412579","title":"Flavonoid and lignin biosynthesis with glucuronidation","description":"Most of the top GO terms cluster around phenylpropanoid metabolism leading to lignin and flavonoid (anthocyanin/cyanidin) biosynthesis and their subsequent glucuronidation/conjugation. Although there is a neuron-related term in the mix, the dominant signal is plant secondary metabolite production and modification, implying a coherent theme of flavonoid/lignin biosynthesis and conjugation.","confidence":"High","size":23,"edges":21,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":14},{"id":"GO:0009808","count":14},{"id":"GO:0009718","count":14},{"id":"GO:0006711","count":14},{"id":"GO:0052697","count":14}]},{"hash":"91210334009536919","title":"Mitochondrial Transport and Metabolic Signaling","description":"The top GO terms cluster around transport across mitochondrial membranes (manganese, heme, CoA, thiosulfate, ATP), mitochondrial apoptotic changes, and metabolic signaling (insulin/IGF response), suggesting proteins coordinating mitochondrial transport/metabolism and regulation of cell survival.","confidence":"High","size":23,"edges":37,"triangles":3,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":16},{"id":"GO:0061179","count":16},{"id":"GO:1990544","count":16},{"id":"GO:0015886","count":16},{"id":"GO:0090152","count":16}]},{"hash":"2099203173345128246","title":"Immune activation and cytokine signaling","description":"The cluster is dominated by immune-related terms: positive regulation of T cell proliferation, cytokine production (including IL-4), and neutrophil clearance, indicating activation of adaptive and innate immune responses. Additional terms like positive regulation of endothelial cell migration and Rho signaling reflect immune cell trafficking and cytoskeletal remodeling. A few terms about cartilage condensation and microtubule localization are supportive context but do not override the central immune theme.","confidence":"High","size":23,"edges":205,"triangles":954,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":23},{"id":"GO:0001502","count":23},{"id":"GO:0097350","count":23},{"id":"GO:0035372","count":23},{"id":"GO:0043068","count":23}]},{"hash":"1993610083333038819","title":"T cell Proliferation and Cytokine Regulation","description":"These proteins are annotated with GO terms centered on immune regulation, notably positive regulation of alpha-beta T cell proliferation, interleukin-4 production, and positive regulation of cytokine production in immune responses, as well as neutrophil clearance and endothelial cell migration. The recurring theme across terms points to coordinated immune signaling and immune cell communication, with supporting roles in cytoskeletal organization (microtubule localization) and Rho signaling.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":23},{"id":"GO:0001502","count":23},{"id":"GO:0097350","count":23},{"id":"GO:0035372","count":23},{"id":"GO:0043068","count":23}]},{"hash":"2000555909482943548","title":"Mitotic machinery and vascular development regulators","description":"The cluster includes terms centered on cell division machinery (kinetochore localization, microtubule localization, and regulation of CDK activity, nuclear export) and terms related to vascular development (angiogenesis and endothelial cell migration), with additional developmental context like cartilage condensation. This suggests a set of proteins that link cell cycle control with developmental signaling. Confidence: Medium","confidence":"","size":23,"edges":59,"triangles":82,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":14},{"id":"GO:0045736","count":14},{"id":"GO:0050830","count":13},{"id":"GO:0071333","count":13},{"id":"GO:0046827","count":13}]},{"hash":"888879439821279112","title":"Immune Activation and Cell Migration","description":"This cluster is dominated by terms about activating immune responses (positive regulation of alpha-beta T cell proliferation; positive regulation of cytokine production involved in immune response), neutrophil clearance, and endothelial cell migration, all of which point to immune cell activation and trafficking. Rho signaling and microtubule localization further support cytoskeletal remodeling required for movement. A developmental term (cartilage condensation) appears but the prevailing signal is immune regulation and cell motility, suggesting these proteins function together in immune surveillance and inflammatory cell migration.","confidence":"Medium","size":23,"edges":73,"triangles":49,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":23},{"id":"GO:0046641","count":18},{"id":"GO:0001502","count":18},{"id":"GO:0097350","count":18},{"id":"GO:0035372","count":18}]},{"hash":"1574046708208365843","title":"T cell activation and cytokine production","description":"This cluster is enriched for adaptive immune terms such as positive regulation of alpha-beta T cell proliferation and interleukin-4 production, along with broader cytokine production in immune responses and neutrophil clearance. Additional terms on actin/cytoskeletal dynamics and endothelial cell migration point to immune cell activation and trafficking during inflammation, supporting a cohesive theme of immune activation and inflammatory signaling.","confidence":"High","size":23,"edges":203,"triangles":949,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":23},{"id":"GO:0001502","count":23},{"id":"GO:0097350","count":23},{"id":"GO:0035372","count":23},{"id":"GO:0043068","count":23}]},{"hash":"986278650948455349","title":"Cell Cycle and Immune Signaling","description":"The top GO terms show a strong emphasis on DNA replication and mitotic cell cycle, suggesting a core proliferative function. Alongside this, there is substantial representation of immune-related processes (positive regulation of T cell proliferation and cytokine production), pointing to immune activation/differentiation. Additional terms involving cytoskeletal dynamics and cell migration (microtubule localization, Rho signaling, endothelial migration) align with cellular behaviors typical of proliferating or activated cells. While some developmental terms like cartilage condensation appear, the dominant theme centers on cell division and immune signaling, justifying the label.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":23},{"id":"GO:0000278","count":23},{"id":"GO:0046641","count":22},{"id":"GO:0001502","count":22},{"id":"GO:0097350","count":22}]},{"hash":"1793508043898314061","title":"Broad Developmental Signaling and Hormone Response","description":"The top GO terms point to developmental processes (multicellular development, heart morphogenesis, pituitary gland development) and hormone-related signaling or responses (cytokinin signaling, gibberellin, salicylic acid). Additional terms about transcriptional regulation and chromatin remodeling suggest regulatory roles during development. The mix across plant and animal terms indicates a broad, non-specific cluster of developmental signaling and hormonal response functions rather than a single coherent pathway. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0003007","count":5},{"id":"GO:0000183","count":5},{"id":"GO:0000122","count":5}]},{"hash":"1359801548330240157","title":"Neural development and dendrite morphogenesis","description":"The proteins here are strongly enriched for nervous system development terms such as neural tube closure, forebrain development, and dendrite morphogenesis, indicating a shared role in neural differentiation and brain wiring. Some outlier terms (phosphorelay signaling, immune regulation, and obsolete apoptotic terms) may reflect annotation noise or distant homology, but the dominant theme is neural development.","confidence":"High","size":23,"edges":77,"triangles":86,"max_degree":14,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007399","count":13},{"id":"GO:0001843","count":13},{"id":"GO:0000160","count":13},{"id":"GO:0002921","count":13},{"id":"GO:0048813","count":13}]},{"hash":"2056225452732338043","title":"Fatty acid metabolism and transport","description":"This cluster is dominated by GO terms tied to lipid metabolism: fatty acid biosynthetic process, long-/medium-chain fatty acid transport, and related lipid metabolic activities (bile acid metabolism, acetyl-CoA biosynthesis from acetate). While a few terms like interleukin-4 response appear peripheral, the core signal points to fatty acid synthesis, activation, and cellular import, suggesting proteins involved in lipid processing pathways.","confidence":"High","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006633","count":11},{"id":"GO:0006813","count":6},{"id":"GO:0071353","count":6},{"id":"GO:0010124","count":6},{"id":"GO:0019427","count":6}]},{"hash":"1696376832417888883","title":"Amino acid catabolism and secondary metabolite biosynthesis","description":"Based on the GO terms, the proteins are enriched for amino acid catabolic pathways (histidine, phenylalanine, tyrosine) and for biosynthesis of diverse secondary metabolites (alkaloids, antibiotics, cinnamic acid, toxins). This suggests a cluster centered on amino-acid\u2013derived metabolism and production of specialized compounds. The protein homotetramerization term is a structural feature of some enzymes and does not override the metabolic theme; a zinc-stress response term is supportive of stress-associated regulation but not central. Overall, the name reflects the core shared function of the cluster.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051289","count":11},{"id":"GO:0009821","count":9},{"id":"GO:1990359","count":9},{"id":"GO:0019557","count":9},{"id":"GO:0006559","count":9}]},{"hash":"2275215708558374410","title":"Plant Growth and Cell Wall Biosynthesis Regulators","description":"The cluster shows a clear pattern of regulatory roles in plant development, including chlorophyll biosynthesis regulation, seed growth, lignin and secondary cell wall biosynthesis, root meristem growth, and leaf senescence. Additional terms about regulation of protein and RNA localization to telomeres and rDNA heterochromatin formation point to broader chromatin/RNA-level regulatory processes. Taken together, these proteins appear to function as regulators of plant growth and cell wall biosynthesis rather than enzymes themselves.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010380","count":7},{"id":"GO:0080113","count":7},{"id":"GO:1901430","count":7},{"id":"GO:1901347","count":7},{"id":"GO:0010082","count":7}]},{"hash":"554828477033116584","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030307","count":2},{"id":"GO:0048507","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009733","count":2},{"id":"GO:0010047","count":2}]},{"hash":"757154820751911246","title":"Plant Transcriptional Regulation and Development Signaling","description":"The top terms cluster around regulation of DNA-templated transcription and epigenetic-related processes (transcription regulation, methylation), with additional plant-developmental themes such as polarity specification and auxin/homeostasis, and signaling aspects like Wnt-like pathways and light-responsive phototransduction. This suggests a broad gene-regulatory and developmental signaling theme in plants rather than a single enzymatic pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:0010252","count":2},{"id":"GO:0009820","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0009944","count":2}]},{"hash":"1134770720364754485","title":"Ubiquitin-Proteasome-Mediated Degradation","description":"Dominant GO terms center on ubiquitin-dependent protein catabolism (including SCF-dependent proteasomal ubiquitination, K48- and K6-linked ubiquitination) and histone turnover, pointing to a cluster of proteins involved in tagging substrates for proteasomal degradation. The presence of autoubiquitination and receptor catabolic processes (e.g., Wnt receptor) suggests broader roles in downregulating signaling components and chromatin dynamics via ubiquitin-mediated proteolysis.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0031146","count":7},{"id":"GO:0036205","count":6},{"id":"GO:0070936","count":6},{"id":"GO:0051865","count":6}]},{"hash":"1713437100120119611","title":"Plant SA signaling transcriptional regulators","description":"This cluster centers on GO terms for cellular response to salicylic acid stimulus and regulation of SA-mediated signaling, combined with DNA-templated transcription and its regulation, pointing to transcription factors/modulators that govern SA-driven defense responses in plants. Seed development is present but secondary; some transport terms appear to be incidental. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071446","count":2},{"id":"GO:2000031","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1930081939271312303","title":"Plant transcriptional regulation and seed development","description":"Top GO terms highlight DNA-templated transcription and its regulation, with seed development and plant-type secondary cell wall biogenesis also represented. The combination suggests a plant-specific regulatory module coordinating transcriptional control during seed development and cell wall formation, rather than a single metabolic enzyme cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0048316","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0043085","count":2}]},{"hash":"1795761495344388570","title":"Actin Cytoskeleton Remodeling during Cytokinesis","description":"The cluster\u2019s top GO terms cluster around actin filament organization, mitotic contractile ring assembly, membrane addition at cytokinesis, and regulation of GTPase activity, indicating coordinated actin remodeling linked to cytokinesis and related cell migration/membrane dynamics.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006930","count":1},{"id":"GO:0043087","count":1},{"id":"GO:0032529","count":1},{"id":"GO:0045769","count":1},{"id":"GO:0001778","count":1}]},{"hash":"2237219237415659654","title":"Clathrin-mediated endocytosis and vesicle trafficking","description":"The GO terms cluster around clathrin-dependent endocytosis, clathrin coat assembly, vesicle cargo loading, and synaptic vesicle maturation, pointing to a shared function in vesicle formation and membrane trafficking. Some terms touch on signaling or stress responses, but the dominant theme is clathrin-mediated vesicle trafficking.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0006915","count":1},{"id":"GO:0098711","count":1},{"id":"GO:2000369","count":1},{"id":"GO:0045742","count":1}]},{"hash":"2235584082304021909","title":"Oocyte maturation and meiotic spindle assembly","description":"These proteins are enriched for ubiquitin-dependent proteolysis and are strongly linked to oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, suggesting a cohesive role in regulating meiosis and oocyte progression through proteasome-mediated degradation and cytoskeletal dynamics. Some brain development terms seem incidental and do not outweigh the core meiotic theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":16},{"id":"GO:0042787","count":10},{"id":"GO:0001556","count":10},{"id":"GO:0046785","count":10},{"id":"GO:0006516","count":10}]},{"hash":"724208548035154033","title":"Oocyte meiosis and spindle assembly","description":"The top GO terms point to meiotic processes in oocytes, including spindle assembly in female meiosis I, oocyte maturation, and microtubule polymerization, along with SCF-dependent ubiquitin-proteasome\u2013mediated protein degradation. These together suggest a cluster of proteins coordinating meiosis, spindle dynamics, and proteolysis, with some broader developmental terms appearing as secondary associations.","confidence":"Medium","size":23,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":16},{"id":"GO:0046785","count":14},{"id":"GO:0007057","count":14},{"id":"GO:0021678","count":14},{"id":"GO:0006516","count":14}]},{"hash":"1963894385707739986","title":"Oocyte meiosis and spindle assembly regulation","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, and ubiquitin-proteasome\u2013mediated protein turnover, plus microtubule dynamics, which together point to meiotic cell-cycle control and spindle organization in oocytes. Some neural development terms appear, but the strongest signal is meiotic spindle and proteolysis machinery.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":14},{"id":"GO:0046785","count":13},{"id":"GO:0007057","count":13},{"id":"GO:0021678","count":13},{"id":"GO:0006516","count":13}]},{"hash":"1534998191290013108","title":"Meiosis and Oocyte Maturation with Spindle Assembly","description":"The cluster is dominated by GO terms related to meiosis and oocyte development such as spindle assembly in female meiosis I, oocyte maturation, microtubule polymerization, and ubiquitin-proteasome\u2013mediated protein degradation. While a few neural development terms appear (e.g., neural tube closure, third ventricle development), the strongest and most frequent signals describe meiotic control and spindle dynamics, plus regulated protein turnover. ","confidence":"High","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":20},{"id":"GO:0046785","count":18},{"id":"GO:0007057","count":18},{"id":"GO:0021678","count":18},{"id":"GO:0006516","count":18}]},{"hash":"27049491972428065","title":"Unknown","description":"The terms are scattered across proteolysis regulation, protein oligomerization, ubiquitin recycling, mitochondrial targeting, metabolism, respiration, and host-symbiont interaction, with no single unifying function or interaction pattern, so a coherent cluster label cannot be determined.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045861","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0007120","count":2},{"id":"GO:1902600","count":2}]},{"hash":"1101563088765167519","title":"Plant hormone biosynthesis during fruit ripening","description":"The top GO terms cluster around major plant hormone production (ethylene, gibberellin, auxin) and related metabolic processes (fruit ripening, secondary metabolite biosynthesis like proanthocyanidin). This suggests the proteins collectively participate in hormone-driven ripening and associated metabolism, despite some noisy terms. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0009835","count":7},{"id":"GO:0042318","count":7},{"id":"GO:1902835","count":7},{"id":"GO:0009686","count":7}]},{"hash":"2240720428527199814","title":"Copper transport and homeostasis","description":"The cluster is enriched for copper-related terms: copper ion import, intracellular copper ion homeostasis, regulation of copper ion transport, and copper-associated xenobiotic transport, with a note of cisplatin response, suggesting a cohesive theme around copper handling and drug response; some DNA-related terms appear incidental rather than central.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0098705","count":1},{"id":"GO:0006855","count":1}]},{"hash":"1483717573416981083","title":"Plant cell wall biosynthesis and remodeling","description":"The top GO terms cluster around plant-type secondary cell wall biogenesis, cell wall organization/modification, and metabolism of major wall polysaccharides (cellulose, xyloglucan, xylan). These point to a cohesive function in constructing and remodeling the plant cell wall, with transcriptional regulation terms suggesting regulatory control during development. Overall, the dominant theme is plant cell wall biosynthesis and remodeling.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0030245","count":3}]},{"hash":"1816831662024720717","title":"Plant Meristem Development and Hormone Signaling","description":"The cluster's terms point to transcriptional regulation of plant development, focusing on floral meristem and bract growth, with hormone signaling (ethylene and ABA) and wax biosynthesis regulation contributing to developmental programs; other terms like mRNA surveillance are present but secondary, suggesting a cohesive module of development linked to hormone response.","confidence":"High","size":23,"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:0000184","count":2},{"id":"GO:0010451","count":2},{"id":"GO:0009873","count":2}]},{"hash":"18195396360678084","title":"T cell activation and cytokine production","description":"This cluster is dominated by immune-related processes: positive regulation of alpha-beta T cell proliferation, cytokine production (including IL-4), and neutrophil clearance, with accompanying Rho signaling and cytoskeletal dynamics that support immune cell movement. While there are a couple of developmental terms (cartilage condensation, endothelial migration), the strongest signals point to T cell activation and cytokine signaling as the core theme. Therefore, this label succinctly captures the shared function of the proteins in the cluster.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":23},{"id":"GO:0001502","count":23},{"id":"GO:0097350","count":23},{"id":"GO:0035372","count":23},{"id":"GO:0043068","count":23}]},{"hash":"548781640337100160","title":"Pollen exine formation and protein glycosylation","description":"This cluster is strongly enriched for pollen development terms, including pollen exine formation and anther dehiscence, alongside protein N-linked glycosylation. The co-occurrence of glycosylation and pollen wall-related processes suggests these proteins function together in glycosylation-dependent pollen wall biosynthesis. The nucleotide-sugar catabolic terms may reflect substrate metabolism for glycosylation, but the dominant theme centers on pollen wall formation via glycosylation pathways.","confidence":"High","size":22,"edges":100,"triangles":291,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006487","count":9},{"id":"GO:0046032","count":9},{"id":"GO:0006256","count":9},{"id":"GO:0010584","count":9},{"id":"GO:0046712","count":9}]},{"hash":"488915284544667682","title":"Plant organelle RNA processing and editing","description":"The cluster is driven by GO terms focused on mitochondrial and chloroplast RNA processing and modification (e.g., mitochondrial mRNA processing, RNA modification, cytidine to uridine editing, chloroplast RNA modification, plastid transcription, polycistronic mRNA processing, chloroplast-nucleus signaling). Together these indicate a shared function in organellar RNA metabolism and coordination between chloroplasts and mitochondria in plants, with the seed dormancy term likely reflecting broader plant developmental context rather than the core function. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":4},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0080156","count":4},{"id":"GO:1905639","count":4}]},{"hash":"2226971713572956415","title":"Viral life cycle and host interaction","description":"The cluster is dominated by GO terms tied to viral processes: virion assembly, viral release and budding via ESCRT, and DNA integration with proviral latency, indicating involvement in the viral life cycle and genome integration. It also includes terms about host transcription and RNA processing (DNA-templated transcription, mRNA splicing, miRNA catabolic process) and host entry, which reflect how viruses manipulate host machinery during infection. This combination suggests a cohesive theme of virus-host interaction and replication.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2}]},{"hash":"1432758121832230924","title":"Plant abiotic-stress RNA processing and translation control","description":"GO terms point to plant abiotic stress responses (abscisic acid signaling, cold acclimation, water deprivation) together with strong signals of RNA processing and translation regulation (splicing, polyadenylation, RNA modification, stabilization, translational elongation, and IRES-dependent initiation), suggesting a coordinated regulation of gene expression at the RNA level under stress.","confidence":"High","size":22,"edges":88,"triangles":66,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0009737","count":4},{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":4},{"id":"GO:1900363","count":4},{"id":"GO:0009631","count":3}]},{"hash":"217419042714454903","title":"Ubiquitin-Dependent Antiviral Signaling and Autophagy","description":"The cluster\u2019s top terms center on ubiquitination processes (K63-linked ubiquitination, autoubiquitination) and degradation/autophagy pathways (ERAD, autophagy), coupled with antiviral defense and innate immune signaling (NF-kappaB pathway, defense response to virus, LPS signaling regulation). This points to a cohesive set of proteins involved in ubiquitin-mediated control of protein fate and immune responses to viral material, including microtubule-associated localization relevant to transport of viral components. Confidence in this label is Medium.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0070534","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":3},{"id":"GO:1901253","count":3},{"id":"GO:0006914","count":3}]},{"hash":"1085644760222644605","title":"ER organization and protein synthesis regulation","description":"The cluster prominently features endoplasmic reticulum\u2013related processes: ubiquitin-dependent ERAD, ER-dependent peroxisome organization, and ER tubular network maintenance. It also includes translation initiation and reinitiation and transcription-related terms, all pointing to ER-associated protein processing and gene expression control. While there are neuronal morphogenesis and steroid biosynthesis terms present, these can be linked to ER-driven cellular growth and metabolism, supporting a cohesive label around ER organization and protein synthesis regulation.","confidence":"Medium","size":22,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0030517","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0051301","count":4}]},{"hash":"1896395811037823329","title":"Photosynthesis-linked organellar translation and redox","description":"This cluster centers on translation functions in organelles, with strong links to photosynthesis and light-responsive signaling (blue, red, far-red). The presence of cytochrome complex assembly and redox homeostasis further points to involvement in chloroplast/mitochondrial electron transport and redox balance, suggesting a cohesive role in organellar protein synthesis tied to photosynthetic and respiratory energy metabolism under light. ","confidence":"High","size":22,"edges":230,"triangles":1520,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0015979","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0010114","count":2}]},{"hash":"2273849383467658071","title":"Membrane trafficking and cytoskeletal remodeling","description":"The cluster is enriched for terms related to membrane trafficking and cytoskeletal dynamics: regulation of Rho signaling, exocytosis, cell shape, receptor internalization, and Golgi retention. There are also mitochondrial fragmentation and sporulation-related membrane formation terms, which are less central but may reflect broader organelle dynamics. Overall, the connectivity points to a membrane trafficking and cytoskeletal remodeling theme.","confidence":"Medium","size":22,"edges":31,"triangles":0,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0035023","count":5},{"id":"GO:0000002","count":4},{"id":"GO:0045921","count":3},{"id":"GO:0008360","count":3}]},{"hash":"789843668131485918","title":"Epigenetic Regulation of T Cell Tolerance","description":"The strongest signals are central and peripheral T cell tolerance induction, pointing to an immune-tolerance theme. Supporting this, several terms relate to DNA methylation and histone modification, indicating chromatin-level regulation of gene expression that can shape T cell fate and tolerance. A few terms about centrosome/spindle assembly and autophagy modulation are present but likely reflect broader cell-cycle context in proliferating immune cells; overall the cluster appears to reflect epigenetic control of immune tolerance rather than a single straightforward pathway.","confidence":"Medium","size":22,"edges":37,"triangles":19,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0010216","count":5},{"id":"GO:1901097","count":5},{"id":"GO:0002509","count":5},{"id":"GO:0070562","count":5},{"id":"GO:0002458","count":5}]},{"hash":"671078786239965972","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2},{"id":"GO:0000398","count":2}]},{"hash":"425616810654270889","title":"Ubiquitin-Proteasome Regulation and Metal Stress Response","description":"This cluster is enriched for ubiquitin-proteasome\u2013related processes (SCF-dependent proteasomal and ubiquitin-dependent protein catabolic pathways) and metal-stress responses (cadmium and arsenic), plus links to cell-cycle/dna-damage signaling and circadian regulation, suggesting a proteostasis module that modulates degradation in response to stress. A minor signal related to synapse assembly is present but peripheral.","confidence":"Medium","size":22,"edges":16,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":18},{"id":"GO:0071276","count":14},{"id":"GO:0042752","count":13},{"id":"GO:0030174","count":13},{"id":"GO:0042787","count":13}]},{"hash":"1722359541499602820","title":"Plastid transcription and photosynthesis","description":"This cluster shows a core signal of DNA-templated transcription and its regulation, alongside photosynthesis-related GO terms, suggesting a plastid-associated module that coordinates gene expression with photosynthetic metabolism. Other terms like various biosynthetic processes and stress responses may reflect peripheral or annotation noise but don\u2019t outweigh the main plastid transcription/photosynthesis theme.","confidence":"Medium","size":22,"edges":142,"triangles":372,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055129","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0090502","count":2}]},{"hash":"2046249214810399470","title":"RNA Splicing and Translation Initiation Regulation","description":"This cluster is strongly enriched for spliceosome-mediated mRNA processing terms (cis and alternative splicing, regulatory splicing) and broader mRNA processing (modification, stabilization), plus terms related to translation initiation and initiation complex assembly. The shared theme appears to be post-transcriptional regulation of gene expression, spanning both RNA processing and the initiation of translation, with possible involvement of regulatory ncRNA pathways.","confidence":"High","size":22,"edges":63,"triangles":46,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":19},{"id":"GO:0048026","count":19},{"id":"GO:0031047","count":19},{"id":"GO:0045292","count":18},{"id":"GO:0016556","count":16}]},{"hash":"2264847839114429869","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:1905639","count":3},{"id":"GO:0009793","count":3},{"id":"GO:1900865","count":3}]},{"hash":"2111379186187816561","title":"Unknown","description":"The GO terms span diverse biological areas (plant leaf development and gibberellin signaling, animal immune signaling and growth factor responses) along with general transcription and translation processes, with no cohesive, cluster-wide function or interaction pattern. Therefore there is no clear representative label beyond Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0048366","count":2},{"id":"GO:0009938","count":2}]},{"hash":"1275838551374895683","title":"Redox Homeostasis and Oxidative Stress Response","description":"This cluster is dominated by GO terms related to oxidation-reduction processes, cellular oxidant detoxification, and cell redox homeostasis, plus the cellular response to oxidative stress and protein deglutathionylation, indicating a core theme of maintaining redox balance and protecting against oxidative damage. A few terms (methylamine metabolism, neural crest migration) are tangential, but the redox-related terms strongly define the group.","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":15},{"id":"GO:0098869","count":15},{"id":"GO:0045454","count":15},{"id":"GO:0030416","count":14},{"id":"GO:2000651","count":12}]},{"hash":"81803583034655672","title":"Plant hormone signaling and growth regulation","description":"The terms cluster around plant hormone signaling (cytokinin, gibberellin, salicylic acid) and growth-related processes (seed growth, root meristem, leaf senescence), along with regulation of chlorophyll biosynthesis and cell wall/lignin biosynthesis, suggesting a cohesive role in hormonal control of plant development and metabolism.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":11},{"id":"GO:0043044","count":8},{"id":"GO:0009751","count":8},{"id":"GO:0009739","count":8},{"id":"GO:0010380","count":7}]},{"hash":"969433619887775872","title":"Embryonic heart and neural development","description":"These proteins cluster around early developmental processes, with strong signals for heart morphogenesis (valve development, outflow tract morphogenesis, cardioblast migration) and neural/mesenchymal differentiation (mesenchyme development, floor plate formation, interneuron and sensory cell fate). While others touch on broader developmental pathways, the dominant pattern is coordinated embryonic organogenesis involving heart tissue and neural lineages, suggesting a shared developmental program. ","confidence":"Medium","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:2000793","count":20},{"id":"GO:2000764","count":20},{"id":"GO:0060375","count":20},{"id":"GO:0060485","count":20},{"id":"GO:0071156","count":20}]},{"hash":"698296898852293618","title":"Unknown","description":"The top GO terms are a mix of transcription regulation (Pol II/III initiation and RNA Pol III preinitiation complex assembly), DNA integration, SMAD signaling, and plant auxin signaling, spanning different kingdoms. Because there is no single cohesive function tying these terms together across the cluster, I cannot assign a specific, representative label.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0060395","count":1},{"id":"GO:0045945","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0060261","count":1}]},{"hash":"1160879810291482303","title":"RNA Splicing and Translation Regulation","description":"This cluster centers on post-transcriptional control of gene expression: spliceosome-mediated and alternative mRNA splicing, regulation of mRNA stability and modification, and initiation of translation (including IRES-dependent initiation and eIF4F complex assembly). The presence of ncRNA-mediated silencing further supports a cohesive RNA metabolism module rather than transcriptional regulation, indicating a focused role in RNA processing and translation control.","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":17},{"id":"GO:0048026","count":14},{"id":"GO:0031047","count":14},{"id":"GO:0016556","count":12},{"id":"GO:0048255","count":12}]},{"hash":"1175112276777191024","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":6},{"id":"GO:0009451","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0090502","count":6},{"id":"GO:0070129","count":6}]},{"hash":"1246966215922653771","title":"Glutathione-driven detoxification and oxidative stress response","description":"The cluster is enriched for glutathione-related processes (glutathione metabolic and derivative biosynthetic) and oxidant detoxification, indicating a redox/ detox theme. Other stress-related terms like response to starvation and DNA damage response by p53 support a protective, stress-adaptation role, making the glutathione-linked detox and oxidative stress label appropriate, despite some unrelated terms nudging the theme.","confidence":"Medium","size":22,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":6},{"id":"GO:1901687","count":5},{"id":"GO:0043651","count":5},{"id":"GO:0042594","count":5},{"id":"GO:0043517","count":5}]},{"hash":"1787183482482263476","title":"Plant Abiotic Stress Signaling","description":"The top GO terms are dominated by plant abiotic stress responses (positive regulation of abscisic acid biosynthesis, response to high light intensity, and response to desiccation), indicating a cluster enriched for environmental stress signaling in plants. The remaining terms (Notch signaling, ectodomain proteolysis, and various development/proliferation processes) are more diverse and contribute less to the core theme, suggesting they are secondary or cross-species annotations. Overall, the strongest signal is plant stress response signaling.","confidence":"Medium","size":22,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010116","count":6},{"id":"GO:0009644","count":6},{"id":"GO:0009269","count":6},{"id":"GO:0007219","count":3},{"id":"GO:0044671","count":2}]},{"hash":"1751659569733415553","title":"Plant Cell Wall Biosynthesis and Pollen Exine Formation","description":"This cluster is dominated by plant-specific cell wall terms: cell wall organization, plant-type secondary cell wall biogenesis, and glucuronoxylan biosynthetic process, plus pollen exine formation, pointing to a cohesive role in cell wall construction and pollen wall development. Some translation-related terms are present but do not define the main theme.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":6},{"id":"GO:0009834","count":3},{"id":"GO:0010417","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0008033","count":3}]},{"hash":"1425689929070873121","title":"RNA Splicing and Translation Machinery","description":"This cluster is dominated by RNA-processing and protein synthesis terms: translation (GO:0006412) and multiple spliceosome-related terms (Group I intron splicing, spliceosome conformational changes) along with ribonucleoprotein complex assembly and regulation of translational fidelity. The strongest signal centers on RNA metabolism, encompassing both splicing and translation components, with a few other terms likely reflecting secondary annotations.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:1990416","count":2},{"id":"GO:0000372","count":2},{"id":"GO:0000388","count":2},{"id":"GO:0055114","count":2}]},{"hash":"679989461893596766","title":"Adaptive immune activation and cytokine signaling","description":"This cluster is dominated by GO terms for T and B cell activation (T cell proliferation, B cell receptor signaling), cytokine responses (interleukin-4 production, interleukin-7 response), and immune synapse/cell death regulation, indicating coordinated adaptive immune signaling. The inclusion of neutrophil clearance and adhesion-related terms suggests broader immune interactions beyond adaptive cells. Overall, it reflects a cohesive immune activation module centered on lymphocyte signaling and cytokine networks.","confidence":"High","size":22,"edges":182,"triangles":804,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":22},{"id":"GO:0097350","count":22},{"id":"GO:0043068","count":22},{"id":"GO:0032633","count":22},{"id":"GO:0050853","count":22}]},{"hash":"2178487716693833651","title":"Plant DNA-Templated Transcription Regulation","description":"The top GO terms center on regulation and execution of DNA-templated transcription, especially the explicit \"regulation of DNA-templated transcription\" and \"DNA-templated transcription.\" Additional terms point to regulatory and metabolic context in plants (phosphorylation, gibberellin response, lipid and ubiquinone/tocopherol-related processes), suggesting a coordination role in transcriptional control within plant signaling networks. Overall, the cluster appears to be defined by transcription regulation rather than a single metabolic pathway. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0016310","count":3},{"id":"GO:0009739","count":3},{"id":"GO:1902171","count":2}]},{"hash":"967588987179197375","title":"Oocyte Meiosis: Spindle Assembly and Ubiquitin-Dependent Proteolysis","description":"The cluster is dominated by terms tied to meiotic spindle dynamics and protein turnover, including microtubule polymerization, spindle assembly in female meiosis I, SCF-dependent ubiquitin-mediated proteolysis, and oocyte maturation, indicating a coherent theme of spindle assembly coupled with ubiquitin-proteasome\u2013mediated proteolysis during oogenesis. Some development-related terms appear but do not override the meiotic/spindle-assembly focus.","confidence":"High","size":22,"edges":20,"triangles":0,"max_degree":5,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0046785","count":16},{"id":"GO:0007057","count":16},{"id":"GO:0031146","count":16},{"id":"GO:0021678","count":16},{"id":"GO:0006516","count":16}]},{"hash":"1469048557241161084","title":"Lipopolysaccharide biosynthesis","description":"Most frequent GO terms point to lipopolysaccharide biosynthesis, including core region and O-antigen assembly, plus related polysaccharide pathways (colanic acid) and sugar-nucleotide biosynthesis (GDP-mannose, dTDP-rhamnose). An obsolete oxidation-reduction term is likely noise. Despite no edges, the core theme is LPS and surface polysaccharide production in Gram-negative bacteria.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":16},{"id":"GO:0009244","count":9},{"id":"GO:0009103","count":9},{"id":"GO:0097171","count":9},{"id":"GO:0019673","count":8}]},{"hash":"1947455303085575211","title":"Lipid biosynthesis and membrane metabolism","description":"The top GO terms are skewed toward lipid-related processes: unsaturated fatty acid biosynthesis, ergosterol biosynthetic regulation, and sphingolipid (MIPC) metabolism, along with lipid-rich tissue functions like CNS myelin maintenance and sebaceous gland differentiation. These collectively suggest a core theme around membrane lipid production and regulation. The remaining terms (nitrate assimilation, nitric oxide biosynthesis, copper ion response, mitochondrial inheritance) are more peripheral, indicating broader metabolism or annotation noise. Overall, lipid metabolism and membrane-related processes best explain the cluster.","confidence":"Medium","size":22,"edges":28,"triangles":4,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0071280","count":3},{"id":"GO:0006675","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0042128","count":2}]},{"hash":"384949460136497019","title":"LPS-driven innate inflammation","description":"The Top Terms are dominated by innate immune response and lipopolysaccharide (LPS)\u2013related terms, including detection of LPS, LPS signaling, cellular response to LPS, inflammatory response, and TNF production. This suggests the cluster's proteins primarily participate in recognizing bacterial components and triggering inflammation. Although there are a couple of cholesterol and DNA repair terms present, the core theme is LPS-triggered innate immunity.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":3},{"id":"GO:0042632","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0033344","count":2}]},{"hash":"2082514267715245689","title":"Meiotic Chromosome Dynamics and Replication Regulation","description":"The top terms point to meiotic chromosome behavior (meiotic sister chromatid cohesion, centromeric; meiotic spindle elongation), together with DNA replication\u2013dependent chromatin assembly and regulation of replication and kinase activity, plus nuclear import. These collectively suggest coordinated control of meiosis-specific chromosome dynamics and replication-associated chromatin processes, with supporting regulatory signaling. The extrinsic apoptotic term is less central to the core theme. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006275","count":3},{"id":"GO:0050790","count":3},{"id":"GO:0006335","count":3},{"id":"GO:0070262","count":3}]},{"hash":"686421310898056285","title":"Glycerolipid catabolism and remodeling","description":"Most terms cluster around breakdown and remodeling of glycerolipids (triglycerides, diacylglycerol, monoacylglycerol, phosphatidylserine) and acyl-chain remodeling, with a contribution from lipid-mediated signaling (endocannabinoid pathway). A few plant-specific terms appear less connected, likely noise. Overall, the dominant theme is glycerolipid catabolism and remodeling. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":8},{"id":"GO:0006660","count":8},{"id":"GO:2000124","count":8},{"id":"GO:0052651","count":8},{"id":"GO:0030245","count":7}]},{"hash":"1002287857686079035","title":"Plant nutrient transport and hormone signaling","description":"This cluster combines multiple transport-related GO terms (nitrate, dipeptide/oligopeptide, xenobiotic transmembrane transport) with plant hormone signaling annotations (auxin-activated signaling, gibberellic acid homeostasis) and herbicide response, suggesting a cohesive theme around nutrient/solute transport alongside hormone- and chemical-response pathways in plants.","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051497","count":2},{"id":"GO:0010336","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0010167","count":2},{"id":"GO:0006855","count":2}]},{"hash":"961138507860702499","title":"Auxin Signaling and Growth Regulation","description":"This cluster shows enrichment for auxin-related GO terms (auxin-activated signaling pathway, response to auxin, auxin polar transport) along with growth and transcription-related terms (regulation of organ growth, cell division, DNA-templated transcription), suggesting a co-regulated set of proteins involved in auxin-driven plant growth and gene expression.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0061668","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046620","count":1}]},{"hash":"202056525181729386","title":"Plant secondary cell wall biosynthesis regulation","description":"This cluster is dominated by terms about regulating secondary cell wall biogenesis and syringyl lignin biosynthesis, with supporting signals in related regulatory processes such as transcription and chlorophyll biosynthesis regulation and seed growth. The recurring emphasis on cell wall and lignin pathways suggests a coherent plant-specific regulatory module.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0043085","count":3},{"id":"GO:0046938","count":3},{"id":"GO:0006508","count":3},{"id":"GO:1904715","count":3}]},{"hash":"1521565758564355444","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0051666","count":2},{"id":"GO:0016197","count":2}]},{"hash":"1173901464928652378","title":"Plant light signaling and membrane transport","description":"The top GO terms emphasize light-responsive processes (red/far-red phototransduction and signaling) and circadian rhythm regulation, together with several membrane transport activities (amino acid export, calcium export, UDP-glucose transport, GDP-fucose import). This points to a cohesive theme of light-regulated transport and timing in plants, though a couple terms (DNA transposition, transcription regulation) are less connected, making the link moderate.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":3},{"id":"GO:1990034","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0015786","count":2},{"id":"GO:0036085","count":2}]},{"hash":"1822507460348999587","title":"Plant Organellar RNA Processing and Modification","description":"The cluster is enriched for organellar RNA metabolism in plants: mitochondrial and chloroplast mRNA processing, RNA modification, cytidine-to-uridine editing, plastid transcription, and polycistronic mRNA processing. These terms point to a cohesive function centered on RNA maturation/editing in plant organelles, with the seed dormancy term possibly reflecting broader developmental context but not altering the core theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090502","count":10},{"id":"GO:0090615","count":7},{"id":"GO:0009451","count":7},{"id":"GO:0016554","count":7},{"id":"GO:0080156","count":7}]},{"hash":"610696097265894683","title":"Plant Development and Hormone-Regulated Transcription","description":"This cluster centers on regulation of DNA-templated transcription and plant development, including floral meristem growth and bract development, with strong links to hormone signaling pathways (ethylene and ABA) and epidermal biosynthesis (wax and cutin). Together, these terms suggest a cohesive theme of transcriptional control guiding plant development and cuticle-related processes, modulated by hormonal cues.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0010451","count":3},{"id":"GO:0009873","count":3},{"id":"GO:0010432","count":3}]},{"hash":"2239136370290029885","title":"Salicylic acid\u2013associated defense signaling","description":"The cluster shows a clear enrichment for GO terms related to salicylic acid stimulus and regulation of SA-mediated signaling, along with regulation of defense responses. This points to a core theme of SA-triggered defense signaling among the proteins, despite some additional, less cohesive terms (e.g., DNA integration, vitamin D response) that may reflect multi-function proteins or annotation noise.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071446","count":3},{"id":"GO:2000031","count":3},{"id":"GO:0031347","count":3},{"id":"GO:0015074","count":2},{"id":"GO:0033280","count":2}]},{"hash":"1011464162442899493","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":5},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0090502","count":4},{"id":"GO:0070129","count":4}]},{"hash":"561856844568587493","title":"Organellar RNA processing and editing in mitochondria and chloroplasts","description":"Based on the GO terms, the cluster is dominated by mitochondrial and chloroplast RNA processing/modification and transcription-related functions (e.g., mitochondrial mRNA processing, chloroplast RNA modification, plastid transcription, polycistronic mRNA processing). This suggests a cohesive role in organellar gene expression, with seed dormancy annotation likely incidental noise.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":4},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0080156","count":4},{"id":"GO:1905639","count":4}]},{"hash":"714982825923430457","title":"Unknown","description":"This cluster's top GO terms span phototropism, gravitropism, P granule assembly, and several mitosis-related processes (sister chromatid biorientation, mitotic spindle orientation checkpoint signaling, septin ring disassembly), plus general signal transduction and protein localization terms. The terms are too diverse to converge on a single clear function, so there isn\u2019t a coherent label beyond Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009638","count":2},{"id":"GO:0009958","count":2},{"id":"GO:0090219","count":2},{"id":"GO:1903863","count":2},{"id":"GO:0007165","count":2}]},{"hash":"28523451740120623","title":"Developmental patterning and Notch signaling","description":"The cluster\u2019s top GO terms cluster around developmental processes and tissue patterning (e.g., ovarian follicle development, intestinal epithelial cell development, hypochord development, female meiotic nuclear division, compartment pattern specification) with recurrent mentions of Notch signaling regulation. This suggests a broad theme of development and cell fate specification with Notch pathway involvement, rather than a single, narrow function. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032092","count":5},{"id":"GO:0007143","count":4},{"id":"GO:0007386","count":4},{"id":"GO:0016267","count":4},{"id":"GO:0001541","count":4}]},{"hash":"2065743919481772573","title":"Endosome-Golgi-Lysosome Vesicle Trafficking","description":"This cluster centers on vesicle transport pathways linking endosomes, the Golgi, lysosomes, and related organelles (including clathrin-coated vesicles and melanosomes), with ancillary links to synaptic vesicle membranes and antigen processing/presentation, suggesting a cohesive vesicle trafficking function.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035646","count":3},{"id":"GO:0098943","count":3},{"id":"GO:0090160","count":3},{"id":"GO:0032438","count":3},{"id":"GO:0061088","count":3}]},{"hash":"2008833002267511852","title":"N-terminal Protein Methylation","description":"The cluster is driven by multiple methylation-related GO terms, especially N-terminal peptidyl methylation variants (e.g., N-terminal peptidyl-alanine/glycine/serine methylation) and a general methylation term. This points to a cohesive theme of protein methylation, particularly at the N-terminus, implying involvement of N-terminal methyltransferases. Some unrelated biosynthetic terms appear (melatonin, lignin, flavonol biosynthesis) but do not define the core function of the cluster. Thus, the label emphasizes the most characteristic function represented by the data.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":7},{"id":"GO:0018012","count":6},{"id":"GO:1901771","count":4},{"id":"GO:0018013","count":4},{"id":"GO:0035572","count":4}]},{"hash":"574344884800650985","title":"Mitochondrial RNA Processing and Translation Regulation","description":"This cluster is dominated by GO terms related to mitochondrial RNA metabolism, including RNA splicing, RNA modification, cytidine-to-uridine editing, mitochondrial mRNA processing and modification, and regulation of mitochondrial translation. Together they indicate a cohesive theme of mitochondrial RNA maturation and control of translation, with a few outliers (e.g., a plant-specific biosynthetic term) that do not fit the core motif. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":2},{"id":"GO:0008380","count":2},{"id":"GO:1901599","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0009451","count":1}]},{"hash":"2248321793568638963","title":"Unknown","description":"The terms span apoptosis, oxidative stress, cell cycle regulation, inflammatory signaling, and insect-specific chitin metabolism, with no single cohesive function tying most terms together, suggesting no clear cluster theme.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031397","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0001836","count":1},{"id":"GO:0042219","count":1},{"id":"GO:0006750","count":1}]},{"hash":"350794928652774262","title":"Transcription and ribosome biogenesis","description":"Top GO terms cluster around gene expression: DNA-templated transcription, RNA guanine-N7 methylation, and ribosome-related processes (nuclear export of the small subunit and rRNA methylation). There are a few peripheral terms (skin development, tellurium ion response, cellular senescence) that seem less central. Overall, the cluster appears to collect proteins involved in transcription and ribosome assembly/processing, so this label reflects the core shared function despite some outwardly related but less connected terms.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046690","count":2}]},{"hash":"2213094005276775231","title":"Iron-sulfur cluster assembly and protein maturation","description":"The cluster is enriched for terms directly tied to iron-sulfur (Fe-S) cluster biogenesis and maturation (assembly and transfer), with ancillary signals for translation, transcription, and photosynthesis that often rely on Fe-S proteins in chloroplasts/mitochondria. The strongest and most coherent theme across the terms is Fe-S cluster biogenesis and maturation, justifying this label.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0016226","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006351","count":2}]},{"hash":"184918338668050416","title":"Neural development and signaling regulation","description":"The terms cluster around brain development and neuronal signaling: hippocampus development, axon extension, Wnt signalosome assembly, focal adhesion regulation, and cytoskeletal dynamics, with dopamine responsiveness and transcriptional/post-transcriptional gene regulation supporting neural differentiation.","confidence":"High","size":21,"edges":33,"triangles":0,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:1903351","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0033138","count":3},{"id":"GO:0035278","count":2}]},{"hash":"72467813154203286","title":"N-terminal peptide methylation","description":"This cluster is dominated by GO terms describing N-terminal peptidyl methylation across several residues (serine dimethylation/trimethylation, alanine trimethylation, glycine methylation), suggesting a common function in methylating protein N-termini. While there are additional terms related to antibiotic and lipopolysaccharide biosynthesis and stress responses, the methylation terms best capture the shared theme among the proteins.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035572","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0035573","count":4},{"id":"GO:0018012","count":4},{"id":"GO:0018013","count":4}]},{"hash":"1109459390434749248","title":"Chromatin regulation and transcription control","description":"The top GO terms point to regulation of transcription (GO:0006355), nucleosome assembly (GO:0006334), histone modification (GO:0051573, GO:0034720), and chromatin binding (GO:0035563), indicating a core theme around chromatin organization and transcription control. Meta-terms like glycolytic process and aerobic electron transport chain are present but likely reflect multifunctional enzymes or annotation noise, so the dominant signal is chromatin-based regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0051573","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0034720","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0006334","count":3}]},{"hash":"517461306354588743","title":"Developmental Signaling and Differentiation","description":"The terms point to signaling events that drive development and cell fate decisions, including imaginal disc fusion and thorax closure, R3/R4 cell fate commitment, and NMJ synaptic assembly, with calcium signaling and transcriptional regulation as common mechanisms. While there are a few outliers (e.g., ABA response, host-mediated viral transcription), the core theme is signaling pathways that coordinate development and differentiation across contexts.","confidence":"Medium","size":21,"edges":197,"triangles":1113,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009737","count":13},{"id":"GO:0071277","count":11},{"id":"GO:0032915","count":10},{"id":"GO:0006990","count":10},{"id":"GO:0046529","count":10}]},{"hash":"1917933272165916142","title":"Synaptic Assembly and Organization","description":"The terms cluster around synapse formation and organization (both inhibitory and excitatory), presynaptic membrane assembly via neurexin clustering, and active zone cytoskeletal arrangement, with related regulation of synaptic transmission, suggesting a cohesive role in synapse assembly and modification.","confidence":"High","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904862","count":4},{"id":"GO:0050808","count":4},{"id":"GO:0097115","count":4},{"id":"GO:1904861","count":4},{"id":"GO:0097151","count":4}]},{"hash":"513962852059239950","title":"Neural development and apoptotic signaling","description":"The top GO terms are dominated by apoptotic processes (intrinsic apoptotic signaling in ER stress; glial and cardiac muscle cell apoptotic processes) and nervous system development (forebrain development; nervous system development). This suggests the proteins function collectively in neural tissue development and programmed cell death, with additional signaling and metabolic context that commonly accompany growth and stress responses. The core theme is neural development intertwined with apoptosis, making this label concise and representative.","confidence":"High","size":21,"edges":195,"triangles":1082,"max_degree":20,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0070059","count":19},{"id":"GO:0030900","count":17},{"id":"GO:0010659","count":17},{"id":"GO:0035006","count":17},{"id":"GO:0033353","count":17}]},{"hash":"7583956441796728","title":"Spliceosome-mediated mRNA processing and regulation","description":"The top GO terms are centered on mRNA splicing via the spliceosome, along with related processing steps (polyadenylation, RNA stability/modification) and regulatory aspects (ncRNA-mediated gene silencing, transcription termination). This pattern suggests a cohesive cluster of proteins involved in splicing and broader mRNA maturation and control, rather than separate pathways. ","confidence":"High","size":21,"edges":174,"triangles":782,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":11},{"id":"GO:0031047","count":11},{"id":"GO:1901407","count":11},{"id":"GO:0006378","count":8},{"id":"GO:0010610","count":8}]},{"hash":"375789568494514844","title":"Plant Hormone Signaling and Chlorophyll Regulation","description":"The top GO terms point to plant hormone signaling (cytokinin-activated and gibberellin-related pathways) and regulation of chlorophyll biosynthesis, suggesting a core function in growth and light-related regulation. Additional terms about photoreceptor localization and ubiquitination imply light-responsive regulation and protein turnover, components often linked to hormone signaling in plants. Overall, the cluster appears to reflect plant signaling pathways tied to light and chlorophyll processes.","confidence":"Medium","size":21,"edges":16,"triangles":13,"max_degree":6,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1903071","count":3},{"id":"GO:1903546","count":3},{"id":"GO:0031400","count":3},{"id":"GO:0006463","count":3},{"id":"GO:0009938","count":3}]},{"hash":"1999472235263824660","title":"Photoreceptor development and energy metabolism","description":"This cluster centers on retina-related functions, with GO terms for retinal rod cell development and protein localization to photoreceptor outer segments, coupled with core metabolic processes (glycolysis and TCA cycle), suggesting a link between photoreceptor maturation and energy production. Some terms are general or outliers (cell division, hormone-related processes), but the prominent retina and metabolism signals define the theme.","confidence":"Medium","size":21,"edges":14,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006099","count":4},{"id":"GO:0006096","count":4},{"id":"GO:1903071","count":4},{"id":"GO:0050689","count":4}]},{"hash":"658223047071275701","title":"Regulation of plant growth and secondary cell wall biosynthesis","description":"Predominant GO terms relate to plant development and regulation of lignin biosynthesis and cell wall formation (seed growth, root meristem growth, leaf senescence, syringal lignin biosynthetic process, and secondary cell wall biogenesis). A few terms (viral process) seem unrelated and may reflect annotation noise. Overall, the cluster best fits regulatory processes governing plant growth and cell wall biosynthesis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0016032","count":6},{"id":"GO:0000183","count":5},{"id":"GO:0030154","count":5},{"id":"GO:0010380","count":4},{"id":"GO:0080113","count":4}]},{"hash":"421276855750752173","title":"Cell cycle and telomere regulation","description":"The cluster is dominated by GO terms related to cell cycle control and telomere maintenance, including mitotic G1 DNA damage checkpoint signaling, regulation of cyclin-dependent kinase activity, and telomere maintenance/capping. This points to a cohesive function in coordinating cell proliferation with genome stability. Some terms such as mRNA processing and cadmium response appear peripheral, possibly reflecting broader stress-related roles, but the core theme centers on cell cycle regulation and telomere integrity.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":4},{"id":"GO:0031571","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0051436","count":3},{"id":"GO:0008285","count":3}]},{"hash":"151072041481975742","title":"Ubiquitin-Proteasome Proteolysis in Meiosis and Development","description":"The cluster is enriched for ubiquitin-dependent protein catabolic processes (including SCF-dependent proteasomal ubiquitin-dependent proteolysis) and meiotic/spindle-related terms (spindle assembly in female meiosis I, oocyte maturation) along with development-related terms (neural tube closure, ventricle development). This points to a core function in regulated protein degradation that drives meiotic progression and developmental processes. Confidence reflects the coherent link between ubiquitin-proteasome\u2013mediated proteolysis and meiotic/oocyte maturation functions.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0046785","count":7},{"id":"GO:0007057","count":7},{"id":"GO:0021678","count":7}]},{"hash":"242844602776129474","title":"Aminoacyl-tRNA charging and translation","description":"The top GO terms are dominated by aminoacyl-tRNA synthetase activities (isoleucyl-, valyl-, leucyl-, methionyl-tRNA charging) along with translation and regulation of translational fidelity, pointing to the core function being protein synthesis and its quality control. A few non-translation terms appear sparsely, likely due to broad or incidental annotations, but the shared theme is clearly translation-related.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006428","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0000372","count":1},{"id":"GO:0006438","count":1},{"id":"GO:0006429","count":1}]},{"hash":"1665194974673911896","title":"Nuclear transcriptional regulation and DNA maintenance","description":"The top GO terms cluster around transcriptional regulation by RNA polymerase II (both positive and negative), DNA replication and recombination, and protein ubiquitination, with supporting signals like calcium response and stress. This combination points to a group of nuclear factors coordinating gene expression and genome maintenance rather than a single cytosolic pathway.","confidence":"Medium","size":21,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006310","count":2}]},{"hash":"67732275239073843","title":"Unknown","description":"This cluster shows several unrelated processes: lipopolysaccharide biosynthesis (bacterial cell envelope), sterol biosynthesis, RNA modification/editing (including mitochondrial RNA), and even developmental and drug-response terms. There isn't a single coherent common function tying most proteins together, so a meaningful specific label is not supported.","confidence":"","size":21,"edges":189,"triangles":979,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0009244","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0097171","count":2}]},{"hash":"2040532248781152726","title":"Plant development and hormone-regulated transcription","description":"The cluster centers on regulation of DNA-templated transcription and development (floral meristem growth, bract development, multicellular organism development) with plant hormone signaling (ethylene and ABA) and epidermal lipid biosynthesis (wax, cutin). This suggests proteins coordinating growth and organ formation via hormone-responsive transcription and epidermal barrier formation, justifying a label focused on plant development and hormone-regulated transcription.","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":4},{"id":"GO:0006351","count":3},{"id":"GO:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010432","count":2}]},{"hash":"980324926948710947","title":"Mesenchymal and neural development","description":"The top terms point to development and differentiation across mesenchymal tissues (mesenchyme development, heart valve morphogenesis, osteoblast-related regulation) and neural lineages (GABAergic interneuron differentiation, auditory receptor fate). Together with core transcription and cell-cycle regulation, the cluster seems to reflect broad developmental regulation spanning mesenchymal and neural fates rather than a single precise pathway.","confidence":"Medium","size":21,"edges":181,"triangles":917,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":16},{"id":"GO:0060766","count":16},{"id":"GO:0006366","count":15},{"id":"GO:2000793","count":14},{"id":"GO:2000764","count":14}]},{"hash":"992241485101362901","title":"Ribosome biogenesis and oxidative phosphorylation","description":"The cluster centers on ribosome assembly and maturation (SSU-rRNA maturation, ribosome biogenesis) alongside energy-generation processes (mitochondrial electron transport, respiratory chain III assembly, aerobic respiration, photosynthesis), suggesting a link between protein synthesis machinery and cellular energy metabolism. Some terms like lipid A biosynthesis and dendrite regulation appear as peripheral noise. Confidence: Medium","confidence":"","size":21,"edges":60,"triangles":29,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0015979","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0006122","count":2}]},{"hash":"2204280084497697627","title":"Lipid and small-molecule metabolism cluster","description":"The top GO terms are dominated by lipid-related pathways (fatty acid biosynthesis, omega-oxidation, prostaglandin metabolism) and various small-molecule catabolic processes (ethanol, formaldehyde, galactose), with retinol metabolism linking to lipid-derived molecules. There is also a signal of xenobiotic/antineoplastic agent response, which fits a broader detoxification/metabolism theme. Taken together, these terms point to a cohesive metabolic cluster centered on lipid and small-molecule catabolism and detoxification rather than a single specific pathway.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0006633","count":21},{"id":"GO:0042572","count":21},{"id":"GO:0010430","count":21},{"id":"GO:0006068","count":21},{"id":"GO:0018119","count":21}]},{"hash":"906352520886227314","title":"Neuronal development and synaptic exocytosis","description":"The cluster is enriched for nervous system development and sensory perception of pain, plus calcium-dependent exocytosis and Rho signaling, pointing to proteins involved in neuronal differentiation and neurotransmission. While there are broader developmental terms present, the strongest theme centers on neural development and synaptic signaling.","confidence":"High","size":21,"edges":167,"triangles":706,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":15},{"id":"GO:0007275","count":15},{"id":"GO:0046827","count":15},{"id":"GO:0006351","count":15},{"id":"GO:0007399","count":12}]},{"hash":"841722442710192346","title":"Ubiquitin-mediated protein degradation and Wnt receptor turnover","description":"The proteins are enriched for ubiquitination-related processes (protein ubiquitination, ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, autoubiquitination) and for Wnt receptor catabolic turnover, suggesting a core theme of ubiquitin-driven protein degradation impacting Wnt signaling. A few terms about peroxisome import or X-inactivation appear, but they seem less connected and may reflect annotation noise.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0038018","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0070936","count":6},{"id":"GO:0051865","count":6}]},{"hash":"859866703976826465","title":"T cell activation and cytokine production","description":"This cluster is strongly enriched for immune-related processes: T cell proliferation and various cytokine production activities (including IL-4), plus neutrophil clearance and inflammatory signaling. The presence of Rho signaling and microtubule localization suggests associated cytoskeletal dynamics in activated immune cells. A few terms like cartilage condensation are less directly connected but may reflect broader developmental overlap. Overall, the dominant theme points to immune activation and cytokine signaling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":21},{"id":"GO:0001502","count":21},{"id":"GO:0097350","count":21},{"id":"GO:0035372","count":21},{"id":"GO:0043068","count":21}]},{"hash":"1165007496769249471","title":"Neuronal development and signaling","description":"The cluster shows enrichment in dendrite morphogenesis, cocaine response, potassium ion transport, glucose metabolism, and nucleocytoplasmic transport, which together point to neuronal growth, signaling, and excitability. Some terms like placenta development or generic chemotaxis are less specific, but the predominant theme centers on neural development and function.","confidence":"Medium","size":21,"edges":181,"triangles":919,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":18},{"id":"GO:0043552","count":14},{"id":"GO:0006935","count":14},{"id":"GO:0045793","count":14},{"id":"GO:0042220","count":14}]},{"hash":"652481840301773374","title":"Neural development and nervous system morphogenesis","description":"The top GO terms are dominated by neural development and nervous system processes (forebrain development, neural tube closure, nervous system development, dendrite morphogenesis), suggesting a cohesive theme around neural formation and wiring. There are also apoptosis and stress signaling terms (ER-stress\u2013induced intrinsic apoptotic signaling, TGF-beta response) that may reflect developmental regulation or stress-responsive modulation, but the strongest, recurring signal centers on neural development.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0030900","count":6},{"id":"GO:0070059","count":6},{"id":"GO:0001843","count":6},{"id":"GO:0006260","count":5}]},{"hash":"911597985992093518","title":"Autophagy and ubiquitin-like protein modifications","description":"The cluster is dominated by autophagy-related terms (macroautophagy, mitophagy, CVT pathway, nucleophagy, piecemeal microautophagy) and includes multiple ubiquitin-like post-translational modification processes (SUMOylation, ufmylation, urmylation) and protein lipidation, suggesting a cohesive theme where autophagy interacts with ubiquitin-like modification pathways. A minor link to immune signaling via MyD88-TLR regulation may reflect broader crosstalk but does not define the core function. ","confidence":"High","size":21,"edges":191,"triangles":1010,"max_degree":20,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0016925","count":7},{"id":"GO:0000422","count":6},{"id":"GO:0032258","count":5},{"id":"GO:0016236","count":5},{"id":"GO:0044805","count":5}]},{"hash":"1089572411763085229","title":"Embryonic Development and Organogenesis","description":"The top GO terms point to broad roles in embryonic development across multiple tissues (brain, heart, palate, pituitary, endoderm, etc.), including neural differentiation and organogenesis processes, suggesting these proteins act as general regulators of development rather than a single tissue-specific function.","confidence":"High","size":21,"edges":83,"triangles":79,"max_degree":15,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007275","count":9},{"id":"GO:0021983","count":8},{"id":"GO:0090009","count":8},{"id":"GO:0060021","count":8},{"id":"GO:0042663","count":7}]},{"hash":"416036330156041153","title":"Ubiquitin-dependent protein degradation","description":"This cluster is enriched for ubiquitination and ubiquitin-dependent degradation pathways (ERAD, protein ubiquitination, ubiquitin-mediated proteolysis) and includes terms related to histone ubiquitination and catabolic processes, as well as signaling pathways (TNF, JNK) and innate immune regulation (RIG-I). The common thread across these terms is ubiquitin-mediated proteostasis and signaling, suggesting proteins in this cluster function in ubiquitin-dependent degradation and related regulatory pathways.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030433","count":8},{"id":"GO:1901253","count":7},{"id":"GO:2000620","count":7},{"id":"GO:0016567","count":7},{"id":"GO:0042787","count":7}]},{"hash":"1472056314899851890","title":"Developmental Differentiation and Cardiac-Neural Lineages","description":"The cluster shows GO terms centered on developmental differentiation across mesenchyme, cardiac (heart valve) development, and neural lineages (GABAergic interneuron differentiation, auditory receptor fate), plus transcription by RNA polymerase II and cell cycle regulation. This suggests a module of proteins coordinating developmental trajectories in mesenchymal, cardiac, and neural tissues, with transcriptional control as a core feature. There is an outlier plant-related term (anthocyanin biosynthesis) that is likely incidental noise rather than reflective of the main theme.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0031542","count":11},{"id":"GO:2001016","count":8},{"id":"GO:2000793","count":7},{"id":"GO:2000764","count":7}]},{"hash":"2209632292282828141","title":"Regulation of chlorophyll and lignin biosynthesis in plants","description":"The cluster\u2019s terms cluster around plant development and regulation of key biosynthetic pathways, notably chlorophyll biosynthesis, seed and root growth, lignin and secondary cell wall biogenesis, and leaf senescence. These converging \u201cregulation of growth and biosynthesis\u201d signals suggest a cohesive theme in plant development rather than a single isolated process.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0035522","count":4},{"id":"GO:0010380","count":3},{"id":"GO:0080113","count":3},{"id":"GO:1901430","count":3},{"id":"GO:1901347","count":3}]},{"hash":"1474731492352326722","title":"Female reproductive development and steroid hormone biosynthesis","description":"The top GO terms cluster around uterus development, female gonad development, and mammary gland development, indicating a primary theme of reproductive tissue development. In addition, there are strong signals for steroid hormone biosynthesis (cortisol, testosterone) and related hormone metabolism (retinoic acid catabolic, vitamin D response), suggesting a cohesive cluster linking reproductive development with hormone production and signaling. Minor terms for xenobiotic metabolism and demethylation appear secondary and do not alter the main theme.","confidence":"High","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060065","count":8},{"id":"GO:0008585","count":8},{"id":"GO:0030879","count":7},{"id":"GO:0071603","count":7},{"id":"GO:0034651","count":7}]},{"hash":"2027361789343368575","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":5},{"id":"GO:0009451","count":4},{"id":"GO:0016554","count":4},{"id":"GO:0070129","count":4},{"id":"GO:0080156","count":4}]},{"hash":"1977446187380144367","title":"Unknown","description":"The terms span disparate areas including plant-specific processes (secondary cell wall biogenesis and cytokinin signaling) alongside general cellular functions (chromatin binding/modification, redox homeostasis, and basic metabolism), with no clear overarching function binding all proteins. Therefore a cohesive label cannot be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1901348","count":6},{"id":"GO:0009736","count":5},{"id":"GO:0045654","count":5},{"id":"GO:0035563","count":5},{"id":"GO:0055114","count":5}]},{"hash":"1329977996733069151","title":"Metal Ion Transport and Redox/Nutrient Uptake","description":"This cluster centers on metal ion transport (copper, iron, arsenate) and redox-associated nutrient uptake (nitrate assimilation, reductive iron assimilation), plus related redox processes, suggesting a theme of metal homeostasis and redox metabolism. A few terms (platelet activation, lignin catabolic process, antibiotic biosynthesis, sporulation) are peripheral noise.","confidence":"Medium","size":21,"edges":13,"triangles":1,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042128","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0006825","count":6},{"id":"GO:0034755","count":6},{"id":"GO:0030435","count":6}]},{"hash":"62446207032593316","title":"Regulation of plant secondary cell wall biosynthesis","description":"This cluster centers on plant-type secondary cell wall formation and its regulation, including positive/negative regulation of cell wall biogenesis, lignin and xyloglucan metabolism, and growth-related processes (seed, root meristem, leaf senescence) with transcriptional control, suggesting a coherent regulatory module for cell wall biosynthesis in plants.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0009834","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0010411","count":3},{"id":"GO:0010380","count":3}]},{"hash":"1155305377388883794","title":"Steroid Hormone and Xenobiotic Metabolism","description":"This cluster centers on hormone biosynthesis and related metabolism, with multiple terms for steroid hormones (cortisol, testosterone), retinoic acid turnover, vitamin D response, and lipid oxidation, alongside xenobiotic catabolic processes. While some GO terms touch broader development or plant-specific pathways (e.g., brassinosteroid biosynthesis), the dominant theme ties to hormone production and metabolic processing of lipids and xenobiotics, suggesting a cohesive group of proteins involved in hormone biosynthesis and detoxification pathways.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":21},{"id":"GO:0071603","count":21},{"id":"GO:0034651","count":21},{"id":"GO:0070989","count":21},{"id":"GO:0042738","count":21}]},{"hash":"1083831306543810902","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0006261","count":2},{"id":"GO:0006094","count":2}]},{"hash":"2284424674641056016","title":"Plant photoperiodic flowering signaling","description":"The proteins show strong representation of photoperiodism (short-day/long-day), regulation of flowering, and far-red light signaling, along with circumnutation and flower development terms, pointing to a shared role in light-driven plant flowering control. A few miscellaneous terms (exocytosis, cell shape) are present but do not define the cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048572","count":1},{"id":"GO:0000160","count":1},{"id":"GO:0048579","count":1},{"id":"GO:0048576","count":1},{"id":"GO:0010031","count":1}]},{"hash":"18919902300677945","title":"Unknown","description":"The GO terms span disparate areas (salicylic acid signaling, heart SA node regulation, telomere and telomeric DNA binding, macrophage protein production, foam cell and brown fat differentiation, membrane protein localization, and proteasome assembly), with no clear common function linking the 21 proteins. The cluster has no edges or triangles, indicating a lack of a cohesive, shared pathway or process. Therefore, there is no single representative function to name this cluster.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071446","count":3},{"id":"GO:2000031","count":3},{"id":"GO:0098907","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0071642","count":2}]},{"hash":"1271912634577182234","title":"Developmental gene regulation and organogenesis","description":"The cluster centers on chromatin remodeling and DNA-templated transcription, with GO terms covering limb bud formation, otic vesicle formation, bile duct development, and definitive endodermal fate, suggesting a set of proteins involved in developmental gene regulation guiding organogenesis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060174","count":1},{"id":"GO:0033234","count":1},{"id":"GO:0030916","count":1}]},{"hash":"1495089649108807499","title":"Floral Meristem Regulation & BR Signaling","description":"The top terms cluster around floral meristem growth and organ specification, including regulation of meristem structure and floral organ number, combined with detection of brassinosteroid stimulus, pointing to a plant developmental module controlled by BR signaling. A subset of terms related to inflammatory and immune responses appears, likely due to annotation noise or cross-species annotations, but they are less representative of the primary cluster signal. Therefore, the label emphasizes floral meristem development and brassinosteroid signaling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009934","count":21},{"id":"GO:0048833","count":21},{"id":"GO:0010080","count":21},{"id":"GO:0009729","count":21},{"id":"GO:0032741","count":20}]},{"hash":"1715034571449909375","title":"Neural development gene regulation and proteostasis","description":"This cluster is enriched for neural development terms (neural tube closure, forebrain development) as well as core gene-expression and protein-regulation processes (DNA-templated transcription, formation of the translation preinitiation complex, ubiquitin-proteasome\u2013mediated degradation, and ERAD). The combination suggests proteins coordinating transcriptional control with protein turnover and quality control during neural development, with some apoptotic signaling modulation fitting developmental remodeling. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0031146","count":3},{"id":"GO:0001731","count":3}]},{"hash":"290615941882682530","title":"Ubiquitin-dependent proteolysis and immune/viral processes","description":"The cluster is strongly enriched for ubiquitin-related catabolic processes, including ubiquitin-dependent protein degradation (K48- and K6-linked ubiquitination) and autoubiquitination, pointing to ubiquitin signaling driving proteolysis. It also features innate and adaptive immune responses and a viral process term, suggesting a theme around ubiquitin-mediated regulation of immune and antiviral functions. While other terms (septin ring assembly, JNK regulation) appear, they supplement but do not override the dominant ubiquitination-immune signal.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0046328","count":7},{"id":"GO:0000921","count":6},{"id":"GO:0036205","count":6},{"id":"GO:0016032","count":5}]},{"hash":"482499738408468209","title":"Oocyte maturation and meiotic spindle assembly","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, and microtubule dynamics, with proteasomal ubiquitin-dependent protein catabolic processes tied to cell-cycle regulation. While development terms appear, the dominant signal is meiosis/oocyte spindle function and related protein turnover, making a label centered on oocyte meiosis appropriate.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":10},{"id":"GO:0046785","count":10},{"id":"GO:0006516","count":10},{"id":"GO:0007057","count":10},{"id":"GO:0070544","count":10}]},{"hash":"88280969797383281","title":"Oocyte maturation and meiotic spindle assembly","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, microtubule dynamics, and ubiquitin-proteasome\u2013mediated protein degradation, indicating a group of proteins focused on meiotic progression and cytoskeletal remodeling during oogenesis. Neural development terms are present but seem less central to the core theme.","confidence":"Medium","size":21,"edges":59,"triangles":30,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":20},{"id":"GO:0046785","count":19},{"id":"GO:0007057","count":19},{"id":"GO:0021678","count":19},{"id":"GO:0006516","count":19}]},{"hash":"1486643171715188368","title":"Unknown","description":"The top GO terms show a mix of ribosome biogenesis, cell wall organization, oxidative detoxification, and calcium signaling-related processes with no clear single function binding the proteins together, so there is no coherent theme to name the cluster confidently.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1903233","count":1}]},{"hash":"986711655859824673","title":"RNA Editing and Processing Under Stress","description":"This cluster is enriched for RNA metabolism terms (mitochondrial mRNA processing, RNA modification, cytidine to uridine editing, RNA phosphodiester hydrolysis) along with stress/defense signals (response to stress, systemic acquired resistance, dormancy entry of symbiont in host) and some proteolysis terms, suggesting a theme around RNA editing/processing coupled to stress responses rather than a single cohesive pathway. The lack of network edges indicates these proteins may share broad functions rather than direct interactions. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0085014","count":2},{"id":"GO:0006950","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0045493","count":2}]},{"hash":"559463982689397964","title":"Plant Cell Wall Biosynthesis & Pollen Development","description":"Most terms cluster around plant cell wall biogenesis and related processes (plant-type primary cell wall biogenesis, cellulose biosynthetic process, cell wall organization, rhamnogalacturonan I side chain metabolism, UDP-glucose metabolism, cell plate assembly, pollen germination), with pollen germination reinforcing a plant reproductive context. A single outlier term references animal prostate biology, which seems noise; overall the signal supports a plant cell wall/pollen-associated cluster.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060770","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0010400","count":1},{"id":"GO:0007299","count":1},{"id":"GO:0000919","count":1}]},{"hash":"1734891737242111009","title":"Plant Cell Wall Biogenesis and Carbohydrate Metabolism","description":"This cluster centers on plant-specific processes: strong enrichment for plant-type secondary cell wall biogenesis and polysaccharide/galactose catabolic processes, indicating roles in building and remodeling cell wall polysaccharides. Additional terms point to developmental and stress-related responses (callus formation, leaf senescence, phytochelatin biosynthesis). Together, these suggest a coherent theme of cell wall formation combined with carbohydrate metabolism and related plant development/stress pathways.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009834","count":3},{"id":"GO:0000272","count":3},{"id":"GO:0019388","count":3}]},{"hash":"804101802008678441","title":"Unknown","description":"The listed GO terms span glycosylation (O-GlcNAc and O-linked), insect cuticle development, plant chloroplast movement, RNA silencing, microtubule dynamics, bone mineralization, and muscle contraction. There are no connecting terms or a dominant shared process, and the cluster has no edges, indicating no cohesive function to label beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097370","count":2},{"id":"GO:0035269","count":2},{"id":"GO:0008363","count":2},{"id":"GO:0080188","count":1},{"id":"GO:0009904","count":1}]},{"hash":"1411941904081707762","title":"Unknown","description":"The top GO terms are scattered across very different biological contexts (animal brain/spinal cord development; plant-specific processes like cutin, lignin, auxin homeostasis; immune-related respiratory burst; general GTPase regulation), with no single, cohesive function tying the cluster together. This makes a confident, specific label inappropriate.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0045730","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0043547","count":2},{"id":"GO:2000114","count":2}]},{"hash":"11519497131621488","title":"Cell-cycle, transcription, and development signals","description":"This cluster is dominated by nuclear processes\u2014DNA replication, DNA-templated transcription, and centrosome/microtubule-associated activities\u2014suggesting a main theme around cell-cycle regulation and gene expression. The presence of embryonic cranial skeleton morphogenesis and chemotaxis/immune-related terms indicates additional development and signaling roles, but the strongest, recurring signal centers on cell-cycle and transcriptional machinery. Confidence: Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006813","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0035372","count":5},{"id":"GO:0007098","count":5}]},{"hash":"1944341103149921616","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2}]},{"hash":"465822436737342287","title":"Fatty Acid Metabolism and Transport","description":"The cluster\u2019s top GO terms are dominated by fatty acid processes: fatty acid biosynthetic process, long-chain fatty acid import, medium-chain fatty acid transport, and carnitine metabolic process, which together point to a cohesive role in fatty acid handling and lipid metabolism. Additional terms like phenylacetate catabolic and phenylpropanoid metabolism suggest broader metabolic connections, but the fatty acid-related terms are most representative. The bioluminescence term appears as an outlier rather than the central function. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008218","count":5},{"id":"GO:0006633","count":4},{"id":"GO:0010124","count":4},{"id":"GO:0019427","count":4},{"id":"GO:0008206","count":4}]},{"hash":"429241506547772983","title":"Sterol and sphingolipid biosynthesis","description":"The top GO terms are strongly lipid-focused: mannosyl-inositol phosphorylceramide metabolic process, unsaturated fatty acid biosynthetic process, and regulation of ergosterol biosynthetic process, along with ergosterol biosynthesis-related terms. These collectively point to membrane lipid metabolism typical of sterol and sphingolipid pathways, particularly in fungi. While a few other terms (nitrate assimilation, transcription, antibiotic response) appear, they are less central to the dominant pattern. Confidence: Medium.","confidence":"","size":20,"edges":102,"triangles":292,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006675","count":4},{"id":"GO:0006636","count":4},{"id":"GO:0001949","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0000001","count":4}]},{"hash":"1064124116148647430","title":"Cofactor and vitamin biosynthesis","description":"The cluster shows multiple, strongly represented biosynthetic processes for vitamins and cofactors (biotin, cobalamin, protoporphyrinogen IX) along with oxaloacetate metabolism, pointing to a shared theme of production of essential cofactors and central carbon metabolism.","confidence":"High","size":20,"edges":152,"triangles":642,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006107","count":10},{"id":"GO:0055114","count":7},{"id":"GO:0019878","count":7},{"id":"GO:0009236","count":6},{"id":"GO:0019518","count":6}]},{"hash":"1653759026664996480","title":"RNA processing and ribosome biogenesis","description":"The proteins are enriched for spliceosome-mediated mRNA splicing and its regulation, multiple rRNA maturation steps, ribosomal subunit biogenesis, and translation initiation/reinitiation, with chromatin remodeling. This points to a coherent module of RNA processing and ribosome assembly, with a link to transcriptional control.","confidence":"Medium","size":20,"edges":17,"triangles":3,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3}]},{"hash":"1766860548526921789","title":"Embryonic Development and Cell Signaling","description":"Based on the prominence of GO terms related to multicellular organism development, skin development, and neural tube closure, combined with signaling-related terms (positive regulation of GTPase activity and kinase activity) and cell proliferation processes, this cluster appears to represent genes involved in embryogenesis and associated signaling networks. While there are additional miscellaneous terms like mRNA transport and hypoxia response, the developmental and signaling themes dominate.","confidence":"High","size":20,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0043547","count":6},{"id":"GO:0071456","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0031954","count":6}]},{"hash":"433631234215490103","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":65,"triangles":52,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0090502","count":2}]},{"hash":"887297403702771316","title":"Ribosome biogenesis and rRNA maturation","description":"The top GO terms are dominated by ribosome biogenesis, maturation of SSU/LSU rRNA (including 5.8S), assembly of large-subunit preribosomes, and related translation initiation/reinitiation steps. This indicates the cluster centers on ribosome assembly and rRNA processing rather than other cellular processes, justifying this label.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0042273","count":4}]},{"hash":"2244219958068324637","title":"Developmental transcriptional regulation and splicing","description":"This cluster centers on transcriptional control and mRNA processing (DNA-templated transcription, regulation of transcription, and spliceosome-mediated splicing) with links to developmental processes (brain and male gonad development). While there are additional signals (ubiquitination, apoptosis, antiviral defense), the dominant terms point to regulation of gene expression in development, making this a cohesive label. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0034316","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0006351","count":2}]},{"hash":"449112318459183885","title":"Cell Cycle Progression and Centrosome Dynamics","description":"The dominant GO terms describe DNA replication, transcription, and centrosome-associated cell cycle steps (centrosome cycle, mitotic centrosome separation, nuclear DNA replication). This points to a cohesive cluster of proteins involved in cell cycle control and centrosome dynamics. Some terms also touch on development and extracellular matrix remodeling (cranial skeleton morphogenesis, hyaluronan metabolism, integrin signaling), suggesting these proteins may coordinate proliferation with morphogenesis. Overall, the cluster centers on cell cycle progression with ancillary developmental/ECM roles.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0006351","count":9},{"id":"GO:0007098","count":7},{"id":"GO:0010571","count":7},{"id":"GO:0048701","count":7}]},{"hash":"1155841422597752912","title":"Central carbon metabolism and energy production","description":"This cluster centers on core metabolic pathways that generate and channel carbon through glycolysis, the pyruvate-to-acetyl-CoA step, and the TCA cycle, with gluconeogenesis and malonyl-CoA biosynthesis also represented. The co-occurrence of these terms, along with protein quality control and stress response to sucrose starvation, suggests a set of proteins involved in energy metabolism and maintenance under nutrient limitation.","confidence":"High","size":20,"edges":167,"triangles":783,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0006515","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0033512","count":3}]},{"hash":"938739493408328233","title":"Oocyte pole plasm mRNA localization and polarization","description":"Most of the top GO terms center on pole plasm, oskar mRNA localization, and pole plasm protein localization, plus oocyte microtubule cytoskeleton polarization, which together point to functions in mRNA localization and cytoskeletal organization during oogenesis. Additional terms about mRNA processing and nonsense-mediated decay align with RNA metabolism processes that accompany RNA localization. Some plant-related terms appear as noise but do not override the core oocyte/pole plasm theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045451","count":3},{"id":"GO:0000184","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0007318","count":3},{"id":"GO:0008103","count":3}]},{"hash":"614376617924560674","title":"mRNA processing and translation in neural development","description":"This cluster\u2019s top GO terms emphasize translation initiation and reinitiation together with mRNA splicing and polyadenylation, pointing to post-transcriptional gene regulation. The neural development terms (forebrain development, neural tube closure) suggest a neural-context role, while TGF-beta signaling and apoptotic regulation indicate broader regulatory functions. Altogether, the proteins likely coordinate RNA processing/translation with neurodevelopmental signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":10},{"id":"GO:0001731","count":10},{"id":"GO:0007584","count":7},{"id":"GO:0006378","count":7},{"id":"GO:0045292","count":7}]},{"hash":"1777438773694573812","title":"Virus entry, uncoating, and genome activation","description":"This cluster prominently includes GO terms related to viral entry and replication processes, such as uncoating of virus, fusion of the viral membrane with the host membrane, and host-mediated activation of viral genome replication. While a few terms are unrelated or obsolete (e.g., sepal formation, some regulatory/UV terms), the core theme is viral infection and host\u2013virus interactions, justifying a focused label around entry and genome activation.","confidence":"Medium","size":20,"edges":12,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0006406","count":2},{"id":"GO:0019061","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0048453","count":2}]},{"hash":"731126461835351713","title":"Vacuolar acidification and ion transport","description":"This cluster is dominated by vacuolar-related processes and ion transport: vacuolar acidification, vacuole organization, protein targeting to vacuole, and proton/sodium transmembrane transport, including proton motive force-driven ATP synthesis. The co-occurrence of these GO terms suggests a cohesive role in maintaining vacuolar pH and ion homeostasis and related organelle targeting.","confidence":"High","size":20,"edges":132,"triangles":471,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":4},{"id":"GO:0006878","count":3},{"id":"GO:0006626","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0015991","count":2}]},{"hash":"1113394290866868539","title":"Metal Ion Detoxification and Transport","description":"This cluster shows enrichment for metal ion handling: mercury ion detoxification and response, copper and zinc ion transport/export, and related detox/oxidative stress processes, suggesting a cohesive role in metal homeostasis. The translation-related terms appear secondary, likely reflecting common cellular components rather than a core function.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0015694","count":3},{"id":"GO:0015680","count":3},{"id":"GO:0070574","count":3}]},{"hash":"1518846122710932242","title":"Chromatin remodeling and immune signaling","description":"The terms show chromatin-related processes (nucleosome assembly, histone exchange) and deubiquitination, suggesting epigenetic regulation, alongside immune-related terms (mucosal immune response, CD40 signaling regulation, IL-1\u03b2 production, germinal center regulation). This points to proteins that bridge chromatin dynamics with immune signaling pathways. The lack of edges may reflect annotation gaps or multi-function proteins. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043486","count":1},{"id":"GO:0010847","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0035523","count":1},{"id":"GO:0032691","count":1}]},{"hash":"398562668650761482","title":"Viral translation initiation and reinitiation","description":"Based on the strongest GO signals, this cluster centers on translation initiation and viral translation processes, including IRES-dependent initiation and translation preinitiation complex formation, as well as translation reinitiation and viral termination-reinitiation. While other terms touch on ubiquitination, interferon response, and development, the concentration of translation-related terms supports labeling around viral translation control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0070979","count":4},{"id":"GO:0046661","count":4},{"id":"GO:0007091","count":4},{"id":"GO:0071357","count":4},{"id":"GO:0006463","count":4}]},{"hash":"865812165344939916","title":"DNA damage response and replication","description":"The top GO terms center on DNA repair and replication: TLS (both error-prone and error-free), nucleotide-excision repair, DNA replication, and responses to UV-C and X-ray, with additional telomere-related context. This suggests a cluster of proteins involved in maintaining genome integrity during replication and in repair of DNA damage.","confidence":"High","size":20,"edges":23,"triangles":12,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042276","count":3},{"id":"GO:0006297","count":3},{"id":"GO:0071897","count":3},{"id":"GO:0071494","count":2},{"id":"GO:0070987","count":2}]},{"hash":"164019064036998875","title":"Apoptosis and Signaling Pathways","description":"Proteins in this cluster are enriched for apoptotic processes and several receptor-mediated signaling pathways (HIPPO, ephrin receptor, neurotrophin TRK receptor, and peptide hormone signaling), suggesting a role in coordinating apoptosis with extracellular signals. Other terms like cell wall organization and glycogen biosynthesis are less central but may reflect broader regulatory or housekeeping functions; the core theme appears to be apoptosis coupled with signaling. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0046677","count":2}]},{"hash":"353373734033321125","title":"DNA Replication and Cell Cycle Regulation","description":"Most terms point to DNA replication and cell-cycle processes, including replication initiation complexes, S-phase progression, and DNA damage checkpoints. While a couple of obsolete terms appear, the core theme is replication initiation and cell-cycle control.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031938","count":1},{"id":"GO:0032508","count":1},{"id":"GO:1900087","count":1},{"id":"GO:0006267","count":1},{"id":"GO:0006277","count":1}]},{"hash":"2090331695306448625","title":"Steroid Hormone Biosynthesis and Lipid Metabolism","description":"This cluster shows strong representation of GO terms for steroid biosynthesis and metabolism (cortisol, testosterone, brassinosteroid), hormone-related processing (retinoic acid, vitamin D response), and lipid oxidation/xenobiotic processing, pointing to a cohesive theme around steroid/hormone production and lipid metabolism with related detoxification pathways.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":15},{"id":"GO:0071603","count":15},{"id":"GO:0034651","count":15},{"id":"GO:0070989","count":15},{"id":"GO:0042738","count":15}]},{"hash":"390647767752061288","title":"Floral Meristem and Bract Development","description":"The GO terms point to floral-specific processes such as floral meristem growth and bract development, coupled with multicellular organism development and transcriptional regulation. The presence of ethylene- and ABA-activated signaling pathways suggests hormone-mediated control of development, aligning with floral organ specification and associated surface wax-related processes. Overall, the cluster appears to represent floral organ development governed by transcriptional programs and hormone signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0015074","count":2},{"id":"GO:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010432","count":2}]},{"hash":"1700709161843369907","title":"Developmental transcriptional regulation and calcium signaling","description":"This cluster is rich in RNA polymerase II\u2013driven transcription terms, including DNA-templated transcription and general transcription by Pol II, along with calcium ion\u2013related signaling and several development-related processes (dorsal identity, imaginal disc fusion, osteoblast differentiation, and TGF-beta2 production). The recurring theme is transcriptional control linked to developmental signaling, with a few outliers (NK cell cytotoxicity) that may reflect broader functional associations. Overall, the label emphasizes the core functions captured by the top GO terms.","confidence":"Medium","size":20,"edges":187,"triangles":1088,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0071277","count":13},{"id":"GO:0006351","count":11},{"id":"GO:0010691","count":9},{"id":"GO:0032915","count":9}]},{"hash":"494962639293955504","title":"Mitochondrial Transporters and Metabolic Regulation","description":"TheTopGO terms are dominated by transport across membranes, especially involving mitochondria (hems transport, manganese ion transport, mitochondrial ATP transmembrane transport, coenzyme A transmembrane transport, thiosulfate transport). There are also terms related to mitochondrial changes in apoptosis and regulation of necroptotic processes, plus insulin/IGF-stimulated metabolic signaling. Together these suggest a cluster of mitochondrial transport functions tied to energy metabolism and apoptotic regulation, hence the label.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":10},{"id":"GO:0006828","count":9},{"id":"GO:0061179","count":9},{"id":"GO:1990544","count":9},{"id":"GO:0090152","count":9}]},{"hash":"947821710787768995","title":"Floral development and hormone signaling","description":"This set centers on plant development\u2014floral meristems, bracts, and epidermal differentiation\u2014tied to hormone signaling (ethylene, ABA) and transcriptional regulation. Even without edges, the recurring GO terms point to a coherent role in floral organogenesis controlled by transcription and hormones.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:1901407","count":3},{"id":"GO:0010451","count":3},{"id":"GO:0009873","count":3},{"id":"GO:0006351","count":3}]},{"hash":"605834119520676929","title":"Transcriptional Regulation in Development and Immune Signaling","description":"This cluster centers on DNA-templated transcription and its regulation, with links to multicellular development, and immune signaling pathways (MyD88-independent TLR signaling and cytokine signaling). The presence of abscisic acid-related signaling also suggests broader stress-response signaling involvement, indicating proteins that coordinate gene expression during development and immune responses.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006355","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0009738","count":5},{"id":"GO:0009620","count":4}]},{"hash":"344441048052791296","title":"Ubiquitin-Dependent Protein Degradation","description":"Most top terms point to ubiquitin-mediated proteolysis (ERAD, autoubiquitination, K48-linked ubiquitination, general protein catabolic process). A few terms involve related regulatory processes (peroxisomal protein import, Wnt receptor turnover, dosage compensation and growth regulation), which are connected to ubiquitin signaling. Together these terms suggest a cluster centered on ubiquitin-driven protein turnover and its regulatory roles.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":15},{"id":"GO:0051865","count":15},{"id":"GO:0042787","count":15},{"id":"GO:0016558","count":14},{"id":"GO:1900095","count":14}]},{"hash":"1309658105015849105","title":"Lipid and Steroid Biosynthesis","description":"Top GO terms converge on lipid-derived metabolite production and steroid-related pathways, including fatty acid elongation, mycolic acid biosynthesis, polyhydroxybutyrate biosynthesis, retinol metabolism, and androgen/testosterone biosynthesis, alongside transcriptional regulation. This points to a cohesive theme of lipid metabolism and steroid biosynthesis across diverse organisms, with a general transcription regulation component. ","confidence":"High","size":20,"edges":75,"triangles":143,"max_degree":11,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0042619","count":13},{"id":"GO:0045150","count":12},{"id":"GO:0042572","count":12},{"id":"GO:0061370","count":12}]},{"hash":"788686537925715230","title":"Diverse solute membrane transporters","description":"The top GO terms indicate transmembrane transport for a wide variety of substrates, including vitamins, xenobiotics, ions, and sugars. This suggests the proteins function collectively as membrane transporters with broad substrate specificity rather than a single, narrow pathway.","confidence":"High","size":20,"edges":73,"triangles":114,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":20},{"id":"GO:0006855","count":20},{"id":"GO:0042891","count":19},{"id":"GO:0042908","count":13},{"id":"GO:0071805","count":13}]},{"hash":"614859809293374853","title":"mRNA Processing and Translation Regulation","description":"This cluster centers on post-transcriptional control: mRNA processing and splicing regulation, polyadenylation, stability and modification of mRNA, and the initiation of translation (including IRES-dependent initiation and eIF4F complex assembly). The convergence of these GO terms suggests a coordinated module governing mRNA life cycle from processing to translation, with potential relevance to development (e.g., blastocyst formation). ","confidence":"High","size":20,"edges":172,"triangles":890,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0000381","count":5},{"id":"GO:0010610","count":5},{"id":"GO:0016556","count":4},{"id":"GO:0048255","count":4}]},{"hash":"1476684462648217899","title":"Bacterial antibiotic and lipid biosynthesis","description":"The cluster shows a strong enrichment for antibiotic biosynthesis and related responses (GO:0017000, GO:0046677), along with lipid/cell envelope and polymer biosynthesis terms (GO:0071768 mycolic acid biosynthetic process, GO:0042619 PHB biosynthetic process). This points to a coherent theme of bacterial secondary metabolism and lipid biosynthesis, including cell-wall\u2013associated processes. Some terms like retinol/testosterone metabolism may be annotations noise, but the core signal supports a bacterial antibiotic/lipid biosynthesis program.","confidence":"High","size":20,"edges":7,"triangles":2,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":18},{"id":"GO:0042619","count":11},{"id":"GO:0017000","count":9},{"id":"GO:0046677","count":7},{"id":"GO:0045150","count":6}]},{"hash":"1419005482201991011","title":"Unknown","description":"The top GO terms span oxidative stress response, RNA processing (snoRNP assembly), photoreceptor localization, protein modification, interferon signaling, immune regulation, and cell division, with no single shared function or pathway uniting them. The cluster has no edges, suggesting the proteins do not participate in a coherent common process, so a single representative function cannot be inferred.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":3},{"id":"GO:1903071","count":2},{"id":"GO:0000492","count":2},{"id":"GO:1903546","count":2},{"id":"GO:0006478","count":2}]},{"hash":"328435572003358737","title":"Nucleic acid repair and tRNA modification","description":"This cluster centers on nucleic acid maintenance and RNA processing/modification: DNA alkylation repair, general DNA repair, RNA repair, tRNA wobble uridine modification, mRNA processing, and regulation of translational initiation by tRNA modification. There is also a hint of programmed cell death regulation, which can connect to stress responses affecting nucleic acid integrity. Overall, the common theme is maintenance and processing of nucleic acids and the translation apparatus, rather than a single isolated pathway. ","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006307","count":1},{"id":"GO:0035553","count":1},{"id":"GO:0012501","count":1},{"id":"GO:0035552","count":1},{"id":"GO:0006397","count":1}]},{"hash":"1671525618519587982","title":"Steroid and lipid metabolism with xenobiotic detox","description":"The top GO terms cluster around steroid hormone biosynthesis (cortisol, testosterone, brassinosteroids), lipid-derived signaling (retinoic acid, vitamin D), and lipid oxidation, plus xenobiotic catabolic processes. This points to a shared function in processing lipid-derived molecules and detoxifying foreign compounds. Some terms about tissue context (mammary gland development, endothelial adhesion) may reflect expression environment rather than core function. The plant-specific brassinosteroid term introduces a cross-kingdom note, but the overall theme remains lipid/hormone metabolism with detox pathways.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":12},{"id":"GO:0071603","count":12},{"id":"GO:0034651","count":12},{"id":"GO:0070989","count":12},{"id":"GO:0042738","count":12}]},{"hash":"1187068756543950722","title":"Unknown","description":"The top GO terms are highly diverse (vascular remodeling, immune regulation, developmental cell fate, protein folding stress responses, eye and sperm differentiation, EGFR ligand maturation, ER-associated proteolysis, chloroplast-related processes) and there are no interactions among the 20 proteins (Edges 0). This lack of a cohesive shared function makes it inappropriate to assign a specific functional label, so Unknown is the best representative name.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097498","count":2},{"id":"GO:0032815","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0034620","count":1},{"id":"GO:0042676","count":1}]},{"hash":"1141064368694854712","title":"Regulation of Plant Growth and Cell Wall Biosynthesis","description":"The GO terms cluster around regulatory roles in plant biology (chlorophyll biosynthesis, seed growth, lignin biosynthesis, secondary cell wall biogenesis, root meristem growth, leaf senescence) with multiple entries specifying positive or negative regulation. Additional terms on chromatin and RNA localization point to broader gene-regulation layers, but the common thread remains regulation of plant growth and cell-wall related processes.","confidence":"High","size":20,"edges":53,"triangles":34,"max_degree":13,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010380","count":6},{"id":"GO:0080113","count":6},{"id":"GO:1901430","count":6},{"id":"GO:1901347","count":6},{"id":"GO:0010082","count":6}]},{"hash":"357501014554857833","title":"Mitochondrial and Chloroplast Protein Import","description":"The top GO terms cluster around import into mitochondrial compartments (inner membrane, matrix) and chloroplast stroma, indicating proteins involved in organelle targeting/import pathways. This suggests the cluster represents components or substrates of organelle protein import rather than other processes; a few unrelated terms appear as noise but do not redefine the main theme.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":7},{"id":"GO:0045037","count":7},{"id":"GO:0000002","count":7},{"id":"GO:0032094","count":7},{"id":"GO:0030150","count":7}]},{"hash":"1103284495762130379","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":3},{"id":"GO:0009734","count":3},{"id":"GO:0009926","count":3},{"id":"GO:0009733","count":3},{"id":"GO:0000494","count":1}]},{"hash":"924753622020652990","title":"Nucleobase and nucleoside transport","description":"The proteins in this cluster are dominated by GO terms for transport of nucleobases and nucleosides across membranes (e.g., adenine, guanine, hypoxanthine, xanthine, uracil, urate), indicating a shared role in importing purines/pyrimidines. There are a few outliers related to ammonium and aromatic acid transport, but the core pattern points to nucleobase/nucleoside transmembrane transport.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070634","count":2},{"id":"GO:1903825","count":1},{"id":"GO:0035344","count":1},{"id":"GO:0098721","count":1},{"id":"GO:0042906","count":1}]},{"hash":"125456925582846165","title":"Ubiquitin-regulated proteolysis and transcription control","description":"Many terms point to ubiquitin-related processes, including deubiquitination (K29-linked), regulation of ubiquitin ligase activity, and ubiquitin-dependent protein catabolic process, plus ERAD-associated unfolded protein handling. There are also hints of transcription regulation (DNA-templated transcription) and a ripoptosome/necroptosis connection. Together these terms suggest a theme of ubiquitin-mediated protein turnover influencing transcription and cell fate.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010226","count":1},{"id":"GO:0035523","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0006355","count":1},{"id":"GO:1901026","count":1}]},{"hash":"4619741649402862","title":"Oocyte maturation and meiotic spindle assembly","description":"The top GO terms cluster around oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, with concurrent SCF\u2011dependent ubiquitin\u2011proteasome\u2013mediated protein catabolism that drives meiotic progression. This combination strongly points to meiotic processes in oocytes and the corresponding spindle/microtubule dynamics, with a few developmental terms appearing secondary to this primary theme.","confidence":"High","size":20,"edges":20,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":16},{"id":"GO:0001556","count":15},{"id":"GO:0046785","count":15},{"id":"GO:0006516","count":15},{"id":"GO:0007057","count":15}]},{"hash":"1416903952378249956","title":"Neurodevelopment and glial apoptosis","description":"The top GO terms are dominated by nervous system development (forebrain development; nervous system development) and glial cell apoptotic process, suggesting a neurodevelopmental focus with glial cell turnover. The other terms (melanization defense response, salivary gland histolysis, L-methionine cycle, TGF-beta stimulus) appear less central and may reflect annotation noise or diverse, non-central functions among cluster members.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":18},{"id":"GO:0010659","count":18},{"id":"GO:0035006","count":18},{"id":"GO:0033353","count":18},{"id":"GO:0071560","count":18}]},{"hash":"1759791641763957172","title":"Ubiquitin-Proteasome Mediated Protein Degradation","description":"Top GO terms cluster around ubiquitin-dependent protein catabolic processes (including autoubiquitination, K48- and K6-linked ubiquitination, and SCF-dependent proteasomal degradation) and histone catabolism, indicating a cohesive function in ubiquitin-proteasome\u2013mediated protein turnover.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051865","count":8},{"id":"GO:0036205","count":7},{"id":"GO:0070936","count":7},{"id":"GO:1903265","count":7}]},{"hash":"679937157590605030","title":"Ubiquitin-Dependent Proteolysis and NF-\u03baB/JNK Signaling","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes and autoubiquitination, plus TNF-mediated signaling, NF-\u03baB-inducing kinase activation, and JNK cascade regulation. This points to proteins involved in ubiquitin-mediated protein turnover that modulate key inflammatory signaling pathways like NF-\u03baB and JNK, rather than a single specific process. Some histone-related terms are obsolete, but the core pattern is ubiquitin-regulated signaling and degradation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0051865","count":6},{"id":"GO:1901253","count":5},{"id":"GO:2000620","count":5},{"id":"GO:0033209","count":5}]},{"hash":"123889269825025485","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017004","count":2},{"id":"GO:0006384","count":1},{"id":"GO:0006383","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0006366","count":1}]},{"hash":"1478532638416175687","title":"Unknown","description":"The top GO terms are very heterogeneous, spanning transcriptional regulation (DNA-templated transcription and its regulation), eye development/visual perception, plant auxin signaling, hormonal secretion, membrane transport, metal ion response, and other diverse processes. With no dominant shared function or pathway, there isn't a coherent biological theme tying these proteins together, so the cluster is best labeled Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0002088","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0009734","count":2}]},{"hash":"650472628533986141","title":"Brain Heparan Sulfate Proteoglycan Biosynthesis","description":"The top GO terms show strong enrichment for heparan sulfate and heparin proteoglycan biosynthesis, which points to a shared role in glycosaminoglycan production and extracellular matrix formation, with brain development supporting a neural context. While some metabolic terms are present, they are less central to the cluster than the proteoglycan biosynthesis signals.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030210","count":3},{"id":"GO:0015012","count":3},{"id":"GO:0007420","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042403","count":2}]},{"hash":"130609112321304771","title":"Cytokinesis Machinery and Membrane Remodeling","description":"Top GO terms point to cytokinesis and cytoskeleton/membrane dynamics, with notable mentions of mitotic contractile ring actin assembly, membrane addition at cytokinesis, and membrane repair, suggesting a cohesive role in cell division and membrane remodeling rather than transcriptional regulation alone. Some transcription-related terms appear but are less central to the dominant 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:0006355","count":2},{"id":"GO:0017004","count":1},{"id":"GO:0006930","count":1},{"id":"GO:0043087","count":1}]},{"hash":"1879940431843999606","title":"Glycosylation and carbohydrate metabolism","description":"The top GO terms cluster around carbohydrate processing and glycosylation-related processes: carbohydrate phosphorylation, glycogen biosynthesis, and UDP-D-xylose metabolism, plus cell wall organization and cell adhesion molecule production, all of which tie into glycan assembly and glycoprotein secretion. Plant-specific terms like root hair development and general extracellular matrix remodeling further support a theme centered on carbohydrate metabolism and glycosylation that underpins cell walls and secreted/glycosylated proteins, with some broader terms reflecting mucosal glycoprotein contexts. Confidence is medium because the cluster mixes plant- and animal-related glycan processes, but the carbohydrate/glycosylation thread remains the strongest unifier.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0042403","count":2}]},{"hash":"1623631575857870231","title":"Angiogenesis and tissue remodeling","description":"GO terms emphasize vascular remodeling and healing (vascular wound healing, VEGF production, blood coagulation) plus ECM remodeling (cell-matrix adhesion, proteoglycan catabolism) and development of skin and bone (hair follicles, osteoblasts). Together these suggest a cluster involved in angiogenesis and tissue repair/regeneration. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0030194","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0010575","count":2},{"id":"GO:0007160","count":2}]},{"hash":"1322789967377065521","title":"Unknown","description":"The GO terms are heterogeneous, spanning xenobiotic transport, redox reactions, transcription, multiple metabolic/biosynthetic processes (glutamine, GDP-mannose, rhamnose, lignans), LPS core biosynthesis, and even hair follicle development, with no clear shared pathway or function. The lack of edges/triangles supports the idea that these proteins do not form a cohesive functional module, so a single interpretable label is not warranted.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006855","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006541","count":2},{"id":"GO:0009244","count":2}]},{"hash":"1542829663445750230","title":"Unknown","description":"The GO terms are highly heterogeneous, covering neural development (spinal cord development, neural tube closure), growth, ribosome biogenesis, DNA integration, lipid transport, immune defense, and mechanotransduction, with no single clear shared function linking the majority of proteins. Because there isn\u2019t a coherent theme that ties the terms together, a specific functional label cannot be confidently assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0015074","count":3}]},{"hash":"945419937456433638","title":"Bacterial metabolite biosynthesis and RNA modification","description":"The top terms cluster around biosynthetic processes for diverse bacterial metabolites (lipopolysaccharide, antibiotics, L-lysine, biotin, serine) as well as RNA modification activities (tRNA and rRNA pseudouridine synthesis). While there are some outliers (zinc transport, stilbene catabolism), the dominant theme is microbial biosynthesis combined with RNA maturation/modification. ","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009244","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009089","count":2},{"id":"GO:0009102","count":2}]},{"hash":"33401797441737773","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to translation and ribosome function (translation, formation of translation preinitiation complex, ribosome biogenesis), plus RNA modification steps (pseudouridine synthesis in snRNA, tRNA, mRNA) which support proper translation. The presence of IRES-dependent translational initiation and related processes further ties the proteins to the translational machinery. While developmental terms like oogenesis appear, the core theme is the assembly and function of the protein synthesis apparatus and its RNA modifications.","confidence":"High","size":19,"edges":75,"triangles":141,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":3},{"id":"GO:0048477","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0030154","count":2}]},{"hash":"152584863150604599","title":"Organelle RNA processing and editing","description":"The terms are dominated by RNA metabolism in organelles: mitochondrial and chloroplast/plastid RNA processing and modification, including RNA editing (cytidine to uridine) and snoRNP assembly. Plastid transcription and polycistronic RNA processing further support a shared role in organellar gene expression. The seed dormancy term is a general plant-development note and does not override the core organellar RNA processing theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000492","count":2},{"id":"GO:0090615","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:1905639","count":2}]},{"hash":"933146406262429592","title":"SNARE-mediated vesicle trafficking and synaptic exocytosis","description":"The dominant GO terms describe ER-to-Golgi transport, Golgi ribbon formation, SNARE complex assembly, vesicle fusion with the Golgi, and exocytic insertion of postsynaptic receptors, all core to secretory and synaptic vesicle pathways. A few cell-cycle/adhesion terms appear but do not define the cluster.","confidence":"High","size":19,"edges":19,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":4},{"id":"GO:0048280","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0090529","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1852238285291016359","title":"Proteostasis and mitochondrial function","description":"This cluster centers on cellular protein quality control and trafficking (ubiquitin-dependent ERAD, proteasome assembly, chaperone-related refolding, Golgi retention) and also includes mitochondrial-related processes (inner membrane protein insertion, mtDNA replication regulation, and oxidative phosphorylation). The mix suggests a theme of maintaining protein homeostasis while supporting mitochondrial energy metabolism.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":11},{"id":"GO:0006260","count":10},{"id":"GO:0006406","count":9},{"id":"GO:0051301","count":9},{"id":"GO:0032979","count":8}]},{"hash":"611291819549150698","title":"Translation machinery and proteostasis","description":"The strongest GO term is translation (GO:0006412), with many proteins likely ribosomal or translation factors, indicating core involvement in protein synthesis. Additional terms point to regulation of degradation and stress responses (proteasomal degradation, autophagy, SUMOylation, ER stress\u2013induced apoptotic signaling) and mitochondrial dynamics, suggesting this cluster coordinates protein production with quality control and stress adaptation. Therefore, the label captures both translation and proteostasis functions.","confidence":"Medium","size":19,"edges":117,"triangles":474,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:1903071","count":4},{"id":"GO:0010216","count":4},{"id":"GO:0045648","count":4},{"id":"GO:1901097","count":4}]},{"hash":"1831615205191233090","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0016554","count":3},{"id":"GO:1905639","count":3},{"id":"GO:0090617","count":3}]},{"hash":"178621432506069966","title":"Metal ion transport and mercury detoxification","description":"The proteins cluster around transport and homeostasis of metal ions, with GO terms for mercury, copper, zinc, and cadmium transport, mercury detoxification, and copper homeostasis, indicating a cohesive theme of metal ion handling and detoxification. A single outlier term for nitrate assimilation does not override the dominant pattern. This label accurately reflects the cluster\u2019s apparent function.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":4},{"id":"GO:0015694","count":3},{"id":"GO:0015680","count":3},{"id":"GO:0070574","count":3},{"id":"GO:0050787","count":3}]},{"hash":"1172193894517485366","title":"DNA-Templated Transcription Regulation Cluster","description":"The strongest terms are DNA-templated transcription and regulation of transcription, indicating a transcriptional regulatory role for the proteins. Additional signals such as insulin signaling and vascular development suggest these factors participate in developmental signaling contexts; some terms seem unrelated (noise) but don't override the core transcription theme.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0060716","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0009736","count":2}]},{"hash":"14359084820855050","title":"RNA Processing and Translation Initiation","description":"This cluster centers on RNA metabolism and the control of translation. Key terms include translation reinitiation and preinitiation complex formation, plus IRES-dependent translation, indicating translation initiation control. Splicing, mRNA modification, and stabilization appear alongside transcription-related terms, suggesting a broader RNA processing and maturation role that feeds into translation.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0006378","count":6},{"id":"GO:0045292","count":5},{"id":"GO:0000398","count":4}]},{"hash":"68249096602546772","title":"Auxin-regulated plant development and transcription","description":"The cluster is enriched for plant-development terms (meristem development, somatic embryogenesis, fruit dehiscence) and hormone signaling (auxin-activated signaling, response to hormone), along with core transcriptional processes (DNA replication, DNA-templated transcription, regulation of transcription) and dephosphorylation. This suggests proteins involved in hormone-driven developmental regulation and gene expression in plants.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0005979","count":3},{"id":"GO:0048507","count":2}]},{"hash":"1400912216497421898","title":"Chloroplast/mitochondrial RNA processing and editing","description":"Most of the top GO terms point to RNA metabolism and post-transcriptional processing in organelles, especially chloroplasts and mitochondria (chloroplast RNA processing, plastid transcription, polycistronic mRNA processing, chloroplast/mitochondrial RNA modification, RNA editing). A few terms about general metabolism appear as noise but are not central to the dominant pattern. Thus the cluster is best described as proteins involved in organellar RNA processing and editing. ","confidence":"High","size":19,"edges":121,"triangles":342,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:1905639","count":2}]},{"hash":"285998099464086606","title":"Ergosterol biosynthesis and lipid metabolism","description":"These proteins are dominated by sterol and lipid biosynthesis terms (ergosterol biosynthetic process, cholesterol biosynthetic via lathosterol, various sterol oxidations, ether lipid metabolism), pointing to a sterol/lipid metabolism cluster. A few outlier terms exist, but the overall theme is sterol production.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046485","count":3},{"id":"GO:0006633","count":3},{"id":"GO:0035754","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0001949","count":3}]},{"hash":"1489276756509237522","title":"RNA processing and editing","description":"Based on the GO terms, several entries cluster around RNA maturation and editing, with mitochondrial mRNA processing, RNA modification, and cytidine-to-uridine editing suggesting a coherent theme. Other terms appear less connected (endocytosis, digestion, cardiac signaling), likely reflecting noise or multifunctional proteins. Overall, the strongest shared function among the terms is RNA processing/editing.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048261","count":2},{"id":"GO:0006919","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0007586","count":2},{"id":"GO:0007205","count":2}]},{"hash":"1363830671072449700","title":"Mercury Detoxification and Metal Ion Transport","description":"The GO terms point to mercury-specific processes (transport, detoxification, response) and to broader metal ion transport/homeostasis (copper, zinc, cadmium, iron), suggesting a cohesive cluster of proteins involved in metal handling and detoxification, with a stress/oxidative component.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015694","count":2},{"id":"GO:0015680","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0050787","count":2},{"id":"GO:0046689","count":2}]},{"hash":"320813531118956439","title":"Floral meristem development and transcription regulation","description":"This cluster is dominated by plant-specific developmental terms tied to floral meristem identity, determinacy, ovule development, and floral organ specification, along with general transcription by RNA polymerase II (including negative regulation). Together, these terms point to a theme of transcriptional control guiding floral development in plants, with some cross-kingdom developmental terms appearing as noise. ","confidence":"Medium","size":19,"edges":167,"triangles":904,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060021","count":7},{"id":"GO:0090009","count":7},{"id":"GO:0006366","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0071277","count":5}]},{"hash":"2229224626064341676","title":"Redox-regulated calcium signaling in muscle","description":"This cluster centers on redox-related processes (glutathione metabolism, cellular oxidant detoxification, protein glutathionylation) and regulation of ryanodine receptor calcium-release channels, pointing to redox control of calcium signaling linked to muscle contraction; prostaglandin biosynthesis and starvation response may reflect metabolic stress context.","confidence":"High","size":19,"edges":135,"triangles":521,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":15},{"id":"GO:0014810","count":11},{"id":"GO:0045454","count":11},{"id":"GO:0042594","count":11},{"id":"GO:0006749","count":11}]},{"hash":"1731453615063994451","title":"Neuronal morphogenesis and signaling","description":"This cluster is enriched in neuronal-related terms such as dendrite morphogenesis, visual perception, and cell migration, with potassium ion transport also aligning with neuronal signaling; transcription and DNA replication-related terms may reflect broader cellular processes in developing or proliferating neural contexts.","confidence":"Medium","size":19,"edges":166,"triangles":888,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":14},{"id":"GO:0000278","count":9},{"id":"GO:0007601","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0043552","count":8}]},{"hash":"1016345350907177576","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"The top GO terms point to multiple plant hormone pathways (gibberellin, ethylene, auxin) and processes related to fruit ripening, along with biosynthesis of related secondary metabolites and stress-associated programmed cell death. Although a stray term like penicillin biosynthesis appears, the dominant theme centers on hormone metabolism and ripening. This cluster likely groups proteins involved in regulating or executing hormone-driven fruit maturation rather than a single enzymatic pathway.","confidence":"High","size":19,"edges":142,"triangles":587,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":17},{"id":"GO:0009835","count":16},{"id":"GO:0042318","count":16},{"id":"GO:1902835","count":16},{"id":"GO:0009686","count":16}]},{"hash":"1030691842892121145","title":"Developmental growth and morphogenesis","description":"Dominant theme is tissue development and morphogenesis, with supporting signals for cell growth, proliferation, cytoskeletal remodeling, and nucleus transport; while some terms touch genome maintenance, the overall cluster centers on developmental growth across multiple organs.","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0051211","count":17},{"id":"GO:0060769","count":17},{"id":"GO:0070602","count":17},{"id":"GO:0006607","count":17},{"id":"GO:0060492","count":17}]},{"hash":"470909249424756194","title":"Neural development and dendrite morphogenesis","description":"The cluster is strongly enriched for nervous system\u2013related terms, including nervous system development, neural tube closure, forebrain development, and dendrite morphogenesis, pointing to a cohesive role in neurodevelopment and neuronal connectivity. While a couple of terms (including some obsolete ones) are less directly related, the dominant theme centers on neural development and dendrite formation, suggesting these proteins work together in neural tissue patterning and neuronal morphogenesis.","confidence":"High","size":19,"edges":57,"triangles":30,"max_degree":10,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007399","count":14},{"id":"GO:0001843","count":14},{"id":"GO:0000160","count":14},{"id":"GO:0002921","count":14},{"id":"GO:0048813","count":14}]},{"hash":"1009142018539511469","title":"Post-transcriptional gene regulation (translation & RNA silencing)","description":"The top GO terms cluster around regulation of translation (including postsynaptic translation and cytoplasmic translation) and RNA silencing (miRNA-mediated), suggesting a shared theme of post-transcriptional control of gene expression. Additional terms touch on RNA genome interactions and cytoskeletal dynamics (filopodium assembly), which can be linked to localized translation and signaling, while an outlier plant ABA signaling term reflects cross-species annotation noise. Overall, the dominant signal is post-transcriptional regulation of gene expression.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0098908","count":1},{"id":"GO:0033129","count":1},{"id":"GO:1901254","count":1},{"id":"GO:0072711","count":1}]},{"hash":"309636606037331244","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0009873","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0000472","count":1},{"id":"GO:0000461","count":1}]},{"hash":"41651601346628657","title":"Plant hormone biosynthesis and fruit ripening","description":"The top GO terms show several plant hormone biosynthesis pathways (ethylene, gibberellin, auxin) and related processes such as fruit ripening, plus secondary metabolite biosynthesis (proanthocyanidin) and stress responses including hydrogen peroxide\u2013mediated programmed cell death. This points to a cohesive theme of hormone-driven maturation and associated metabolic and stress pathways in plants, even though one term (penicillin biosynthetic process) appears unrelated and may be an outlier. Overall, a cohesive label is plant hormone\u2013mediated ripening and metabolism.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0009835","count":8},{"id":"GO:0042318","count":8},{"id":"GO:1902835","count":8},{"id":"GO:0009686","count":8}]},{"hash":"1146396071171812388","title":"Lipid metabolism and signaling regulation","description":"The proteins show enrichment for lipid-related catabolic processes (triglyceride, monoacylglycerol, phosphatidylserine) and lipid signaling pathways (endocannabinoid signaling, vitamin D receptor signaling), suggesting a primary theme around lipid metabolism and lipid-mediated signaling. Additional terms like DNA-templated transcription and biofilm-related adhesion/tubulin regulation are present but less central, so the dominant interpretation is lipid metabolism and signaling regulation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070562","count":2},{"id":"GO:0019433","count":2},{"id":"GO:0006660","count":2},{"id":"GO:0010223","count":2},{"id":"GO:2000124","count":2}]},{"hash":"1734741935067709399","title":"Chitin-based cuticle development and molting","description":"Dominant GO terms cluster around chitin metabolism and cuticle biology (chitin catabolic process, chitin-based cuticle development, ecdysis), indicating a core theme of cuticle formation/remodeling and molting. Additional terms related to immune signaling and apoptosis may reflect stress or regulatory responses during these processes, but the primary signal is chitinous cuticle biology.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0006032","count":3},{"id":"GO:0040003","count":3},{"id":"GO:0071347","count":3}]},{"hash":"1957985731607370840","title":"Xylem and Phloem Development","description":"The terms point to plant vascular differentiation, with emphasis on xylem (protoxylem development, xylem vessel differentiation, secondary cell wall biogenesis) and phloem components (sieve element enucleation). The presence of transcription regulation terms supports a coordinated developmental program controlling these tissues, while related traits like fruit dehiscence and leaf senescence reflect broader plant development contexts. Overall, the cluster aligns with vascular tissue development and differentiation in plants.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0010047","count":4},{"id":"GO:1990110","count":3}]},{"hash":"1654744219679245306","title":"Pectin metabolism and pollen tube growth","description":"The top GO terms center on pollen tube growth and pectin-associated cell wall processes (mucilage pectin biosynthesis, pectin catabolic process, and cell wall modification), pointing to plant-specific cell wall remodeling and pectin dynamics as the core function. The other terms appear as noise or broader, non-overlapping processes, but the strongest signal is plant pollen tube\u2013related. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002091","count":2},{"id":"GO:0043086","count":1},{"id":"GO:0009860","count":1},{"id":"GO:0048358","count":1},{"id":"GO:0042545","count":1}]},{"hash":"1775760289017889358","title":"Mitochondrial RNA editing and mRNA modification","description":"This cluster is dominated by mitochondrial RNA processing functions, including cytidine-to-uridine editing and mRNA modification, with related roles in mitochondrial protein import and folding. Minor terms reference salt-stress response and spermatid development, but the core signal points to mitochondrial gene expression regulation.","confidence":"Medium","size":19,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901001","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0030150","count":2}]},{"hash":"2099424435419262742","title":"Plant transcriptional control, ribosome biogenesis, and immunity","description":"The top GO terms point to transcription regulation (GO:0006355), translation initiation and ribosome biogenesis (GO:0006413, GO:0042273), and innate immune response (GO:0045087), with plant-development hints (cuticle development, callus formation) suggesting a cohesive theme of gene expression and protein synthesis engaging immunity and development in plants.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0018171","count":1},{"id":"GO:0070483","count":1},{"id":"GO:0006413","count":1}]},{"hash":"412713169620472544","title":"TLR signaling and macrophage activation","description":"The top GO terms are dominated by innate immune functions: response to fungus, regulation of cytokine production, TLR8 signaling, MyD88-independent TLR signaling, macrophage activation, and IL-18 production. This points to a cohesive theme of Toll-like receptor\u2013driven innate immunity and cytokine responses. Some neural development terms appear, likely due to multifunctional annotations, but the central signal is immune signaling. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":17},{"id":"GO:0050707","count":17},{"id":"GO:0034158","count":17},{"id":"GO:0022038","count":17},{"id":"GO:0002756","count":17}]},{"hash":"2073300745137114688","title":"Developmental signaling pathways","description":"The proteins cluster around signaling processes that govern development and neural connectivity, highlighted by nervous system development, axonogenesis, Roundabout and Smoothened pathways, and Rab-mediated signal transduction, with supporting cues from vesicle trafficking terms. While there are broader signaling terms like T cell receptor signaling and kidney development, the dominant theme centers on developmental signaling and neural patterning.","confidence":"Medium","size":19,"edges":31,"triangles":5,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0035385","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0007107","count":4},{"id":"GO:0032482","count":4}]},{"hash":"614855278581519859","title":"Unknown","description":"There is no single dominant function linking the top GO terms; they cover nitrate assimilation, immune response, development, RNA processing, telomere regulation, stress responses, and cell migration, indicating a heterogeneous or random cluster. The absence of edges also suggests these proteins do not form a cohesive pathway. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042128","count":4},{"id":"GO:2001275","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006397","count":3}]},{"hash":"155099019795386364","title":"Plant development and auxin signaling","description":"This cluster has terms centered on plant growth and patterning: meristem development, auxin-activated signaling and auxin response, leaf vascular tissue pattern formation, longitudinal axis specification, and fruit dehiscence, along with transcriptional regulation terms. These collectively point to a plant development/hormone signaling theme. A couple of non-plant terms (RIG-I signaling and miRNA silencing) may reflect annotation noise or cross-species matches, but the dominant signal is plant development, so the label captures the core function of the cluster with moderate confidence.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900246","count":2},{"id":"GO:2000637","count":2},{"id":"GO:0048507","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0009733","count":1}]},{"hash":"834871947513175289","title":"Plant light-regulated transcription and RNAi silencing","description":"The top GO terms point to plant-specific regulation through RNAi pathways (ta-siRNA processing, siRNA-directed DNA methylation, RNAi antiviral response) in concert with light signaling and circadian regulation (far-red light signaling, phototransduction, circadian rhythm), plus developmental processes (wax biosynthesis, vegetative phase change), suggesting a cohesive theme of light-regulated transcription and RNAi-mediated gene control in plants.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0010267","count":1},{"id":"GO:0010025","count":1},{"id":"GO:0010050","count":1},{"id":"GO:0080188","count":1}]},{"hash":"1304259018987979944","title":"Floral Development and Cuticle Biosynthesis Regulation","description":"This cluster is enriched for plant developmental processes (floral meristem growth, bract development, multicellular organism development) and transcription regulation, plus hormonal signaling (ABA, ethylene) and positive regulation of wax/cutin biosynthesis, pointing to coordinated transcriptional control of floral development and epidermal cuticle formation. ","confidence":"High","size":19,"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:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010432","count":2}]},{"hash":"2038093951202310549","title":"Oocyte maturation and meiotic spindle assembly","description":"The top terms cluster around microtubule polymerization and spindle assembly in female meiosis I, along with processes of oocyte maturation and ubiquitin-proteasome\u2013mediated protein turnover that regulate the cell cycle. A few neural development terms appear but the dominant signal is meiosis/oocyte maturation, justifying this label.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046785","count":12},{"id":"GO:0007057","count":12},{"id":"GO:0031146","count":12},{"id":"GO:0021678","count":12},{"id":"GO:0006516","count":12}]},{"hash":"1940862179489199134","title":"Plant oxidative stress response and lignin degradation","description":"The dominant GO terms are about responding to oxidative stress and detoxifying oxidants, including hydrogen peroxide catabolism, plus lignin catabolic process and plant-type cell wall organization. This points to a plant-specific oxidative defense coupled with lignin-related cell wall remodeling/degradation. Minor terms are incidental noise. ","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":16},{"id":"GO:0098869","count":16},{"id":"GO:0046274","count":16},{"id":"GO:0042744","count":16},{"id":"GO:0055114","count":16}]},{"hash":"1384739132162603883","title":"Diverse catabolic and detoxification processes","description":"This cluster is dominated by GO terms for breaking down a variety of substrates (chlorophyll, cellulose, triglycerides, glucuronosides) and for detoxification activities (cellular oxidant detoxification) plus proteolysis, suggesting a broader theme of catabolic metabolism and detox pathways. Some signals related to signaling or host interaction appear, but the core pattern centers on diverse catabolic/detox functions.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":8},{"id":"GO:0015996","count":7},{"id":"GO:0030245","count":6},{"id":"GO:0006508","count":6},{"id":"GO:0019433","count":6}]},{"hash":"235440292974717490","title":"Lipid and small-molecule metabolism","description":"The cluster shows multiple terms tied to lipid-related processing, including triglyceride and monoacylglycerol catabolism, phosphatidylserine catabolic process, and the epoxygenase P450 pathway, as well as endocannabinoid signaling regulation (lipid-derived signaling). There are also biosynthetic and catabolic terms for biotin, antibiotics, and alkaloids, suggesting a broader theme of small-molecule metabolism. The mix points most strongly to lipid and related small-molecule metabolism, though the presence of diverse biosynthetic terms introduces some ambiguity. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":4},{"id":"GO:2000124","count":3},{"id":"GO:0019373","count":3},{"id":"GO:0019433","count":3}]},{"hash":"839116980696418384","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":3},{"id":"GO:0090502","count":2},{"id":"GO:0070129","count":2},{"id":"GO:0001682","count":2}]},{"hash":"401095023785903037","title":"Petal development and floral organ morphogenesis","description":"Dominant terms center on petal development, floral organ formation, and petal number specification, indicating involvement in floral organ morphogenesis; other terms suggest regulatory and trafficking roles supporting this process.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000071","count":2},{"id":"GO:0006620","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0009299","count":1},{"id":"GO:0090698","count":1}]},{"hash":"1864432526653982911","title":"Transcriptional Regulation and ER-Golgi Transport","description":"This cluster shows strong signals for DNA-templated transcription and its regulation, with additional terms for vesicle transport between the endoplasmic reticulum and Golgi, protein transport, and development-related processes (including synaptic potentiation). The combination suggests proteins involved in nuclear gene expression control alongside components of the secretory pathway, possibly connected to neuronal development and function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0006888","count":2}]},{"hash":"148004415477588611","title":"Plant immune signaling and ROS response","description":"The terms point to plant defense signaling, including transcriptional regulation during immunity, hypersensitive response, SA-mediated systemic acquired resistance, and ROS-based responses to oomycete attack.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0015074","count":1},{"id":"GO:0010602","count":1},{"id":"GO:0034051","count":1},{"id":"GO:0009626","count":1}]},{"hash":"2145852304628504592","title":"GA-regulated seed germination and plant development","description":"GA-regulated seed germination and plant development is suggested by GO terms on gibberellin response, seed dormancy regulation, and seed germination, along with leaf development and various developmental patterning processes, indicating a cohesive theme of GA-mediated control of seed and shoot development.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010187","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0048366","count":2},{"id":"GO:2000033","count":2},{"id":"GO:0009956","count":2}]},{"hash":"1766234920672309757","title":"Organelle RNA editing and processing (mitochondria and chloroplasts)","description":"The cluster is dominated by GO terms for mitochondrial mRNA processing, RNA modification, cytidine to uridine editing, and chloroplast/plastid RNA modification, as well as plastid transcription and chloroplast-nucleus signaling, indicating a cohesive theme of organellar gene expression regulation in plants (mitochondria and chloroplasts). The embryo development/seed dormancy term may reflect plant developmental context but does not override the central organellar RNA processing signal.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":13},{"id":"GO:0009451","count":13},{"id":"GO:0016554","count":13},{"id":"GO:0080156","count":13},{"id":"GO:1905639","count":13}]},{"hash":"1463403143990557665","title":"Immune activation and cytokine signaling","description":"The proteins are enriched for immune-related processes: positive regulation of T cell proliferation, cytokine production (including IL-4), and neutrophil clearance, alongside endothelial cell migration and Rho-mediated signaling that support inflammatory responses and cell movement. This suggests a cohesive theme around immune activation and inflammatory signaling, with some ancillary roles in cell migration and cytoskeletal dynamics.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":19},{"id":"GO:0001502","count":19},{"id":"GO:0097350","count":19},{"id":"GO:0035372","count":19},{"id":"GO:0043068","count":19}]},{"hash":"296639222098890156","title":"Epigenetic control of B cell antibody diversification","description":"The cluster\u2019s top GO terms point to epigenetic regulation (histone methylation) and transcriptional control, plus B cell\u2013specific processes such as somatic hypermutation and IgA isotype switching, suggesting a role in B cell maturation and antibody diversification governed by chromatin regulation. Some terms relate to broader immune regulation, fitting a context of epigenetic transcription control in immune cells, but the B cell\u2013centric terms are the strongest signal here.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051573","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0002692","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0060313","count":2}]},{"hash":"1362110434852140551","title":"Plant organellar RNA processing and editing","description":"The cluster is dominated by GO terms for mitochondrial mRNA processing, RNA modification, and cytidine-to-uridine editing, plus chloroplast RNA modification, plastid transcription, and chloroplast-nucleus signaling. This points to a cohesive theme of organellar (mitochondrial and plastid) RNA maturation/editing and associated retrograde signaling in plants. The embryo dormancy term is less central to the core theme but may reflect broader developmental contexts.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0080156","count":2},{"id":"GO:1905639","count":2}]},{"hash":"801779702427794147","title":"Unknown","description":"The Top Terms span immune sensing (TLR8 signaling, LPS detection, cytokine regulation) and inflammation alongside seemingly unrelated processes (kidney development, dopamine response, vestibuloocular reflex). There isn\u2019t a single coherent biological theme tying all terms together, so a specific functional label isn\u2019t supported.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0010596","count":16},{"id":"GO:0009620","count":16},{"id":"GO:0050929","count":16},{"id":"GO:0072237","count":16},{"id":"GO:0050707","count":16}]},{"hash":"2178239278349389180","title":"Transcription Regulation","description":"Dominant GO terms center on DNA-templated transcription and its regulation, including transcription by RNA polymerase II and III, and mRNA transport; additional terms point to related signaling and regulatory processes. This suggests the proteins form a module focused on controlling gene expression, with secondary involvement in signaling pathways.","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:0070262","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0038202","count":2}]},{"hash":"503868539339898981","title":"Plant Developmental Transcription Regulation","description":"Top GO terms emphasize DNA-templated transcription and regulation by RNA Pol II, with plant development processes such as meristem development, leaf vascular patterning, somatic embryogenesis, auxin response, fruit dehiscence, and root cap development. This suggests a cluster of proteins that coordinate transcriptional control during plant growth and organ formation, particularly in auxin-mediated pathways.","confidence":"High","size":19,"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:0071157","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0010305","count":1}]},{"hash":"2149055585630754105","title":"Unknown","description":"GO terms span diverse, unrelated processes (circadian rhythm regulation, nervous system and tissue development, immune germinal center formation, viral latency, protein catabolism, renal/distal tubule biology, and plant glucosinolate metabolism), with no edges or cohesive pathway connecting them. There is no single common function tying these proteins.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000312","count":2},{"id":"GO:0042752","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0002467","count":2},{"id":"GO:0019762","count":2}]},{"hash":"146970697657597913","title":"RNA splicing and mRNA stability with translation initiation","description":"This cluster is dominated by spliceosome- and splicing-related processes (cis-splicing, alternative splicing, negative regulation of splicing) along with mRNA processing/modification and stability, plus components involved in translation initiation (eIF4F complex assembly, IRES-dependent initiation). Together these terms point to a cohesive group centered on RNA maturation and regulation, linking splicing and mRNA turnover to initiation of translation.","confidence":"High","size":18,"edges":85,"triangles":226,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":9},{"id":"GO:0006378","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0048025","count":7},{"id":"GO:0016556","count":6}]},{"hash":"615507188085098735","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":41,"triangles":42,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0046689","count":2}]},{"hash":"170195792339286092","title":"DNA replication, repair, and chromatin remodeling","description":"This cluster centers on DNA metabolism and genome maintenance: chromatin remodeling, DNA replication, various DNA repair processes (including replication-born DSB repair and SOS response), DNA topological changes, and telomere-associated disassembly, with additional signals of transcription regulation and viral genome replication reflecting broader DNA-damage responses. These terms together point to a cohesive set of proteins involved in genome replication, maintenance, and chromatin state regulation.","confidence":"Medium","size":18,"edges":52,"triangles":36,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0043044","count":4},{"id":"GO:1990414","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0006306","count":3}]},{"hash":"201819385513678595","title":"Cardiac electrophysiology and calcium signaling regulators","description":"The top GO terms converge on heart rhythm and excitability: regulation of atrial cardiac muscle cell membrane repolarization, regulation of heart rate by cardiac conduction, and cellular responses to calcium and cGMP, along with related ion transport. While cortisol biosynthesis and circadian sleep regulation appear, the strongest, common theme across the cluster is cardiac ion signaling and rhythm control. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060372","count":6},{"id":"GO:0034651","count":6},{"id":"GO:0051592","count":6},{"id":"GO:0045188","count":6},{"id":"GO:0050955","count":6}]},{"hash":"1481550538540745466","title":"Organelle RNA Editing and Processing (Mitochondria & Plastids)","description":"The cluster is heavily enriched for mitochondrial mRNA processing, RNA modification, and C-to-U editing, plus plastid/chloroplast RNA modification and polycistronic mRNA processing, indicating a shared function in organellar RNA maturation and editing in both mitochondria and plastids. The presence of plastid transcription and chloroplast-nucleus signaling terms further supports a coordinated organellar gene expression theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":7},{"id":"GO:0009451","count":7},{"id":"GO:0016554","count":7},{"id":"GO:0080156","count":7},{"id":"GO:1905639","count":7}]},{"hash":"1815146431171593116","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":4},{"id":"GO:0009451","count":4},{"id":"GO:0080156","count":4},{"id":"GO:0016554","count":4},{"id":"GO:1905639","count":4}]},{"hash":"335950853223271501","title":"Nuclear RNA Export and Protein Quality Control","description":"The top GO terms cluster around nucleocytoplasmic RNA handling (mRNA export, tRNA re-export, splicing factor import) and protein quality control pathways (unfolded protein response, ERAD, chaperone-dependent refolding). Together these suggest a theme of coordinating RNA processing/export with protein quality control in the nucleus/ER, despite a few mismatched terms like DNA replication or phototaxis. Overall, the label captures the dominant functional threads in the cluster.","confidence":"Medium","size":18,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034620","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070389","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1223332865123024288","title":"Mitochondrial and Chloroplast RNA Editing and Processing","description":"This cluster centers on RNA processing, modification, and editing in mitochondria and chloroplasts (plastids), including mRNA processing, cytidine-to-uridine editing, and plastid transcription, with evidence of chloroplast-nucleus signaling, suggesting a cohesive plant organelle gene-expression module.","confidence":"High","size":18,"edges":144,"triangles":681,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:1905639","count":3}]},{"hash":"732018117223088000","title":"RNA processing and translation machinery","description":"The top GO terms cluster around mRNA splicing, translation initiation/reinitiation, preinitiation complex formation, mRNA export, and ribosome biogenesis, indicating a core theme of RNA metabolism and protein synthesis. Viral and retroelement terms appear as secondary associations, but the dominant signal is RNA processing and translation machinery.","confidence":"High","size":18,"edges":8,"triangles":2,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0006406","count":4},{"id":"GO:0015074","count":4}]},{"hash":"1998548583421703871","title":"Genome Replication and Energy Metabolism under Stress","description":"The cluster centers on core processes of DNA replication and viral genome replication, coupled with mitochondrial import and energy-related pathways (ATP metabolism, regulation of aerobic respiration) as well as proteostasis and stress responses (proteasome assembly, heat acclimation, cadmium stress). This suggests a broad coordination between genome maintenance and cellular energy/protein-homeostasis mechanisms under stress, rather than a single narrow function.","confidence":"Medium","size":18,"edges":19,"triangles":26,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0019079","count":7},{"id":"GO:1990171","count":5},{"id":"GO:0032979","count":5},{"id":"GO:1903715","count":5}]},{"hash":"1808136167634154103","title":"Translation Initiation and Preinitiation Complex Assembly","description":"Most terms cluster around initiation of protein synthesis, including IRES-dependent initiation, translation reinitiation, and formation of the translation preinitiation complex. A few terms touch on related processes like ER-to-Golgi trafficking and splicing, but the dominant signal is translation initiation machinery.","confidence":"High","size":18,"edges":125,"triangles":473,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0031954","count":2}]},{"hash":"2117897184367381433","title":"Synaptic vesicle dynamics and neurotransmitter release","description":"This cluster is dominated by GO terms related to presynaptic vesicle processes and neurotransmission, including neurotransmitter secretion, synaptic vesicle maturation, and regulation of synaptic transmission (GABAergic). Lipid biosynthesis terms (phosphatidylethanolamine and phosphatidylcholine) align with membrane and vesicle formation, while other terms touch on vesicle fusion and exocytosis. A few terms (autophagy, granuloma formation, Ras/VEGF signaling) appear peripheral, but the core theme points to synaptic vesicle function and neurotransmitter release.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006646","count":1},{"id":"GO:0046580","count":1},{"id":"GO:1990927","count":1},{"id":"GO:0007269","count":1},{"id":"GO:0046470","count":1}]},{"hash":"35370373129894017","title":"Proteostasis and Protein Quality Control","description":"Top GO terms cluster around proteostasis: misfolded protein transport, ubiquitin-dependent degradation, and chaperone-assisted refolding signals, all key to protein quality control. The presence of protein complex oligomerization also fits with assembly processes linked to proteostasis. A few terms relate to specific signaling or stress responses and are less central, but do not outweigh the proteostasis theme. ","confidence":"Medium","size":18,"edges":65,"triangles":128,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":7},{"id":"GO:0051259","count":7},{"id":"GO:0070843","count":7},{"id":"GO:0010198","count":7},{"id":"GO:0070389","count":7}]},{"hash":"295699011538733752","title":"Unknown","description":"The top terms are diverse (viral process, symbiont entry into host cell, metabolism and protein oligomerization) and there are no edges among proteins, indicating no single shared function. Therefore a reliable label cannot be inferred.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0009060","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0009086","count":2}]},{"hash":"1276507912260894716","title":"Viral Genome Integration and Latency","description":"The cluster is dominated by GO terms tied to viral entry and genome integration, including viral penetration into the host nucleus, DNA recombination, DNA integration, and establishment of integrated proviral latency, which together suggest a viral genome integration/latency theme. Other terms present (defense response to fungus, symbiont entry, muscle development) are less central to this core signal, so the overall coherence centers on host\u2013virus genome interaction. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":3},{"id":"GO:0000272","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0048741","count":2},{"id":"GO:1903704","count":2}]},{"hash":"1150265072757998694","title":"DNA replication and cell cycle regulation","description":"The top GO terms cluster around DNA replication, centrosome cycle, and positive regulation of nuclear cell cycle DNA replication, with supporting terms for meiotic DNA break formation, growth signaling (TORC1), and stress responses (amino acid starvation, apoptosis). Immune signaling and development terms appear but are secondary, suggesting the core theme is cell cycle control and DNA metabolism with related regulatory pathways.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0007098","count":11},{"id":"GO:0010571","count":11},{"id":"GO:0048701","count":11},{"id":"GO:0046827","count":10}]},{"hash":"1063516405300483538","title":"Neuronal Oxidative Stress and Autophagy","description":"Most terms cluster around oxidative stress response, autophagy, and neural signaling (membrane depolarization), with hints of dopamine-related metabolism. The overarching theme is a neuronal stress-response/maintenance program coupling redox balance and autophagic processes.","confidence":"Medium","size":18,"edges":43,"triangles":3,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":1},{"id":"GO:0033234","count":1},{"id":"GO:2000679","count":1},{"id":"GO:0006914","count":1},{"id":"GO:1903197","count":1}]},{"hash":"1927667831760854302","title":"Root Cell Wall and Membrane Biosynthesis","description":"This cluster is enriched for cell wall organization and root hair development, along with multiple lipid- and glycolipid-biosynthetic processes (GPI anchors, phospholipids, glycolipids) and sugar metabolism. The combination suggests a coordinated program for building and remodeling the plant cell wall and plasma membrane in root cells, potentially tied to root hair formation and drought-related membrane/wall adaptations. Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":6},{"id":"GO:0005978","count":4},{"id":"GO:0080147","count":4},{"id":"GO:0006506","count":3},{"id":"GO:0009414","count":3}]},{"hash":"473838171018890109","title":"Auxin Response and Transport in Plants","description":"Top GO terms indicate a cohesive auxin-related theme, including response to auxin, auxin-activated signaling, auxin polar transport, and regulation of organ growth. These collectively suggest a module centered on auxin signaling and its transport in plant cells, despite a few RNA processing and mitochondrial terms that likely reflect background housekeeping functions. Confidence in this label is Medium.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006891","count":2},{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1}]},{"hash":"1411505391552241411","title":"Plant flavonoid and lignin biosynthesis","description":"Most GO terms indicate phenylpropanoid metabolism, with lignin and flavonoid/anthocyanin biosynthesis as prominent processes, suggesting a cluster of proteins involved in plant secondary metabolism; a few xenobiotic-related annotations are likely ancillary.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":11},{"id":"GO:0009808","count":11},{"id":"GO:0009718","count":11},{"id":"GO:0006711","count":11},{"id":"GO:0052697","count":11}]},{"hash":"766819227905275543","title":"RNA processing and ubiquitin regulation in plant defense","description":"This cluster centers on processes regulating RNA metabolism (polyadenylation, stability, splicing, cap-independent translation) together with ubiquitin-mediated protein modification and degradation, including autoubiquitination and proteasomal pathways, within a context that includes plant defense responses (hypersensitive response). The combination suggests coordinated control of gene expression and protein turnover during plant stress/immune signaling, despite some obsolescent GO terms.","confidence":"Medium","size":18,"edges":16,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:0044829","count":2},{"id":"GO:1903679","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0034052","count":2}]},{"hash":"2238998000673594330","title":"Nuclear RNA processing and chromatin regulation","description":"This cluster centers on nuclear processes: mRNA splicing, maturation of rRNA, termination of RNA Pol II transcription, and nuclear import, all indicative of RNA processing and transcription control. Additional terms about histone mRNA metabolism and pericentric heterochromatin formation point to chromatin organization. Some plant-specific stress response terms (abscisic acid response, water deprivation) and a hair cycle term are present but seem peripheral to the core theme, suggesting the cluster mainly groups nuclear RNA processing and chromatin regulation.","confidence":"Medium","size":18,"edges":93,"triangles":201,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0051170","count":4},{"id":"GO:0008334","count":4},{"id":"GO:1990141","count":4},{"id":"GO:0009737","count":4}]},{"hash":"2137768097207183364","title":"Immune Response Regulation","description":"The cluster\u2019s GO terms cluster around immune signaling and regulation: negative regulation of IL-1\u03b2 and IL-2 production, regulation of CD40 signaling, germinal center formation, and mucosal immune response, plus a response to muramyl dipeptide, all pointing to regulatory roles in both innate and adaptive immunity. The presence of K63-linked deubiquitination supports regulatory control of signaling pathways rather than core effector functions. These together suggest a cohesive theme of modulating immune activation and signaling. ","confidence":"High","size":18,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0032691","count":1},{"id":"GO:0002634","count":1},{"id":"GO:0032495","count":1},{"id":"GO:0002385","count":1}]},{"hash":"1492181600263911863","title":"Neural development and CNS apoptosis","description":"This cluster is enriched for neural development terms (neural tube closure, forebrain development) alongside CNS-specific apoptotic processes (glial cell apoptotic process, neuron apoptotic process) and regulation of apoptotic signaling, plus a role for SCF-dependent ubiquitin-proteasome\u2013mediated protein turnover. The presence of cellular response to TGF-beta and mitotic cell cycle signals suggests proliferating neural progenitors undergoing development with coordinated apoptosis and protein turnover. These together imply a neural development/apoptosis regulatory program.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0001843","count":2},{"id":"GO:2001235","count":2},{"id":"GO:0030900","count":2},{"id":"GO:1902510","count":2}]},{"hash":"121163927948685821","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":4},{"id":"GO:0050832","count":4},{"id":"GO:0007601","count":3},{"id":"GO:0031640","count":3},{"id":"GO:0052889","count":3}]},{"hash":"461164069735357463","title":"Plant organelle RNA editing and modification","description":"This cluster is dominated by terms for mitochondrial and chloroplast RNA processing and editing (e.g., mitochondrial mRNA processing/modification, chloroplast RNA modification, RNA modification, cytidine to uridine editing), pointing to a core function in organelle gene expression in plants; related terms like seed dormancy and sterol biosynthesis appear as secondary contexts but do not override the main theme.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006695","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2}]},{"hash":"1656815501540900718","title":"Floral Development and Cuticle Biosynthesis Regulation","description":"This cluster centers on transcriptional regulation (DNA-templated transcription and its regulation) linked to floral meristem growth and bract development, with signaling inputs from ethylene and abscisic acid. It also includes regulation of wax and cutin biosynthesis, and defense-related transcriptional regulation, suggesting a coordinated network governing flower formation and cuticle deposition.","confidence":"High","size":18,"edges":63,"triangles":76,"max_degree":15,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0006355","count":8},{"id":"GO:0010451","count":5},{"id":"GO:0009873","count":5},{"id":"GO:0010432","count":5}]},{"hash":"667937906795040391","title":"Plant Polarity and Nuclear RNA Processing","description":"The top terms strongly pair plant organ polarity and meristem initiation (adaxial/abaxial axis specification and meristem initiation) with nuclear RNA handling (ribosomal subunit export, mRNA export, tRNA re-export, and splicing factor import). This suggests a cohesive theme around plant developmental regulation that is tightly linked to RNA processing and trafficking within the nucleus, with ancillary signals related to environmental response. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009944","count":5},{"id":"GO:0000056","count":4},{"id":"GO:1900370","count":3},{"id":"GO:0035048","count":3},{"id":"GO:0034501","count":3}]},{"hash":"429008293153850766","title":"Plant Terpene Biosynthesis and GA Signaling","description":"This cluster centers on terpene biosynthesis (sesquiterpene, camphor, monoterpene) with gibberellin biosynthesis and GA-mediated signaling, plus related fatty acid biosynthesis and herbivore-response terms, suggesting a plant-focused secondary metabolite and hormone signaling module.","confidence":"High","size":18,"edges":71,"triangles":65,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051762","count":1},{"id":"GO:0046211","count":1},{"id":"GO:0009686","count":1},{"id":"GO:0033383","count":1},{"id":"GO:0043693","count":1}]},{"hash":"316218811336756776","title":"Developmental Transcription Regulators","description":"This cluster is dominated by DNA-templated transcription, with several terms pointing to regulation of differentiation across tissues (muscle, bone marrow, cartilage) and even plant reproduction, suggesting a set of proteins that broadly regulate development through transcriptional control, with calcium signaling as a common modulatory theme.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":12},{"id":"GO:0006351","count":12},{"id":"GO:2001016","count":9},{"id":"GO:0080155","count":8},{"id":"GO:0002634","count":8}]},{"hash":"1057829911102367095","title":"Cell Cycle and Neural-Immune Regulation","description":"The cluster centers on cell cycle control (kinetochore localization and CDK activity regulation) and also includes neural development signals (Bergmann glial differentiation, cerebellar cortex formation) alongside immune signaling (T cell receptor signaling, T cell proliferation), suggesting proteins that coordinate cell division with neural differentiation and immune responses.","confidence":"Medium","size":18,"edges":135,"triangles":567,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":16},{"id":"GO:0045736","count":16},{"id":"GO:2001275","count":13},{"id":"GO:0060020","count":13},{"id":"GO:0008285","count":13}]},{"hash":"2274211231558626189","title":"Immune activation and cytokine signaling","description":"This cluster is dominated by immune-related GO terms: positive regulation of T cell proliferation, cytokine production (including IL-4), neutrophil clearance, and immune response regulation, with supporting roles for Rho signaling and microtubule localization that link to immune cell migration and activation. While a few terms relate to development or cytoskeletal organization, the overarching theme is immune activation and cytokine signaling. ","confidence":"High","size":18,"edges":25,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":18},{"id":"GO:0001502","count":18},{"id":"GO:0097350","count":18},{"id":"GO:0035372","count":18},{"id":"GO:0043068","count":18}]},{"hash":"1157307795266121855","title":"Immune activation and cytokine signaling with cytoskeletal dynamics","description":"The cluster is dominated by immune-related terms: positive regulation of T cell proliferation, cytokine production including IL-4, neutrophil clearance, and endothelial cell migration, all pointing to immune activation and inflammatory signaling. Rho signaling and microtubule localization suggest underlying cytoskeletal changes typical of immune cell movement and signaling. A developmental term like cartilage condensation is less aligned but may reflect broader cell\u2013cell or ECM-related processes; overall the theme centers on immune response and cytokine regulation with cytoskeletal involvement.","confidence":"Medium","size":18,"edges":52,"triangles":50,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":18},{"id":"GO:0001502","count":18},{"id":"GO:0097350","count":18},{"id":"GO:0035372","count":18},{"id":"GO:0043068","count":18}]},{"hash":"1868850479816379391","title":"Cell Division and Immune Regulation","description":"The cluster is dominated by core cell cycle terms (DNA replication and mitotic cell cycle), indicating involvement in cell division. At the same time, terms related to immune signaling (T cell proliferation, cytokine production) and tissue remodeling/angiogenesis (endothelial migration, cartilage condensation, neutrophil clearance) suggest a broader role in coordinating proliferation with immune responses and vascular remodeling.","confidence":"Medium","size":18,"edges":118,"triangles":406,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":18},{"id":"GO:0000278","count":18},{"id":"GO:0046641","count":17},{"id":"GO:0001502","count":17},{"id":"GO:0097350","count":17}]},{"hash":"715689679330065717","title":"Angiogenesis and developmental signaling with cytoskeletal remodeling","description":"This cluster is dominated by GO terms for angiogenesis and multicellular organism development, with a strong PI3K/AKT signaling signature and cortical actin cytoskeleton organization, suggesting a module of signaling pathways that drive tissue formation and vascular development coupled to cytoskeletal changes and metabolic regulation. While some terms are regulatory, the core theme centers on development and angiogenesis mediated by cell signaling and structural remodeling.","confidence":"High","size":18,"edges":21,"triangles":6,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032436","count":16},{"id":"GO:0043491","count":16},{"id":"GO:0043433","count":16},{"id":"GO:0001525","count":16},{"id":"GO:0007275","count":16}]},{"hash":"1038519446403764264","title":"Immune activation and cytokine signaling","description":"The top terms are dominated by immune-related processes, including positive regulation of T cell proliferation, interleukin-4 production, and cytokine production in immune responses, along with neutrophil clearance and endothelial migration\u2014traits of inflammatory signaling and immune cell coordination. Some cytoskeletal and development terms (Rho signaling, microtubule localization, cartilage condensation) likely reflect cellular changes during immune responses rather than a separate pathway, but overall the cluster centers on immune activation and cytokine-mediated communication.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":18},{"id":"GO:0001502","count":18},{"id":"GO:0097350","count":18},{"id":"GO:0035372","count":18},{"id":"GO:0043068","count":18}]},{"hash":"471592395995266965","title":"Developmental Transcriptional Regulators Across Taxa","description":"These terms cluster around regulation of development through transcription and signaling, spanning plant meristem identity (flower and inflorescence maintenance), vernalization responses, and embryonic processes like primitive streak formation, plus broader roles in germinal center regulation and bone marrow proliferation. The common thread is transcriptional control and signaling that guide cell fate and proliferation during development across taxa, rather than a single pathway.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0071277","count":7},{"id":"GO:2001016","count":7},{"id":"GO:0010076","count":6},{"id":"GO:0090009","count":6}]},{"hash":"1181576818228586005","title":"Unknown","description":"The top GO terms cover a wide and seemingly unrelated mix, including transcription regulation, chemotaxis, telomerase assembly, protein folding, signaling regulation, and development. This lack of a coherent shared function or pathway implies the cluster is heterogeneous, so a specific, representative label cannot be determined.","confidence":"","size":18,"edges":25,"triangles":9,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006935","count":2},{"id":"GO:1905323","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0032092","count":2}]},{"hash":"774645295990946664","title":"Neural development and differentiation","description":"The prominent GO terms center on development and nervous system formation (cell differentiation, multicellular organism development, forebrain development, glial cell apoptotic process). This points to proteins involved in neural development and differentiation; other terms in the list (melanization defense, salivary gland histolysis, L-methionine cycle) are more general or species-specific annotations, so the overall theme is neural development with differentiation as core.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030154","count":12},{"id":"GO:0007275","count":12},{"id":"GO:0030900","count":10},{"id":"GO:0010659","count":10},{"id":"GO:0035006","count":10}]},{"hash":"2135443370154304199","title":"Steroid and Prostaglandin Biosynthesis with Lipid Metabolism","description":"The GO terms cluster around biosynthesis and breakdown of lipid- and hormone-related compounds (prostaglandin, cortisol, testosterone, retinoic acid, vitamin D) and related oxidation/catabolic processes, alongside lipid-focused pathways like fatty acid omega-oxidation. The presence of mammary gland development and endothelial cell adhesion suggests a tissue-contextual aspect, but the core theme appears to be hormone and lipid metabolism related to development and signaling.","confidence":"Medium","size":18,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":15},{"id":"GO:0030879","count":14},{"id":"GO:0071603","count":14},{"id":"GO:0034651","count":14},{"id":"GO:0070989","count":14}]},{"hash":"1774667755195894552","title":"Exocyst-Mediated Vesicle Trafficking","description":"Top GO terms cluster around exocyst- and vesicle trafficking: exocyst localization/assembly, exocytosis, Golgi-to-plasma membrane transport, vesicle tethering, and protein transport, with Rho signaling linking to cytoskeletal regulation. Some plant-specific terms (flower development, cell differentiation) may reflect broader developmental roles of trafficking. Overall this cluster represents exocyst-mediated vesicle delivery to the plasma membrane.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051601","count":1},{"id":"GO:0006887","count":1},{"id":"GO:0006893","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0007266","count":1}]},{"hash":"1813591895903504052","title":"ER-Golgi Traffic and Translation Initiation","description":"The top terms cluster around vesicle-mediated transport between the ER and Golgi and general protein transport, plus processes tied to initiating translation (formation of the translation preinitiation complex) and associated RNA processing (RNA guanine-N7 methylation). A few DNA-related terms are present but do not dominate, so the core theme appears to be fundamental intracellular trafficking linked to early stages of protein synthesis. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0015031","count":1},{"id":"GO:0042147","count":1}]},{"hash":"1650808169114100257","title":"Plant secondary cell wall biosynthesis and vascular development","description":"The top terms cluster around plant-specific processes: secondary cell wall biogenesis with positive regulation, protoxylem development, xylem vessel differentiation, and related plant developmental events like callus formation and leaf senescence. This points to a cohesive theme of plant vascular development and cell wall formation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009834","count":5},{"id":"GO:1901348","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006334","count":3},{"id":"GO:1990110","count":3}]},{"hash":"1008087885059282942","title":"Plant Growth and Development Regulation","description":"The top GO terms cluster around regulatory processes governing plant development and growth, including cytokinin signaling, chlorophyll biosynthesis regulation, seed and root meristem growth, leaf senescence, and modulation of secondary cell wall/lignin pathways. This suggests a cohesive theme of controlling plant growth and developmental programs rather than a single metabolic pathway.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":7},{"id":"GO:0010380","count":5},{"id":"GO:0080113","count":5},{"id":"GO:1901430","count":5},{"id":"GO:1901347","count":5}]},{"hash":"1571346630912657782","title":"Unknown","description":"The term set is a broad mix: several developmental processes (roof of mouth development, multicellular organism development, pituitary gland development) paired with diverse metabolic and transport processes (nitrate assimilation, cellulose catabolic, copper/iron ion transport, arsenate transport) and even sporulation. With no clear, single functional theme linking the proteins, there isn\u2019t a coherent cluster function to name beyond Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0060021","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0030245","count":5}]},{"hash":"182530227092434368","title":"Regulation of plant growth and development","description":"The cluster is dominated by terms about regulation of transcription and multiple plant-specific developmental processes (chlorophyll biosynthesis, seed growth, lignin biosynthesis, secondary cell wall biogenesis, root meristem growth, and leaf senescence). This pattern suggests these proteins act as regulators coordinating plant growth and tissue development rather than a single metabolic pathway.","confidence":"High","size":18,"edges":18,"triangles":0,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0010380","count":6},{"id":"GO:0080113","count":6},{"id":"GO:1901430","count":6},{"id":"GO:1901347","count":6}]},{"hash":"314617104726606607","title":"Plant signaling and carbohydrate metabolism","description":"This cluster\u2019s top GO terms center on plant-specific signaling (cytokinin-activated signaling, MAPKKK cascade regulation) and on carbohydrate-related catabolic processes (cellulose, lactose via tagatose-6-phosphate, glucosinolate catabolism). The combination suggests proteins tied to plant growth signaling and sugar/defense metabolite processing. Some terms like chromatin remodeling and metal ion transport are present but appear peripheral to the dominant plant signaling and carbohydrate metabolism theme.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030245","count":10},{"id":"GO:0009736","count":10},{"id":"GO:0090080","count":7},{"id":"GO:0008286","count":7},{"id":"GO:0019512","count":7}]},{"hash":"1019717569760166717","title":"Plant transcriptional regulation and chromatin dynamics","description":"The top GO terms point to transcriptional control (DNA-templated transcription; negative regulation of transcription by RNA Pol II) and chromatin-related processes (nucleosome assembly; subtelomeric heterochromatin formation), combined with plant hormone signaling (cytokinin- and auxin-activated pathways) indicating regulation of growth and development at the transcriptional level in plants. The viral process term appears less connected to the core theme and may reflect annotation noise, but the dominant signals support transcriptional regulation and chromatin dynamics with hormonal signaling. ","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:0016032","count":3},{"id":"GO:0010082","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0000122","count":2}]},{"hash":"369010348145027818","title":"Unknown","description":"The top GO terms span DNA integration, development, abscisic acid biosynthesis, various transport processes, and growth responses, with no single shared function linking the proteins. The absence of edges and the heterogeneous functional signals suggest there is no coherent module to label beyond Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0009688","count":2},{"id":"GO:0072488","count":1},{"id":"GO:0007124","count":1}]},{"hash":"275959906845845707","title":"Developmental signaling and ECM biosynthesis","description":"The top GO terms point to developmental processes (BMP signaling, endoderm development, embryonic skeletal joint development, gastrulation-related regulation) as well as biosynthetic processes for extracellular matrix components (GPI anchors, xyloglucan, xylogalacturonan, proteoglycans), suggesting a cluster centered on development coupled with ECM-related biosynthesis across species. This mixture implies a common theme of how signaling directs development and how the extracellular matrix is built to support it, rather than a single, narrow function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010075","count":1},{"id":"GO:0006506","count":1},{"id":"GO:1904103","count":1},{"id":"GO:0010398","count":1},{"id":"GO:0009863","count":1}]},{"hash":"1994704573105880341","title":"Developmental signaling and hormone maturation","description":"These GO terms cluster around organismal development, growth, and signaling (e.g., multicellular development, angiogenesis, axis determination), with associated hormone-related processes (nerve growth factor production, insulin processing). Regulatory aspects like chromatin binding and receptor recycling suggest modulation of signaling during development. Overall, the theme points to developmental signaling and maturation rather than a single canonical pathway. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0035562","count":2},{"id":"GO:1905598","count":2},{"id":"GO:0032902","count":2}]},{"hash":"1901191169392432353","title":"Plant Cuticle Biosynthesis and Desiccation Stress Response","description":"The GO terms cluster around cutin and suberin biosynthesis and regulatory processes tied to abscisic acid and abiotic stress (high light, desiccation), pointing to a cohesive plant-specific function in constructing the protective cuticle and mediating drought/abiotic stress responses. A couple of outlier terms (DNA integration, MHC II antigen processing) likely reflect annotation noise rather than core cluster function.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0010116","count":1},{"id":"GO:0009644","count":1},{"id":"GO:0009269","count":1},{"id":"GO:0010345","count":1}]},{"hash":"1509169318831153824","title":"Plant cell wall biosynthesis and metabolism","description":"The top GO terms strongly emphasize plant-related cell wall biology (cell wall organization; cell wall polysaccharide biosynthetic process; arabinan biosynthesis), with supporting pathways in plant metabolism (L-ascorbic acid biosynthesis; alkaloid metabolism) and related redox/metabolic processes. This suggests a cluster centered on plant cell wall formation and its associated metabolism, though some general metabolic terms introduce some ambiguity.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0009820","count":5},{"id":"GO:0008360","count":4},{"id":"GO:0071555","count":4}]},{"hash":"377821155037863686","title":"Meiosis, Spindle Assembly, and Ubiquitin-Proteasome Degradation","description":"This cluster is dominated by GO terms tied to oocyte maturation and female meiosis I spindle assembly, with a prominent signal for SCF-dependent ubiquitin-proteasome protein catabolic processes and microtubule polymerization. The co-occurrence of meiosis-related processes and proteolytic regulation of proteins suggests a functional module coordinating cell cycle control, spindle dynamics, and protein turnover in oocytes and early developmental contexts.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0001556","count":7},{"id":"GO:0046785","count":7},{"id":"GO:0006516","count":7},{"id":"GO:0007057","count":7}]},{"hash":"42624411498341420","title":"Ubiquitination and TNF/JNK signaling modulation","description":"Proteins in this cluster are enriched for ubiquitin-dependent proteolysis and related processes (including autoubiquitination and various ubiquitin linkages) as well as histone catabolic and ubiquitination events, with links to TNF-mediated signaling and JNK cascade regulation. This points to a cohesive group of ubiquitin-system components that influence inflammatory signaling and chromatin dynamics, justifying a label centered on ubiquitination-driven regulation of TNF/JNK signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0036205","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0085020","count":5},{"id":"GO:1903265","count":5}]},{"hash":"2130610420181273798","title":"Sensory signaling and ion transport","description":"The cluster has strong representation of GO terms related to sensory perception (pain, touch) along with ion transport across membranes (sodium import, potassium export) and signaling via cAMP/cGMP with membrane potential dynamics, including cardiac repolarization. This pattern points to a cohesive theme of electrophysiological signaling and sensory transduction, despite some broader annotations such as development or aerotaxis.","confidence":"Medium","size":18,"edges":24,"triangles":5,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019233","count":11},{"id":"GO:0007275","count":11},{"id":"GO:0098719","count":9},{"id":"GO:0097623","count":9},{"id":"GO:0071321","count":8}]},{"hash":"151724702429139133","title":"Lipid catabolism and endocannabinoid signaling","description":"This cluster is dominated by GO terms for lipid breakdown (triglyceride, monoacylglycerol, phosphatidylserine catabolic processes, phospholipid dephosphorylation) and includes regulation of endocannabinoid signaling, pointing to lipid metabolism and lipid-derived signaling as the common theme. Some plant-specific catabolic terms are present but do not override the lipid-centric pattern.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":7},{"id":"GO:0006660","count":6},{"id":"GO:2000124","count":6},{"id":"GO:0052651","count":6},{"id":"GO:0046272","count":4}]},{"hash":"497134749241344932","title":"Synaptic Organization and Assembly","description":"Most terms point to synapse formation and organization (excitatory/inhibitory synapse assembly, synapse organization, neurexin clustering in presynaptic membrane assembly, active zone cytoskeletal matrix organization, and protein localization to synapse). A few metabolic terms (lipid, starch, cellulose catabolic processes) appear incidental and less related to the core function. Overall, the cluster is best described by synaptic assembly/organization.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016042","count":2},{"id":"GO:0005983","count":2},{"id":"GO:1904862","count":1},{"id":"GO:0050808","count":1},{"id":"GO:0097115","count":1}]},{"hash":"755531562966437250","title":"Secretory and Endosomal Vesicle Trafficking","description":"The dominant GO terms point to movement of vesicles along the secretory and endocytic pathways (ER-Golgi transport, Golgi-to-plasma-membrane transport, COPII budding, endosomal fusion/recycling, and endosome-to-lysosome trafficking). While a couple terms touch on neuronal processes, the overall signal is cohesive around intracellular vesicle trafficking and membrane traffic.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0006893","count":4},{"id":"GO:0032456","count":4},{"id":"GO:1902824","count":3},{"id":"GO:0048227","count":3}]},{"hash":"281754258506641656","title":"Cell growth and division machinery","description":"The terms converge on fundamental cellular processes: translation initiation and reinitiation (protein synthesis), mitotic and replication-related activities (Okazaki fragment processing in mitotic DNA replication, APC/C-dependent catabolic process, and general cell division), cytoskeletal dynamics (actin filament depolymerization), membrane trafficking (COPII-coated vesicle budding), and growth signaling (positive regulation of TORC1). A developmental cue (lens fiber differentiation) and an aging-related term further support a broad view of cellular growth, division, and differentiation rather than a single narrow pathway. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":8},{"id":"GO:0002188","count":8},{"id":"GO:1903461","count":5},{"id":"GO:1904263","count":5},{"id":"GO:0051301","count":5}]},{"hash":"1152946937810616848","title":"Strigolactone-regulated shoot formation and chloroplast development","description":"The cluster centers on strigolactone biosynthesis and secondary shoot formation, implying regulation of shoot architecture by strigolactones, while also including chloroplast-related processes (chloroplast organization, protein import into chloroplast stroma, light-response de-etiolation, and related transport/metabolic terms), suggesting a functional module linking hormone signaling to chloroplast biogenesis and light-responsive growth.","confidence":"High","size":18,"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:0009658","count":1},{"id":"GO:1904216","count":1},{"id":"GO:0009704","count":1}]},{"hash":"492932010521968931","title":"Cell-cycle control with antiviral defense","description":"The GO terms cluster around cell-cycle regulation (G2/M transition of the mitotic cell cycle) and transcriptional control (DNA-templated transcription), with notes on negative regulation of translation. They are complemented by several immune-related terms (defense response to virus/fungus, regulation of defense response to virus, killing of cells of another organism), suggesting an innate-defense component. A few terms touch on development and growth (muscle fiber development, mammary gland proliferation), which may reflect broader cellular growth programs but do not override the core signal of cell-cycle and immune-related functions. Overall, there is a coherent but mixed signal for a functional module combining cell-cycle control with antiviral/antifungal defense, justifying the chosen name.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0031640","count":2},{"id":"GO:0050688","count":2},{"id":"GO:0050832","count":2}]},{"hash":"2204597562539586965","title":"Oxidative Stress Response and Detoxification","description":"The cluster is enriched with GO terms tied to oxidative stress response, cellular oxidant detoxification, and hydrogen peroxide catabolic processes, indicating a core theme of reactive oxygen species management. A few plant-specific or unrelated terms appear, which may reflect annotation noise, but do not override the central ROS-related signal.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0046274","count":2},{"id":"GO:0042744","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1254737557686900909","title":"Plant cell wall biosynthesis and modification","description":"The top GO terms are dominated by plant-type secondary cell wall biogenesis, xyloglucan metabolism, plant-type cell wall modification, and xylan biosynthesis, all pointing to synthesis and remodeling of plant cell wall polysaccharides (especially xyloglucan and xylan). While a few terms relate to transcription or chromatin, the strongest signal describes cell wall biosynthetic processes, suggesting the cluster represents proteins involved in cell wall formation and modification in plants.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":4},{"id":"GO:0010411","count":3},{"id":"GO:0009827","count":3},{"id":"GO:0050826","count":3},{"id":"GO:0045492","count":3}]},{"hash":"1228163412552370274","title":"Organelle RNA editing and processing (mitochondria and chloroplasts)","description":"The top GO terms cluster around mitochondrial mRNA processing, RNA modification, cytidine-to-uridine editing, and plastid/chloroplast RNA modification, plus chloroplast-nucleus signaling and plastid transcription. This points to a cohesive role in RNA processing/editing within plant organelles (mitochondria and chloroplasts) and related inter-organellar communication, with one outlier term likely due to annotation noise (seed dormancy). ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:1905639","count":3}]},{"hash":"599566902126380113","title":"Plant secondary metabolism and vacuolar transport","description":"The terms include lignin and cutin biosynthesis (cell-wall/cuticle components), flavonoid biosynthesis, and transmembrane amino acid transport into/out of vacuoles. This combination suggests a cluster of plant-specific metabolic pathways coupled with metabolite compartmentalization, rather than a single, unified function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":3},{"id":"GO:0010143","count":3},{"id":"GO:0080088","count":3},{"id":"GO:0009809","count":3},{"id":"GO:0009963","count":3}]},{"hash":"1761698702776793725","title":"Plant cell wall polysaccharide biosynthesis","description":"This cluster shows a cohesive theme around plant cell wall biogenesis and polysaccharide synthesis, with multiple GO terms for glucuronoxylan, xyloglucan, xylogalacturonan, and plant-type secondary cell wall biogenesis. A few terms (salicylic acid signaling, BMP signaling, embryonic development) are less aligned and may reflect annotation noise or cross-species labels, but the dominant signal points to plant cell wall biosynthesis.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010417","count":4},{"id":"GO:0009834","count":4},{"id":"GO:0010398","count":2},{"id":"GO:0009863","count":2},{"id":"GO:0008101","count":2}]},{"hash":"1893802686878979418","title":"Mitotic Sister Chromatid Cohesion Factors","description":"This cluster is best labeled by the strong representation of mitotic sister chromatid cohesion terms (GO:0007064 and GO:0034087), indicating a group involved in cohesion of sister chromatids during mitosis. A number of obsolete or unrelated terms appear, but the dominant modern annotations point to chromosome cohesion machinery rather than other processes.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":1},{"id":"GO:0034087","count":1},{"id":"GO:0044376","count":1},{"id":"GO:1990022","count":1},{"id":"GO:1901621","count":1}]},{"hash":"618477345054154123","title":"Plant defense and cell wall remodeling via protease regulation","description":"The top GO terms point to plant defense against fungi and to remodeling of the cell wall, with proteolysis and coordination of endopeptidase activity. The combination suggests a functional cluster where defense responses are linked to cell wall loosening/modification, controlled by protease regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":4},{"id":"GO:0006508","count":3},{"id":"GO:0050832","count":3},{"id":"GO:0006869","count":2},{"id":"GO:0019953","count":2}]},{"hash":"1778646835575462697","title":"Regulation of TLR and cytokine signaling","description":"This cluster is dominated by innate immune signaling terms, including response to fungus, MyD88-independent TLR signaling, cytokine- and chemokine-mediated signaling, and negative regulation of receptor signaling pathways (e.g., JAK-STAT). The pattern points to modulation or suppression of immune receptor pathways, despite a few outliers related to nervous system processes and other unrelated terms.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":18},{"id":"GO:0050929","count":18},{"id":"GO:0060007","count":18},{"id":"GO:0002756","count":18},{"id":"GO:0019221","count":18}]},{"hash":"632137097674731432","title":"Plant biosynthesis and defense responses","description":"This cluster mixes plant-specific defense and developmental terms (defense response to fungus, plant-type cell wall loosening, meristem development, secondary cell wall biogenesis) with various biosynthetic processes (ubiquinone, biotin, antibiotic biosynthesis) suggesting a group of proteins involved in plant metabolism that supports growth and defense rather than a single pathway. The common theme is plant growth-related remodeling coupled with antimicrobial and biosynthetic activities. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0019953","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0006949","count":2}]},{"hash":"266405713048496686","title":"T Cell Activation and Cytokine Signaling","description":"The cluster shows strong enrichment for adaptive immune functions: positive regulation of alpha-beta T cell proliferation, interleukin-4 production, and cytokine production involved in immune response. Neutrophil clearance and endothelial migration support an inflammatory/immune context, with other terms hinting at signaling and cytoskeletal dynamics that accompany immune cell behavior. Overall, it points to immune activation and cytokine signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":18},{"id":"GO:0001502","count":18},{"id":"GO:0097350","count":18},{"id":"GO:0035372","count":18},{"id":"GO:0043068","count":18}]},{"hash":"876455945536696236","title":"Organelle gene expression in mitochondria and chloroplasts","description":"This cluster is dominated by GO terms for mitochondrial transcription and translation, mitochondrial ribosome assembly, and chloroplast organization, highlighting a cohesive theme of organellar gene expression and ribosome biogenesis. Some terms are unrelated outliers, but the core signal points to organelle-specific expression machinery.","confidence":"High","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0030420","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0009658","count":1}]},{"hash":"1561600888534943893","title":"Insect chitin-based cuticle development and molting","description":"The top GO terms center on chitin catabolic process, chitin-based cuticle development, and ecdysis (molting), with related polysaccharide catabolic processes and cuticle remodeling signals. This combination strongly suggests roles in exoskeleton formation and shedding in insects, rather than intracellular signaling alone. While some terms like NF-kappaB-related activities and interleukin responses appear, they seem ancillary to the core theme of cuticle biosynthesis and molt-related processes.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0006032","count":3},{"id":"GO:0040003","count":3},{"id":"GO:0071347","count":3},{"id":"GO:0072606","count":3}]},{"hash":"635175107586186653","title":"RNA splicing and post-transcriptional regulation","description":"The cluster has strong representation of mRNA processing and regulatory processes, including spliceosome-mediated splicing, regulatory control of splicing, mRNA export, stress-responsive mRNA stability, translation initiation regulation, and RNA modification, indicating a coordinated post-transcriptional gene expression program.","confidence":"High","size":17,"edges":4,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":11},{"id":"GO:0045292","count":11},{"id":"GO:0048026","count":10},{"id":"GO:0031047","count":10},{"id":"GO:0010610","count":9}]},{"hash":"179050435189550201","title":"Neural development and immune signaling","description":"The cluster includes terms tied to neural differentiation (oligodendrocyte differentiation, dendrite development) alongside immune signaling pathways (NOD2 signaling, NF-kappaB regulation) and responses like vitamin D signaling. Additional terms touching proteasome assembly and endocytic processes suggest broader cellular regulation, but the strongest common theme appears to be a cross-talk between neural development and immune signaling. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":3},{"id":"GO:0050955","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0007253","count":3},{"id":"GO:0070431","count":3}]},{"hash":"1632420384928453769","title":"Neural differentiation and mesenchymal development","description":"Reason: The top GO terms point to differentiation programs in neural lineages (GABAergic interneuron differentiation, auditory receptor cell fate determination, astrocyte differentiation regulation) alongside mesenchymal and heart-related development (mesenchyme development, heart valve development). This pattern suggests a cluster of proteins involved in coordinating neural and mesenchymal organogenesis rather than a single pathway.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0048712","count":13},{"id":"GO:2001038","count":13},{"id":"GO:2000793","count":12},{"id":"GO:2000764","count":12}]},{"hash":"2119252734438309842","title":"Unknown","description":"The top GO terms span diverse biosynthetic pathways (glutamine, galactose, thiamine, phenylpropanoid, anthocyanin, colanic acid) and transcription-related processes, with no clear shared function. The mixture of plant secondary metabolism and bacterial processes suggests no single cohesive theme for the cluster. ","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:1901006","count":3},{"id":"GO:0006541","count":2},{"id":"GO:0009718","count":2},{"id":"GO:0009699","count":2}]},{"hash":"1450036974269747272","title":"Cell cycle transitions (G1/S, G2/M)","description":"Most terms point to control of cell cycle progression, especially G1/S transition and G2/M transition, with regulation of G2/M and epithelial cell proliferation supporting a cell cycle\u2013centered theme. A few unrelated terms (metabolic processes, viral transcription) appear as noise, but the dominant pattern is cell cycle control in epithelial contexts.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000082","count":5},{"id":"GO:0030245","count":4},{"id":"GO:0046340","count":4},{"id":"GO:0042136","count":4},{"id":"GO:0033598","count":3}]},{"hash":"691359103837026341","title":"Carbohydrate metabolism and energy production","description":"This cluster is dominated by GO terms for glycolysis (GO:0061621), gluconeogenesis (GO:0006094), and related fructose metabolism, NADH-related processes, and overall ATP-oriented activity, pointing to central carbohydrate catabolism and energy generation; auxiliary terms (antibiotic biosynthesis, V-type ATPase assembly) reflect broader microbial metabolism but do not override the core carbohydrate- and energy-focused theme.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":7},{"id":"GO:0061621","count":7},{"id":"GO:0017000","count":6},{"id":"GO:0032781","count":5},{"id":"GO:0030388","count":5}]},{"hash":"2091980298309609244","title":"Unknown","description":"The top GO terms are highly diverse, spanning lipid transport, fungal defense and cell wall processes, enzyme regulation, plant cell wall metabolism, cell division, metal/ hormone responses, and tissue development. There isn\u2019t a single clear functional theme tying these terms together, suggesting the cluster may be functionally heterogeneous or multi-domain, not representing a cohesive module.","confidence":"","size":17,"edges":30,"triangles":17,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006869","count":4},{"id":"GO:0050832","count":4},{"id":"GO:0010951","count":4},{"id":"GO:0045493","count":2},{"id":"GO:0071970","count":1}]},{"hash":"1872503523617583792","title":"Nuclear DNA Replication and Chromatin Regulation","description":"These proteins are annotated with GO terms centered on nucleus-based activities, including regulation of DNA replication, chromatin assembly during replication, maintenance of rDNA, and nuclear import (NLS-bearing proteins). The presence of synaptonemal complex assembly also points to meiotic chromosome organization within the nucleus. A couple of terms (visual learning, gravitropism) seem unrelated and may reflect cross-species annotations, but the dominant signal is nuclear chromatin and replication regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0008542","count":2},{"id":"GO:0006275","count":2},{"id":"GO:0050790","count":2},{"id":"GO:0006335","count":2}]},{"hash":"327883769840169017","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is enriched for ubiquitin-dependent proteolysis, including SCF-dependent proteasomal degradation, K48- and K6-linked ubiquitination, and histone catabolic processes, all pointing to proteasome-mediated protein turnover. Autoubiquitination and various ubiquitin-related regulation terms support roles in signaling and stress responses, but the dominant theme is targeted protein degradation via the ubiquitin\u2013proteasome system.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0031146","count":9},{"id":"GO:0036205","count":8},{"id":"GO:0070936","count":8},{"id":"GO:0051865","count":8}]},{"hash":"381536220649238542","title":"mRNA Splicing and Translation Regulation","description":"This cluster centers on RNA maturation and gene expression control, with strong signals for mRNA splicing (spliceosome, alternative splicing), mRNA modification and stabilization, polyadenylation, and translation initiation (eIF4F complex assembly, IRES-dependent initiation), plus regulatory ncRNA-mediated gene silencing, suggesting a linked program of RNA processing and translation regulation.","confidence":"High","size":17,"edges":81,"triangles":175,"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:1901407","count":10},{"id":"GO:0016556","count":9},{"id":"GO:0048255","count":9}]},{"hash":"1039418477536308404","title":"Unknown","description":"The top GO terms span nervous system development, apoptosis in multiple tissues, immune defense, metabolism, TGF-beta signaling, and other disparate processes. With no interactions among proteins (Edges 0, Triangles 0, Max Degree 0) and no cohesive common theme, there isn\u2019t a clear, single function to name this cluster. Confidence: None","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":5},{"id":"GO:0010659","count":5},{"id":"GO:0035006","count":5},{"id":"GO:0033353","count":5},{"id":"GO:0071560","count":5}]},{"hash":"1657548265633201094","title":"Developmental differentiation and genome maintenance","description":"The top GO terms show clear development-related processes (oligodendrocyte differentiation, dendritic cell differentiation, branching morphogenesis) alongside genome maintenance and cell cycle processes (DNA repair, mitotic cell cycle, telomere maintenance, apoptosis regulation). This mix suggests proteins involved in coordinating developmental differentiation with genome integrity and proliferation control, justifying a label that covers both themes.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048709","count":2},{"id":"GO:0006281","count":2},{"id":"GO:2001200","count":2},{"id":"GO:1902042","count":2},{"id":"GO:0090190","count":2}]},{"hash":"2150583697078583941","title":"Plant development and cuticle biosynthesis regulation","description":"These GO terms cluster around plant developmental processes (floral meristem growth, bract development) and transcriptional regulation, with hormone signaling (ethylene, ABA) and cuticle biosynthesis (wax/cutin). Together they suggest a coordinated plant development program controlling floral structures and cuticle formation through transcriptional regulation and hormone signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010432","count":2}]},{"hash":"824809397942331683","title":"Developmental transcription regulation","description":"Many top terms relate to transcription by RNA polymerase II (and its negative regulation), indicating a transcriptional-control function. Others point to diverse developmental processes (primitive streak formation; inner ear morphogenesis; pharyngeal system development; neuron specification; ureteric bud and organ differentiation). Together they suggest proteins coordinating transcriptional programs during embryonic development and tissue morphogenesis.","confidence":"High","size":17,"edges":43,"triangles":20,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0090009","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0006366","count":4},{"id":"GO:0021902","count":4}]},{"hash":"841207980684499184","title":"Proteostasis and Cell Cycle Regulation","description":"The cluster's top GO terms point mainly to ubiquitin-proteasome\u2013mediated protein turnover (ERAD and SCF-dependent pathways) and processes related to mitotic cell division. While kinase signaling and some metal ion transport terms appear, the clearest, most consistent theme is regulated protein degradation linked to cell-cycle control. ","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0031915","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2}]},{"hash":"306815238850489337","title":"SA-Mediated Defense and Amino Acid Biosynthesis","description":"The cluster features GO terms tied to systemic acquired resistance and salicylic acid signaling, alongside multiple amino acid biosynthetic and catabolic processes (lysine, tyrosine, aspartate, glutamate, and kynurenine/kynurenic acid), plus fatty acid homeostasis. This suggests a functional theme linking defense signaling with core metabolic pathways, rather than a single narrow process, justifying a label that spans both defense and amino acid metabolism.","confidence":"Medium","size":17,"edges":129,"triangles":583,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":7},{"id":"GO:0009102","count":6},{"id":"GO:0019550","count":5},{"id":"GO:0097053","count":5},{"id":"GO:0009862","count":5}]},{"hash":"1368654422638287945","title":"Plant Development and DNA Repair","description":"The terms predominantly point to developmental processes in plants (petal development, organ boundary specification, chorion development) along with DNA maintenance activities (UV-damage excision repair, DNA ligation in recombination, cytokinesis). Although there are outliers and obsolete terms, the overall theme connects development with genome maintenance, suggesting a cohesive, multi-functional cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010199","count":1},{"id":"GO:0048441","count":1},{"id":"GO:0045666","count":1},{"id":"GO:0070914","count":1},{"id":"GO:0060717","count":1}]},{"hash":"1911186401326641071","title":"Growth and division with vesicle trafficking","description":"This cluster combines growth/development terms (multicellular growth, spinal cord development) with cell-cycle and mitotic processes, ribosome biogenesis, and vesicle transport (COPII budding, Golgi-ER traffic). The shared theme centers on cellular growth and proliferation linked to intracellular trafficking and protein synthesis, justifying a label that emphasizes growth/division with vesicle trafficking.","confidence":"Medium","size":17,"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:0090114","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1482435640382554200","title":"Transcription Regulation and Chromatin Remodeling","description":"The top GO terms cluster around transcription control by RNA polymerase II (DNA-templated transcription, regulation of transcription, preinitiation complex assembly) and chromatin dynamics (chromatin remodeling, nucleosome mobilization, heterochromatin formation), with sporulation as a developmental context and some signaling hints. This points to a cohesive theme of regulating gene expression via transcriptional and chromatin mechanisms.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0030435","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0043044","count":2}]},{"hash":"728830277541942219","title":"Mitochondrial Membrane Permeability and Transport","description":"The cluster shows strong enrichment for GO terms tied to mitochondria, including regulation of mitochondrial membrane permeability, mitochondrial ATP transmembrane transport, and apoptotic mitochondrial changes, plus various transport processes (heme, manganese, CoA, thiosulfate) across mitochondrial membranes. This points to a cohesive theme of mitochondrial membrane dynamics and transport as the core function of these proteins, with metabolic signaling links (insulin/IGF stimuli) reinforcing the energy-centric context.","confidence":"High","size":17,"edges":42,"triangles":16,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":7},{"id":"GO:0006828","count":6},{"id":"GO:0061179","count":6},{"id":"GO:1990544","count":6},{"id":"GO:0015886","count":6}]},{"hash":"2032472423037662292","title":"Mitochondrial Translation and tRNA Charging","description":"The cluster is dominated by translation-related GO terms, especially mitochondrial tRNA aminoacylation (histidyl- and threonyl-tRNA charging) and overall translation, plus mitochondrial-specific processes such as respiratory electron transport and mitochondrial DNA metabolism. The presence of selenocysteine biosynthesis terms also links to specialized mitochondrial translation. This suggests the proteins collectively participate in mitochondrial protein synthesis and its regulation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0022904","count":2},{"id":"GO:0016260","count":2},{"id":"GO:0006450","count":2}]},{"hash":"2152204875232996607","title":"Organelle RNA Modification and Plastid Signaling","description":"The cluster centers on RNA editing and modification in mitochondria and chloroplasts, with terms like mitochondrial mRNA processing/modification, cytidine-to-uridine editing, polycistronic mRNA processing, and plastid transcription, plus chloroplast-nucleus signaling, indicating coordinated organelle RNA processing and plastid-to-nucleus communication in plants. A single seed dormancy term appears as a broader developmental context but does not alter the main theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":10},{"id":"GO:0009451","count":10},{"id":"GO:0016554","count":10},{"id":"GO:0080156","count":10},{"id":"GO:1905639","count":10}]},{"hash":"677749340644807623","title":"Immune Activation and Cytokine Production","description":"The top GO terms are dominated by immune-related processes: positive regulation of T cell proliferation, cytokine production (including IL-4), and neutrophil clearance. Additional terms include endothelial cell migration, Rho protein signaling, and protein localization to microtubules, all of which relate to immune cell activation and movement, as well as regulation of programmed cell death in immune contexts. A cartilage condensation term is less central but may reflect developmental overlap; overall, the cluster coherently represents immune activation and inflammatory signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":17},{"id":"GO:0001502","count":17},{"id":"GO:0097350","count":17},{"id":"GO:0035372","count":17},{"id":"GO:0043068","count":17}]},{"hash":"2181222859488956884","title":"T cell activation and cytokine signaling","description":"The top GO terms are dominated by immune-related processes, including positive regulation of T cell proliferation, interleukin-4 production, and positive regulation of cytokine production, along with neutrophil clearance. While a few terms touch on development or cytoskeletal localization, the strongest signal points to immune activation and cytokine-mediated regulation, justifying a label centered on T cell and cytokine signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":17},{"id":"GO:0001502","count":17},{"id":"GO:0097350","count":17},{"id":"GO:0035372","count":17},{"id":"GO:0043068","count":17}]},{"hash":"615026392961787297","title":"RNA Pol II Transcription Regulation","description":"Most of the topGO terms center on transcription by RNA polymerase II and its regulation, suggesting the proteins in this cluster are enriched for transcription initiation and control activities. Several terms indicate regulatory processes affecting transcription (positive/negative regulation, DNA-templated transcription), supporting a cohesive theme of transcriptional control. A few outliers relate to differentiation and immune signaling, which may reflect broader transcriptional regulatory roles across contexts.","confidence":"Medium","size":17,"edges":25,"triangles":6,"max_degree":11,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0010691","count":3},{"id":"GO:0032915","count":3}]},{"hash":"925741676252140630","title":"Plant cuticle and secondary metabolite biosynthesis","description":"The terms cluster around plant-specific biosynthetic processes (cutin, lignin, flavonoids, and hydroxycinnamate conjugates) and auxin homeostasis, with ROP/Rho signaling supporting plant-specific development; together they point to plant cuticle formation and phenylpropanoid metabolism as the core theme, despite a few general processes being present.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":7},{"id":"GO:0010143","count":7},{"id":"GO:0080088","count":7},{"id":"GO:0009809","count":7},{"id":"GO:0009963","count":7}]},{"hash":"729432337288363400","title":"Developmental and neuronal signaling","description":"The top GO terms suggest involvement in embryonic and organ development (mesoderm formation, heart and skeletal system development) together with nervous system development and synaptic processes (long-term potentiation), plus signaling (Rho pathway) and calcium-dependent exocytosis. While a couple terms point to general cellular processes, the overall theme appears to be development coupled with neural signaling and regulation, justifying a combined label that is specific yet broad enough to cover the cluster\u2019s functions.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001707","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0007266","count":3},{"id":"GO:0007507","count":3}]},{"hash":"668386692718621114","title":"Basic cellular metabolism and gene expression","description":"The terms cluster around fundamental cellular processes, including protein synthesis (translation and translational fidelity), transcription, and carbohydrate metabolism (fructose/glucose phosphate pathways and fructose import), plus a membrane protein modification process (GPI anchor biosynthesis). This mix suggests a general cellular maintenance module rather than a single, specific pathway, hence a label capturing both expression and metabolism.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010050","count":2}]},{"hash":"1174990689228492841","title":"Ubiquitin-dependent protein degradation and receptor turnover","description":"Most frequent GO terms center on tagging and degrading proteins via ubiquitination (ubiquitin-dependent protein catabolic process, autoubiquitination, K48-linked ubiquitination, ERAD). The presence of Wnt receptor catabolic process reinforces a theme of ubiquitin-driven receptor turnover. Some terms about peroxisome import and X-chromosome dosage compensation seem less connected, likely noise or distant associations.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051865","count":10},{"id":"GO:0030433","count":10},{"id":"GO:0038018","count":9},{"id":"GO:0070936","count":9}]},{"hash":"1844229131076070274","title":"Secretory peptide maturation and endocytic signaling","description":"This cluster centers on peptide hormone processing (insulin processing; peptide pheromone maturation) and secretion (renin secretion) as well as receptor-mediated endocytosis and regulation of cholesterol transport (LDL receptor pathways). Although some terms are plant- or embryo-specific (stomatal morphogenesis; zygotic axis), the common thread appears to be secretory/peptide maturation processes and endocytic trafficking that modulate signaling, which justifies a unified label around secretory peptide maturation and endocytic signaling.","confidence":"Medium","size":17,"edges":20,"triangles":4,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0010103","count":9},{"id":"GO:0030070","count":9},{"id":"GO:0007323","count":9},{"id":"GO:0032805","count":9},{"id":"GO:0032804","count":9}]},{"hash":"2002569030127964277","title":"Plant membrane transporters and stomatal regulation","description":"The top GO terms point to multiple plasma membrane transport activities (succinate, malate, malonic acid, sulfite) alongside environmental-response terms such as regulation of stomatal opening and responses to CO2 and humidity. This pattern suggests a module of transporter proteins mediating metabolite uptake and stomatal signaling, with ion homeostasis supporting the transport function. The presence of an outlier term like neurotransmitter secretion may be noise or cross-annotation, but the dominant theme is membrane transport linked to stomatal and environmental response.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007269","count":2},{"id":"GO:0009395","count":2},{"id":"GO:0098720","count":1},{"id":"GO:0010037","count":1},{"id":"GO:0009270","count":1}]},{"hash":"1440100711931277191","title":"Chromatin regulation and viral lifecycle factors","description":"This cluster centers on transcription regulation and chromatin remodeling (regulation of DNA-templated transcription, DNA-templated transcription, nucleosome disassembly, histone acetylation) and includes RNA processing and several viral-life-cycle terms (virion assembly, viral release, proviral latency). The mix suggests proteins involved in transcription/chromatin control with connections to viral processes or host-virus interactions, rather than a single cohesive pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071442","count":2},{"id":"GO:0006337","count":2},{"id":"GO:0019068","count":1}]},{"hash":"2290666136620492132","title":"Developmental gene regulation and neural differentiation","description":"The cluster is enriched for development-related GO terms (pituitary gland development, multicellular organism development, primitive streak formation, neural differentiation) and transcriptional control (regulation of DNA-templated transcription, transcription by RNA polymerase II), pointing to proteins involved in developmental gene expression programs and neural lineage specification. Some terms like nitrate assimilation, oxidation-reduction, and ABA response are less connected and may reflect annotation noise, but the dominant signal supports a developmental transcriptional theme.","confidence":"Medium","size":17,"edges":39,"triangles":22,"max_degree":10,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":8},{"id":"GO:0007275","count":7},{"id":"GO:0006355","count":7},{"id":"GO:0006366","count":6},{"id":"GO:0090009","count":6}]},{"hash":"286080149810591816","title":"Unknown","description":"TheGO terms are highly diverse, spanning endosomal transport, viral processes, plant development, hormone signaling, and transcription, with no single dominant function uniting the proteins. There are no edges or clear interactions in the cluster, and the terms come from disparate biological contexts, making a cohesive theme unlikely. Therefore, Unknown with None. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032511","count":1},{"id":"GO:0048672","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0009838","count":1}]},{"hash":"454127775581620428","title":"Clathrin-mediated endocytosis and vesicle trafficking","description":"The strongest signals in this cluster point to clathrin-dependent processes: endocytosis, clathrin coat assembly, and synaptic vesicle maturation, with related regulation of EGFR signaling. While there are a couple of transcription-related terms and an iron transport term, the dominant theme is vesicle trafficking and clathrin-mediated internalization, making this label representative though not exclusively exclusive of other functions. ","confidence":"Medium","size":17,"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:0006915","count":1},{"id":"GO:0098711","count":1},{"id":"GO:2000369","count":1}]},{"hash":"1747798705620434766","title":"Plant Hormone Signaling and Defense Development","description":"The terms highlight plant hormone signaling (gibberellin, salicylic acid, and ethylene precursor ACC) and its regulatory roles, alongside developmental processes such as atrichoblast and sclerenchyma differentiation, and defense-related responses to chitin and fungal invasion. This combination suggests a cluster of proteins tied to hormone-mediated development and immune readiness in plants.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080169","count":1},{"id":"GO:0009961","count":1},{"id":"GO:0010055","count":1},{"id":"GO:0009751","count":1},{"id":"GO:0009739","count":1}]},{"hash":"1116064903615101826","title":"Oocyte maturation and meiotic spindle assembly","description":"This cluster is dominated by GO terms for oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, with supporting SCF-dependent ubiquitin\u2013proteasomal protein degradation; these together suggest a coherent role in oocyte meiosis and spindle dynamics, despite a few broader developmental terms present. ","confidence":"High","size":17,"edges":36,"triangles":7,"max_degree":7,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0001556","count":6},{"id":"GO:0046785","count":6},{"id":"GO:0006516","count":6},{"id":"GO:0007057","count":6}]},{"hash":"661511211700181262","title":"Oocyte Meiosis and Spindle Assembly","description":"The terms show strong enrichment for oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, with proteolysis via SCF-ubiquitin-proteasome machinery shaping meiosis progression. A few neural development terms appear, but the core signal points to meiotic division and spindle dynamics in oocytes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031146","count":10},{"id":"GO:0001556","count":8},{"id":"GO:0046785","count":8},{"id":"GO:0006516","count":8},{"id":"GO:0007057","count":8}]},{"hash":"362348388365968080","title":"Meiosis spindle assembly and oocyte maturation","description":"The cluster shows strong enrichment for processes tied to meiotic progression in oocytes: SCF-dependent ubiquitin-proteasome\u2013mediated protein catabolic activity, microtubule polymerization, spindle assembly in female meiosis I, and explicit oocyte maturation. While a few neural development terms appear, the dominant signals point to a core module governing protein turnover, cytoskeletal dynamics, and meiotic maturation in oocytes. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0046785","count":9},{"id":"GO:0007057","count":9},{"id":"GO:0021678","count":9},{"id":"GO:0006516","count":9}]},{"hash":"1463721381491834316","title":"Oocyte Meiosis with Spindle Assembly and Proteasome Degradation","description":"The dominant GO terms point to meiosis/oocyte maturation, spindle assembly in female meiosis I, and microtubule dynamics, all tied together by ubiquitin-proteasome\u2013mediated protein degradation. This suggests a core theme of meiotic cell division coupled with proteostasis; a few neural development terms appear peripheral to this main signal. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":12},{"id":"GO:0001556","count":9},{"id":"GO:0046785","count":9},{"id":"GO:0006516","count":9},{"id":"GO:0007057","count":9}]},{"hash":"373205377860788011","title":"Sphingolipid Signaling and Metabolism","description":"These proteins strongly associate with sphingolipid and lipid metabolic processes, including sphingoid catabolic and diacylglycerol pathways, and lipid signaling (GPCR/thrombin signaling, lipid phosphorylation). The presence of terms related to angiogenesis, fibroblast proliferation, and IL-1\u03b2 production suggests a lipid-mediated signaling module involved in vascular and inflammatory regulation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0046521","count":3},{"id":"GO:0046339","count":3},{"id":"GO:2000182","count":3},{"id":"GO:0045766","count":3},{"id":"GO:0048146","count":3}]},{"hash":"177769298558104582","title":"Plant cell wall biosynthesis and modification","description":"This cluster is enriched for plant-type secondary cell wall biogenesis, xyloglucan and xylan biosynthetic processes, and cell wall modification, suggesting a cohesive role in constructing and remodeling the plant cell wall. Some terms about freezing response and storage carbohydrates appear but are likely secondary to the dominant cell wall-related functions.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":4},{"id":"GO:0010411","count":3},{"id":"GO:0009827","count":3},{"id":"GO:0050826","count":3},{"id":"GO:0045492","count":3}]},{"hash":"1336451047594672358","title":"T Cell Activation and Cytokine Regulation","description":"Top terms point to adaptive immune activation (T cell proliferation, IL-4 production, cytokine regulation) with related inflammation and tissue remodeling (neutrophil clearance, endothelial migration). While a couple terms are non-immune, the shared theme is immune activation and cytokine signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":17},{"id":"GO:0001502","count":17},{"id":"GO:0097350","count":17},{"id":"GO:0035372","count":17},{"id":"GO:0043068","count":17}]},{"hash":"248847123335243535","title":"Neuronal vesicle trafficking and synaptic signaling","description":"The cluster shows strong representation of neuronal-specific processes: intracellular protein transport, regulation of GABAergic synaptic transmission, neurotransmitter secretion, and brain development. Additional terms related to calcium-regulated lysosome exocytosis and Ras/Rho signaling modulations suggest coordination of signaling pathways with vesicle trafficking. Lipid biosynthesis (phosphatidylethanolamine and phosphatidylcholine) supports membrane dynamics essential for vesicle budding and release, further linking to the synaptic function theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":6},{"id":"GO:0032228","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0006646","count":4}]},{"hash":"2054156619135238980","title":"Plant Nutrient Transport and Hormone Signaling","description":"The cluster centers on plant-specific processes: nitrate transport and assimilation, oligopeptide/dipeptide transport, and hormone signaling (auxin-activated pathways and gibberellin homeostasis), complemented by defense responses to fungus and herbicides and seed coat mucilage biosynthesis, suggesting a coherent theme of nutrient handling coupled with growth and stress responses in plants.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0010336","count":2},{"id":"GO:0035672","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0080055","count":2}]},{"hash":"402598576858123967","title":"Unknown","description":"The GO terms span metabolism (cellulose catabolic process, gluconeogenesis), proteolysis, autophagy regulation, metal detoxification (phytochelatin), and biofilm formation, with an outlier term for synapse assembly. These diverse functions do not point to a single coherent theme or biological role for the cluster, so a specific label is not justifiable.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0006094","count":2},{"id":"GO:0043085","count":2},{"id":"GO:0046938","count":2},{"id":"GO:0006508","count":2}]},{"hash":"1480580041989850343","title":"Innate immune signaling and NF-kappaB regulation","description":"The strongest recurring themes are NF-kappaB regulation, NOD2 signaling, and proteasome-related processes, which together point to innate immune signaling and NF-kappaB pathway control; other terms (mRNA processing, oligodendrocyte differentiation, thermoception, vitamin D response) appear as less direct associations or broad annotations, indicating a mostly immune-signaling cluster with some noise.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006397","count":5},{"id":"GO:0032088","count":5},{"id":"GO:0033280","count":4},{"id":"GO:0050955","count":4},{"id":"GO:0070682","count":4}]},{"hash":"1591481327089488687","title":"Plant cell wall biosynthesis and freezing response","description":"The dominant GO terms\u2014xyloglucan metabolic process, xylan biosynthetic process, and plant-type secondary cell wall biogenesis\u2014point to proteins involved in cell wall synthesis and remodeling. The accompanying term, response to freezing, suggests these proteins also participate in plant cold-stress adaptation, indicating a cohesive cluster of cell wall\u2013related factors enriched for cold response. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010411","count":4},{"id":"GO:0009827","count":4},{"id":"GO:0050826","count":4},{"id":"GO:0045492","count":4},{"id":"GO:0009834","count":4}]},{"hash":"1938469025510883475","title":"Synaptic signaling and plasticity","description":"The top GO terms cluster around neuronal communication and plasticity: ionotropic glutamate receptor signaling, regulation of synaptic vesicle fusion, cellular response to electrical stimulus, and long-term neuronal synaptic plasticity. Sensory processing terms like visual learning and phototaxis, plus prepulse inhibition and ethanol response, reinforce a neural signaling/theme. A couple of terms about imaginal disc morphogenesis and cell wall organization seem peripheral, but the core signal is clearly synaptic signaling and experience-dependent plasticity.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":1},{"id":"GO:0008542","count":1},{"id":"GO:0060134","count":1},{"id":"GO:0007476","count":1},{"id":"GO:0035235","count":1}]},{"hash":"775635762888796967","title":"Regulation of Plant Growth and Metabolism","description":"These proteins appear enriched for GO terms that describe regulatory roles across multiple plant processes (regulation of chlorophyll biosynthesis, seed growth, lignin biosynthesis, secondary cell wall biogenesis, root meristem growth, leaf senescence, and chromatin/telomere localization). The common thread is the act of regulation rather than a single biosynthetic pathway, suggesting the cluster represents factors modulating plant development and metabolism rather than a specific metabolic route.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010380","count":1},{"id":"GO:0080113","count":1},{"id":"GO:1901430","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0010082","count":1}]},{"hash":"1513914971398773982","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000492","count":2},{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0090502","count":2}]},{"hash":"1118966344871024528","title":"Unknown","description":"The terms span muscle development (skeletal muscle fiber development, ventricular heart tissue morphogenesis), immune processes (type 2 immune response, germinal center formation, regulation of mast cell cytokine production), and RNA modification (tRNA/rRNA pseudouridine synthesis), plus circadian rhythm and a plant-embryo term, with no clear single functional theme. The lack of edges/structure suggests no cohesive biological module, so a generic Unknown label is most appropriate.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0055010","count":2},{"id":"GO:0009793","count":2},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1}]},{"hash":"339708223912007150","title":"Exocyst-Mediated Vesicle Trafficking","description":"The dominant GO terms point to vesicle trafficking and secretion: exocytosis, Golgi to plasma membrane/vacuole transport, exocyst localization/assembly, and general protein transport, all coordinated by Rho signaling. A few terms about differentiation regulation are present but likely incidental to the core trafficking theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048712","count":2},{"id":"GO:0048715","count":2},{"id":"GO:0006896","count":2},{"id":"GO:0051601","count":1},{"id":"GO:0006887","count":1}]},{"hash":"2032836779672177559","title":"Transcriptional regulation of floral development and cuticle biosynthesis","description":"The cluster shows strong signals for DNA-templated transcription and its regulation, coupled with plant-specific developmental terms such as floral meristem growth and bract development, and epidermal barrier biosynthesis (wax and cutin). The inclusion of hormone signaling terms (ethylene and ABA) further supports a cohesive role in coordinating floral development with cuticle formation and epidermal responses.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":6},{"id":"GO:0010451","count":3},{"id":"GO:0009873","count":3},{"id":"GO:0010432","count":3}]},{"hash":"1750661216759217214","title":"ER-Golgi Vesicle Trafficking","description":"The top GO terms center on vesicle movement between the ER and Golgi (anterograde and retrograde transport) and related trafficking steps (endocytosis, Golgi to vacuole, and synaptic vesicle budding), indicating intracellular vesicle trafficking as the cluster\u2019s core function, with a few outlier terms reflecting broader roles in pigmentation or neural development.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1374493043674825051","title":"Unknown","description":"The listed GO terms span diverse biological themes, including innate immune sensing (TLR8 signaling, detection of LPS, response to fungus) and cytokine regulation, vascular processes, kidney development, dopamine signaling, neural/vestibular functions, and reproductive apoptosis. There isn\u2019t a single coherent function or pathway tying all proteins together, making a specific, representative label difficult.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0010596","count":17},{"id":"GO:0009620","count":17},{"id":"GO:0050929","count":17},{"id":"GO:0072237","count":17},{"id":"GO:0050707","count":17}]},{"hash":"954299267124239331","title":"Unknown","description":"The top GO terms are highly diverse and partially conflicting, including immune signaling (TLR8 signaling, NOD-like receptor signaling, regulation of cytokine production, response to fungus) alongside unrelated terms about plant and kidney development (lateral root morphogenesis, metanephric proximal tubule development) and reproductive processes. With no shared, cohesive function across the 17 proteins and zero edges, there isn\u2019t a clear, representative theme to name the cluster beyond Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010102","count":2},{"id":"GO:0010596","count":1},{"id":"GO:0009620","count":1},{"id":"GO:0050929","count":1},{"id":"GO:0072237","count":1}]},{"hash":"1618714150996831950","title":"Microtubule dynamics and cytoskeleton organization","description":"The terms are dominated by microtubule-related processes\u2014centrosome separation, meiotic spindle orientation, and regulation of microtubule-based processes\u2014plus axonemal microtubule depolymerization and cytoskeleton polarity, with some neuron-structure hints (cerebellar layer organization). This points to a coherent theme of microtubule regulation shaping cell division, polarity, and neuronal architecture.","confidence":"High","size":16,"edges":90,"triangles":277,"max_degree":15,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007100","count":14},{"id":"GO:0051296","count":14},{"id":"GO:0032886","count":14},{"id":"GO:0001560","count":14},{"id":"GO:0035617","count":14}]},{"hash":"2110535555426094354","title":"Plant cell wall synthesis and carbohydrate metabolism","description":"The top GO terms cluster around plant-type secondary cell wall biogenesis, cellulose biosynthesis, and cell wall organization, with additional carbohydrate metabolism processes (sucrose, starch, maltose, glycogen). This suggests proteins involved in building plant cell walls and general sugar metabolism, even though the network shows no edges. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":3},{"id":"GO:0071555","count":2},{"id":"GO:0006011","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0051692","count":2}]},{"hash":"1804748882550176229","title":"Neural development and hypoxia-responsive cell-cycle regulation","description":"The top GO terms point to neural development (neural tube closure, forebrain development) combined with stress-response pathways (hypoxia, TGF-beta signaling) and checks on cell cycle and apoptosis (cell division, regulation of cell cycle, regulation of apoptotic signaling). This suggests a cluster of proteins involved in neural development integrated with hypoxia-related signals and cell-cycle/apoptosis control.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0001843","count":2},{"id":"GO:0035948","count":2}]},{"hash":"1654147272999397196","title":"Spliceosome-Mediated mRNA Splicing","description":"These proteins are enriched for GO terms centered on mRNA splicing via the spliceosome, including cis splicing and positive regulation of splicing, indicating a core splicing machinery/processing function. While there are additional terms related to transcription initiation and other RNA-based processes, the strongest and most representative signal is spliceosome-driven RNA splicing.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0006367","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0048026","count":3}]},{"hash":"1705978525505348459","title":"DNA metabolism and developmental-immune signaling","description":"The top GO terms point to core DNA processing activities (replication, transcription, repair, mitotic cell cycle) alongside diverse developmental processes (nervous system development, dendrite morphogenesis, embryonic cranial skeleton morphogenesis) and immune/migration signals (B cell receptor signaling, chemotaxis). This suggests a cluster of proteins involved in DNA metabolism that also participate in or coordinate developmental and immune-related pathways. Confidence: Medium","confidence":"","size":16,"edges":8,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":14},{"id":"GO:0006351","count":13},{"id":"GO:0006281","count":12},{"id":"GO:0007399","count":12},{"id":"GO:0048813","count":12}]},{"hash":"805643066179780267","title":"Antiviral Defense Signaling and Autophagy","description":"The top GO terms cluster around defense response to virus, activation of NF-kappaB signaling, ubiquitination, autophagy, and membrane repair, all of which are central to host antiviral responses and cellular stress remodeling. The combination of NF-kB\u2013related signaling, protein ubiquitination, and autophagy points to innate immune signaling and vesicle/homeostasis processes that limit viral infection, rather than a single metabolic pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0016567","count":3},{"id":"GO:1901253","count":2}]},{"hash":"1164392959294402693","title":"Plant innate immune signaling and defense","description":"Although some terms reflect general cellular processes (cell division, transcription) or odd annotations (spinal cord development), the strongest common thread is plant immunity: defense response to bacterium, plant-type hypersensitive response, and innate immune response-activating signaling pathway. Other terms like pollination, aluminum cation transport, and growth appear less central and may represent background functions or annotation noise. Overall, the cluster seems to group proteins involved in plant innate immune signaling and defense.","confidence":"Medium","size":16,"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:0009856","count":1},{"id":"GO:0015690","count":1},{"id":"GO:0034051","count":1}]},{"hash":"146112166428887647","title":"Plant signaling, development, and defense","description":"The top GO terms cluster around signaling pathways (positive regulation of GTPase activity, GPCR signaling), developmental processes (multicellular organism development, pollination), and defense responses (defense response to fungus), with additional hints from protein interactions and exocytosis. These collectively suggest a set of plant proteins involved in coordinating growth, reproduction, and immunity, though the mix of diverse terms and the lack of interaction data mean the assignment is plausible but not narrowly defined.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0009856","count":1}]},{"hash":"2144197633394138403","title":"Unknown","description":"The terms span across multiple kingdoms and disparate processes (transcription regulation, cell wall biogenesis, various ion transports, sporulation, antibiotic biosynthesis, platelet activation), with no single unifying function. This wide mix suggests no coherent cluster theme can be discerned from the GO terms, so the label Unknown is appropriate.","confidence":"","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":4},{"id":"GO:1901348","count":4},{"id":"GO:0006825","count":4},{"id":"GO:0034755","count":4},{"id":"GO:0030435","count":4}]},{"hash":"1009303170820930912","title":"Unknown","description":"The top terms come from a wide mix of processes across plants and animals (cardiac regulation, multicellular development, flower patterning, skin development) plus plant cell wall and polysaccharide metabolism (alginic/pectin catabolism, cell wall organization) and mitochondrial RNA processing. There is no clear, shared function tying these 16 proteins together, suggesting annotation noise or a heterogeneous cluster rather than a single cohesive theme.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0042121","count":3},{"id":"GO:0060773","count":3}]},{"hash":"1474289630367129694","title":"DNA Replication and Cell Cycle Regulation","description":"This cluster is dominated by GO terms for DNA replication, DNA-templated transcription, DNA repair, and mitotic processes, plus centrosome cycle and centrosome separation, pointing to nuclear DNA processing and mitotic control as the core theme. A few terms related to development or immune-related proliferation appear but are likely peripheral annotations, with the main signal centered on replication and cell cycle regulation.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0048701","count":9},{"id":"GO:0007100","count":9},{"id":"GO:0046827","count":9}]},{"hash":"1759585614657150281","title":"Microtubule assembly and signaling-driven cytoskeletal remodeling","description":"This cluster centers on microtubule nucleation and spindle assembly (mitotic spindle pole body duplication) and includes terms tied to cytoskeletal regulation (cell shape) as well as signaling and vesicle trafficking (cAMP/epinephrine responses and exocytosis). The mix suggests proteins coordinating spindle/cytoskeleton dynamics with signaling pathways and post-translational regulation (dephosphorylation, sumoylation). Confidence: Medium","confidence":"","size":16,"edges":60,"triangles":85,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007020","count":9},{"id":"GO:1903087","count":9},{"id":"GO:0043388","count":8},{"id":"GO:0006470","count":7},{"id":"GO:0014850","count":7}]},{"hash":"505455486758715392","title":"ER Stress Response and Protein Trafficking","description":"The top GO terms show a cluster centered on ER stress\u2013related regulation, including positive regulation of translation initiation in response to ER stress, COPII-coated vesicle budding (ER-to-Golgi trafficking), and K11-linked ubiquitination as part of protein quality control. Phosphorylation/dephosphorylation also points to regulatory signaling linked to stress responses. While some terms like DNA repair and viral processes are less coherent with this theme, the strongest signal ties to ER stress\u2013driven proteostasis and trafficking mechanisms, suggesting proteins involved in managing protein folding, degradation, and transport under stress.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0009405","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0016310","count":3}]},{"hash":"1649962841436816683","title":"Neural development and synaptic signaling","description":"The top GO terms point to neural-related functions: axonogenesis, visual perception, Schwann cell development, excitatory postsynaptic potentials, and regulation of synaptic vesicle exocytosis/endocytosis, indicating a theme of neural development and synaptic activity. A few terms (mitotic cell cycle, apoptosis, abscisic acid signaling, heart development) seem peripheral or annotated broadly, likely representing background processes rather than core cluster function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0060079","count":3},{"id":"GO:2000300","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0043065","count":2}]},{"hash":"2086796228116160526","title":"Neuronal vesicle trafficking and spine morphogenesis","description":"The top GO terms cluster around regulation of synaptic vesicle exocytosis, dendritic spine morphogenesis, and hippocampus development, with supporting signals from actin remodeling (lamellipodium/ruffle assembly) and membrane trafficking. Together these suggest roles in synaptic vesicle transport and the structural development/modulation of neuronal synapses, despite some broader/obsolete terms present. ","confidence":"High","size":16,"edges":27,"triangles":5,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":8},{"id":"GO:0031384","count":8},{"id":"GO:0010796","count":8},{"id":"GO:0097178","count":7},{"id":"GO:0000060","count":7}]},{"hash":"2123554033028081901","title":"Host Immune Signaling and Autophagy Regulation","description":"The top GO terms cluster around modulation of immune signaling (LPS-mediated pathways, MIP-1 alpha production), autophagy, and membrane/vesicular dynamics, suggesting these proteins regulate host defense and intracellular turnover in response to stress or pathogens. Some terms reflect broader signaling regulation (IGF, vitamin D receptor) and membrane repair, with a couple of outliers like short-day photoperiodism and viral entry regulation, which may reflect pleiotropy or annotation noise. Overall, the common theme appears to be regulation of immune signaling and autophagy-related processes, giving a plausible, coherent label.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":2},{"id":"GO:0046598","count":2},{"id":"GO:0048572","count":2},{"id":"GO:0006914","count":2},{"id":"GO:0007026","count":2}]},{"hash":"583419161260222157","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0010923","count":1},{"id":"GO:0006869","count":1},{"id":"GO:0050832","count":1}]},{"hash":"160276278870454375","title":"Cytokinin-Regulated Plant Growth and Chlorophyll/Seed Biosynthesis","description":"The top GO terms are centered on cytokinin-activated signaling and regulation of key developmental processes in plants (chlorophyll biosynthesis, seed growth, root meristem growth, and leaf senescence) as well as regulation of cell wall biosynthesis (lignin, secondary cell wall). This points to a cohesive theme of cytokinin-driven regulation of plant growth and metabolism, rather than a single enzymatic function, justifying a label that emphasizes cytokinin-mediated developmental regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":9},{"id":"GO:0010380","count":7},{"id":"GO:0080113","count":7},{"id":"GO:1901430","count":7},{"id":"GO:1901347","count":7}]},{"hash":"1313304106369912622","title":"Bacterial LPS core and sugar-nucleotide biosynthesis","description":"The top GO terms cluster around lipopolysaccharide biosynthesis and related sugar-nucleotide pathways (LPS core region, ADP-L-glycero-manno-heptose, dTDP-rhamnose, GDP-mannose), plus other bacterial polysaccharide-related processes (poly-hydroxybutyrate biosynthesis, antibiotic biosynthesis). This suggests a coherent theme of bacterial envelope component and nucleotide-sugar biosynthesis. The lone plant-specific term (anthocyanin-containing compound biosynthesis) appears to be noise. ","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0009718","count":6},{"id":"GO:0009244","count":5},{"id":"GO:0009103","count":5},{"id":"GO:0042619","count":5}]},{"hash":"1619485068029225469","title":"Unknown","description":"The top GO terms are highly diverse, spanning biosynthetic processes (riboflavin, heme), plant-specific cell wall assembly, fatty acid transport, ubiquitination/deubiquitination, and various immune-related responses. With only a couple of edges and no clear shared function, the cluster does not converge on a single biological theme, suggesting noise or mixed annotations rather than a cohesive module.","confidence":"","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009231","count":1},{"id":"GO:0071668","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0070453","count":1}]},{"hash":"660925534717390802","title":"G2/M Cell Cycle Regulation in Epithelial Proliferation","description":"The top GO terms point to strong involvement in G2/M transition, mitosis, and cell division (e.g., GO:0000086, GO:0010389, GO:0051301) together with mammary gland epithelial cell proliferation (GO:0033598) and regulation of CDK activity, indicating a cluster focused on cell cycle control driving epithelial proliferation. Some terms touch on broader differentiation signals (e.g., Leydig cell differentiation, epithelial differentiation), and an outlier related to early viral transcription, but the dominant theme remains cell cycle\u2013linked proliferation in epithelial contexts.","confidence":"Medium","size":16,"edges":20,"triangles":1,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033598","count":4},{"id":"GO:0030857","count":4},{"id":"GO:0010389","count":4},{"id":"GO:0000086","count":4},{"id":"GO:0019085","count":4}]},{"hash":"640138258318475269","title":"Unknown","description":"The top GO terms are highly diverse, spanning plant cell wall biosynthesis, corneocyte development, apoptotic process, peptide hormone signaling, DNA recombination, lipid signaling, and metabolic regulation, with several entries being obsolete. There is no single cohesive function or theme connecting these proteins, so a specific, representative label cannot be assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":5},{"id":"GO:0071555","count":4},{"id":"GO:0009834","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0046856","count":3}]},{"hash":"242561577417464780","title":"Bacterial lipid and steroid metabolism","description":"The top GO terms cluster around lipid-related biosynthesis and metabolism: lipopolysaccharide biosynthesis, mycolic acid biosynthesis, retinol metabolic process, testosterone biosynthetic process, and androgen metabolic process, along with polyhydroxybutyrate biosynthesis and acetoin catabolic processes typical of bacterial metabolism. This suggests a theme of lipid and small-molecule biosynthesis/metabolism in bacteria. Some entries (e.g., regulation of transcription, antibiotic response) are broader or ancillary and do not reflect a unifying lipid/steroid theme, leaving some noise around the core signal. ","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0042619","count":6},{"id":"GO:0046677","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0045150","count":4}]},{"hash":"276891892966509365","title":"Immune signaling and lymphocyte activation","description":"The top terms cluster around immune signaling and lymphocyte activity: JNK cascade, B cell receptor signaling, interleukin-4 production, and T cell proliferation, with additional terms for neutrophil clearance and apoptosis regulation. These collectively point to adaptive immune activation and regulation, despite some ancillary terms like angiogenesis and DNA repair that may reflect broader stress responses linked to immune contexts. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007254","count":6},{"id":"GO:0045766","count":6},{"id":"GO:0014068","count":6},{"id":"GO:0006281","count":5},{"id":"GO:0032436","count":5}]},{"hash":"2173166534572944292","title":"Plant Developmental Transcription Regulators","description":"This cluster is enriched for DNA-templated transcription and regulation of transcription, along with ABA- and ethylene-activated signaling, seed development, floral meristem growth, bract development, and wax biosynthesis regulation. The combination points to plant developmental control by transcriptional regulators responsive to hormone signaling, rather than core metabolic enzymes, hence a label emphasizing plant developmental transcription regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0009738","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0048316","count":3},{"id":"GO:0043966","count":3}]},{"hash":"988117773066354809","title":"Plant Hormone Signaling and Stress Responses","description":"The top GO terms center on plant-specific signaling and defense: cytokinin-activated signaling, gibberellin response, salicylic acid response, and far-red light signaling indicate hormone and light-regulated pathways; chitin response and phytochelatin biosynthesis point to defense and metal-detox processes in plants. While some entries (e.g., sporulation) are less typical for plants, the overall theme is coherent around plant hormone signaling coupled with stress responses and defense.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":3},{"id":"GO:0046938","count":3},{"id":"GO:0006508","count":3},{"id":"GO:1904715","count":3},{"id":"GO:0030435","count":2}]},{"hash":"1361706217078424282","title":"Mitotic control and ubiquitin-proteasome regulation","description":"The cluster is dominated by GO terms tied to cell-cycle control: negative regulation of cell proliferation, spindle/polynomial assembly in meiosis, regulation of DNA replication initiation, and mitotic G1 checkpoint signaling, along with robust indications of ubiquitin-dependent proteolysis including SCF-mediated pathways. Together these point to a group of proteins coordinating cell-cycle progression and targeted degradation, with some secondary associations to circadian and metal-stress responses. Confidence in this being the core theme is High.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":4},{"id":"GO:0042752","count":3},{"id":"GO:0046785","count":3},{"id":"GO:0007057","count":3},{"id":"GO:0030174","count":3}]},{"hash":"2095845620404315489","title":"Steroid and lipid hormone biosynthesis and metabolism","description":"The top GO terms cluster around biosynthesis of lipid-derived hormones (cortisol, testosterone, brassinosteroids) and related metabolic/detoxification pathways (retinoic acid catabolism, vitamin D response, fatty acid omega-oxidation, xenobiotic metabolism). This suggests proteins in the group participate in lipid-hormone production, processing, and detoxification across species, with additional terms like mammary gland development and endothelial adhesion likely reflecting downstream hormone-regulated processes. Therefore, a unifying label is steroid and lipid hormone biosynthesis and metabolism.","confidence":"Medium","size":16,"edges":12,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":16},{"id":"GO:0071603","count":16},{"id":"GO:0034651","count":16},{"id":"GO:0070989","count":16},{"id":"GO:0042738","count":16}]},{"hash":"922690512621177085","title":"Membrane Transporters","description":"The cluster shows a strong enrichment for transmembrane transport activities across diverse substrates (sialic acid, urate, galactose, vitamins, 4-hydroxyphenylacetate) and for neurotransmitter loading into synaptic vesicles, pointing to a common theme of membrane transport proteins and vesicular transport components. A few terms like cell division are less related and may reflect background annotations. Overall, the dominant pattern is transport across membranes.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0051301","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0015747","count":3}]},{"hash":"393174317480223834","title":"Transcriptional Regulation in Development","description":"This cluster features multiple GO terms tied to regulation of transcription (GO:0006355, GO:0006351) and several developmental processes (uterus development, digestive tract development, female gonad development), suggesting a general theme of gene expression control during development. Additional terms point to regulatory layers such as proteolysis and autophagy regulation, which fits with proteins involved in controlling cellular functions rather than a single metabolic pathway. Some plant-specific terms (phytochelatin biosynthetic process, camphor catabolic process) appear but do not define a cohesive single pathway, so the main recognizable theme is transcriptional regulation in development. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0043085","count":4},{"id":"GO:0046938","count":4},{"id":"GO:0006508","count":4},{"id":"GO:1904715","count":4},{"id":"GO:0006355","count":3}]},{"hash":"80757453409189296","title":"Unknown","description":"The top GO terms span neural development (forebrain and nervous system development) and glial apoptosis, but also include diverse, seemingly unrelated processes (cardiac muscle cell apoptosis, melanization defense, L-methionine cycle, salivary gland histolysis, TGF-beta response, obsolete aging terms). With no clear single functional theme and no network connectivity, there isn\u2019t a coherent label to represent this cluster beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":13},{"id":"GO:0010659","count":13},{"id":"GO:0035006","count":13},{"id":"GO:0033353","count":13},{"id":"GO:0071560","count":13}]},{"hash":"2091265105596522217","title":"Glycolysis and autophagy regulation","description":"The most represented terms point to energy metabolism (glycolytic process, carbohydrate phosphorylation, fructose 2,6-bisphosphate metabolism, PPP shunt), with autophagy/mitophagy regulation also prominent, suggesting a cluster wired to metabolic control and mitochondrial turnover. Less central terms like brain development and cobalamin biosynthesis appear but don't override the core theme. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:1901525","count":3},{"id":"GO:0006003","count":3},{"id":"GO:0006564","count":3},{"id":"GO:0006914","count":3},{"id":"GO:1902153","count":3}]},{"hash":"415507317203878198","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning plant cell wall biogenesis, transcription, DNA repair, endothelial migration, fungal response, chemotaxis, kidney development, cytokine regulation, and dopamine signaling. This wide mix does not reveal a coherent shared function or pathway for the cluster, so a specific, unified label isn\u2019t justifiable. Therefore, Unknown with no confidence. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000652","count":1},{"id":"GO:0070816","count":1},{"id":"GO:0006360","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0010596","count":1}]},{"hash":"337611588943901821","title":"DNA transcription regulation and repair proteins","description":"This cluster centers on DNA-templated transcription and its regulation, plus DNA repair via homologous recombination, indicating a core theme of transcription control linked to genome maintenance. Additional terms hint at broader roles in growth and development, but the core signals point to transcription regulation and DNA repair as the defining theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0006355","count":2},{"id":"GO:1901348","count":2},{"id":"GO:1900056","count":2}]},{"hash":"502031009228645102","title":"Ubiquitin-dependent protein degradation","description":"The cluster is dominated by terms for ubiquitination and proteasomal protein catabolism (e.g., GO:0042787, GO:0031146, GO:0016567), including SCF-dependent proteasomal ubiquitin-dependent degradation. The presence of related regulatory terms and immune signaling connections (TNF, RIG-I pathways) further supports a unifying role in ubiquitin-mediated protein turnover and regulation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0090073","count":8},{"id":"GO:0031146","count":8},{"id":"GO:1901253","count":7},{"id":"GO:2000620","count":7}]},{"hash":"1111777722372661236","title":"Oocyte meiosis and spindle assembly","description":"The cluster is dominated by terms tied to oocyte maturation and meiotic spindle assembly in female meiosis I, plus a proteasome/ubiquitin-dependent protein degradation pathway and microtubule polymerization\u2014consistent with proteins regulating meiosis, spindle dynamics, and cell cycle control in oocytes. While some neural development terms appear, the strongest, most representative signals center on meiosis and spindle organization during oocyte development.","confidence":"Medium","size":16,"edges":20,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":15},{"id":"GO:0046785","count":13},{"id":"GO:0007057","count":13},{"id":"GO:0021678","count":13},{"id":"GO:0006516","count":13}]},{"hash":"1382523430841858561","title":"Ubiquitin-mediated proteolysis and histone modification","description":"The cluster centers on ubiquitin-dependent protein degradation and protein ubiquitination, with strong signals from histone modifications (H4-K16 acetylation, H2A K63 ubiquitination) and links to inflammatory signaling pathways (NF-kappaB, JNK, TNF). This suggests a cohesive module where ubiquitination governs proteolysis and chromatin regulation, influencing cellular signaling and histone dynamics.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:1901253","count":9},{"id":"GO:2000620","count":9},{"id":"GO:0016567","count":9},{"id":"GO:0038018","count":9}]},{"hash":"1724373217035158275","title":"Lipid and polysaccharide catabolism with stress signaling","description":"The top GO terms show clear enrichment for lipid catabolism (triglyceride, phosphatidylserine, monoacylglycerol) and various polysaccharide degradation (cellulose, xylogalacturonan), alongside stress and signaling pathways (salicylic acid signaling, BMP signaling, endocannabinoid regulation). This points to a cohesive theme of metabolic breakdown combined with stress-response signaling, despite some cross-species signaling terms.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:0006660","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0052651","count":4},{"id":"GO:0085014","count":3}]},{"hash":"1266750893796767768","title":"Lipid Catabolism and Acylglycerol Remodeling","description":"The GO terms are dominated by lipid-focused catabolic processes (triglyceride, monoacylglycerol, diacylglycerol, phosphatidylserine) and acylglycerol remodeling, suggesting a cohesive theme of lipid turnover and membrane lipid metabolism; a few plant-specific or unrelated terms appear but do not override the lipid-centric signal.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":8},{"id":"GO:0019433","count":8},{"id":"GO:0006660","count":8},{"id":"GO:2000124","count":8},{"id":"GO:0052651","count":8}]},{"hash":"1713395746586033215","title":"Unknown","description":"The Top Terms span RNA processing, mitochondrial assembly, cytochrome c release regulation, and several distinct metabolic pathways (glutamine, lipopolysaccharide, and lignan biosynthesis), with no clear shared function across all proteins. The lack of cohesive pathway/theme and zero edges suggest the proteins do not form a single functional cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0006388","count":2},{"id":"GO:0000379","count":2},{"id":"GO:0033617","count":2},{"id":"GO:0097250","count":2}]},{"hash":"1569803276824352469","title":"Steroid and fatty acid biosynthesis","description":"The cluster is dominated by GO terms for lipid metabolism, including fatty acid elongation, methyl-branched fatty acid biosynthesis, mycolic acid biosynthesis, retinol metabolism, and steroid-related processes (testosterone biosynthetic and androgen metabolic/catabolic). This points to a cohesive theme around lipid and steroid biosynthesis, with a few more general metabolic or regulatory terms that may reflect broader cellular context. Confidence in this label: High.","confidence":"","size":16,"edges":64,"triangles":116,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045150","count":16},{"id":"GO:0042572","count":16},{"id":"GO:0061370","count":16},{"id":"GO:0071768","count":16},{"id":"GO:0006355","count":16}]},{"hash":"478823093826990246","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":15,"triangles":0,"max_degree":11,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0090615","count":6},{"id":"GO:0009451","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0090502","count":6},{"id":"GO:0070129","count":6}]},{"hash":"1718868482693654566","title":"Mitotic Cell Cycle Regulation","description":"In this cluster, the top GO terms center on G2/M transition, mitotic cell cycle, and cell division, indicating proteins involved in entry into and progression through mitosis. There are a couple of unrelated terms (e.g., mRNA stabilization, taste perception) that may be annotation noise, but the dominant signal points to mitotic control. Therefore, a concise label is \u201cMitotic Cell Cycle Regulation.\u201d","confidence":"High","size":16,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":1},{"id":"GO:1905287","count":1},{"id":"GO:0045792","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0051301","count":1}]},{"hash":"1571497909970572146","title":"Unknown","description":"This cluster\u2019s top GO terms span diverse biosynthetic and metabolic processes across different kingdoms (bacteria, plants, animals), including PHB, wax, lipid, and polysaccharide biosynthesis and even hair follicle development, with no clear shared pathway or interaction (edges/triangles = 0). There isn\u2019t a cohesive theme linking the proteins, so Unknown with None confidence is appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0042619","count":9},{"id":"GO:0009718","count":8},{"id":"GO:1902987","count":8},{"id":"GO:0006541","count":7}]},{"hash":"531177275452857270","title":"Unknown","description":"The top GO terms describe a highly diverse set of functions, including immune signaling, muscle/stretch responses, adipocyte differentiation, telomere maintenance, DNA replication, and metabolism, with several terms being obsolete. There is no clear, cohesive biological theme linking these proteins into a single interpretable pathway or process, and the lack of network edges further reduces confidence in a unified function. Therefore, this cluster appears to be an assortment of disparate signals rather than a distinct biological module.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0032088","count":3}]},{"hash":"1652069126853611829","title":"Membrane Ion Transport and Homeostasis","description":"The cluster is dominated by terms for ion transport across membranes (sodium and potassium import/export, proton transmembrane transport) and processes underlying cell volume and ion concentration homeostasis, including vacuolar acidification and intracellular potassium homeostasis. This points to a coherent functional theme of membrane transport and ionic regulation. A minority of terms (BDNF signaling and heart conduction regulation) may reflect tissue-specific signaling roles associated with ion channels.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006884","count":5},{"id":"GO:0007035","count":3},{"id":"GO:0051595","count":3},{"id":"GO:0097623","count":3},{"id":"GO:1902600","count":3}]},{"hash":"489802745515902476","title":"Diverse Substrate Membrane Transporters","description":"GO terms point to broad transmembrane transport activities across diverse substrates (ions, sugars, vitamins, xenobiotics) and vesicular neurotransmitter loading, indicating a cluster of membrane transport proteins; an outlier term (T cell costimulation) is unlikely to define the group.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031295","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0098700","count":2},{"id":"GO:0006855","count":2}]},{"hash":"1393333516033317161","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0050684","count":3},{"id":"GO:0080156","count":3},{"id":"GO:0001889","count":3}]},{"hash":"1267597671331328834","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":9},{"id":"GO:0009451","count":9},{"id":"GO:0016554","count":9},{"id":"GO:0090502","count":9},{"id":"GO:0070129","count":9}]},{"hash":"439708298395459764","title":"Fungal Cell Wall Biogenesis and Glucan Metabolism","description":"The top GO terms are dominated by fungal-type cell wall organization, fungal-type cell wall biosynthesis and assembly, and beta-D-glucan biosynthesis/catabolism, indicating a cohesive theme of fungal cell wall biogenesis and remodeling; division septum assembly also fits growth/division processes tied to cell wall dynamics.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0031505","count":3},{"id":"GO:0006076","count":3},{"id":"GO:0000917","count":3}]},{"hash":"1649510906252551475","title":"Plant developmental transcriptional regulation","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, along with plant-specific developmental processes such as vernalization response, seed dormancy and germination, leaf development, and radial pattern formation. The combination suggests a module where transcription control coordinates key developmental timing and organ patterning in plants. Secondary associations to chloroplast-related processes and transport appear peripheral to the main theme. ","confidence":"High","size":16,"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:0010048","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0006855","count":2}]},{"hash":"896288654826431505","title":"Unknown","description":"Top GO terms are diverse and span immunity, proteolysis, signaling, and organism-specific processes (plants, cardiovascular, neuroscience); there is no clear shared function tying all proteins together, so Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002803","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0070305","count":2},{"id":"GO:0002016","count":2},{"id":"GO:0042985","count":2}]},{"hash":"1668908981952139418","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning lipid transport, membrane organization and repair, signaling (GTPase regulation, ABA signaling), immune defense, development (cell division), and proteolysis regulation, with no single cohesive function tying the cluster together. Therefore, no clear, representative label can be assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006869","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0010951","count":1},{"id":"GO:0032434","count":1},{"id":"GO:0009788","count":1}]},{"hash":"1417894978518430967","title":"Floral development and cuticle biosynthesis regulation","description":"These proteins appear linked to plant development and epidermal barrier formation: terms for floral meristem growth and bract development indicate floral/inflorescence timing, while wax and cutin biosynthesis regulation point to epidermal cuticle control. The presence of ABA and ethylene signaling hints at hormone-regulated coordination of these processes, likely via transcriptional regulation. Confidence: Medium","confidence":"","size":16,"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:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0010432","count":2}]},{"hash":"2004410110553629078","title":"Peroxisomal Fatty Acid Oxidation and Lipid Metabolism","description":"The proteins here cluster around lipid catabolism and energy production, with strong signals for fatty acid beta-oxidation, acetyl-CoA and propionyl-CoA metabolism, and glyoxysome/peroxisome organization. Additional terms hint at tissue-level development (liver, adipose) and mitochondrial stress regulation, all pointing to a coherent theme of lipid metabolism and energy homeostasis across cells and tissues. The antibiotic biosynthetic term appears incidental rather than central.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0006635","count":6},{"id":"GO:0001889","count":4},{"id":"GO:0042594","count":4},{"id":"GO:1902860","count":3}]},{"hash":"882990836638817887","title":"Neural development and neurotransmitter secretion","description":"The dominant GO terms point to nervous system and brain development, as well as neuronal differentiation and neurotransmitter secretion, suggesting a neural development-focused cluster. Some terms (plant ABA signaling, lipid metabolism, lysosome exocytosis) are peripheral but do not outweigh the neural theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0009738","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0006646","count":1}]},{"hash":"1134510265840176285","title":"Ribosome Biogenesis and RNA/Protein Methylation","description":"This cluster centers on ribosome biogenesis and RNA/protein methylation, evidenced by rRNA methylation, ribosomal small subunit export, and several methylation processes. Growth signaling (TORC1) and cellular senescence contexts tie nutrient status to ribosome production, while a few terms appear as noise.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0035572","count":2},{"id":"GO:0046690","count":2},{"id":"GO:0090398","count":2}]},{"hash":"2109416926793176806","title":"Translation machinery and ribosome processing","description":"Based on the prominent GO terms, the cluster centers on translation and ribosome-related processes: general translation, rRNA import into mitochondria, diphthamide modification of histidine (a factor in translation), and regulation of translational fidelity. While some auxiliary terms (e.g., photosynthesis, glial proliferation) appear, they are likely annotations or broader context signals and do not override the core link to protein synthesis and ribosome function. Confidence is Medium.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0035928","count":1}]},{"hash":"1597342183807434314","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster is dominated by GO terms for LSU-rRNA maturation, ribosome biogenesis, translation reinitiation, and preinitiation complex formation, pointing to a core function in assembling and initiating protein synthesis. Other terms such as cell wall and lipid biosynthesis may reflect linked growth processes but do not change the central ribosome-focused theme.","confidence":"High","size":15,"edges":39,"triangles":33,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0008283","count":3}]},{"hash":"920499926727869943","title":"RNA processing and rRNA maturation","description":"The top terms are dominated by RNA processing: maturation of 5.8S and LSU rRNA and splicing via the spliceosome, indicating a core function in RNA maturation. Immune signaling terms are present but appear less central, suggesting potential secondary roles or annotations, with RNA processing as the main theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":1},{"id":"GO:0000470","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0071347","count":1},{"id":"GO:0032720","count":1}]},{"hash":"684166963437315368","title":"Organelle mRNA processing and editing","description":"The leading terms cluster around mitochondrial and chloroplast RNA processing, modification, and editing (e.g., mitochondrial mRNA processing, RNA modification, cytidine-to-uridine editing), with related plastid transcription and chloroplast-nucleus signaling, suggesting proteins involved in organellar RNA maturation and gene expression. An embryo dormancy term is present but not central to the main theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":6},{"id":"GO:0009451","count":6},{"id":"GO:0016554","count":6},{"id":"GO:0080156","count":6},{"id":"GO:1905639","count":6}]},{"hash":"313263703140043935","title":"Xenobiotic detox and small-molecule catabolism","description":"The main signals are detoxification and metabolism of xenobiotics or organic compounds (cellular oxidant detoxification, xenobiotic stimulus response, nicotine/cellulose/formaldehyde catabolic processes), suggesting a cluster focused on processing external or environmental chemicals; additional terms hint at host interaction and adhesion, which may reflect broader functional context. Confidence: Medium","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0030245","count":4},{"id":"GO:0019608","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0043542","count":3}]},{"hash":"2270936526793133447","title":"Neurodevelopment and vesicle trafficking","description":"The cluster is enriched for neural development terms (brain development, spinal cord development, neural tube closure) and vesicle trafficking from ER to Golgi (COPII vesicle budding, ER-to-Golgi transport), suggesting proteins involved in neural differentiation that rely on secretory pathways. Additional terms on ribosome biogenesis and signaling regulation may reflect broader cellular maturation in developing neural tissue, but the common theme centers on neural development linked to vesicular transport. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0070262","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0035264","count":3},{"id":"GO:0021510","count":3}]},{"hash":"163962955365116009","title":"DNA/RNA processing and ribosome biogenesis","description":"This cluster is enriched for core gene expression and genome maintenance functions, including DNA replication, DNA-templated transcription, DNA integration, RNA processing (mRNA splicing, nonfunctional rRNA decay), and ribosome biogenesis, plus proteolysis. While multicellular development and antibiotic response terms are broader, the central theme ties to the machinery of genome expression and protein synthesis.","confidence":"High","size":15,"edges":42,"triangles":28,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0046677","count":3}]},{"hash":"294068093989009119","title":"Photosynthetic Quinone Biosynthesis","description":"This cluster centers on photosynthesis-related processes and the biosynthesis of quinone cofactors (phylloquinone/plastoquinone and menaquinone) used in photosynthetic electron transport, along with associated redox and metabolic activities (e.g., photosystem I assembly, redox response, TCA cycle). The GO terms point to chloroplast/cyanobacterial\u2013like metabolism, tying energy capture to quinone biosynthesis.","confidence":"High","size":15,"edges":53,"triangles":71,"max_degree":12,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0048564","count":2},{"id":"GO:0051775","count":2},{"id":"GO:0006099","count":2}]},{"hash":"2087257846067045740","title":"ER protein processing and proteasome degradation","description":"This cluster centers on GO terms linked to the endoplasmic reticulum and protein quality control, including protein targeting to the ER, ER tubular network maintenance, ER-dependent peroxisome organization, and ubiquitin-/proteasome-mediated protein catabolism. While ribosome biogenesis and a couple of lineage-specific terms appear, the dominant theme is ER-associated protein processing and degradation. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1},{"id":"GO:0033033","count":1},{"id":"GO:0045721","count":1}]},{"hash":"124108473197306945","title":"Spliceosome-regulated RNA processing proteins","description":"Proteins in this cluster are dominated by GO terms related to splicing regulation via the spliceosome, including both positive regulation and alternative splicing. They also show broader RNA processing features (mRNA modification, stabilization, even rRNA methylation) and some translation initiation associations (eIF4F complex assembly, IRES-dependent initiation), suggesting a cohesive theme around RNA maturation and processing with a link to translation. ","confidence":"Medium","size":15,"edges":50,"triangles":74,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0048255","count":2}]},{"hash":"2302220043098879199","title":"Oxidative stress response and redox homeostasis","description":"This cluster is dominated by GO terms related to redox biology: cellular redox homeostasis, cellular response to oxidative stress, oxidant detoxification, and deglutathionylation, indicating a module focused on managing cellular oxidation and detoxification. While other terms touch on metabolism and development, the redox theme is clear and representative of the cluster's core function.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0030416","count":8},{"id":"GO:0045454","count":8},{"id":"GO:0098869","count":8},{"id":"GO:2000651","count":6}]},{"hash":"1082974533929502323","title":"Ubiquitin-dependent proteolysis and cell cycle control","description":"The top GO terms are dominated by ubiquitin-dependent protein degradation (including SCF-dependent proteasomal ubiquitin-mediated catabolism and positive regulation of polyubiquitination) and cell cycle-related processes (mitotic spindle assembly, regulation of DNA replication initiation, and DNA damage checkpoints). There are also microtubule polymerization terms, which align with mitotic/spindle dynamics. While stress response terms to metals and circadian regulation appear, the clearest common theme is proteostasis coupled to cell-cycle regulation, suggesting these proteins function together in controlling protein turnover during cell division and related checkpoints.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0042752","count":7},{"id":"GO:0046785","count":7},{"id":"GO:0007057","count":7},{"id":"GO:0030174","count":7}]},{"hash":"1180738854714775030","title":"Organelle RNA Editing and Processing (Mitochondria and Chloroplasts)","description":"The cluster\u2019s top GO terms cluster around RNA modification and processing specifically in mitochondria and chloroplasts, including mitochondrial mRNA processing, cytidine-to-uridine editing, and plastid/chloroplast RNA modification, as well as polycistronic mRNA processing and chloroplast transcription. This points to a cohesive function in organellar RNA maturation and editing in plants, with some terms touching on plastid-to-nucleus signaling and seed development as broader plant-context connections.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":15},{"id":"GO:0009451","count":15},{"id":"GO:0016554","count":15},{"id":"GO:0080156","count":15},{"id":"GO:1905639","count":15}]},{"hash":"149918545398563340","title":"DNA replication and SOS response","description":"The top GO terms are dominated by DNA replication-related processes (DNA replication, primer synthesis, topological changes, unwinding) and the SOS response, indicating a cohesive cluster of replication and DNA damage signaling activities. Some terms like spliceosome-related mRNA splicing and protein import appear incidental, but the core signal clearly centers on replication and damage response functions.","confidence":"High","size":15,"edges":90,"triangles":301,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":12},{"id":"GO:0006260","count":12},{"id":"GO:0006269","count":12},{"id":"GO:0006268","count":12},{"id":"GO:0009432","count":12}]},{"hash":"822051174382429248","title":"Transcription and Mitotic Signaling Regulators","description":"The top terms emphasize mitotic cell cycle and DNA-templated transcription, plus regulation of DNA binding and kinase activities, pointing to a module of regulators coordinating gene expression with cell-cycle signaling; the additional terms on mRNA transport, development, and stress responses suggest context-dependent modulation during development and cellular stress.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0043388","count":5},{"id":"GO:0045454","count":5},{"id":"GO:0021510","count":4}]},{"hash":"518208807553192433","title":"Mitochondrial Translation and Fe-S Cluster Biogenesis","description":"The cluster is dominated by mitochondrial translation and general translation terms, with additional terms for Fe-S cluster assembly and maturation (2Fe-2S), suggesting a coherent module of mitochondrial protein synthesis coupled to Fe-S biogenesis. A few ancillary terms (stress response, dormancy) appear ancillary rather than central to the core function.","confidence":"High","size":15,"edges":89,"triangles":278,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006950","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0085014","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0097428","count":1}]},{"hash":"1661209144189591220","title":"Ubiquitin-dependent protein degradation and turnover","description":"The GO terms are strongly centered on ubiquitination and ubiquitin-mediated protein catabolism (K48-linked ubiquitination, autoubiquitination, ubiquitin-dependent ERAD pathway, ubiquitin-dependent protein catabolic process) and include related peroxisomal protein import, pointing to a cluster focused on protein quality control and turnover via the ubiquitin-proteasome system. Some terms are obsolete or tangential, but the core signal is cohesive around degradation and regulation through ubiquitination.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090073","count":9},{"id":"GO:0038018","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0070936","count":9},{"id":"GO:0051865","count":9}]},{"hash":"919532808756551235","title":"Immune signaling and leukocyte migration","description":"The top GO terms point to immune regulation (positive regulation of cytokine production in immune response, T cell proliferation, neutrophil clearance) and cell movement/cytoskeleton dynamics (Rho signaling, microtubule localization, endothelial cell migration). Together these suggest proteins coordinating immune signaling with leukocyte movement, with a few developmental/metabolic terms as possible context. Confidence is medium due to some heterogeneity and a metabolic outlier.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010898","count":6},{"id":"GO:0046641","count":5},{"id":"GO:0001502","count":5},{"id":"GO:0097350","count":5},{"id":"GO:0035372","count":5}]},{"hash":"506975235499488047","title":"Growth signaling and transcription regulation","description":"The top GO terms point to a mix of nuclear processes (DNA replication, transcription regulation) and signaling pathways (Wnt signaling, angiogenesis, PI3K signaling) along with cellular responses (glucose stimulus, apoptosis) and defense. This suggests a cluster of proteins coordinating growth, proliferation, and gene expression through signaling networks, rather than a single, specific pathway. Confidence: Medium","confidence":"","size":15,"edges":21,"triangles":6,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0046827","count":4},{"id":"GO:0071333","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0014068","count":4}]},{"hash":"899951103685944969","title":"Membrane Transporters","description":"This cluster shows a cohesive pattern of membrane transport activities across substrates (nitrate, sialic acid, vitamins, urate, organic cations, galactose, 4-hydroxyphenylacetate) and a vesicle-related process (neurotransmitter loading), indicating proteins that function broadly as solute transporters and vesicular transporters.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0015739","count":4},{"id":"GO:0035461","count":4},{"id":"GO:0015747","count":4},{"id":"GO:0070715","count":4}]},{"hash":"694911658145246349","title":"Heavy metal detox and metal ion transport","description":"GO terms point to detoxification and transport of several heavy metal ions (mercury, cadmium, copper, zinc) and maintaining copper homeostasis, with processes like detoxification of mercury ion, response to mercury ion, copper ion export, intracellular copper ion homeostasis, and zinc/cadmium transport driving the theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0015694","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1}]},{"hash":"28835788381989290","title":"Unknown","description":"The top GO terms span leaf development, apoptosis, translation, ribosomal large subunit assembly, mitochondrial respiratory chain complex IV assembly, and aerobic respiration, with only one protein per term. There is no clear shared function or pathway linking the proteins, and the lack of edges suggests an unconnected set. Therefore the cluster cannot be cleanly named beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048366","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0033617","count":1}]},{"hash":"928129306955352819","title":"SCF-ubiquitin regulation of GA signaling and plant immunity","description":"The top GO terms point strongly to ubiquitin-dependent protein degradation, especially SCF-dependent pathways, which are key for regulating gibberellin signaling. Additionally, terms about responses to gibberellin, ACC (ethylene precursor), salicylic acid, and antifungal innate immunity indicate plant hormone signaling intersects with immune responses. Developmental cues like atrichoblast differentiation and boron deprivation further support a plant-specific regulatory cluster centered on proteasome/SCF-mediated control of hormone signaling and immunity.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0045815","count":2},{"id":"GO:0080169","count":2},{"id":"GO:0009961","count":2}]},{"hash":"1809357999838680600","title":"ER Proteostasis and Redox-Regulated Transcription","description":"The top GO terms point to ER protein folding, protein repair, and redox processes (redox homeostasis, oxidation-reduction, deglutathionylation), indicating a proteostasis/redox module. Simultaneously, transcription-related terms (DNA-templated transcription, regulation of DNA binding, RNA polymerase II regulation) suggest these proteins may also influence gene expression, aligning with ER stress responses that couple protein quality control with transcriptional regulation.","confidence":"Medium","size":15,"edges":25,"triangles":9,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034975","count":9},{"id":"GO:0045454","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0030091","count":6},{"id":"GO:0043388","count":6}]},{"hash":"413628602374551677","title":"Synapse formation and actin regulation","description":"The terms point to neuronal development and synapse assembly, with strong emphasis on regulating synaptic vesicle exocytosis and actin cytoskeleton dynamics (actin polymerization, formin-nucleated cables, stress fiber assembly, and GTPase activity). This combination suggests proteins involved in building and remodeling synapses in the brain, where actin remodeling underpins vesicle release and synaptic maturation; some obsolete terms likely reflect cross-species annotations but do not outweigh the primary neuronal/cytoskeletal signal.","confidence":"High","size":15,"edges":56,"triangles":70,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0007416","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0031384","count":3}]},{"hash":"1079345395020966650","title":"Enhancement of Glutamatergic Synaptic Transmission","description":"The cluster\u2019s top GO terms are dominated by neuronal synaptic functions, especially learning, positive regulation of glutamatergic transmission, AMPA receptor activity, and excitatory postsynaptic potentials, pointing to proteins that modulate excitatory synapses. Some mitochondrial RNA processing and a seed dormancy term appear as outliers, but the strongest signal is glutamatergic signaling. Confidence reflects this clear synaptic theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007612","count":2},{"id":"GO:0051968","count":2},{"id":"GO:2000463","count":2},{"id":"GO:0051262","count":2},{"id":"GO:2000969","count":2}]},{"hash":"918552027695329329","title":"Immune Cytokine Signaling and Leukocyte Trafficking","description":"The terms cluster around immune activation and cytokine production (T cell proliferation, IL-4 production, cytokine production), neutrophil clearance, and endothelial cell migration, with supporting roles for cytoskeletal signaling (Rho) and microtubule localization. This suggests a cohesive theme of immune signaling coordinating leukocyte activity and vascular remodeling.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":15},{"id":"GO:0001502","count":15},{"id":"GO:0097350","count":15},{"id":"GO:0035372","count":15},{"id":"GO:0043068","count":15}]},{"hash":"1413125658048378167","title":"T Cell Activation and Cytokine Production","description":"The cluster is dominated by GO terms related to adaptive immunity, especially T cell proliferation, IL-4 production, and cytokine regulation, indicating a module of T cell activation and cytokine signaling. While there are also terms pointing to inflammatory remodeling (neutrophil clearance, endothelial migration) and cytoskeletal dynamics (Rho signaling, microtubule localization), the strongest signal centers on T cell\u2013driven immune activation and cytokine production.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":15},{"id":"GO:0001502","count":15},{"id":"GO:0097350","count":15},{"id":"GO:0035372","count":15},{"id":"GO:0043068","count":15}]},{"hash":"1046258180999381200","title":"Vitamin biosynthesis and redox metabolism","description":"The cluster shows strong enrichment for biosynthetic processes of vitamins and antioxidants (retinol, L-ascorbic acid, glutathione, and related lactones), indicating a core theme of vitamin/cofactor biosynthesis and redox regulation. Other terms (JAK-STAT signaling, endothelial apoptosis, renal water homeostasis) suggest broader signaling and organ-physiology contexts among these proteins, but the dominant shared function appears to be biosynthesis and redox metabolism.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:2000353","count":15},{"id":"GO:0042572","count":15},{"id":"GO:0044597","count":15},{"id":"GO:0009414","count":15},{"id":"GO:0061370","count":15}]},{"hash":"1699442631548896038","title":"Mitochondrial Energy Metabolism","description":"This cluster is dominated by GO terms tied to mitochondrial function and energy production, notably mitochondrial translation and the tricarboxylic acid cycle, suggesting a group of proteins involved in mitochondrial energy metabolism. Other metabolic and catabolic terms may reflect broader metabolic roles, but the central theme appears to be mitochondrial energy processes.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0032543","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0019391","count":4},{"id":"GO:0046272","count":4}]},{"hash":"1603275120500373046","title":"Redox homeostasis and central carbon metabolism","description":"The cluster is dominated by redox-related GO terms (oxidation-reduction, cellular oxidant detoxification, and redox homeostasis), suggesting a core theme of maintaining cellular redox balance. There are accompanying central carbon metabolism terms (gluconeogenesis, pyruvate decarboxylation to acetyl-CoA, malonyl-CoA biosynthesis), indicating linkage to energy metabolism. Obsolete terms appear, but the redox-focused signals strongly define the group\u2019s function.","confidence":"High","size":15,"edges":11,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006094","count":1},{"id":"GO:0033512","count":1}]},{"hash":"2050180226665174188","title":"Neural development with glial apoptosis","description":"The top GO terms are heavily weighted toward nervous system development (forebrain development, nervous system development) and glial cell apoptotic process, suggesting a neural development-focused cluster. Other terms (e.g., TGF-beta response, various organ-related processes) appear as less central or cross-species annotations, but do not override the main neural theme. Thus, the cluster is best described as neural development with glial apoptosis signals.","confidence":"Medium","size":15,"edges":52,"triangles":57,"max_degree":12,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":12},{"id":"GO:0010659","count":12},{"id":"GO:0035006","count":12},{"id":"GO:0033353","count":12},{"id":"GO:0071560","count":12}]},{"hash":"1154910403698283725","title":"Nucleosome dynamics and chromatin remodeling","description":"The terms are centered on nucleosome assembly/disassembly and regulation of histone acetylation, pointing to chromatin remodeling activity. A few other terms (sperm DNA decondensation, microtubule polymerization regulation) are less directly tied to chromatin but can be connected to nuclear dynamics and cell division, so the core theme remains chromatin-related.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043085","count":1},{"id":"GO:0035041","count":1},{"id":"GO:0006337","count":1},{"id":"GO:0007117","count":1},{"id":"GO:0071442","count":1}]},{"hash":"1790216687453621852","title":"Membrane Signaling and Trafficking","description":"The top GO terms point to membrane-associated processes: cell surface receptor signaling, Notch and integrin signaling, and regulation of cell motility, along with intracellular trafficking like endosome-to-melanosome transport and junction assembly. The terms collectively suggest functions at the plasma membrane and in trafficking/adhesion pathways, rather than a single highly cohesive process, so a broad but specific label \u201cMembrane Signaling and Trafficking\u201d fits. ","confidence":"Medium","size":15,"edges":22,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035646","count":1},{"id":"GO:1904352","count":1},{"id":"GO:0046813","count":1},{"id":"GO:0007166","count":1},{"id":"GO:0045747","count":1}]},{"hash":"1829206530692221260","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0032981","count":1},{"id":"GO:0019918","count":1}]},{"hash":"624292102877991784","title":"Plant Hormone Biosynthesis and Fruit Ripening","description":"Dominant GO terms point to hormone-driven plant development and ripening (gibberellin, ethylene, auxin), alongside secondary metabolism (proanthocyanidin) and stress-associated hydrogen peroxide\u2013mediated programmed cell death. An outlier term (penicillin biosynthetic process) is likely an annotation artifact. Overall, the proteins cluster around plant hormone signaling and fruit maturation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0009835","count":5},{"id":"GO:0042318","count":5},{"id":"GO:1902835","count":5},{"id":"GO:0009686","count":5}]},{"hash":"967898585951887831","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000447","count":2}]},{"hash":"502700718286961142","title":"Regulation of Plant Growth and Lignin Biosynthesis","description":"The top GO terms cluster around regulatory processes in plants\u2014cytokinin signaling, regulation of chlorophyll biosynthesis, seed growth, syringal lignin biosynthesis, and secondary cell wall biogenesis\u2014along with regulation of root meristem growth and leaf senescence. The presence of multiple \u201cregulation\u201d terms, including negative regulation of some processes, suggests a cohesive theme of developmental and cell-wall metabolism control rather than a single enzymatic function.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:0010380","count":3},{"id":"GO:0080113","count":3},{"id":"GO:1901430","count":3},{"id":"GO:1901347","count":3}]},{"hash":"1008650687619436221","title":"Pseudouridine Synthesis and Transcription Regulation","description":"The cluster is enriched for RNA modification terms related to pseudouridine synthesis on rRNA and tRNA (GO:0000455, GO:0031119) and transcription-related terms (GO:0006353, GO:0006351, GO:0032784, GO:0031564), pointing to a core role in RNA maturation linked to transcription control. The presence of photosynthesis and sterol biosynthetic terms suggests chloroplast-associated functions, which can involve nuclear-encoded, organelle-targeted RNA-processing enzymes. Overall, the functional theme centers on RNA modification and transcription regulation, giving a Medium confidence.","confidence":"Medium","size":15,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000455","count":3},{"id":"GO:0006353","count":2},{"id":"GO:0006977","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0031119","count":2}]},{"hash":"1548308605953268357","title":"Mitotic cell cycle regulation","description":"The top GO terms center on G2/M transition, cell division, and regulation of CDK activity, indicating a shared function in controlling mitotic progression. While there are a few tissue-specific terms, the dominant signal is regulation of the mitotic cell cycle and proliferation.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033598","count":4},{"id":"GO:0030857","count":4},{"id":"GO:0010389","count":4},{"id":"GO:0000086","count":4},{"id":"GO:0019085","count":4}]},{"hash":"253532933925846620","title":"Placental development and embryonic morphogenesis","description":"The top GO terms point to placental lineage and morphogenesis, with trophoblast giant cell differentiation, cartilage morphogenesis, left-right patterning, and EMT in embryonic placental contexts, suggesting a cluster of proteins involved in placental development and early embryogenesis. A few additional terms on mRNA splicing and translational fidelity appear but are less central to the cluster\u2019s primary function. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0060536","count":2},{"id":"GO:0060972","count":2},{"id":"GO:0060806","count":2},{"id":"GO:0003198","count":2}]},{"hash":"388463736517848728","title":"Plant meristem and embryogenesis development","description":"The cluster is enriched for meristem development, somatic embryogenesis, auxin-activated signaling pathway, and fruit dehiscence, pointing to plant growth and developmental processes. Supportive terms like DNA replication and transcription reflect general cellular activities. Overall, the dominant theme is plant organogenesis and differentiation, especially meristem activity and embryogenesis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015937","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0030154","count":2}]},{"hash":"1859486818400163783","title":"Pituitary hormone regulation and stress response","description":"This cluster is dominated by GO terms related to pituitary gland development and hormone biosynthesis regulation, including response to corticosterone, signaling an endocrine/neuroendocrine module. Additional terms on chromatin binding regulation and neuron projection extension suggest coordinated transcriptional control and neural connectivity involved in stress and hormonal pathways.","confidence":"Medium","size":15,"edges":67,"triangles":133,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0045654","count":5},{"id":"GO:0035563","count":5},{"id":"GO:0051412","count":5},{"id":"GO:0051572","count":5}]},{"hash":"1234120276128290224","title":"Hormone biosynthesis and tissue development","description":"This cluster is enriched for prostaglandin biosynthetic and cortisol biosynthetic processes, pointing to lipid/hormone signaling. The presence of tissue development terms (uterus and mammary gland development, type II pneumocyte differentiation) and endothelial adhesion suggests a theme where hormone biosynthesis and signaling guide tissue differentiation and vascular interactions, with redox-related terms appearing as a broader cellular context.","confidence":"Medium","size":15,"edges":88,"triangles":282,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":8},{"id":"GO:0098869","count":8},{"id":"GO:0001516","count":6},{"id":"GO:0060065","count":6},{"id":"GO:0060510","count":5}]},{"hash":"1474072587100388823","title":"Synapse formation and neurotransmitter secretion","description":"The top GO terms cluster around synaptic biology (synapse assembly, regulation of synaptic vesicle exocytosis, neurotransmitter secretion) and brain development, with supporting signals from membrane trafficking and lipid biosynthesis (phosphatidylethanolamine/phosphatidylcholine) and calcium-regulated lysosome exocytosis. This points to proteins coordinating synapse formation and presynaptic vesicle exocytosis, with membrane-dynamics and signaling components involved in neurotransmitter release.","confidence":"High","size":15,"edges":96,"triangles":355,"max_degree":14,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007416","count":10},{"id":"GO:2000300","count":10},{"id":"GO:0031384","count":10},{"id":"GO:0010796","count":10},{"id":"GO:0007420","count":10}]},{"hash":"1869816421133589372","title":"Auxin signaling and organ growth","description":"The top GO terms cluster around auxin biology\u2014auxin-activated signaling, response to auxin, auxin polar transport\u2014and related regulation of organ growth, which together point to a module centered on auxin-mediated development and growth control. Some outliers exist (e.g., L-arabinose metabolism, DNA ADP-ribosylation), but the dominant theme is clearly auxin signaling and growth regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010274","count":1},{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1}]},{"hash":"1135315413571967106","title":"Sphingolipid Biosynthesis","description":"The strongest common signal among the GO terms is sphingosine and phytosphingosine biosynthesis, indicating a sphingolipid metabolism focus. The related term keratinocyte differentiation hints at skin/epidermal contexts where sphingolipids are important, supporting a cohesive theme around sphingolipid biology, while other terms are more peripheral. Overall, this cluster most coherently aligns with sphingolipid biosynthesis, albeit with some noise from unrelated or obsolete terms. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0035563","count":2},{"id":"GO:0035690","count":1},{"id":"GO:0001953","count":1},{"id":"GO:0090285","count":1}]},{"hash":"1515085972669721375","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001253","count":1},{"id":"GO:0031440","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0006362","count":1}]},{"hash":"1111413406516430966","title":"Floral organ development and transcription control","description":"The cluster is enriched for plant floral development terms (petal development) and organ boundary specification between lateral organs and the meristem, along with DNA-templated transcription and its regulation. This points to transcriptional control governing floral organ formation, with chromatin modification (histone acetylation) as a supporting mechanism, and a minor stress-response signal. ","confidence":"Medium","size":15,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0010199","count":2},{"id":"GO:0048441","count":2},{"id":"GO:0044154","count":1},{"id":"GO:0043982","count":1}]},{"hash":"627026771643068891","title":"Plant light signaling and transcriptional growth regulation","description":"The cluster is enriched in plant-related light signaling terms (red/far-red phototransduction, far-red signaling), leaf development, circadian rhythm regulation, and gibberellin response, along with transcriptional regulation. This suggests a cohesive theme of light- and hormone-driven transcriptional programs governing plant growth and development, with the other terms accounting for shared cellular processes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0048366","count":2},{"id":"GO:0009585","count":2},{"id":"GO:0042753","count":2}]},{"hash":"1352914073951183680","title":"Transcription Regulation and RNA Splicing","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, plus mRNA processing, RNA splicing, and spliceosomal tri-snRNP assembly, pointing to a cohesive role in gene expression control at both transcriptional and post-transcriptional levels. The histone H3-K9 modification terms suggest chromatin-level regulation as well. A few terms (e.g., developmental process, deep water response) are incidental. Overall, the recurrent theme is transcription regulation and RNA processing.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051573","count":2},{"id":"GO:2000616","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006397","count":1}]},{"hash":"82799216516703821","title":"Ribosome Biogenesis and Cell Cycle","description":"The top terms cluster around ribosome assembly/export (ribosomal subunit biogenesis and export from nucleus) and cell division/cell cycle, suggesting proteins tied to ribosome production that also participate in cell cycle progression. Transport-related terms (amino acid and calcium export) are present but secondary to the dominant ribosome/ cell cycle theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":4},{"id":"GO:1990034","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0007049","count":2}]},{"hash":"870273514506193528","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning plant developmental processes (organ boundary specification, petal development) and animal-related events (embryonic pregnancy, extrinsic apoptotic signaling), along with various stress responses (singlet oxygen, hypoxia, arsenite) and organelle-related processes. There isn\u2019t a single cohesive biological function linking these proteins, suggesting a non-cohesive cluster rather than a functionally unified group.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010199","count":3},{"id":"GO:0048441","count":3},{"id":"GO:0032418","count":1},{"id":"GO:0097345","count":1},{"id":"GO:0048490","count":1}]},{"hash":"868140910918015582","title":"Plant innate immunity and hypersensitive response","description":"This cluster centers on plant defense against bacteria, the plant-type hypersensitive response, and innate immune signaling, with links to regulation of cell death and protein ubiquitination, suggesting components of plant immune signaling and HR execution rather than basic metabolic roles.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034051","count":1},{"id":"GO:0009816","count":1},{"id":"GO:0009626","count":1},{"id":"GO:0010204","count":1},{"id":"GO:0043066","count":1}]},{"hash":"989538413243944636","title":"Steroid Hormone Biosynthesis and Female Reproductive Development","description":"The top GO terms point to steroid hormone production (cortisol and testosterone biosynthesis) and development of female reproductive tissues (uterus, female gonad, mammary gland), suggesting an endocrine-reproductive theme. Additional terms for vitamin D response and endothelial cell adhesion appear related but secondary, while xenobiotic and carbazole catabolism indicate detox pathways that can be co-expressed in steroidogenic tissues. Overall, the cluster seems best described by endocrine hormone biosynthesis linked to female reproductive development, with some ancillary processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":8},{"id":"GO:0060065","count":7},{"id":"GO:0033280","count":7},{"id":"GO:0008585","count":7},{"id":"GO:0030879","count":6}]},{"hash":"336588433243866197","title":"Nervous system development and glial apoptosis","description":"This cluster is dominated by neural-development terms: forebrain development, nervous system development, and glial cell apoptotic process, suggesting proteins involved in brain formation and glial regulation. Other terms like cellular response to transforming growth factor beta stimulus and L-methionine cycle appear, but the strongest signal points to neural development.","confidence":"High","size":15,"edges":80,"triangles":216,"max_degree":14,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":13},{"id":"GO:0010659","count":13},{"id":"GO:0035006","count":13},{"id":"GO:0033353","count":13},{"id":"GO:0071560","count":13}]},{"hash":"2256755568618666110","title":"Oocyte Maturation and Meiotic Spindle Assembly","description":"Several top GO terms point to the meiotic cell cycle in oocytes: spindle assembly in female meiosis I, microtubule polymerization, oocyte maturation, and SCF-dependent proteasomal ubiquitin-dependent protein degradation. A few neural development terms appear, but the dominant theme is meiosis and oocyte maturation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":11},{"id":"GO:0046785","count":10},{"id":"GO:0007057","count":10},{"id":"GO:0021678","count":10},{"id":"GO:0006516","count":10}]},{"hash":"483712221015266611","title":"Unknown","description":"The proteins are linked to a highly mixed set of GO terms (neural development, glial/apoptotic processes, cardiac apoptosis, immune/melanization responses, metabolism, and signaling) with no single coherent theme, and there are no edges connecting them, so there isn\u2019t a unifying function to name beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":6},{"id":"GO:0010659","count":6},{"id":"GO:0035006","count":6},{"id":"GO:0033353","count":6},{"id":"GO:0071560","count":6}]},{"hash":"1682063883434956644","title":"Oocyte maturation and meiotic spindle assembly","description":"This cluster is dominated by GO terms tied to oocyte maturation and the spindle assembly process in female meiosis I, with amino contributions from microtubule polymerization and proteasomal protein catabolism (SCF-dependent) linked to meiotic cell cycle regulation. While a couple of terms (neural development) are less related, the core signal points to meiosis progression and spindle dynamics in oocytes.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":10},{"id":"GO:0046785","count":10},{"id":"GO:0006516","count":10},{"id":"GO:0007057","count":10},{"id":"GO:0070544","count":10}]},{"hash":"928401773581960254","title":"Ubiquitin-Dependent Degradation and TNF Signaling","description":"This cluster is dominated by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, autoubiquitination) and TNF signaling terms, suggesting a core theme of ubiquitin-driven protein turnover and inflammatory signaling. Additional terms touch histone ubiquitination and peroxisomal protein import, which can be connected to ubiquitin pathways but are less central, reinforcing a primary focus on ubiquitin-mediated regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0016558","count":5}]},{"hash":"1297892631803662911","title":"Lipid and steroid metabolism","description":"This cluster is driven by lipid-centric biosynthetic and catabolic processes: mycolic acid biosynthesis, fatty acid elongation, methyl-branched fatty acid biosynthesis, retinol metabolism, and testosterone/androgen biosynthesis and catabolism, pointing to a cohesive set of enzymes involved in lipid and steroid metabolism (with a note that transcription regulation terms may reflect co-regulated gene groups or annotations). ","confidence":"Medium","size":15,"edges":71,"triangles":171,"max_degree":14,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045150","count":15},{"id":"GO:0042572","count":15},{"id":"GO:0061370","count":15},{"id":"GO:0071768","count":15},{"id":"GO:0006355","count":15}]},{"hash":"1191674517818194392","title":"Plant Cell Wall Biogenesis","description":"The top GO terms include xyloglucan biosynthetic process, glucuronoxylan biosynthetic process, and plant-type secondary cell wall biogenesis, which together point to synthesis and assembly of the plant cell wall. While other terms (cellular responses and immune-related terms) appear, they are less representative of the core theme. Overall, the strongest signal is plant cell wall biosynthesis, supporting this label.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0098586","count":5},{"id":"GO:0032092","count":5},{"id":"GO:0071333","count":5},{"id":"GO:0009969","count":4},{"id":"GO:0010417","count":4}]},{"hash":"1233492932734845895","title":"Plant light-response and photosynthesis","description":"This cluster is dominated by GO terms related to light perception and light-driven processes (red/blue/UV-A/light intensity responses, nonphotochemical quenching) and photosynthesis, including light harvesting in photosystem I and phytol/phytol biosynthesis components. The shared theme is light sensing and the photosynthetic machinery, suggesting proteins function together in light-driven energy capture. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010218","count":1},{"id":"GO:0010114","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0071486","count":1}]},{"hash":"1921760313473240010","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014806","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006438","count":2},{"id":"GO:0010236","count":2},{"id":"GO:0010193","count":2}]},{"hash":"1359519152397189313","title":"Membrane solute transporters","description":"These proteins show enrichment for transmembrane transport of ions and small metabolites (potassium, acetate, glycerol) and include related signaling and secretion terms (cAMP response, corticotropin secretion). While there are some tissue-development terms (lens and metanephric kidney), the common thread is membrane-based transport of solutes and its regulation, so a concise label is \"Membrane solute transporters.\" ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":8},{"id":"GO:0051458","count":6},{"id":"GO:0002088","count":6},{"id":"GO:0071288","count":6},{"id":"GO:0070295","count":6}]},{"hash":"489305291015519098","title":"Immune Activation and Cytokine Production","description":"The top GO terms cluster around immune stimulation and cytokine regulation, such as positive regulation of T cell proliferation, interleukin-4 production, and broader positive regulation of cytokine production in immune responses. While some terms touch on neutrophil clearance, endothelial migration, and cytoskeletal signaling, the dominant theme is immune activation and cytokine signaling, justifying a label focused on immune modulation rather than metabolic or developmental processes.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":15},{"id":"GO:0001502","count":15},{"id":"GO:0097350","count":15},{"id":"GO:0035372","count":15},{"id":"GO:0043068","count":15}]},{"hash":"1752395736401403157","title":"T cell activation and cytokine signaling","description":"The terms show strong enrichment for adaptive immune processes, including positive regulation of alpha-beta T cell proliferation, IL-4 production, and broader positive regulation of cytokine production in immune responses. Additional hints of immune cell movement and signaling come from Rho pathway activity and microtubule localization, with neutrophil clearance and programmed cell death regulation supporting immune regulation. A cartilage condensation term seems incidental; overall, the cluster centers on immune activation and cytokine regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":15},{"id":"GO:0001502","count":15},{"id":"GO:0097350","count":15},{"id":"GO:0035372","count":15},{"id":"GO:0043068","count":15}]},{"hash":"507055882321582818","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":2},{"id":"GO:2000344","count":2},{"id":"GO:0016042","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0010336","count":2}]},{"hash":"1753015636536775720","title":"Unknown","description":"The Top Terms span a wide range of unrelated processes (exocytosis regulation, cell shape, protein sumoylation, sporule membrane formation, membrane tubulation, heart rate regulation, nuclear import, methylmercury response, astrocyte activation, and adenylate cyclase activation), with no clear shared pathway or function. The lack of shared themes and zero edges suggest no cohesive cluster function can be inferred.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045921","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0033234","count":1},{"id":"GO:0032120","count":1},{"id":"GO:1903525","count":1}]},{"hash":"195214234713336416","title":"Plant jasmonate/oxylipin signaling and lipid metabolism","description":"Several top GO terms point to lipid transport, jasmonic acid biosynthesis, and oxylipin biosynthetic processes, with accompanying fatty acid beta-oxidation. Additional hints come from stress- and defense-related terms (defense response to fungus, response to ozone, response to toxic substance) and a note of stamen development, which aligns with jasmonate signaling in plants. Taken together, this cluster appears to reflect plant-specific lipid signaling via jasmonate/oxylipin pathways and related lipid metabolism, underpinning defense responses.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006869","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0010951","count":2},{"id":"GO:0030245","count":1},{"id":"GO:0009695","count":1}]},{"hash":"730307944748849832","title":"Plant light signaling and membrane transport","description":"The dominant terms point to membrane transport (amino acid, calcium, and general transmembrane transport) and plant-specific light/circadian signaling (red/far-red phototransduction, far-red signaling, circadian rhythm regulation) with auxin export as a key hormone transport process. These together suggest a cluster focused on plant membrane transport linked to light- and circadian-regulated signaling. Some outlier terms (DNA transposition, transcription regulation) are likely annotation noise and do not outweigh the main theme.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":2},{"id":"GO:1990034","count":2},{"id":"GO:0006313","count":1},{"id":"GO:0042753","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1226024211953990805","title":"T cell activation and cytokine signaling","description":"This cluster is dominated by adaptive immune terms, including positive regulation of alpha-beta T cell proliferation, interleukin-4 production, and positive regulation of cytokine production in immune response, pointing to proteins involved in T cell\u2013mediated signaling and inflammation. Additional terms on neutrophil clearance, endothelial cell migration, and Rho signaling suggest coordinated immune cell trafficking and cytoskeletal regulation, with a few terms like cartilage condensation and microtubule localization that are less central but may reflect broader developmental/cytoskeletal context. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":15},{"id":"GO:0001502","count":15},{"id":"GO:0097350","count":15},{"id":"GO:0035372","count":15},{"id":"GO:0043068","count":15}]},{"hash":"1994283643368812774","title":"Fungal cell wall biosynthesis and sphingolipid metabolism","description":"These proteins cluster around fungal-specific biology: fungal-type cell wall assembly and beta-D-glucan biosynthesis, along with sphingolipid biosynthesis and regulation of sphingolipid signaling. Lipid transport and calcium export support membrane processes common in fungal cells, and defense response to fungus fits with host\u2013fungal interactions. Together, the terms point to a cohesive theme of fungal cell wall construction and associated lipid signaling pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006869","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0010951","count":1},{"id":"GO:0032973","count":1},{"id":"GO:1990034","count":1}]},{"hash":"308213957958488150","title":"Organelle RNA Editing and Processing","description":"Top GO terms cluster around RNA metabolism in mitochondria and chloroplasts/plastids, including mitochondrial mRNA processing/modification, cytidine-to-uridine editing, chloroplast RNA modification, and plastid transcription. This suggests a cohesive role in organellar RNA maturation/editing, with plastid-nucleus signaling reflecting plastid regulation. A single term about seed dormancy appears less related and may be an artifact.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:1905639","count":3}]},{"hash":"518488981369642640","title":"Deubiquitination and ubiquitin signaling","description":"The cluster is dominated by GO terms for deubiquitination across multiple lysine linkages (K29, K6, K11, K48) and associated ubiquitination regulation, indicating a cohesive theme around ubiquitin modification/editing and ubiquitin-cycle control. While there are related terms touching on transcription regulation and necroptosis, the strongest signal is deubiquitinase activity and ubiquitin pathway regulation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035523","count":3},{"id":"GO:0044313","count":3},{"id":"GO:0035871","count":3},{"id":"GO:0071108","count":3},{"id":"GO:0006397","count":3}]},{"hash":"1987584969785140324","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006979","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0046274","count":4},{"id":"GO:0042744","count":4}]},{"hash":"1218260404885023505","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010411","count":1},{"id":"GO:0009827","count":1},{"id":"GO:0050826","count":1},{"id":"GO:0045492","count":1},{"id":"GO:0009834","count":1}]},{"hash":"427797694282892083","title":"Plant primary carbon metabolism and hormone biosynthesis","description":"The top GO terms cluster around central carbon metabolism (glycolysis, pyruvate to acetyl-CoA, glyoxylate cycle) and plant-specific biosynthetic processes (auxin biosynthesis and phylloquinone biosynthesis). This combination suggests a cohesive group of proteins involved in core metabolism and plant hormone/vitamin pathways, indicating a plant-focused metabolic module rather than a single enzymatic function.","confidence":"Medium","size":14,"edges":73,"triangles":241,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006086","count":4},{"id":"GO:0006096","count":3},{"id":"GO:0033611","count":3},{"id":"GO:0019310","count":3},{"id":"GO:0019596","count":3}]},{"hash":"100491314144051047","title":"Spindle assembly and microtubule regulation","description":"The cluster is dominated by GO terms tied to microtubule dynamics and spindle-related processes, including regulation of microtubule-based processes, establishment/maintenance of microtubule cytoskeleton polarity, mitotic centrosome separation, and meiotic spindle orientation. Karyogamy and DNA replication appear but the unifying theme is microtubule-driven organization of the spindle during cell division, with some axonemal/microtubule dynamics context as well. This suggests a coherent function in spindle assembly and microtubule regulation across mitosis and meiosis.","confidence":"High","size":14,"edges":34,"triangles":36,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":11},{"id":"GO:0006260","count":7},{"id":"GO:0035617","count":6},{"id":"GO:0070389","count":6},{"id":"GO:0007100","count":5}]},{"hash":"1368041446170803197","title":"Lipid, quinone, and polymer biosynthesis","description":"The top GO terms point to diverse biosynthetic processes: antibiotic, phylloquinone/menaquinone biosynthesis, fatty acid and long-chain fatty-acyl-CoA biosynthesis, sporopollenin and chalcone biosynthesis, and DIM/DIP cell wall layer assembly, with some related catabolic terms like glyoxylate. This pattern suggests a cluster focused on synthesizing a range of lipid, quinone, and protective polymer components, rather than a single cohesive pathway, hence a broad \u201clipid, quinone, and polymer biosynthesis\u201d label.","confidence":"Medium","size":14,"edges":82,"triangles":273,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0042372","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0006633","count":4},{"id":"GO:0035336","count":4}]},{"hash":"821906089719524451","title":"Bacterial cell envelope biosynthesis and antibiotic production","description":"The top GO terms point to biosynthesis of cell wall and envelope components (cell wall organization; teichoic acid D-alanylation; lipoteichoic acid biosynthesis; lipid A biosynthetic processes) together with antibiotic-related pathways (antibiotic biosynthetic process; nonribosomal peptide biosynthetic process; amino acid activation for NRPS). This pattern suggests a cluster of proteins involved in building the bacterial cell envelope and in producing NRPS-derived antibiotics, a theme common in Gram-positive bacteria. ","confidence":"High","size":14,"edges":69,"triangles":221,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0006633","count":5},{"id":"GO:0071555","count":5},{"id":"GO:0070400","count":5},{"id":"GO:1902987","count":5}]},{"hash":"1135954205945134537","title":"Gene Expression Machinery","description":"The cluster\u2019s top GO terms cluster around transcription and translation processes\u2014DNA-templated transcription and termination, transcription, translation, ribosome biogenesis, tyrosyl-tRNA aminoacylation, rRNA pseudouridylation, and maintenance of translational fidelity. These collectively point to components of gene-expression machinery and ribosome biogenesis. A few outlier terms (alkane catabolic process, GPCR signaling, oxidation-reduction) are minor and do not define the overall theme. ","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006353","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0007200","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0043448","count":1}]},{"hash":"2152234458781235318","title":"mRNA processing and translation initiation","description":"The GO terms are dominated by mRNA maturation processes (polyadenylation, modification, stabilization, and spliceosome-mediated splicing) and components involved in initiating translation (eIF4F complex assembly, IRES-dependent initiation). This points to a cluster of proteins coordinating mRNA maturation and subsequent translation, rather than distinct unrelated functions. The presence of a blastocyst formation term may reflect developmental roles of mRNA regulation. Overall, the core theme is mRNA processing-upstream events linked to translation.","confidence":"High","size":14,"edges":6,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":11},{"id":"GO:0016556","count":10},{"id":"GO:0048255","count":10},{"id":"GO:0075522","count":10},{"id":"GO:1905663","count":10}]},{"hash":"1239102699861895902","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":45,"triangles":80,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":6},{"id":"GO:0071320","count":6},{"id":"GO:0005978","count":6},{"id":"GO:0006541","count":5},{"id":"GO:0044205","count":5}]},{"hash":"175979423005110969","title":"Ubiquitin-Proteasome Regulation in Meiosis and Differentiation","description":"The dominant GO terms point to ubiquitin-dependent protein catabolic processes, especially SCF-dependent proteasomal degradation, coupled with meiosis-related functions like oocyte maturation and spindle assembly. This suggests a core theme of regulated proteolysis governing meiosis and cell differentiation, with some additional roles in development and immune responses. Confidence: High","confidence":"","size":14,"edges":69,"triangles":168,"max_degree":13,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0007399","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0030154","count":4},{"id":"GO:0051607","count":3}]},{"hash":"1301644365867688665","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0048568","count":2}]},{"hash":"1707334029179991449","title":"Immune activation and cell proliferation signals","description":"Explanation: The dominant terms indicate immune activation and signaling (positive regulation of T cell proliferation, cytokine production, neutrophil clearance) along with cytoskeletal and migration-related processes (Rho signaling, protein localization to microtubules, endothelial cell migration). The presence of DNA replication and cartilage condensation suggests concurrent proliferation and development in related pathways. Overall, the cluster centers on immune signaling with proliferative/developmental cues.","confidence":"Medium","size":14,"edges":12,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":14},{"id":"GO:0046641","count":10},{"id":"GO:0001502","count":10},{"id":"GO:0097350","count":10},{"id":"GO:0035372","count":10}]},{"hash":"80420820277382101","title":"Plant cell wall biosynthesis and arabinogalactan proteins","description":"The cluster is dominated by plant-specific processes: plant-type secondary cell wall biogenesis, arabinogalactan protein metabolism, root hair development, seed coat mucilage biosynthesis, and NG related glycosylation. These points together suggest a coherent theme of AGP-rich cell wall assembly and mucilage production in plants, with supporting roles in adhesion and polarity. ","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0080147","count":2}]},{"hash":"1482985911409552777","title":"Developmental Growth Regulation","description":"Although the proteins span both plant and animal processes, the recurring terms emphasize regulation of growth and developmental signaling across tissues (meristem/flower development, hormone response) plus broader regulatory processes (cytokine production, migration). This suggests a cluster tied to developmental regulation rather than a single, specific pathway.","confidence":"Low","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009934","count":6},{"id":"GO:0048833","count":6},{"id":"GO:0009729","count":6},{"id":"GO:0010080","count":6},{"id":"GO:0010596","count":5}]},{"hash":"710648329273585742","title":"Neural development and apoptotic signaling","description":"These proteins cluster around neural development terms (neural tube closure, forebrain development) and apoptosis-related processes (neuron/glial apoptotic processes, regulation of apoptotic signaling, intrinsic ER-stress\u2013driven apoptotic signaling, DNA fragmentation). While some terms are general (aging, homooligomerization), the dominant signals point to coordinated regulation of neural maturation with programmed cell death. This label captures the core theme without overextending to unrelated functions.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0007568","count":10},{"id":"GO:0051260","count":10},{"id":"GO:0001843","count":9},{"id":"GO:2001235","count":9},{"id":"GO:0030900","count":9}]},{"hash":"384923552684124290","title":"Nuclear Transport and Cell Cycle Regulation","description":"This cluster shows a strong emphasis on nuclear processes (positive regulation of nuclear protein export, centrosome cycle, and positive regulation of nuclear DNA replication within the mitotic cell cycle), suggesting a core theme of coordinating nuclear transport with cell division. While there are additional terms related to development and immune functions, the dominant signal appears to be regulation of the cell cycle and nuclear transport, with supporting links to microtubule-associated localization and cell fate decisions.","confidence":"Medium","size":14,"edges":32,"triangles":17,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046827","count":12},{"id":"GO:0007098","count":10},{"id":"GO:0010571","count":10},{"id":"GO:0007601","count":10},{"id":"GO:0000278","count":10}]},{"hash":"367981305646602824","title":"Developmental signaling and organogenesis","description":"The top GO terms cluster around development across tissues (axonogenesis, Schwann cell and heart development, visual perception) and associated signaling processes (positive regulation of phosphorylation, apoptotic regulation). This points to a broad theme of developmental programs and signaling rather than a single, narrow pathway. A plant-specific term (abscisic acid-activated signaling) may reflect cross-species annotation noise rather than a core function of this protein cluster. Overall, the proteins appear linked by developmental signaling across multiple organ systems.","confidence":"Medium","size":14,"edges":8,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007409","count":11},{"id":"GO:0007275","count":11},{"id":"GO:0043065","count":10},{"id":"GO:0014044","count":10},{"id":"GO:0007601","count":10}]},{"hash":"1780043305445806621","title":"Chaperone-assisted proteostasis","description":"The cluster is enriched for protein folding and refolding terms (chaperone-mediated folding, protein refolding) and a redox-response term, pointing to a proteostasis role under oxidative stress. Additional terms on sumoylation and steroid signaling (steroid hormone receptor assembly, prostate development) suggest links between proteostasis and signaling/growth pathways, indicating a cohesive function in maintaining protein homeostasis with signaling ties.","confidence":"High","size":14,"edges":82,"triangles":263,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0051775","count":4},{"id":"GO:0061077","count":4},{"id":"GO:0061179","count":4},{"id":"GO:0022417","count":4},{"id":"GO:0006463","count":4}]},{"hash":"117863563095264276","title":"Neuronal vesicle trafficking and development","description":"The Top Terms show a clear emphasis on synaptic vesicle exocytosis regulation, brain and dendrite development, and multiple intracellular transport processes (ER-Golgi, Golgi-plasma membrane, endosomes), suggesting a cohesive role in vesicle trafficking tied to neuronal development. A couple of terms (mating projection growth, Cvt pathway) are sponge-like cross-species annotations but do not override the central vesicle trafficking theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000300","count":4},{"id":"GO:0031384","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0032258","count":4}]},{"hash":"1959765779676363922","title":"mRNA processing and translation initiation","description":"The top GO terms point to post-transcriptional gene regulation: mRNA polyadenylation, modification, splicing, stabilization, and the assembly of the eIF4F complex for translation initiation, including IRES-dependent initiation. Together these suggest a cluster centered on mRNA maturation and control of translation rather than transcriptional regulation. Some terms are labeled obsolete, but the core theme remains mRNA processing and translation initiation. ","confidence":"Medium","size":14,"edges":22,"triangles":6,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0075522","count":2},{"id":"GO:1905663","count":2}]},{"hash":"2149354319920082112","title":"Oxidative Stress Response and Detoxification","description":"The top GO terms point to oxidative stress and detoxification activities (cellular oxidant detoxification, response to toxic substance, UV protection), suggesting a stress-response module. Some terms appear peripheral (menaquinone biosynthesis, transcription, tetramerization, developmental processes), likely contributing noise. Overall, the dominant signal supports a detox/oxidative stress theme.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0006351","count":2}]},{"hash":"2217223438495361715","title":"Hormone signaling and protein regulation","description":"Most terms point to hormone signaling networks (cytokinin, gibberellin, steroid hormone receptors) and regulation of protein modification/ubiquitination. A few terms touch on plant-specific processes (chlorophyll biosynthesis, cadmium response) but overall the theme is signaling and regulatory control of protein function.  ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0009736","count":5},{"id":"GO:1903071","count":4},{"id":"GO:0031400","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0009938","count":4}]},{"hash":"949832832532890696","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":84,"triangles":293,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0000463","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0001825","count":2}]},{"hash":"887180981203043960","title":"Neurodevelopmental RNA processing and apoptosis","description":"This cluster shows strong signals for neural development terms (neural tube closure, forebrain development) alongside RNA processing functions (translation initiation, spliceosome-mediated mRNA splicing) and apoptotic regulation (positive regulation of apoptotic signaling, glial apoptotic process). The combination suggests a set of proteins involved in neurodevelopment with coordinated RNA processing and apoptosis control, justifying a label that links these themes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0002188","count":9},{"id":"GO:0001731","count":9},{"id":"GO:0001843","count":5},{"id":"GO:2001235","count":5},{"id":"GO:0000398","count":5}]},{"hash":"278232059683852507","title":"Metal ion transport and redox processes","description":"The cluster shows several GO terms centered on transporting metal ions (copper, iron, arsenate) and related iron assimilation, plus oxidation-reduction and nutrient assimilation processes. This common theme suggests a function in metal homeostasis and redox metabolism in microbes, even though some terms (platelet activation, lignin catabolic process, sporulation) may reflect annotation noise or broader context.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0042128","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006825","count":4},{"id":"GO:0034755","count":4}]},{"hash":"1136371571721192948","title":"Organelle RNA editing and modification","description":"This cluster is weighted by GO terms tied to RNA modification and editing in organelles, especially mitochondrial and chloroplast contexts (cytidine-to-uridine editing; mitochondrial and chloroplast mRNA/chloroplast RNA modification; organelle RNA modification), suggesting a cohesive function in organellar RNA processing. The other biosynthetic terms are less cohesive with the main theme but do not override the clear RNA-modification signal.","confidence":"High","size":14,"edges":23,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0014075","count":2},{"id":"GO:0046654","count":2},{"id":"GO:0006633","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009451","count":2}]},{"hash":"2023674231636018691","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":2},{"id":"GO:1990034","count":2},{"id":"GO:0010116","count":1},{"id":"GO:0009644","count":1},{"id":"GO:0009269","count":1}]},{"hash":"87119423523306555","title":"Organogenesis and neural differentiation","description":"The top GO terms center on development and morphogenesis across multiple tissues\u2014neuronal fate specification in the forebrain, inner ear morphogenesis, pharyngeal system development, ureteric bud formation, pancreatic beta-cell differentiation, and gonad/uterus development\u2014indicating a shared theme of organogenesis and neural differentiation. A few plant-hormone related terms are present, but they do not define the cluster's primary function; the dominant signal is broad developmental programs.","confidence":"Medium","size":14,"edges":18,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009938","count":3},{"id":"GO:0009751","count":3},{"id":"GO:0009739","count":3},{"id":"GO:0021902","count":3},{"id":"GO:0072107","count":3}]},{"hash":"326897585180019419","title":"Fungal cell wall biosynthesis","description":"The strongest recurring signals are fungal-type cell wall assembly and beta-D-glucan biosynthesis, with a related term on division septum assembly, suggesting involvement in fungal cell wall biogenesis and cytokinesis. The other terms (mRNA splicing, DNA-related processes, transport) are more diverse and do not form a single cohesive alternative theme, so the fungal cell wall biosynthesis label best captures the core signal, albeit with some annotation noise.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":2},{"id":"GO:0000398","count":1},{"id":"GO:0046944","count":1},{"id":"GO:0032973","count":1},{"id":"GO:0071970","count":1}]},{"hash":"23200183834469578","title":"Neural development and DNA regulation","description":"Top GO terms include axonogenesis, Schwann cell development, and visual perception, which strongly point to neural development and retina-related functions. The cluster also shows nuclear/cellular regulation terms (DNA-templated transcription, positive regulation of DNA binding) and DNA repair, along with microtubule-related processes (microtubule nucleation, mitotic spindle pole body duplication), suggesting coordinated transcription, genome maintenance, and cytoskeletal dynamics that support neural differentiation and cell division.","confidence":"Medium","size":14,"edges":21,"triangles":12,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0046826","count":7},{"id":"GO:0006281","count":7},{"id":"GO:0007020","count":6},{"id":"GO:1903087","count":6}]},{"hash":"136082340831751782","title":"Unknown","description":"The top terms cover ion transport (K+, Ca2+, Mn2+), mechanosensing and cell migration, and separate nuclear processes (protein export, mRNA processing, telomere maintenance) as well as pain signaling. The terms lack a single cohesive function or pathway, indicating a heterogeneous cluster rather than a specific biological module.","confidence":"","size":14,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0071260","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0010163","count":3},{"id":"GO:0098703","count":3}]},{"hash":"205993678526190248","title":"ABA-driven abiotic stress response","description":"The cluster's top GO terms center on ABA biosynthesis regulation and responses to high light and desiccation, indicating a clear plant abiotic stress signaling theme. Other terms (DNA replication/repair, transcription, mitochondrial protein insertion, proteasome assembly, Golgi retention) are more general cellular processes and do not define a cohesive alternative function. Therefore, the dominant signal is ABA-mediated stress response in plants.","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0010116","count":4},{"id":"GO:0009644","count":4},{"id":"GO:0009269","count":4},{"id":"GO:0006260","count":2},{"id":"GO:0006281","count":2}]},{"hash":"2278647024138692923","title":"Auxin signaling and photoperiodic flowering","description":"This cluster is characterized by GO terms for auxin-activated signaling, auxin transport, and responses to auxin, together with photoperiod-related flowering regulation (short-day/long-day). The combination suggests a set of proteins coordinating hormone signaling with flowering time in response to day length.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":2},{"id":"GO:0009734","count":2},{"id":"GO:0009926","count":2},{"id":"GO:0009733","count":2},{"id":"GO:0048572","count":2}]},{"hash":"85971046455486689","title":"Ubiquitin-Proteasome\u2013Immune Signaling","description":"The cluster contains GO terms for deubiquitination, SCF-dependent proteasomal turnover, and NF-\u03baB/TNF/TCR signaling, pointing to a core theme of proteostasis linked with immune signaling; ancillary terms (hypoxia, cadmium response, amino acid regulation) reflect broader stress-related modulation.","confidence":"High","size":14,"edges":51,"triangles":115,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":6},{"id":"GO:0038061","count":5},{"id":"GO:0006521","count":4},{"id":"GO:0080129","count":4},{"id":"GO:0061418","count":4}]},{"hash":"986237540945600969","title":"Regulation of signaling and membrane dynamics","description":"The terms emphasize regulatory control across signaling and membrane-associated processes\u2014negative regulation of kinase activity, exocytosis, cell shape, and membrane remodeling (tubulation) plus nuclear import and protein modification\u2014suggesting a cluster centered on how cells regulate signaling pathways and membrane trafficking. Some items (fungal sporulation membrane formation, astrocyte activation, methylmercury response) point to broader contexts, but the core theme remains regulatory control of signaling and membrane dynamics.","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:0045921","count":5},{"id":"GO:0008360","count":5},{"id":"GO:0033234","count":5},{"id":"GO:0032120","count":5}]},{"hash":"1029725513930975475","title":"ER-Golgi vesicle trafficking and intracellular transport","description":"The listed GO terms center on secretory pathway movement: ER to Golgi and Golgi to plasma membrane transport, COPII budding, SNARE disassembly, and retrograde Golgi\u2013ER trafficking, plus CVT/autophagy\u2013related vesicle targeting. Together these indicate a cohesive theme of intracellular vesicle trafficking within the secretory/autophagy pathways, rather than a single enzyme function or signaling process. The amino acid starvation term and cell division term are secondary context rather than defining features.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0034198","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0035494","count":4},{"id":"GO:0090114","count":4}]},{"hash":"800679293968995128","title":"Immune signaling and leukocyte migration","description":"Consisting of proteins associated with immune signaling and cell movement, the top GO terms emphasize activation and regulation of immune responses (positive regulation of T cell proliferation; neutrophil clearance; positive regulation of cytokine production; interleukin-4 production) and processes that govern leukocyte and endothelial cell migration (Rho signaling, cytoskeletal localization to microtubules, endothelial cell migration). While a few terms touch development or metabolism, the strongest signal is immune activation and leukocyte trafficking.","confidence":"High","size":14,"edges":55,"triangles":84,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":14},{"id":"GO:0001502","count":14},{"id":"GO:0097350","count":14},{"id":"GO:0035372","count":14},{"id":"GO:0043068","count":14}]},{"hash":"1770986608754055635","title":"Immune activation and cell cycle signaling","description":"The top GO terms point to immune-related activities (positive regulation of T cell proliferation, cytokine production, neutrophil clearance) alongside cell cycle and cytoskeleton dynamics (DNA replication, Rho signaling, microtubule localization) and developmental processes (cartilage condensation, endothelial migration, apoptosis). This suggests a cluster of proteins that tie immune responses to cell proliferation and cytoskeletal remodeling during development or tissue remodeling.","confidence":"Medium","size":14,"edges":39,"triangles":20,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":14},{"id":"GO:0046641","count":13},{"id":"GO:0001502","count":13},{"id":"GO:0097350","count":13},{"id":"GO:0035372","count":13}]},{"hash":"878728224492977474","title":"Lipid and small-molecule biosynthesis","description":"These proteins are enriched for biosynthetic processes, including fatty acid biosynthesis, fructose biosynthesis, retinol metabolism, and even antibiotic/phosphinothricin biosynthesis, suggesting a core theme of producing diverse small molecules. While some catabolic terms appear, the dominant signal is biosynthesis, making this label representative overall.","confidence":"Medium","size":14,"edges":80,"triangles":278,"max_degree":13,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0006633","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0042572","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0019518","count":4}]},{"hash":"1519999927637969042","title":"Diverse Metabolic and Signaling Cluster","description":"The top GO terms center on various metabolic processes (TCA cycle, amino acid catabolism, GABA biosynthesis, alkaloid and phytoalexin metabolism, kynurenine catabolism) with a few development/signaling terms (Notch pathway, Leydig cell differentiation, pigmentation regulation). This suggests a cluster driven by metabolism with some associated signaling or lineage-specific roles rather than a single cohesive pathway. Confidence: Medium","confidence":"","size":14,"edges":89,"triangles":341,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0097053","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0007219","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0052314","count":4}]},{"hash":"153184738802054055","title":"Steroid and hormone metabolism","description":"Based on GO terms, the proteins are enriched for biosynthesis and turnover of lipid- and steroid-derived signals (cortisol, testosterone, brassinosteroids, retinoic acid, vitamin D responses, fatty acid omega-oxidation, xenobiotic catabolic processes). This suggests a common theme of hormone and lipid metabolism driving the cluster\u2019s function, with other terms like mammary development or endothelial adhesion likely reflecting downstream effects rather than core activity.","confidence":"High","size":14,"edges":23,"triangles":10,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":12},{"id":"GO:0071603","count":12},{"id":"GO:0034651","count":12},{"id":"GO:0070989","count":12},{"id":"GO:0042738","count":12}]},{"hash":"784237543063664112","title":"Oxidative and Heat Stress Response with Axonal Transport","description":"The cluster is enriched for stress-response terms including stress-activated MAPK cascade, hydrogen peroxide, UV-A, and heat response, along with transport regulation (anterograde axonal transport, intracellular transport). This suggests proteins involved in cellular defense against oxidative/thermal stress and regulation of neuronal transport.","confidence":"Medium","size":14,"edges":20,"triangles":18,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051403","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0032387","count":4},{"id":"GO:0032355","count":4},{"id":"GO:0099641","count":4}]},{"hash":"1758625904126739926","title":"Neuronal Stress Signaling and Axonal Transport Regulation","description":"This cluster centers on stress-responsive signaling and transport regulation in neurons. The top GO terms point to a stress-activated MAPK cascade, oxidative and heat stress responses, UV response, and regulation of intracellular/axonal transport (notably anterograde transport). Also present are estradiol response and regulation of amyloid fibril formation, hints of broader proteostasis involvement. Overall, the proteins likely coordinate cellular stress signaling with axonal transport and proteostasis in neuronal contexts.","confidence":"Medium","size":14,"edges":72,"triangles":196,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051403","count":6},{"id":"GO:0007568","count":6},{"id":"GO:0032387","count":6},{"id":"GO:0032355","count":6},{"id":"GO:0099641","count":6}]},{"hash":"1661672988707011133","title":"Steroid hormone metabolism and detoxification","description":"This cluster is dominated by GO terms related to steroid biosynthesis and hormone-related metabolism (cortisol, testosterone, brassinosteroid) along with catabolic and detoxification processes (retinoic acid, vitamin D response, xenobiotic catabolic, fatty acid omega-oxidation, oxidative demethylation). While some terms (e.g., mammary gland development, endothelial adhesion) touch on development and tissue remodeling, the strongest signal is lipid/hormone metabolism and detoxification pathways. The presence of a plant-specific term (brassinosteroid biosynthesis) suggests broad annotation coverage, but the core theme still centers on steroids and related metabolic/detoxification processes. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":14},{"id":"GO:0071603","count":14},{"id":"GO:0034651","count":14},{"id":"GO:0070989","count":14},{"id":"GO:0042738","count":14}]},{"hash":"1542765283124940738","title":"Plant metabolite catabolism and detoxification","description":"The proteins are enriched for catabolic processing of plant-derived compounds (chlorophyll, stilbene, glucuronoside) and detoxification pathways (P450 epoxygenase pathway, cellular oxidant detoxification), suggesting a cohesive function in metabolizing and detoxifying plant/metabolite xenobiotics.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019391","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0015996","count":3},{"id":"GO:0019373","count":3}]},{"hash":"1759209453813974829","title":"Floral development and epidermal lipid biosynthesis regulation","description":"This cluster centers on plant development terms like floral meristem growth, bract development, and multicellular organism development, combined with regulation of wax and cutin biosynthesis and hormone signaling (abscisic acid and ethylene). This suggests a cohesive program linking floral/inflorescence development with epidermal lipid barrier formation, modulated by hormonal pathways.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0006355","count":10},{"id":"GO:0010451","count":8},{"id":"GO:0009873","count":8},{"id":"GO:0010432","count":8}]},{"hash":"1634352846047199879","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The most represented GO terms are ubiquitin-related catabolic processes, including protein ubiquitination and SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, which together point to proteasome-mediated protein turnover. While a few other terms are diverse and could reflect multifunctional annotations or species-specific contexts, the dominant signal is ubiquitin tagging and proteasomal degradation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007568","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0030900","count":3}]},{"hash":"576973827036870258","title":"Plant Development and Cuticle Biosynthesis Regulation","description":"The top GO terms point to plant-specific developmental processes (floral meristem growth, bract development, multicellular organism development) and transcriptional regulation, alongside epidermal barrier biosynthesis processes (positive regulation of cutin and wax biosynthetic processes) and hormone signaling (ethylene- and abscisic acid-activated pathways). This pattern suggests a coherent theme of coordinating plant organ development with epidermal cuticle biosynthesis and related regulatory signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010451","count":1},{"id":"GO:0009873","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0010432","count":1},{"id":"GO:0007275","count":1}]},{"hash":"55949096601032510","title":"Leaf development and cell wall remodeling","description":"The top GO terms are dominated by plant-specific processes: pectin catabolic process and cell wall modification, together with leaf development, suggesting a focus on leaf growth and cell wall remodeling. The various transport terms appear as secondary themes, reflecting membrane transport capabilities for metabolites, but do not override the core plant developmental/cell wall signal. Thus, naming the cluster around leaf development and cell wall remodeling captures the main functional theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0042545","count":2},{"id":"GO:0048366","count":2},{"id":"GO:0015739","count":1},{"id":"GO:0035461","count":1}]},{"hash":"772243015978385102","title":"Plant meristem identity and flowering regulation","description":"Top GO terms indicate shoot/root meristem maintenance and identity, embryonic patterning, cell fate specification, and flowering/vernalization responses. Taken together, these terms point to a cohesive theme of plant developmental regulation focused on meristem identity and the timing of developmental transitions, with one outlier term (virus transport) likely incidental. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048575","count":1},{"id":"GO:0010071","count":1},{"id":"GO:0046740","count":1},{"id":"GO:0009880","count":1},{"id":"GO:0080022","count":1}]},{"hash":"954869268798910365","title":"T cell activation and cytokine production","description":"These proteins are collectively enriched for adaptive immune functions, especially T cell proliferation and cytokine production (including IL-4), along with broader immune signaling such as neutrophil clearance and regulation of cytokine production. Additional terms point to immune-related cell signaling (Rho pathways) and cytoskeletal dynamics (microtubule localization) that support T cell\u2013driven immune responses and inflammation. Overall, a cohesive theme of T cell\u2013mediated immune activation and cytokine signaling emerges.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":13},{"id":"GO:0001502","count":13},{"id":"GO:0097350","count":13},{"id":"GO:0035372","count":13},{"id":"GO:0043068","count":13}]},{"hash":"1176597769589111701","title":"Meiosis-related spindle assembly and cell cycle control","description":"These proteins show strong signals for microtubule dynamics and spindle assembly in female meiosis I, plus processes linked to oocyte maturation and ubiquitin-dependent protein turnover during the cell cycle, suggesting a core role in meiotic progression and early developmental regulation. Some broader developmental terms appear, but the dominant theme is meiosis/spindle assembly coupled with cell cycle control.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046785","count":8},{"id":"GO:0007057","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0021678","count":8},{"id":"GO:0006516","count":8}]},{"hash":"1102523819250971496","title":"Plant nutrient and xenobiotic transport with hormone signaling","description":"This cluster is dominated by transmembrane transport terms for nutrients and xenobiotics (nitrate transmembrane transport, nitrate assimilation, oligopeptide transport, xenobiotic transport) and by stress- and hormone-related terms (response to nitrate, osmotic stress, herbicide response, auxin signaling, gibberellin homeostasis). The combination suggests a functional theme around membrane transport coupled to nutrient handling and hormone-mediated stress responses, with an outlier viral process term that does not define the core function. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0006855","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0010336","count":2}]},{"hash":"1851834513703125050","title":"Plant Actin Dynamics and ER-Golgi Trafficking","description":"Top terms show actin cytoskeleton organization, lamellipodium assembly, and positive regulation of GTPase activity, plus ER-to-Golgi vesicle transport, suggesting coordinated cytoskeletal remodeling with vesicle trafficking. The presence of plant development and hormone-response terms implies these processes contribute to growth and development in plants (meristem development, somatic embryogenesis, auxin signaling). ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0048507","count":2}]},{"hash":"804556428117044580","title":"Seed development, hormone signaling, and nitrate transport","description":"The top GO terms cluster around seed development and transcriptional regulation, with auxin-activated signaling and gibberellin homeostasis highlighting plant hormone control. Nitrate transport, assimilation, and nitrate response indicate nutrient signaling integration. Together, these terms point to a plant-specific growth and developmental module where transcriptional control, hormone cues, and nutrient signaling coordinate seed development and growth. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048316","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0010336","count":1},{"id":"GO:0035672","count":1}]},{"hash":"720636382228444484","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031426","count":3},{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0090502","count":2}]},{"hash":"852342319138726960","title":"Neuronal endosomal trafficking and synaptic recycling","description":"This cluster centers on neuronal endosomal trafficking and receptor handling, as indicated by terms for endosome transport and size regulation, receptor recycling, and glutamatergic synaptic transmission, with supporting roles for GTPase activity and dendrite morphogenesis. A few terms like bradykinin catabolism and insulin processing seem incidental rather than defining for the cluster.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":1},{"id":"GO:0030070","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0035646","count":1},{"id":"GO:0050775","count":1}]},{"hash":"1752576202698572790","title":"Auxin-regulated transcription in plant development","description":"This cluster's top GO terms cluster around transcriptional regulation and auxin signaling (DNA-templated transcription, regulation of transcription, response to auxin, auxin-activated signaling) along with developmental processes (meristem development, fruit dehiscence). These together point to proteins involved in auxin-controlled gene expression during plant growth and development. Some metabolic terms are present but likely peripheral to the main theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0010047","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1454904183220848393","title":"Innate immune sensing and inflammatory signaling","description":"This cluster is driven by innate immune terms: detection of lipopolysaccharide, TLR8 signaling, response to fungus, and regulation of cytokine production, pointing to an immune/inflammatory theme. A few terms relate to broader physiological processes, but the core signal is innate immune sensing and inflammatory response.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0010596","count":13},{"id":"GO:0009620","count":13},{"id":"GO:0050929","count":13},{"id":"GO:0072237","count":13},{"id":"GO:0050707","count":13}]},{"hash":"1941207381156422959","title":"Ubiquitin-Dependent Protein Regulation and Chromatin Modification","description":"The cluster is driven by ubiquitin-related processes (ubiquitination and ubiquitin-dependent protein catabolic processes), suggesting protein turnover via the proteasome/ERAD pathway. Histone modification terms (acetylation and methylation) imply chromatin remodeling and transcriptional regulation, while signaling terms like regulation of JNK cascade and NF-kappaB activation indicate ubiquitin-linked signaling pathways. A few terms (peroxisome import, actin cable regulation) may reflect broader regulatory roles rather than a single pathway, making the set heterogeneous. Overall, the theme centers on ubiquitin-mediated regulation with chromatin modification as a key associated function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0016567","count":4},{"id":"GO:2000620","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0046328","count":4}]},{"hash":"1594043726577827553","title":"Mitochondrial and Plastid Gene Expression","description":"This cluster centers on transcription and ribosome-related processes in organelles, with GO terms for mitochondrial transcription and termination, mitochondrial ribosome assembly, plastid rRNA transcription, and chloroplast organization, plus RNA processing (RNA splicing) and related protein folding (peptidyl-prolyl isomerase). These collectively suggest a common theme of organellar gene expression and RNA processing in mitochondria and plastids.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000413","count":2},{"id":"GO:0046521","count":1},{"id":"GO:0009658","count":1},{"id":"GO:0006393","count":1},{"id":"GO:0061668","count":1}]},{"hash":"1240833612965534620","title":"Actin Cytoskeleton Remodeling and Cell Polarity","description":"Top terms indicate strong enrichment for actin filament polymerization and Arp2/3-mediated nucleation, along with neuronal-related dendritic spine development and bipolar cell polarity establishment/maintenance. These shared functions point to regulation of the actin cytoskeleton to shape cell morphology and polarity, justifying the label as a concise, representative cluster description.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0030838","count":1},{"id":"GO:0007096","count":1},{"id":"GO:0007232","count":1},{"id":"GO:2000601","count":1}]},{"hash":"1113995967199942659","title":"TLR-Mediated Innate Immune Signaling","description":"Despite a mix of terms, the cluster is characterized by innate immune sensing features: TLR8 signaling, detection of LPS, response to fungus, and cytokine production regulation, suggesting a shared role in pathogen recognition and inflammatory signaling; several terms (development, vestibuloocular reflex, luteolysis) may be incidental.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010596","count":2},{"id":"GO:0009620","count":2},{"id":"GO:0050929","count":2},{"id":"GO:0072237","count":2},{"id":"GO:0050707","count":2}]},{"hash":"179676048699152586","title":"Coagulation and Fibrinolysis Regulation","description":"Top terms point to proteolytic processes governing clot formation and dissolution (fibrinolysis, negative regulation of plasminogen activation, blood coagulation, and regulation of extracellular matrix secretion). While a few plant-defense terms appear (defense response to oomycetes, SA biosynthesis regulation, systemic acquired resistance), these are minority and likely noise; the dominant theme is coagulation/fibrinolysis control. Overall, the cluster aligns with proteolytic regulation of coagulation pathways.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042730","count":2},{"id":"GO:0003331","count":2},{"id":"GO:0051918","count":2},{"id":"GO:0010757","count":2},{"id":"GO:0007596","count":2}]},{"hash":"1301543567114159230","title":"DNA Damage Response and Ubiquitin-Proteasome Regulation","description":"This cluster centers on DNA damage response and proteostasis: terms point to homologous recombination\u2013mediated repair and DNA unwinding, as well as ubiquitination and SCF-dependent proteasomal degradation, with protein oligomerization. The presence of Arp2/3-mediated actin nucleation suggests linked cytoskeletal remodeling, possibly related to repair signaling or chromatin dynamics. Cadmium ion response and embryonic development terms imply broader stress signaling and developmental regulation, but the core theme appears to be DNA repair coupled with controlled protein turnover and remodeling. ","confidence":"Medium","size":13,"edges":56,"triangles":118,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006268","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0000209","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0032508","count":3}]},{"hash":"484661063718760039","title":"Nuclear import and RNA processing","description":"This cluster includes GO terms tied to nuclear transport and RNA handling, such as NLS-bearing protein import into the nucleus, splicing factor import, Ran signaling, and tRNA re-export from the nucleus, pointing to a common theme of nuclear import/export and RNA processing. Some terms (e.g., phototaxis, meristem initiation, adaxial/abaxial polarity, phosphatidylcholine biosynthesis) are less clearly connected and may reflect broader or incidental associations, which keeps the overall signal moderate rather than strong.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900370","count":1},{"id":"GO:0035048","count":1},{"id":"GO:0034501","count":1},{"id":"GO:0071528","count":1},{"id":"GO:0042331","count":1}]},{"hash":"675263736396668005","title":"Ribosome biogenesis and rRNA processing","description":"This cluster is dominated by GO terms related to ribosome assembly and pre-rRNA maturation (ribosome biogenesis, ribosomal subunit biogenesis, SSU/LSU rRNA maturation, and ITS1 cleavage), indicating proteins mainly involved in ribosome production and rRNA processing. Additional terms for spliceosome-mediated splicing and microtubule severing are present but secondary to ribosome-focused functions.","confidence":"High","size":13,"edges":35,"triangles":40,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0048568","count":2},{"id":"GO:0000447","count":2}]},{"hash":"104066971767964983","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":44,"triangles":65,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2},{"id":"GO:0075713","count":2}]},{"hash":"1770142533076211349","title":"Immune-ECM Remodeling and Cell Adhesion","description":"The cluster mixes immune activity (complement activation; T cell activation) with extracellular matrix remodeling and adhesion processes (metallopeptidase activity, ECM assembly regulation, hyaluronan metabolism, cell-matrix and cell-cell adhesion, migration). Some cartilage-related terms appear, suggesting tissue remodeling contexts; overall, the set reflects immune responses intertwined with ECM remodeling and adhesion.","confidence":"Medium","size":13,"edges":12,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006956","count":4},{"id":"GO:0002291","count":4},{"id":"GO:1905050","count":4},{"id":"GO:1901202","count":4},{"id":"GO:0006929","count":4}]},{"hash":"2300864110223789398","title":"Neural development and trafficking","description":"This cluster's top GO terms are dominated by neural development: spinal cord development, neural tube closure, neuron projection development, embryonic organ development, and multicellular organism growth, indicating a neural-development theme. Additional terms (COPII vesicle budding, peroxisome targeting, ribosomal subunit biogenesis) point to trafficking and general cellular processes that accompany development. The primary signal is neural development with some supporting trafficking/biogenesis roles.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0035264","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0090114","count":3}]},{"hash":"291926647593766649","title":"MAPK/ERK pathway regulation and immune signaling","description":"Based on GO terms such as negative regulation of ERK1/ERK2 cascade, regulation of MAPK activity, cellular response related to T cell receptor signaling, and regulation of GTPase activity, the proteins in this cluster appear to modulate key signaling pathways involved in immune responses and stress signaling (including cadmium response). Development terms like placenta and thymus are broad/less specific in this context, so the core theme centers on signaling control and immune-related regulation.","confidence":"Medium","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":6},{"id":"GO:0000187","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0048538","count":6},{"id":"GO:0070373","count":5}]},{"hash":"2014119080811665497","title":"Mitochondrial and plastid RNA editing and transcription","description":"These proteins cluster around organelle gene expression, showing involvement in RNA processing/modification and transcription in both mitochondria and chloroplasts, plus chloroplast-nucleus signaling. The top GO terms emphasize mitochondrial mRNA processing/editing, plastid/chloroplast RNA modification, and plastid transcription, indicating a coherent role in organellar RNA metabolism and gene expression. Embryo dormancy annotation may be incidental noise.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":8},{"id":"GO:0009451","count":8},{"id":"GO:0016554","count":8},{"id":"GO:0080156","count":8},{"id":"GO:1905639","count":8}]},{"hash":"474031193362903412","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0090502","count":3},{"id":"GO:0070129","count":3}]},{"hash":"399020934559555108","title":"Embryonic development and cell cycle control","description":"This cluster is enriched for DNA replication and centrosome cycle (cell cycle) terms, plus transcriptional regulation and nuclear transport, all of which are active during cell division in development. The presence of embryonic cranial skeleton morphogenesis and angiogenesis terms suggests a developmental context, with innate immune signals also present, so the label reflects both developmental gene regulation and cell-cycle coordination.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0048701","count":5},{"id":"GO:0045944","count":4},{"id":"GO:0035372","count":4},{"id":"GO:0007098","count":4}]},{"hash":"2265450676961012530","title":"Vesicle trafficking and autophagy regulators","description":"The cluster is dominated by GO terms for ER-to-Golgi and endosome-to-Golgi transport, along with autophagy and positive regulation of GTPase activity, suggesting proteins that coordinate vesicle trafficking and autophagic processes via GTPase regulation. Some terms (developmental processes, DNA recombination, and viral entry) seem less connected, likely reflecting multifunctionality or annotation noise, but the core theme remains vesicle transport and autophagy.","confidence":"Medium","size":13,"edges":13,"triangles":1,"max_degree":12,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0090502","count":8},{"id":"GO:0006310","count":3},{"id":"GO:0034498","count":2},{"id":"GO:0016358","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1229646061092938359","title":"DNA replication and genome maintenance","description":"The cluster is dominated by GO terms tied to DNA replication (DNA replication, DNA duplex unwinding) and chromatin dynamics (histone exchange). A secondary signal is nonsense-mediated decay for mRNA surveillance, along with ubiquitination, and stress-related processes (hypoxia) and development signals, suggesting a set of proteins involved in genome maintenance, transcriptional regulation, and cellular stress responses. The MDA-5 signaling term may reflect RNA sensing aspects or broader stress signaling, but the core connection appears to be DNA replication and genome stability.","confidence":"Medium","size":13,"edges":64,"triangles":158,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000184","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006268","count":4},{"id":"GO:0001666","count":4},{"id":"GO:0000209","count":3}]},{"hash":"1772415738112183409","title":"Nutrient and neurotransmitter membrane transporters","description":"The top GO terms are dominated by membrane transport activities, including vitamin, sugar, sialic acid, urate, galactose, and other nutrient/metabolite transmembrane transport, plus a vesicular neurotransmitter loading term. This pattern suggests a cohesive role for these proteins as diverse membrane transporters moving nutrients and metabolites, with the neurotransmitter loading term fitting the broader transporter/trafficking theme. ","confidence":"High","size":13,"edges":12,"triangles":6,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019852","count":6},{"id":"GO:0015739","count":5},{"id":"GO:0035461","count":5},{"id":"GO:0015747","count":5},{"id":"GO:0070715","count":5}]},{"hash":"1621000226776727564","title":"Antiviral Stress-Response and Translational Regulation","description":"The cluster highlights innate immune activity together with translational control mechanisms, including innate immune response, negative regulation of viral genome replication, translation, mRNA processing, and regulation of translational initiation by eIF2 alpha phosphorylation, suggesting a shared role in antiviral defense via stress-induced translation regulation. Some terms like facial nerve morphogenesis seem less connected and may reflect annotation noise, but the dominant pattern supports a link between immune signaling and control of protein synthesis under stress.","confidence":"Medium","size":13,"edges":19,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0006397","count":4}]},{"hash":"154759687344592599","title":"ER Stress and Chaperone Folding","description":"The top GO terms point to proteostasis: misfolded protein handling, chaperone-assisted refolding, and translation initiation in response to ER stress, plus protein complex assembly. Although some terms are obsolete or peripheral (e.g., development and hormone signaling), the dominant theme is ER-associated quality control and folding. This suggests the cluster represents a proteostasis network centered on ER stress response and chaperone-mediated folding.","confidence":"Medium","size":13,"edges":62,"triangles":155,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":4},{"id":"GO:0051259","count":4},{"id":"GO:0070843","count":4},{"id":"GO:0070389","count":4},{"id":"GO:1900035","count":4}]},{"hash":"328231734640122604","title":"Mitochondrial protein synthesis and metabolism","description":"The cluster is anchored by mitochondrial translation and tRNA processing/transamidation, plus fatty acid catabolism, pointing to a mitochondrial gene expression and metabolic theme. Some other terms (ER organization, epithelial polarity, muscle regeneration) may reflect broader cellular context or annotation noise, but the core signals are mitochondrial protein synthesis and energy metabolism.","confidence":"Medium","size":13,"edges":30,"triangles":21,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0009405","count":3},{"id":"GO:0090162","count":2},{"id":"GO:0043403","count":2},{"id":"GO:0007029","count":2}]},{"hash":"1101421592977656503","title":"Unknown","description":"The GO terms span diverse processes\u2014from regulation of cell growth and cell cycle transitions to translation and various developmental or stress-related activities\u2014without a clear, single functional theme tying all proteins together. This heterogeneity suggests the cluster does not represent a cohesive biological function, making a concise informative label difficult to justify.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060770","count":2},{"id":"GO:0030308","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0051245","count":1},{"id":"GO:1901001","count":1}]},{"hash":"1233105797488502125","title":"Membrane Transport and Ion Homeostasis","description":"The GO terms are dominated by transmembrane transport (chloride, sulfate, fructose) and processes regulating membrane potential and intracellular pH, pointing to a coherent function in membrane transport and ion balance. Some terms (sperm capacitation, sensory perception of sound) are less clearly related and may reflect cross-species annotations; overall the label captures the main shared function of the cluster.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0046677","count":4},{"id":"GO:1902476","count":3},{"id":"GO:0051454","count":3}]},{"hash":"1627560897240278282","title":"COPI-mediated ER-Golgi trafficking","description":"The top GO terms cluster around secretory pathway organization and vesicle trafficking between the ER and Golgi, including COPI vesicle budding/coating, ER-to-Golgi transport, and regulation of protein exit from the ER, plus Golgi ribbon formation and Wnt secretion. This points to a cohesive set of proteins involved in COPI-mediated ER-Golgi trafficking and Golgi function, with a few developmental terms likely incidental. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":1},{"id":"GO:1902003","count":1},{"id":"GO:0001893","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0070863","count":1}]},{"hash":"1118917511725653326","title":"RNA Processing and Maturation","description":"Based on GO terms, the cluster is enriched for RNA-centric processes: nuclear-transcribed mRNA catabolic process (RNase MRP-dependent), box C/D snoRNA processing, tRNA processing, and RNA hydrolysis. These indicate components of RNA maturation, processing, and turnover. While a few terms touch on other areas (chromosome condensation, lipid biosynthesis, signaling, vesicle exocytosis), the majority center on RNA metabolism, suggesting the proteins act together in RNA processing pathways.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0030261","count":2},{"id":"GO:0000294","count":2},{"id":"GO:0048235","count":2},{"id":"GO:0034965","count":2},{"id":"GO:0090502","count":1}]},{"hash":"495265292787486207","title":"Plant nitrate transport and defense signaling","description":"Based on the GO terms, the cluster centers on plant-specific processes such as nitrate transmembrane transport, nitrate assimilation, and response to nitrate, along with defense and biotic stimulus responses. The presence of gibberellic acid homeostasis and pollen tube reception hints at broader hormone signaling and reproductive context. Together, these terms suggest a cohesive theme around plant nutrient uptake/metabolism coupled with defense signaling, with additional hormonal/reproductive associations reflecting functional cross-talk in plants.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010483","count":1},{"id":"GO:0009607","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0010336","count":1}]},{"hash":"1274488035926405500","title":"Plant cell wall remodeling and defense","description":"Based on top GO terms centered on cell wall dynamics (cell wall organization, plant-type cell wall loosening), carbohydrate catabolism (cellulose and polysaccharides), and defense against fungi, the proteins appear to function in remodeling and degradation of the plant cell wall and related defense responses.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0071555","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0000272","count":2},{"id":"GO:0019953","count":2}]},{"hash":"1305331782931803911","title":"DNA Replication and Cell Cycle Proteins","description":"The top terms are dominated by DNA replication, cell division, DNA recombination, and DNA integration, pointing to a cluster enriched for genome duplication and cell-cycle progression. Supporting terms like ATP metabolic process and ribosomal large subunit assembly fit the broader cellular growth context, while a cadmium-stress\u2013related SCF disassembly term may be an annotation peculiarity. Overall, the cluster appears to represent DNA metabolism and cell-cycle machinery.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0015074","count":2},{"id":"GO:1990171","count":2}]},{"hash":"1634657127944552401","title":"Developmental Signaling and Differentiation","description":"The cluster centers on developmental signaling pathways (Hippo, Wnt) together with tissue differentiation events (keratinocyte differentiation, cartilage condensation) and cell growth regulation (DNA replication, apoptosis, cardiac proliferation). While there are immune-related terms, the dominant signal points to developmental growth and patterning across tissues.","confidence":"Medium","size":13,"edges":24,"triangles":16,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0046827","count":7},{"id":"GO:0035329","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0030216","count":6}]},{"hash":"88583469655304657","title":"Epithelial morphogenesis and cell cycle control","description":"The cluster combines terms tied to epithelial growth and organ development (lung induction, fungiform papilla formation, prostate-related epithelial proliferation) with core cell cycle and DNA damage response processes (regulation of cell cycle, chromatid cohesion, DNA damage response). There are also hints of nuclear transport and actin cytoskeleton rearrangements via cell adhesion, all of which support coordinated morphogenesis in epithelial tissues. This suggests a cohesive theme of epithelial development intertwined with cell cycle regulation.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007050","count":10},{"id":"GO:0051211","count":6},{"id":"GO:0060769","count":6},{"id":"GO:0070602","count":6},{"id":"GO:0006607","count":6}]},{"hash":"2132949082991960425","title":"Lipopolysaccharide Core and Heptose Biosynthesis","description":"The top GO terms are strongly centered on lipopolysaccharide biosynthesis, especially core region and ADP-L-glycero-beta-D-manno-heptose biosynthesis, indicating a cohesive LPS assembly module. Some other biosynthesis terms appear, but they likely reflect broad annotations across species rather than a separate function, so the LPS core/heptose focus best explains the cluster.","confidence":"Medium","size":13,"edges":53,"triangles":112,"max_degree":12,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009103","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0009244","count":5},{"id":"GO:0097171","count":5},{"id":"GO:0055114","count":5}]},{"hash":"322307651911296704","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":23,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0061091","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0098709","count":1},{"id":"GO:0051515","count":1},{"id":"GO:0052889","count":1}]},{"hash":"498357254805968853","title":"Unknown","description":"The listed GO terms span lipid biosynthesis, various forms of transport, protein complex formation, sulfur amino acid metabolism, nuclear import, and cell-cycle regulation, showing little cohesion around a single biological process. This diversity suggests the cluster does not represent one clear function, hence the Unknown label with no confidence.","confidence":"","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006633","count":13},{"id":"GO:0031460","count":13},{"id":"GO:0051289","count":13},{"id":"GO:0043418","count":13},{"id":"GO:0055114","count":13}]},{"hash":"2137862443265955669","title":"T cell activation and inflammatory signaling","description":"The cluster\u2019s top GO terms cluster around adaptive immune activation (positive regulation of T cell proliferation, IL-4 production, cytokine production) and inflammatory processes (neutrophil clearance, endothelial cell migration). Rho signaling ties into cytoskeletal and motility changes common in immune cells. While cartilage condensation is less related, the dominant theme is immune activation and inflammation, justifying this label as a concise, representative summary.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":13},{"id":"GO:0001502","count":13},{"id":"GO:0097350","count":13},{"id":"GO:0035372","count":13},{"id":"GO:0043068","count":13}]},{"hash":"1196553306922913509","title":"Plant growth signaling and development regulation","description":"This cluster combines GO terms that center on regulatory signaling pathways (negative regulation of BMP signaling, non-canonical NF-kappaB, MAPK cascades) and developmental control (maintenance of meristem identity), along with related enzymatic activity (peptidyl-threonine dephosphorylation) and organelle-associated processes (photosystem stoichiometry adjustment, vacuole fusion). The recurring theme is coordinated signaling control affecting plant development and organelle dynamics, supporting a cohesive label around plant growth signaling and development regulation.","confidence":"Medium","size":13,"edges":39,"triangles":35,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":12},{"id":"GO:0080005","count":11},{"id":"GO:0000173","count":11},{"id":"GO:0071560","count":11},{"id":"GO:0010991","count":11}]},{"hash":"936773266568583516","title":"Chromatin regulation and transcription control","description":"Top terms indicate a core theme of chromatin state and gene expression regulation, including rDNA heterochromatin formation, histone modification, transcriptional repression by RNA Pol II, and localization of proteins to chromatin, with additional signals for centromere regulation. Some development-related terms (vitellogenesis, spermatid development, multicellular growth) appear but seem secondary to the chromatin-focused function.","confidence":"Medium","size":13,"edges":16,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":6},{"id":"GO:0043966","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0071169","count":5},{"id":"GO:1900446","count":4}]},{"hash":"157836711585563839","title":"Neuronal spine morphogenesis and actin remodeling","description":"Top terms converge on actin-driven remodeling (ruffle and lamellipodium assembly, Rac signaling, actin cortical patch localization) and neuronal development (dendritic spine morphogenesis and hippocampus development). Golgi-to-plasma membrane transport aligns with membrane delivery needed for spine growth, while adhesion-related terms reflect broader developmental processes. This suggests the cluster represents proteins coordinating spine formation and cytoskeletal dynamics in neurons.","confidence":"High","size":13,"edges":64,"triangles":164,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0097178","count":5},{"id":"GO:0061001","count":5},{"id":"GO:0043001","count":5},{"id":"GO:0045792","count":5},{"id":"GO:0060999","count":5}]},{"hash":"1115405706764287275","title":"Mitochondrial ROS stress response and mitophagy","description":"The top GO terms center on mitochondrial autophagy (mitophagy), responses to oxidative stress (hydrogen peroxide, ROS), and stress signaling (MAPK cascade, radiation/UV response), with an axonal transport component. Together they point to a coordinated mitochondrial quality-control program activated by oxidative and radiation stress, especially in neural contexts.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":6},{"id":"GO:0000422","count":6},{"id":"GO:0051403","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0032387","count":4}]},{"hash":"1664972429510591832","title":"Proteolysis and peptide hormone maturation","description":"These proteins converge on proteolytic processing and maturation of peptide signals: autoprocessing and membrane proteolysis indicate protease activity, while angiotensin maturation and blood-volume regulation point to peptide hormone processing. Digestion and general proteolysis support a common post-translational processing role, and antigen processing via MHC II highlights proteolysis in generating immune-presented peptides. Together, the GO terms suggest a shared theme of proteolytic processing across endocrine, digestive, and immune contexts.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016540","count":3},{"id":"GO:0002016","count":2},{"id":"GO:0007193","count":2},{"id":"GO:0060736","count":2},{"id":"GO:0033619","count":2}]},{"hash":"1716253103405128496","title":"Vacuolar Amino Acid Transporters","description":"The strongest signal is the set of GO terms for transmembrane import of various amino acids into the vacuole (tyrosine, arginine, glutamate, histidine, asparagine, lysine), suggesting this cluster groups proteins that transport amino acids across the vacuolar membrane. A few terms about actin filament network formation and general transport are present but do not override the central theme of vacuolar amino acid transport.","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0051639","count":2},{"id":"GO:0090514","count":1},{"id":"GO:1901481","count":1},{"id":"GO:0090518","count":1}]},{"hash":"908282244442377029","title":"Protein acetylation and chromatin modification","description":"The top GO terms are dominated by acetylation-related processes (peptidyl-lysine N6-acetylation, N-terminal acetylation, spermine acetylation, histone acetylation) and subtelomeric heterochromatin formation, indicating a core theme around acetyltransferase activity and chromatin state regulation. A few outlier terms describe unrelated metabolic processes, likely noise, but the strongest signal points to acetylation-driven chromatin modification.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":12},{"id":"GO:0006348","count":11},{"id":"GO:0032919","count":11},{"id":"GO:0043967","count":11},{"id":"GO:0018002","count":11}]},{"hash":"1601347664373144456","title":"Multi-tissue embryonic organogenesis and differentiation","description":"This cluster includes GO terms spanning diverse embryonic development and tissue differentiation across organs (palate, endoderm, cortex interneurons, axon guidance, muscle progenitors, heart AV node, kidney morphogenesis, cerebellar neuron signaling) and retinoic acid\u2013regulated processes, suggesting a general role in broad developmental programs rather than a single pathway.","confidence":"Medium","size":13,"edges":19,"triangles":6,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":4},{"id":"GO:0042663","count":3},{"id":"GO:0021892","count":3},{"id":"GO:0030516","count":3},{"id":"GO:0014813","count":3}]},{"hash":"1671020428262021562","title":"Steroid and lipid biosynthesis","description":"This cluster is enriched for GO terms tied to steroid (testosterone/androgen) biosynthesis and metabolism, alongside various lipid and fatty acid-related biosynthetic processes (retinol metabolism, fatty acid elongation, mycolic acid, poly-hydroxybutyrate). While a transcription regulation term is present, the dominant pattern is lipid and steroid metabolic pathways across diverse contexts, suggesting a cohesive theme around lipid/steroid biosynthesis. ","confidence":"High","size":13,"edges":22,"triangles":22,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0061370","count":8},{"id":"GO:0008209","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0042619","count":8},{"id":"GO:0045150","count":7}]},{"hash":"345142333026612721","title":"Root hair tip growth with cytoskeletal and mitochondrial stress responses","description":"The top GO terms point to plant root hair tip growth and cortical microtubule organization, indicating a cytoskeletal role in polarized growth. Additional terms indicate osmotic and nutrient stress responses (mannitol, sorbitol, magnesium starvation), suggesting stress adaptation. Mitochondrial-associated terms (cytochrome c release, outer membrane protein insertion) imply changes in mitochondrial dynamics during stress. Together, these terms describe a cluster of proteins involved in root hair growth coupled with cytoskeletal and mitochondrial stress responses.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071325","count":1},{"id":"GO:0010350","count":1},{"id":"GO:0048768","count":1},{"id":"GO:0072709","count":1},{"id":"GO:0051511","count":1}]},{"hash":"166186150587413150","title":"Chloroplast Photosynthesis Core","description":"The cluster is dominated by GO terms tied to photosynthesis and photosystem I function (photosynthetic electron transport, NADP+ reduction, and stabilization of photosystem I), indicating chloroplast-based photosynthetic machinery as the central theme; other terms appear peripheral (cell wall, chitin response, pollination) and do not override the primary photosynthesis signal.","confidence":"High","size":13,"edges":13,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009773","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0009780","count":1},{"id":"GO:0042550","count":1},{"id":"GO:0009856","count":1}]},{"hash":"394874416593879035","title":"Plant Hormone Signaling and Biotic Responses","description":"This cluster's top GO terms are dominated by plant hormone signaling pathways (abscisic acid, cytokinin, gibberellin) and biotic-related processes (response to biotic stimulus, defense, nodulation), suggesting proteins involved in hormone-regulated growth and legume biotic interactions. The presence of both hormone signaling and defense-related terms supports a cohesive theme around hormone-mediated biotic responses, even though the network edges are absent.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":4},{"id":"GO:0009736","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0080163","count":2},{"id":"GO:0043086","count":2}]},{"hash":"550949189067193361","title":"ER stress\u2013related protein folding and maturation","description":"The terms cluster around protein handling and quality control in the secretory pathway, including misfolded protein transport, chaperone-assisted refolding, translation initiation during ER stress, and maturation processes (e.g., iron-sulfur cluster transfer), with protein oligomerization as a general theme. A couple of developmental or DNA-related terms are present but do not define the main function of the cluster, which centers on protein folding/maturation under stress.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0051259","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0070389","count":2}]},{"hash":"1147899201689191990","title":"Cell wall polysaccharide biosynthesis and glycosylation","description":"The terms are dominated by biosynthesis of cell wall components such as galactomannan, galactoglucomannan, and xyloglucan, along with protein glycosylation (N-linked and galactosylation). A few terms related to division and budding appear, which can accompany cell wall remodeling in fungi. Overall, the cluster seems to group proteins involved in cell wall component synthesis and post-translational modification, with a fungal/yeast-biased theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0000032","count":1},{"id":"GO:0010192","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0010392","count":1}]},{"hash":"49094214796428821","title":"Retroviral DNA Integration and Latency","description":"The cluster is dominated by GO terms for DNA integration and establishment of integrated proviral latency, with additional signals for DNA replication and host gene regulation via miRNA silencing and DNA methylation. These together suggest a core theme around viral DNA integrating into the host genome and the establishment of latent states, with some ancillary links to germ cell development and signaling pathways that may reflect broader cellular contexts rather than a primary focus of the cluster. Confidence: Medium","confidence":"","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0035279","count":1}]},{"hash":"1074580103515412931","title":"Plant Growth and Cell Wall Biosynthesis Regulation","description":"This cluster is dominated by regulatory GO terms tied to plant development, including chlorophyll biosynthesis regulation, seed growth, root meristem growth, and leaf senescence, plus regulation of lignin and secondary cell wall biosynthesis. The common theme is regulatory control of growth and cell wall assembly in plants, with a few telomere-related regulatory terms that are less central to the main pattern.","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010380","count":5},{"id":"GO:0080113","count":5},{"id":"GO:1901347","count":5},{"id":"GO:0010082","count":5},{"id":"GO:1901430","count":5}]},{"hash":"1527221149703038902","title":"Unknown","description":"The top GO terms are diverse (immune response, circadian rhythm, kidney development, ubiquitin turnover) with no clear, shared function or enrichment, and the cluster has no edges or connections to tie these proteins together. This supports labeling the cluster as Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000312","count":1},{"id":"GO:0042092","count":1},{"id":"GO:0042748","count":1},{"id":"GO:0032764","count":1},{"id":"GO:0002467","count":1}]},{"hash":"394549925524244687","title":"Mitochondrial respiration and protein import","description":"The top GO terms show NADH dehydrogenase to ubiquinone electron transport, assembly of the respiratory chain, and import of proteins into the mitochondrial inner membrane/matrix, plus heme biosynthesis regulation. These point to mitochondrial biogenesis and energy production; a few terms about chloroplast import or plant cell wall appear less representative noise. Overall, a cohesive theme around mitochondrial respiration and protein trafficking.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006120","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0000002","count":1}]},{"hash":"242242417217658533","title":"Meiosis and oocyte maturation machinery","description":"The top GO terms strongly point to meiotic processes and oocyte development, including microtubule polymerization, spindle assembly in female meiosis I, and oocyte maturation, along with ubiquitin-proteasome\u2013mediated protein catabolic processes that regulate the meiotic cell cycle. A few neural development terms are present but appear less central to the cluster\u2019s core theme. Confidence: High","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046785","count":6},{"id":"GO:0007057","count":6},{"id":"GO:0031146","count":6},{"id":"GO:0021678","count":6},{"id":"GO:0006516","count":6}]},{"hash":"136751106228704899","title":"Unknown","description":"The top GO terms include neural development (forebrain and nervous system development), glial and cardiac apoptosis, metabolism (L-methionine cycle), immune-related melanization, and general responses to TGF-beta, plus some unrelated terms. The terms point to no single cohesive function or pathway for the cluster, making a specific, representative label inappropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":13},{"id":"GO:0010659","count":13},{"id":"GO:0035006","count":13},{"id":"GO:0033353","count":13},{"id":"GO:0071560","count":13}]},{"hash":"516544417510763640","title":"Lipid Catabolism and Endocannabinoid Regulation","description":"Strong emphasis on lipid catabolism (triglyceride, diacylglycerol, monoacylglycerol) and related remodeling, plus regulation of endocannabinoid signaling; other terms (detox, immune activation) are present but less central, so the lipid/endocannabinoid theme best fits the cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0030245","count":5},{"id":"GO:0019433","count":5},{"id":"GO:0046340","count":5},{"id":"GO:2000124","count":5}]},{"hash":"1494277005209962680","title":"GPI-anchor and glycolipid biosynthesis","description":"This cluster is driven by GO terms for GPI-anchor biosynthesis and glycolipid biosynthesis, with additional hints of carbohydrate metabolism (glucose/glycogen) in the set. Together, these terms suggest proteins involved in membrane-related lipid and glycan biosynthesis pathways, rather than signaling or transport alone.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0006506","count":1},{"id":"GO:0010037","count":1},{"id":"GO:0009414","count":1},{"id":"GO:0009247","count":1}]},{"hash":"1300080307505244331","title":"Mitochondrial Transport and Membrane Permeability","description":"The dominant GO terms center on mitochondria: regulation of mitochondrial membrane permeability, mitochondrial ATP transmembrane transport, apoptotic mitochondrial changes, and various membrane transports (manganese, heme, CoA, thiosulfate). Together these suggest proteins involved in mitochondrial membrane transport and regulation, linked to metabolism and apoptosis.","confidence":"High","size":13,"edges":29,"triangles":16,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":10},{"id":"GO:0006828","count":9},{"id":"GO:0061179","count":9},{"id":"GO:1990544","count":9},{"id":"GO:0015886","count":9}]},{"hash":"1400880108759477134","title":"Regulation of signaling and membrane dynamics","description":"This cluster centers on modulation of signaling pathways and membrane-related processes. The top GO terms include negative regulation of protein kinase activity and sumoylation, which affect signaling, along with exocytosis, membrane tubulation, and cell shape regulation, indicating a cohesive theme of controlling intracellular signaling and membrane organization. A few terms about nuclear import and sporulation membranes reflect deeper aspects of membrane trafficking and organization, supporting the overall theme.","confidence":"Medium","size":13,"edges":10,"triangles":1,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":7},{"id":"GO:0000272","count":7},{"id":"GO:0045921","count":6},{"id":"GO:0008360","count":6},{"id":"GO:0033234","count":6}]},{"hash":"1979288346729429522","title":"Plant RNA silencing and cell-wall biosynthesis","description":"The GO terms are dominated by plant-specific RNA silencing pathways (ta-siRNA processing, siRNA-directed DNA methylation, RNAi antiviral response) and by cell-wall/cuticle biosynthesis (xyloglucan, wax) with some developmental terms, suggesting a cluster of plant proteins involved in RNA silencing and cell-wall-related processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":2},{"id":"GO:1990034","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0009832","count":1},{"id":"GO:0009969","count":1}]},{"hash":"686708626755187221","title":"Organelle gene expression in chloroplasts and mitochondria","description":"The cluster shows a coherent theme around organellar transcription and RNA processing (chloroplast/plastid and mitochondrial transcription, plastid rRNA transcription, RNA splicing) and ribosome assembly, plus protein import into the mitochondrial intermembrane space. These together point to functions in expression and maturation of organellar gene products in chloroplasts and mitochondria; some terms like de-etiolation or CAAX-box processing are broader but do not override this central theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009658","count":3},{"id":"GO:0071586","count":2},{"id":"GO:0006393","count":2},{"id":"GO:0061668","count":2},{"id":"GO:1903108","count":2}]},{"hash":"1685543653823550828","title":"Membrane Ion Transport and Homeostasis","description":"The top GO terms cluster around ion movement across membranes (sodium and potassium import/export, proton translocation) and organelle pH regulation (vacuolar acidification), as well as intracellular potassium homeostasis, pointing to a shared function in maintaining ion gradients and membrane potential. A few terms (mitotic cell cycle, BDNF signaling) are less related, likely reflecting multifunctionality or annotation noise, but do not override the core theme of membrane ion transport and homeostasis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0006884","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0051595","count":1},{"id":"GO:0097623","count":1}]},{"hash":"2033267191360151924","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0070129","count":2}]},{"hash":"2175678524798110579","title":"Unknown","description":"The top terms cover diverse biological processes from different kingdoms and tissues (bone/eye development, plant leaf and cell wall processes, alkaloid metabolism, insulin processing, transferrin transport), with no obvious shared pathway or function. The cluster has no edges or triangles (degree 0), suggesting no cohesive functional theme. Therefore I cannot assign a single meaningful label beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002076","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0009820","count":2},{"id":"GO:0055114","count":2}]},{"hash":"990372009819869889","title":"Neural development and synaptic signaling","description":"The cluster\u2019s GO terms cluster around neural development and neuronal signaling: axonogenesis, Schwann cell development, and visual perception point to neural growth and function; excitatory postsynaptic potential indicates synaptic activity; positive regulation of peptidyl-threonine phosphorylation suggests signaling modulation in neurons. Some terms about cell cycle and apoptosis reflect general cellular regulation common in proliferating neural cells, but the dominant theme remains neural development and signaling, justifying the label. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0010800","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0014044","count":2},{"id":"GO:0000086","count":2}]},{"hash":"145736193279366282","title":"Plant oxidative stress response and lignin degradation","description":"The cluster is dominated by GO terms tied to oxidative stress and lignin breakdown in plants: response to oxidative stress, cellular oxidant detoxification, hydrogen peroxide catabolic process, and lignin catabolic process. The plant-type cell wall organization term further supports a plant-specific remodeling/defense context, suggesting proteins involved in detoxifying reactive oxygen species and remodeling cell walls during stress.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":10},{"id":"GO:0098869","count":10},{"id":"GO:0046274","count":10},{"id":"GO:0042744","count":10},{"id":"GO:0055114","count":10}]},{"hash":"272853824223971060","title":"Ubiquitin-regulated proteostasis and necroptosis","description":"The cluster shows enrichment for ubiquitin-related processes (deubiquitination, regulation of ubiquitin ligase activity, ubiquitin-dependent protein catabolic process) and protein quality control (chaperone-mediated assembly, transport of polyubiquitinated misfolded proteins), plus necroptosis-related signaling (ripoptosome assembly, hydrogen peroxide\u2013mediated programmed cell death). Although there are some transcription-related terms, the ubiquitin/proteostasis and necroptosis themes dominate, supporting this label.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035523","count":1},{"id":"GO:0090035","count":1},{"id":"GO:0070845","count":1}]},{"hash":"2181639055628318840","title":"LPS and O-antigen biosynthesis","description":"This cluster is dominated by GO terms for lipopolysaccharide biosynthesis, including core region and O-antigen biosynthesis, plus related sugar-nucleotide pathways (GDP-mannose, dTDP-rhamnose) and colanic acid biosynthesis, pointing to a common function in bacterial cell envelope polysaccharide assembly. Some terms related to plant secondary metabolite biosynthesis appear incidental, but the LPS-related terms strongly tie the cluster together.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006541","count":2},{"id":"GO:0009244","count":2},{"id":"GO:0019673","count":2},{"id":"GO:0019305","count":2}]},{"hash":"2056499926742884430","title":"Vesicle trafficking and signaling regulation","description":"The top GO terms cluster around membrane trafficking: COPII-coated vesicle cargo loading, plasma membrane-to-endosome transport, and retrograde transport from the plasma membrane to the Golgi, with additional notes on cilium assembly regulation. There are also signaling modulation terms (NFAT pathway, CDK kinase activity) and transcription regulation, suggesting a broader theme where trafficking processes are coordinated with signaling and gene regulation. Overall, the core signal is intracellular transport and its regulation, with peripheral signaling connections.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0009585","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0090630","count":1},{"id":"GO:0035526","count":1}]},{"hash":"427392907955883787","title":"TLR-Mediated Innate Immune Response","description":"This cluster is dominated by GO terms related to innate immunity and Toll-like receptor signaling (response to fungus, defense against virus, TLR3 signaling, and MyD88-independent TLR signaling), plus general innate immune response and B cell involvement. A few developmental terms appear but are likely incidental; the core theme is innate immune recognition and signaling through TLR pathways.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":12},{"id":"GO:0002756","count":12},{"id":"GO:1900155","count":12},{"id":"GO:1904887","count":12},{"id":"GO:0051607","count":12}]},{"hash":"1871167827840635176","title":"Plant morphogenesis and proteolysis","description":"The cluster shows strong representation of plant-specific developmental processes (post-embryonic morphogenesis, organ boundary specification, floral organ formation) alongside proteolysis and protein catabolic processes, with additional hints of cell-wall remodeling (xylan catabolic process) and defense (systemic acquired resistance). This combination suggests proteins involved in plant growth and tissue remodeling, with proteolytic activity as a common mechanism, justifying a label that emphasizes both morphogenesis and proteolysis.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0030163","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0009627","count":2},{"id":"GO:0016540","count":2}]},{"hash":"1299126927773016650","title":"Apoptosis Regulation and Stress Signaling","description":"The cluster prominently features GO terms for positive/negative regulation of apoptosis and responses to toxic substances, suggesting a shared role in cell fate decisions under stress. Additional terms point to broader signaling and developmental processes (cell polarity regulation, ribosomal gene transcription) that can intersect with stress responses, though some annotations (placenta development, abscisic acid signaling) appear less directly related, indicating a somewhat mixed but cohesive theme around cell survival and signaling under stress.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0034351","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0009636","count":2}]},{"hash":"1789498285705879442","title":"Ribosome biogenesis and translation","description":"Dominant GO terms are translation and ribosome biogenesis, indicating the cluster mainly comprises components of the protein synthesis machinery and ribosome assembly. The few single-mention terms (DNA repair, transcription termination, immune responses) appear incidental rather than defining the cluster. ","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006281","count":1},{"id":"GO:0071549","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0033119","count":1}]},{"hash":"1386510424324477897","title":"Neural development and apoptotic regulation","description":"These proteins are enriched for neural development terms (neural tube closure, forebrain development) alongside strong apoptotic signals (glial and neuron apoptotic processes, regulation of apoptotic signaling, ER-stress\u2013related intrinsic pathway). This pattern suggests a cluster of neurodevelopmental proteins that also coordinate apoptosis and stress-induced cell death, with TGF-beta signaling contributing to the regulation. The aging term appears as noise and does not define the core theme.","confidence":"High","size":12,"edges":15,"triangles":2,"max_degree":6,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0001843","count":5},{"id":"GO:2001235","count":5},{"id":"GO:0030900","count":5},{"id":"GO:1902510","count":5},{"id":"GO:0071560","count":5}]},{"hash":"1369103916486914","title":"Unknown","description":"The Top Terms are a mix of retina-related terms (retinal rod cell development and photoreceptor outer segment localization) and many unrelated processes (prostate development, fat pad development, cell division, centrosome microtubule anchoring), with no single cohesive function emerging. This makes it unclear what common theme defines this cluster, so an Unknown label is most appropriate.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":2},{"id":"GO:0050689","count":2},{"id":"GO:1903546","count":2},{"id":"GO:0046548","count":2},{"id":"GO:0070389","count":2}]},{"hash":"601290431500629028","title":"Nuclear import and nuclear pore assembly","description":"The top GO terms are dominated by nuclear import processes (NLS-bearing protein import into nucleus, ribosomal protein import into nucleus) and nuclear pore complex assembly, pointing to a cohesive theme of proteins involved in transporting cargo into the nucleus and assembling the nuclear pore. Related terms on desumoylation regulation and protein catabolic processes fit with regulatory aspects of nuclear transport proteins, while a few outliers (intraciliary transport, nitrate assimilation) are less central. Overall, the cluster centers on nuclear import machinery and pore assembly functions.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":3},{"id":"GO:0060188","count":3},{"id":"GO:0042176","count":3},{"id":"GO:0000060","count":3},{"id":"GO:0051292","count":3}]},{"hash":"551411951946707384","title":"Heat stress response and ubiquitin-proteasome quality control","description":"The top GO terms cluster around heat/thermoception, protein ubiquitination, and proteasome assembly/ERAD, suggesting a module focused on stress-induced protein quality control via ubiquitin/proteasome pathways. Some terms related to immune signaling (NF-kappaB, NOD2) and development (oligodendrocyte differentiation) are present but appear ancillary, while vitamin D response and cell growth may reflect broader regulatory roles. Overall, the dominant theme is heat-induced stress response coupled with ubiquitin-proteasome\u2013mediated protein processing.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":4},{"id":"GO:0033280","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0050955","count":3}]},{"hash":"1923723800855532050","title":"Translation Machinery and Ribosome Biogenesis","description":"The cluster is strongly enriched for GO terms related to translation and ribosome biogenesis, including cytosolic and mitochondrial translation, as well as regulatory steps in elongation and termination and even selenocysteine incorporation, pointing to core translation machinery and ribosome maturation across compartments. A couple of outliers (glial proliferation and antibiotic response) are present but do not define the main theme.","confidence":"High","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0046677","count":5},{"id":"GO:0045903","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0014009","count":2}]},{"hash":"1001653268861060702","title":"Unknown","description":"The GO terms cover a wide range of processes\u2014from development (lung induction, papilla formation, epithelial proliferation) to cell cycle and genome maintenance (DNA damage response, centromeric cohesion), cytoskeletal regulation (actin, cell adhesion), nuclear transport (NLS import), vesicle trafficking (Cvt vesicle assembly), and even physiology (heart rate regulation). There isn\u2019t a single cohesive theme tying these functions together, so a specific label isn\u2019t justifiable. ","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051211","count":9},{"id":"GO:0060769","count":9},{"id":"GO:0070602","count":9},{"id":"GO:0006607","count":9},{"id":"GO:0060492","count":9}]},{"hash":"128569198349111367","title":"Neural tube development and RNA processing","description":"Two strong themes stand out: neural development terms (spinal cord development, neural tube closure) and RNA processing/biogenesis (RNA guanine-N7 methylation, ribosomal large subunit biogenesis). Additional terms related to growth and vesicle trafficking (COPII-coated vesicle budding) align with a broader developmental program requiring RNA metabolism and protein synthesis. Thus, the label captures the neural development emphasis while acknowledging RNA-processing roles. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0036265","count":4},{"id":"GO:0007584","count":4},{"id":"GO:0035264","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0051441","count":3}]},{"hash":"2114842438641602113","title":"Developmental transcriptional regulation and stress signaling","description":"This cluster is enriched for developmental processes (neural tube closure, forebrain and skeletal system development) and for general transcriptional regulation (DNA-templated transcription and cell cycle). The presence of ER stress\u2013related intrinsic apoptotic signaling and cellular responses to cadmium suggests stress signaling is linked to these developmental programs. Overall, the dominant theme is regulation of gene expression during development with stress-responsive modulation.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0001403","count":3}]},{"hash":"2098953164323657110","title":"mRNA decay and translation regulation","description":"The top terms cluster around mRNA turnover and translational control: deadenylation and decapping of nuclear-transcribed mRNA, poly(A) tail shortening, negative regulation of translation, and assembly of processing bodies. These point to post-transcriptional regulation of gene expression as the core theme. A few terms about transcription elongation and differentiation are present but appear ancillary to the dominant mRNA processing signal.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000289","count":1},{"id":"GO:0017148","count":1},{"id":"GO:0031087","count":1},{"id":"GO:0010606","count":1},{"id":"GO:0000749","count":1}]},{"hash":"1660696449728443962","title":"Ribosome biogenesis and translation regulation","description":"The strongest signals are translation and ribosome assembly (translation initiation/elongation and ribosomal large subunit biogenesis). Additional terms point to transcription elongation/termination and transcription antitermination, suggesting some shared factors or coordinated regulation of gene expression at both transcriptional and translational levels. A couple of entries reference obsolete p53-mediated DNA damage response annotations, likely historical noise. Overall, the cluster centers on ribosome biogenesis and control of translation, with a broader link to transcription-related processes.","confidence":"High","size":12,"edges":63,"triangles":190,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006353","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0032784","count":2},{"id":"GO:0045727","count":2}]},{"hash":"1453204034719222021","title":"Plant stress metabolism and redox signaling","description":"The cluster centers on cellular responses to environmental cues and redox/metabolic adjustments: responses to cAMP, hydrogen peroxide, nutrients, and xenobiotic stimuli, along with metabolic processes like malate and lactate production, and regulation of photorespiration. This combination points to a cohesive module where stress signaling, redox responses, and metabolic reprogramming intersect, characteristic of plant stress adaptation. The mention of photorespiration strongly supports a plant-specific context, making the theme fairly coherent despite a few broader terms.","confidence":"Medium","size":12,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051591","count":6},{"id":"GO:0043065","count":6},{"id":"GO:0080093","count":5},{"id":"GO:0048569","count":5},{"id":"GO:0019244","count":5}]},{"hash":"1619194466500687280","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006355","count":1},{"id":"GO:0050832","count":1}]},{"hash":"673565657693452591","title":"Glycan biosynthesis and proteoglycans","description":"The top GO terms are dominated by biosynthetic processes for various glycans and proteoglycans (xyloglucan, xylogalacturonan, arabinan, heparan sulfate/heparin proteoglycans), pointing to a core theme of glycan assembly and extracellular matrix components. Although there are also signaling and development terms (e.g., BMP signaling, endoderm development, salicylic acid signaling) these can be linked to how glycans and proteoglycans modulate signaling and tissue development. Thus, the cluster most coherently centers on glycan biosynthesis and proteoglycan formation as a representative function.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0010398","count":1},{"id":"GO:0009863","count":1},{"id":"GO:0008101","count":1},{"id":"GO:0072498","count":1}]},{"hash":"411513518157058802","title":"Immune signaling and cytoskeletal remodeling","description":"This cluster's GO terms cluster around immune-related processes (regulation of T cell proliferation, neutrophil clearance, cytokine production, and endopeptidase activity regulation) and cytoskeletal/microtubule dynamics (Rho signaling, protein localization to microtubules, endothelial cell migration, and programmed cell death). The combination suggests proteins that coordinate immune responses with cytoskeletal reorganization and cell movement, rather than a single narrow function; note that a developmental term (cartilage condensation) may reflect context rather than a core cluster function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010951","count":2},{"id":"GO:0046641","count":1},{"id":"GO:0001502","count":1},{"id":"GO:0097350","count":1},{"id":"GO:0035372","count":1}]},{"hash":"483268963083808228","title":"Unknown","description":"The GO terms are highly diverse, including translation, antibiotic response, several distinct metabolic pathways (glutamine, acetoin, retinol, GDP-mannose), and biosynthesis processes (LPS core, mycolic acids) as well as transcription regulation. This lack of a cohesive, single-function theme suggests these proteins do not share a common, well-defined function at the GO level, so a generic Unknown label is appropriate.","confidence":"","size":12,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0006541","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0042572","count":2}]},{"hash":"2304256572093339867","title":"Unknown","description":"The top GO terms span metabolism (glutamine, glycerol, NAD+, riboflavin), protein processing (proteolysis, dephosphorylation), development in specific tissues (substantia nigra, skeletal muscle), and signaling (interleukin-13 response, quorum sensing), with no clear single function tying all proteins together. This broad, mixed functional signal suggests there is no coherent cluster theme.","confidence":"","size":12,"edges":47,"triangles":80,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0016311","count":2}]},{"hash":"2287179169988976033","title":"Plant flavonoid and lignin biosynthesis","description":"The top GO terms point to plant-specific phenylpropanoid metabolism, including anthocyanin/cyanidin biosynthesis and lignin formation, suggesting a cluster centered on flavonoid and lignin biosynthetic pathways; a few terms are obsolete or peripheral, but the core signal is flavonoid/lignin biosynthesis.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":3},{"id":"GO:0009808","count":3},{"id":"GO:0009718","count":3},{"id":"GO:0006711","count":3},{"id":"GO:0052697","count":3}]},{"hash":"1660358860169231254","title":"Developmental signaling and stress responses","description":"The cluster highlights both development-related processes (multicellular organism development, substantia nigra development) and signaling/stress response activities (cellular response to xenobiotic stimulus, calcium ion, corticosterone, hydrogen peroxide biosynthetic process, ABA signaling) along with transcriptional regulation and modulation of kinase activity. This suggests a cohesive module where developmental programs are tuned by signaling and stress pathways, with epigenetic regulation via protein methylation contributing to the control. Although some terms span different kingdoms (e.g., ABA signaling), the shared theme centers on development linked to stress- and signal-mediated regulation.","confidence":"Medium","size":12,"edges":8,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0006479","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0071277","count":3}]},{"hash":"1717666747445757727","title":"Unknown","description":"Top terms are diverse, spanning apoptotic processes in myeloid and hepatocytes, cell migration, epithelial polarity, plant GA signaling, vitamin D response, thermoception, and broad transcription regulation terms. With zero edges and no dominant shared function across all proteins, there isn't a single coherent biological theme tying these proteins together. Therefore a reliable descriptive label cannot be inferred.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033028","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0009739","count":2}]},{"hash":"1373215530297463579","title":"Multi-substrate Transporters for Xenobiotics and Metabolites","description":"The top GO terms cluster around transport activities across membranes, including xenobiotic transport, sodium-dependent organic cation transport, trehalose and urate transport, and dehydroascorbic acid transport, plus related trafficking terms like nuclear import and mRNA transport. This suggests a shared function in moving diverse substrates rather than a single substrate or pathway, justifying a label of multi-substrate transporters even though interconnections are sparse. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0015747","count":2}]},{"hash":"773179459289087046","title":"Translation and stress response regulation","description":"The cluster\u2019s top GO terms cluster around regulation of translation (translational elongation; regulation of translational initiation in response to stress) and growth signaling (TOR signaling), with supporting roles in protein homeostasis (protein deubiquitination) and general gene regulation (mRNA splicing, regulation of DNA binding) and cell fate/survival (apoptosis regulation; telomere maintenance). This suggests a shared theme of post-transcriptional control and stress-responsive regulation of protein synthesis and genome stability, even though not every term maps to a single function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":1},{"id":"GO:0045843","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0016579","count":1},{"id":"GO:0031929","count":1}]},{"hash":"1727288006741531011","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2}]},{"hash":"1420920950839603958","title":"Symbiont-driven host immune modulation","description":"The top terms center on symbiont interactions with the host immune system, including perturbation of ubiquitin-like modification, suppression of adaptive immunity (MHC II related processes), antigen presentation, and tolerance regulation. A minority of terms relate to barrier biosynthesis (suberin/cutin), but the dominant signal points to immune modulation by symbionts and host defense regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010345","count":1},{"id":"GO:0039648","count":1},{"id":"GO:1900490","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0002495","count":1}]},{"hash":"506696819133800452","title":"RNA processing and translation regulation","description":"The top terms point to RNA processing (spliceosomal tri-snRNP assembly) and translation-related alterations (diphthamide modification of histidine on EF2 and regulation of translational fidelity), with a minority of terms relating to RNA-based chromatin regulation and some differentiation processes as potential noise. The connection is suggestive but not uniformly strong across all proteins, so a Medium confidence is appropriate.","confidence":"Medium","size":12,"edges":20,"triangles":13,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009089","count":2},{"id":"GO:0019877","count":2},{"id":"GO:0014009","count":1},{"id":"GO:0017183","count":1}]},{"hash":"2117727031113421518","title":"Lipid and steroid metabolism","description":"The top GO terms point to lipid biosynthesis and modification (poly-hydroxybutyrate, mycolic acid, fatty acid elongation) along with steroid-related processes (retinol, androgen, testosterone metabolism), suggesting a shared focus on lipid-based metabolism; a broad transcription regulation term is present but secondary. Confidence: Medium","confidence":"","size":12,"edges":6,"triangles":1,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0042619","count":8},{"id":"GO:0045150","count":7},{"id":"GO:0042572","count":7},{"id":"GO:0061370","count":7}]},{"hash":"1765529657453890518","title":"Immune activation and cytokine signaling","description":"Many terms point to immune system activation and cytokine regulation, including T cell proliferation, IL-4 production, cytokine production in immune response, neutrophil clearance, and endothelial cell migration, along with Rho signaling and microtubule localization that support immune cell movement and signaling. The cartilage condensation term appears as an outlier, but the overall theme is immune activation and cytokine pathways.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":12},{"id":"GO:0001502","count":12},{"id":"GO:0097350","count":12},{"id":"GO:0035372","count":12},{"id":"GO:0043068","count":12}]},{"hash":"1403663428546616404","title":"Forebrain development with retinoid and neurotransmitter metabolism","description":"The proteins cluster around brain development terms (forebrain, nucleus accumbens) and neural metabolic processes (retinol metabolism, GABA catabolic process, ethanol catabolic/oxidation). While some terms are broader developmental categories, the strongest signals emphasize forebrain formation and neural metabolism, suggesting these proteins function in early brain development linked to retinoid and neurotransmitter turnover.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":12},{"id":"GO:0042572","count":12},{"id":"GO:0001936","count":12},{"id":"GO:0006068","count":12},{"id":"GO:0009450","count":12}]},{"hash":"1872101446178456910","title":"Plant oxidative stress response and lignin catabolism","description":"The top GO terms cluster around oxidative stress-related processes (response to oxidative stress, cellular oxidant detoxification, hydrogen peroxide catabolic) indicating a defense role against reactive oxygen species. The inclusion of plant-type cell wall organization and lignin catabolic process points to cell wall remodeling or lignin turnover in a plant context, often linked to stress responses. Some terms are obsolete, but the dominant theme supports oxidative stress defense coupled with cell wall\u2013associated metabolism.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006979","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0046274","count":3}]},{"hash":"680841114149943298","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":17,"triangles":5,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0050843","count":2},{"id":"GO:0019354","count":2},{"id":"GO:0017183","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000453","count":2}]},{"hash":"324314262093427028","title":"Regulated neuronal synaptic vesicle cycling","description":"This cluster\u2019s top GO terms are centered on regulation of synaptic vesicle exocytosis and endocytosis, and on excitatory postsynaptic potential, all pointing to neuronal synaptic vesicle trafficking and signaling. Additional terms about cell polarity and brain development (substantia nigra development) fit neuronal morphology, while xenobiotic response and cell cycle terms are less central but can appear in brain-related protein sets. Overall, the data suggest proteins involved in controlled synaptic vesicle cycling in neurons.","confidence":"High","size":12,"edges":14,"triangles":7,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000300","count":7},{"id":"GO:0010796","count":6},{"id":"GO:0031384","count":6},{"id":"GO:1900242","count":6},{"id":"GO:0060079","count":6}]},{"hash":"589807822367168350","title":"Oocyte mRNA processing and localization","description":"The cluster centers on mRNA processing and post-transcriptional regulation (splicing, modification, stabilization, poly(A) tail dynamics) and on localization/translation control in oocytes (oskar mRNA localization, axis specification, translation initiation). This combination points to a cohesive module governing mRNA metabolism and localized translation during oogenesis. ","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0016556","count":5},{"id":"GO:0048255","count":5},{"id":"GO:0060213","count":5},{"id":"GO:0075522","count":5}]},{"hash":"661095286920448455","title":"Rab-mediated vesicle trafficking (ER\u2013Golgi and endocytosis)","description":"This cluster is dominated by GO terms for intracellular transport between the ER and Golgi, Golgi-to-Plasma Membrane trafficking, endocytosis, and Rab protein signaling, indicating a vesicle trafficking module regulated by Rab proteins. Nervous-system development terms are present but far less representative, so the core theme is Rab-driven vesicle transport.","confidence":"High","size":12,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0032482","count":3},{"id":"GO:0050771","count":3}]},{"hash":"962002879080405023","title":"Diverse substrate membrane transporters","description":"The top terms indicate transmembrane transport across a wide range of substrates\u2014vitamins, sugars, urate, galactose, xenobiotics, and even neurotransmitter loading into vesicles\u2014along with nitrate assimilation. This pattern supports labeling the cluster as membrane transporters with diverse substrates rather than a single specific function.","confidence":"High","size":12,"edges":14,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":12},{"id":"GO:0042891","count":12},{"id":"GO:0006855","count":12},{"id":"GO:0015739","count":8},{"id":"GO:0015747","count":8}]},{"hash":"1885719876486481045","title":"Sterol and fatty acid lipid metabolism","description":"The strongest signal in this cluster is lipid and sterol metabolism: ether lipid metabolic process, fatty acid biosynthetic process, ergosterol biosynthetic process, and sterol oxidation terms point to membrane lipid and sterol biosynthesis pathways. Some other terms (bradykinin catabolic process, B cell chemotaxis, sebaceous gland differentiation, CNS myelin maintenance) appear less related and may reflect broader or cross-annotated functions, but the dominant theme is lipid/sterol metabolism. Confidence reflects this partial coherence; while the lipid theme is clear, the presence of several unrelated terms makes the label not universally representative across all proteins. ","confidence":"Medium","size":12,"edges":37,"triangles":50,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":5},{"id":"GO:0045453","count":5},{"id":"GO:0046485","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0035754","count":5}]},{"hash":"1913626288218618019","title":"Vacuolar amino acid transporters","description":"Proteins here are linked by GO terms for transmembrane import of various amino acids into the vacuole (tyrosine, glutamate, arginine, histidine, lysine, asparagine), indicating a shared role in vacuolar amino acid uptake. A lithium ion transport term appears but is less representative. ","confidence":"High","size":12,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090514","count":1},{"id":"GO:1901481","count":1},{"id":"GO:0090518","count":1},{"id":"GO:0089708","count":1},{"id":"GO:0006867","count":1}]},{"hash":"2028088293262090321","title":"Chromatin modification and signaling regulation","description":"The top terms include histone H4-K16 acetylation and H4-K20 methylation, as well as histone catabolic processes, suggesting a chromatin modification theme. There are also entries referencing regulatory signaling pathways (RIG-I, JNK, NF-kappaB). Some other terms (peroxisome import, ERAD) seem less connected, making the cluster somewhat heterogeneous, but the core appears to center on chromatin regulation tied to cellular signaling responses.","confidence":"Low","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000620","count":5},{"id":"GO:0039536","count":5},{"id":"GO:0036205","count":5},{"id":"GO:0046328","count":5},{"id":"GO:0007250","count":5}]},{"hash":"368291818413667622","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035321","count":1},{"id":"GO:0060412","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0031440","count":1}]},{"hash":"851800959902097308","title":"Unknown","description":"The GO terms are very diverse, spanning lipid/fatty acid biosynthesis, growth, vitamin D response, thermoception, proteasome assembly, NF-kappaB signaling, NOD2 signaling, oligodendrocyte differentiation, and kinase activity regulation. There is no clear single biological process or pathway tying the cluster together, 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:0016049","count":2},{"id":"GO:0009245","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0033280","count":1},{"id":"GO:0050955","count":1}]},{"hash":"613843027696413382","title":"Peptide catabolism and ECM remodeling","description":"The leading terms include bradykinin and neuropeptide catabolic processes, signaling peptide degradation. Additional terms point to extracellular matrix remodeling (bone resorption, basement membrane disassembly) and developmental/immune contexts (lung branching, T cell cytotoxicity, macrophage apoptosis), suggesting a common theme of peptide degradation intertwined with ECM remodeling in tissue contexts. Confidence: Medium","confidence":"","size":12,"edges":55,"triangles":128,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":9},{"id":"GO:0050790","count":8},{"id":"GO:0010813","count":8},{"id":"GO:0045453","count":8},{"id":"GO:0001913","count":8}]},{"hash":"241084997697077212","title":"Steroidogenesis and xenobiotic metabolism","description":"The top terms cluster around biosynthesis of steroid hormones (cortisol, testosterone, brassinosteroids) and related lipid/hormone metabolism, as well as catabolic and detoxification processes (retinoic acid catabolic, fatty acid omega-oxidation, xenobiotic catabolic, vitamin D response). This suggests a cohesive theme of hormone production and lipid/ xenobiotic processing that can influence tissues like mammary glands and vasculature. Confidence: High","confidence":"","size":12,"edges":41,"triangles":60,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":12},{"id":"GO:0071603","count":12},{"id":"GO:0034651","count":12},{"id":"GO:0070989","count":12},{"id":"GO:0042738","count":12}]},{"hash":"1096152298098085105","title":"Membrane transporters for ions and metabolites","description":"The GO terms are dominated by transmembrane transport across membranes for diverse substrates (nitrate, sodium/potassium ions, sialic acid, vitamins, galactose, xenobiotics, and other metabolites) plus a note on neurotransmitter loading into synaptic vesicles, collectively pointing to a cluster of transporter proteins rather than enzymes or receptors.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0071805","count":4},{"id":"GO:0015739","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0015757","count":3}]},{"hash":"2158844074060760489","title":"Plant fungal defense and cell wall degradation","description":"The top GO terms cluster around antifungal defense (defense response to fungus, defense response, killing of cells of another organism) and cell wall/chitin remodeling (chitin catabolic process, cell wall macromolecule catabolic process), indicating roles in defending against fungal pathogens via cell wall degradation and pathogen-triggered cell death. Additional terms like phytochelatin biosynthetic process and response to amitrole reflect broader stress responses but do not override the core antifungal defense theme.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":3},{"id":"GO:0043085","count":2},{"id":"GO:0046938","count":2},{"id":"GO:0006508","count":2},{"id":"GO:1904715","count":2}]},{"hash":"1532044128761209546","title":"Chromatin Regulation and DNA Repair","description":"The terms largely point to chromatin regulation and genome maintenance (rDNA heterochromatin formation, DNA-templated transcription, cell cycle, double-strand break repair), with a few outliers and obsolete annotations; together they suggest a nuclear chromatin/regulatory function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0055114","count":3}]},{"hash":"953504369669051933","title":"Plant development and cuticle biosynthesis regulation","description":"This cluster centers on transcriptional regulation in plants, with GO terms for DNA-templated transcription and its regulation. It also features developmental processes such as floral meristem growth, bract development, and multicellular organism development, plus hormone signaling via ethylene- and abscisic acid-activated pathways. The presence of regulation of wax and cutin biosynthetic processes points to coordination of epidermal cuticle formation, while the positive regulation of cellular defense hints at stress-related regulatory roles. Together, these terms suggest a set of transcriptional regulators controlling plant development and surface lipid biosynthesis.","confidence":"High","size":12,"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:0010451","count":3},{"id":"GO:0009873","count":3},{"id":"GO:0010432","count":3}]},{"hash":"909363562672534307","title":"Auxin-regulated plant development and transcription","description":"The GO terms point to developmental processes driven or influenced by auxin signaling (GO:0009733, GO:0009734) including meristem development, leaf vascular patterning, and axis specification. Also present are terms for DNA-templated transcription and its regulation, suggesting transcriptional control as a core mechanism. The combination supports a cluster of proteins involved in auxin-dependent plant development with transcriptional regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0048507","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0009733","count":1}]},{"hash":"31558068223954463","title":"Neural development and apoptosis","description":"This cluster is dominated by neural-related processes: forebrain development, nervous system development, and glial cell apoptotic process, suggesting a neurodevelopmental and cell-survival/remodeling theme. Additional terms like cellular response to TGF-beta stimulus and tissue remodeling concepts (e.g., salivary gland histolysis) fit into developmental signaling and morphogenesis, while other terms are broader or less central. Overall, the data point to a neurodevelopmental/apoptotic core with some peripheral developmental signals.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":8},{"id":"GO:0010659","count":8},{"id":"GO:0035006","count":8},{"id":"GO:0033353","count":8},{"id":"GO:0071560","count":8}]},{"hash":"511214683872460455","title":"Neural development and dendrite morphogenesis","description":"The top GO terms converge on neural development\u2014nervous system development, forebrain development, neural tube closure, and dendrite morphogenesis\u2014suggesting these proteins function together in neural development pathways. Some annotations appear noisy or obsolete, but the dominant signal supports a neural-development theme.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0007399","count":9},{"id":"GO:0001843","count":9},{"id":"GO:0000160","count":9},{"id":"GO:0002921","count":9},{"id":"GO:0048813","count":9}]},{"hash":"1962364649118939795","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000685","count":1},{"id":"GO:0036297","count":1},{"id":"GO:0031860","count":1},{"id":"GO:0010833","count":1},{"id":"GO:0031627","count":1}]},{"hash":"1322092822637856697","title":"Plant defense and hormone signaling in nodulation","description":"This cluster shows enrichment for plant-specific processes such as cytokinin-activated signaling, gibberellin-mediated signaling, defense response, and nodulation, indicating proteins involved in plant immune signaling and legume symbiosis; note that some terms are obsolete or noisy, but the dominant theme is plant hormonal signaling linked to defense and nodulation.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0006952","count":3},{"id":"GO:0009877","count":3},{"id":"GO:0009740","count":3}]},{"hash":"1624741838241284613","title":"Plant cell wall biosynthesis and remodeling","description":"The top terms cluster around plant-specific processes: xyloglucan metabolism, cell wall biogenesis, and plant-type cell wall modification involved in growth, plus stamen filament development. This points to a cohesive theme of plant cell wall construction and remodeling, with a supplementary hint of defense against fungi (detection of fungal origin). Confidence: High","confidence":"","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032491","count":4},{"id":"GO:0031505","count":4},{"id":"GO:0010411","count":4},{"id":"GO:0080086","count":4},{"id":"GO:0042546","count":4}]},{"hash":"391715568127633030","title":"Cell Growth and Vesicle Trafficking","description":"The top GO terms point to processes involved in growth and organization (positive regulation of axon extension, maintenance of cell polarity, mitotic cell cycle, cell proliferation) as well as intracellular transport and trafficking (regulation of synaptic vesicle exocytosis, endosome to lysosome transport), plus cytoskeletal dynamics (stress fiber assembly) and ribosome biogenesis. This suggests a cohesive theme around growth, structural organization, and vesicle-based transport, even though there is some diversity among terms. Confidence: Medium.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045773","count":2},{"id":"GO:0030011","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0008283","count":2},{"id":"GO:2000300","count":2}]},{"hash":"311411595056828792","title":"Plant defense signaling and hormone pathways","description":"The terms center on defense and responses to biotic stimuli, along with plant hormone signaling (cytokinin- and gibberellin-mediated pathways) and nodulation, suggesting a cohesive theme of plant signaling in defense and growth, despite some broad or cross-kingdom terms present.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0009877","count":1},{"id":"GO:0009740","count":1}]},{"hash":"976750632246879777","title":"Mitochondrial RNA editing and processing","description":"The cluster is dominated by GO terms for mitochondrial mRNA processing and modification, plus cytidine-to-uridine editing and RNA modification, pointing to a shared role in mitochondrial RNA maturation/editing. Some plant-development and transcription-regulation terms appear but are less central, so the mitochondrial RNA processing/editing theme best represents the group.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":3},{"id":"GO:0048235","count":2},{"id":"GO:0040015","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010047","count":2}]},{"hash":"1888430556566814622","title":"Vesicle trafficking and Golgi-ER transport","description":"The GO terms cluster around endomembrane system processes: ER-to-Golgi transport, Golgi organization, retrograde transport, and Cvt pathway, with vesicle recycling and related trafficking steps. Occasional terms like pollen tube growth and male meiosis cytokinesis likely reflect secretion demands in development, but the dominant theme is intracellular vesicle trafficking within the secretory pathway.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":1},{"id":"GO:0033227","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0009860","count":1},{"id":"GO:0007030","count":1}]},{"hash":"128892017653302093","title":"Retina and retinoid metabolism","description":"The terms cluster around retina function and retinoid metabolism (retina homeostasis, retinal and retinol metabolism, carotene/xanthophyll catabolism, phototransduction, and visual perception). This points to proteins involved in the retinal visual cycle and maintenance of the visual system; an outlier term (abscisic acid biosynthesis) is present but does not outweigh the vision-related theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001895","count":2},{"id":"GO:0016121","count":2},{"id":"GO:0016124","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0007604","count":2}]},{"hash":"570728580943347711","title":"Heme/Porphyrin Biosynthesis","description":"This cluster is strongestly associated with porphyrin and heme production, as evidenced by the presence of protoporphyrinogen IX biosynthetic process and heme biosynthetic process terms. The other terms are quite diverse (lipid signaling, transport, detoxification, germ cell repulsion, etc.), which do not cohere into a single clear function, suggesting the heme-related terms capture the main signal while the rest may reflect annotation noise. Therefore, the label is plausible but not definitively representative of a unified function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0018160","count":1},{"id":"GO:1902068","count":1},{"id":"GO:0044329","count":1}]},{"hash":"1638354136521108851","title":"Transcriptional & Cell Cycle Regulation","description":"The terms cluster around DNA-templated transcription, regulation of the cell cycle, and replication-related chromatin assembly, with supporting roles for deubiquitination and serine dephosphorylation. This suggests a cohesive theme of coordinating gene expression with DNA replication/chromatin maintenance and post-translational control, rather than a single isolated process.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0016579","count":1},{"id":"GO:0006275","count":1}]},{"hash":"474415540146907497","title":"ER tubular network organization","description":"The top GO terms strongly point to endoplasmic reticulum (ER) tubule formation, maintenance, and membrane organization, indicating the proteins share a role in shaping ER morphology. While a few neural development terms appear, the dominant signal is ER tubular network organization. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032581","count":1},{"id":"GO:0071788","count":1},{"id":"GO:2000172","count":1},{"id":"GO:0006694","count":1},{"id":"GO:0060317","count":1}]},{"hash":"52456136354803108","title":"Starch, sucrose, and glycogen metabolism","description":"Most of the top GO terms in this cluster relate to carbohydrate metabolism\u2014starch catabolic process, sucrose metabolic/catabolic processes, maltose metabolic process, and glycogen biosynthetic process\u2014suggesting a common theme of processing these carbohydrates and energy storage. There are a couple of outlier terms (proteasome assembly, DNA transposition) that are less represented, and one plant-associated term (positive regulation of secondary cell wall biogenesis), but they do not outweigh the central carbohydrate-metabolism signal. Confidence is Medium.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901348","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0006313","count":2},{"id":"GO:0000278","count":1},{"id":"GO:0051692","count":1}]},{"hash":"2048862122126678376","title":"Mitochondrial phospholipid biosynthesis and remodeling","description":"The cluster shows repeated representation of phospholipid-related processes (phosphatidylcholine acyl-chain remodeling, cardiolipin acyl-chain remodeling, CDP-diacylglycerol biosynthetic process) and mitochondrial ATP synthesis, which together point to mitochondrial membrane lipid metabolism and remodeling as the common theme. Some terms (like cerebellum morphogenesis or cutin biosynthesis) are outliers but do not override the lipid/mitochondrial signal. Confidence: High","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070236","count":1},{"id":"GO:2001246","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0021587","count":1}]},{"hash":"743135999181105138","title":"Unknown","description":"The GO terms show a highly diverse set of functions\u2014from xenobiotic transport and plasminogen activation to immune regulation, embryonic and gland morphogenesis, and even plant pollen rejection\u2014without a unifying biological theme. This diversity makes it inappropriate to assign a coherent, specific label. Confidence: None","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0010758","count":1},{"id":"GO:0016476","count":1},{"id":"GO:0060707","count":1},{"id":"GO:0060763","count":1}]},{"hash":"1333810054843932727","title":"ER stress, unfolded protein response, and calcium signaling","description":"The top GO terms indicate stress-related protein handling and trafficking (unfolded protein response and SRP-dependent targeting to membrane) along with a cellular calcium response, all pointing to ER-associated protein folding and signaling under stress. While some development-related terms appear, the dominant signal is ER stress/UPR and calcium-mediated response, which likely ties these proteins together in a membrane-associated, protein-folding context with apoptotic regulation linked to stress.","confidence":"Medium","size":11,"edges":40,"triangles":65,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":7},{"id":"GO:0021762","count":4},{"id":"GO:0048741","count":4},{"id":"GO:0071277","count":4},{"id":"GO:1900035","count":3}]},{"hash":"1823680487264708528","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0008615","count":6},{"id":"GO:0035606","count":6},{"id":"GO:0042823","count":6},{"id":"GO:0009089","count":6},{"id":"GO:0051402","count":6}]},{"hash":"1892537778224384861","title":"Embryonic neural and cardiac development","description":"This cluster shows strong representation of developmental processes in neural tissues (floor plate development, cortical interneuron differentiation, auditory receptor fate) and heart formation (valve development, outflow tract morphogenesis), plus mesenchyme-related development. The combination suggests a cohesive theme of embryonic tissue differentiation across neural, cardiac, and mesenchymal lineages.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045668","count":11},{"id":"GO:0060766","count":11},{"id":"GO:2000793","count":8},{"id":"GO:2000764","count":8},{"id":"GO:0060375","count":8}]},{"hash":"557229875171819467","title":"Folate-mediated one-carbon metabolism","description":"These terms cluster around serine\u2013folate\u2013one-carbon flux: serine biosynthesis and catabolism provide one-carbon units to tetrahydrofolate, which drives dTMP and purine biosynthesis and methylation, as well as folate/interconversion pathways. This pattern suggests a cohesive role in folate-driven one-carbon metabolism.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":5},{"id":"GO:0006565","count":4},{"id":"GO:1904482","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0006231","count":3}]},{"hash":"1151413670400989000","title":"Redox balance and oxidative stress response","description":"The top GO terms cluster around oxidation-reduction processes, detoxification of oxidants, and cellular responses to oxidative stress, plus protein repair and deglutathionylation, indicating involvement in maintaining redox homeostasis and repairing oxidative damage; the viral process term may reflect broad host-virus interactions or annotation noise, but the core theme is redox regulation. ","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016032","count":8},{"id":"GO:0055114","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0045454","count":6},{"id":"GO:1903026","count":6}]},{"hash":"1174035068878655400","title":"Mitotic spindle checkpoint and septin ring assembly","description":"This cluster is dominated by mitotic and cytokinesis-related processes: multiple GO terms point to spindle assembly checkpoint signaling and spindle orientation checkpoint signaling, as well as septin ring assembly, suggesting a core role in mitosis and cytokinesis. While a few terms touch unrelated pathways (viral transport, TNF signaling, histone ubiquitination), the strongest and most recurrent signals pertain to spindle dynamics and checkpoint control.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":4},{"id":"GO:0044810","count":4},{"id":"GO:1902364","count":4},{"id":"GO:2000620","count":4},{"id":"GO:0038018","count":4}]},{"hash":"1624943892783189050","title":"Ubiquitin-Dependent Degradation and Signaling Regulation","description":"The cluster is enriched for ubiquitin-related processes (protein ubiquitination and ubiquitin-dependent protein catabolic process) and signaling regulation, including NF-kappaB and JNK pathways, with additional ties to chromatin modification via ubiquitination. This suggests a cohesive role in ubiquitin-mediated protein turnover and modulation of signaling and chromatin states.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:1901253","count":5},{"id":"GO:2000620","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0038018","count":5}]},{"hash":"1250811322348993832","title":"Actin dynamics and COPII vesicle trafficking","description":"This cluster is anchored by actin-related terms (actin nucleation; barbed-end actin filament capping) alongside COPII vesicle loading and coating regulation, pointing to a coordinated role of cytoskeletal remodeling in ER-to-Golgi vesicle trafficking. The other tissue-development terms are less central but may reflect context-specific roles; the core signal remains cytoskeleton-transport coupling.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045010","count":2},{"id":"GO:0051016","count":1},{"id":"GO:0021747","count":1},{"id":"GO:0035909","count":1},{"id":"GO:0045654","count":1}]},{"hash":"202556363180359412","title":"Ubiquitin-Dependent Protein Regulation","description":"The top GO terms are dominated by ubiquitination and ubiquitin\u2011dependent protein catabolism, including protein ubiquitination and ubiquitin\u2011dependent protein catabolic process, with related regulation of receptor turnover (Wnt receptor catabolic process) and ubiquitin\u2011regulated signaling (TNF and RIG\u2011I pathways). A few terms are obsolete or less directly connected (histone modifications, spindle checkpoint), but the overall theme points to ubiquitin-mediated control of protein fate and signaling.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":3},{"id":"GO:0044810","count":3},{"id":"GO:1902364","count":3},{"id":"GO:2000620","count":3},{"id":"GO:0016567","count":3}]},{"hash":"859970289914161613","title":"Unknown","description":"The top GO terms are a scattered mix across plant pigment and lignin biosynthesis, xenobiotic and antibiotic metabolism, hormone catabolism, and even neuronal protein localization, with several obsolete terms. There is no clear, cohesive function connecting all proteins, so a unified, intuitive label isn\u2019t supported.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":6},{"id":"GO:1902987","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0002175","count":3},{"id":"GO:0009808","count":3}]},{"hash":"1080613349730993329","title":"Unknown","description":"The terms show a mix of membrane transport for diverse substrates (e.g., methionine, glycine betaine, cobalt, taurine, vitamins), DNA damage/stress responses (SOS, nucleotide-excision repair, mercury ion response), together with unrelated processes (fatty acid catabolism, stem cell proliferation). This lack of a single cohesive function makes a confident, specific label inappropriate.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":4},{"id":"GO:0006289","count":4},{"id":"GO:0015821","count":3},{"id":"GO:0031460","count":3},{"id":"GO:0006824","count":3}]},{"hash":"1671327205611435974","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":29,"triangles":44,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0000105","count":3},{"id":"GO:0000162","count":3},{"id":"GO:0044205","count":2},{"id":"GO:0014075","count":2}]},{"hash":"179501797629603198","title":"RNA modification and ribosome biogenesis","description":"This cluster is characterized by RNA processing and modification terms (tRNA wobble uridine modification, tRNA methylation, rRNA methylation) and ribosome assembly/export (ribosomal small subunit export from nucleus), suggesting a shared function in RNA modification and ribosome biogenesis; xenobiotic and senescence signals indicate a stress-responsive context, but the core theme remains RNA-based regulation of the ribosome. ","confidence":"High","size":11,"edges":9,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":6},{"id":"GO:0002098","count":6},{"id":"GO:0046690","count":5},{"id":"GO:0090398","count":5},{"id":"GO:0006656","count":5}]},{"hash":"590465935793854947","title":"Ubiquitin-proteasome regulation of the cell cycle","description":"This cluster is dominated by ubiquitin-related degradation processes: SCF-dependent ubiquitination, K11- and K48-linked ubiquitination, APC-dependent catabolic processes, and autoubiquitination, plus neddylation, all linking to proteasome-mediated protein turnover that drives cell cycle progression. ER stress-induced apoptosis and peroxisomal import appear ancillary; overall, the common theme is ubiquitin-mediated proteolysis coordinating cell cycle control and stress responses.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070059","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0070979","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0016032","count":5}]},{"hash":"1877772702002953105","title":"Ribosome Biogenesis and Translation Machinery","description":"The cluster is strongly enriched for GO terms tied to ribosome function and protein synthesis, including translation, ribosome biogenesis, large-subunit assembly, and LSU-rRNA maturation, plus mitochondrial translation and snoRNP assembly. These themes consistently point to ribosome assembly and translation machinery as the core function of the proteins in this group, with a few related terms (like antibiotic response and selenocysteine incorporation) reflecting translation-related regulation. ","confidence":"High","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0032543","count":3},{"id":"GO:0006415","count":3}]},{"hash":"1652715971703994895","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":1},{"id":"GO:0009553","count":1},{"id":"GO:0030010","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000920","count":1}]},{"hash":"1600733385267881657","title":"Nucleotide Salvage and Biosynthesis","description":"The cluster is dominated by nucleotide metabolism terms: AMP salvage, nucleoside monophosphate phosphorylation, ADP and CDP biosynthesis, purine ribonucleotide interconversion, and ITP metabolic process, suggesting a core role in nucleotide production and turnover. The brain and liver development terms seem incidental and likely reflect broader tissue-specific associations rather than defining the cluster\u2019s function. Confidence: Medium","confidence":"","size":11,"edges":36,"triangles":50,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":4},{"id":"GO:0046940","count":4},{"id":"GO:0046939","count":4},{"id":"GO:0015937","count":4},{"id":"GO:0015951","count":3}]},{"hash":"1621386391025027000","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":37,"triangles":55,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0099132","count":2},{"id":"GO:0034656","count":1},{"id":"GO:0006203","count":1},{"id":"GO:0009240","count":1},{"id":"GO:1901911","count":1}]},{"hash":"1670876794798285504","title":"mRNA processing and translation initiation control","description":"This cluster centers on RNA maturation and processing (splicing, export, polyadenylation) and on regulation of translation initiation, including formation of the preinitiation complex and translation reinitiation, with an additional note of ncRNA-mediated gene silencing, suggesting a coordinated role in mRNA lifecycle and translation control.","confidence":"High","size":11,"edges":22,"triangles":9,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":8},{"id":"GO:0001731","count":8},{"id":"GO:1901407","count":8},{"id":"GO:0006378","count":8},{"id":"GO:0045292","count":7}]},{"hash":"1081167994446731114","title":"Cell wall and surface polysaccharide biosynthesis","description":"The GO terms cluster around synthesis and assembly of carbohydrate-based surface structures: cell wall organization, mannoprotein biosynthesis, GDP-mannose and UDP-glucose pathways, lipopolysaccharide and lipid A biosynthesis, and related glycogen/starch biosynthesis. This suggests a cohesive function in producing cell-wall and extracellular polysaccharides across different organisms, rather than cytosolic carbohydrate metabolism alone.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0005978","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0009298","count":2},{"id":"GO:0000032","count":2}]},{"hash":"1759813846105986758","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0015074","count":3},{"id":"GO:0019068","count":2},{"id":"GO:0019076","count":2},{"id":"GO:0010587","count":2}]},{"hash":"339674798543131070","title":"Ribosome Biogenesis and Translational Regulation","description":"The top GO terms cluster around translation and ribosome-related processes: translation, ribosome biogenesis, translational termination/elongation, and mitochondrial translation, pointing to a core group of proteins involved in protein synthesis machinery and its fidelity/regulation. A couple of terms (glial cell proliferation, regulation of heterochromatin formation) are less central and may reflect secondary annotations or pleiotropy.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0045903","count":6},{"id":"GO:0046677","count":6},{"id":"GO:0042254","count":4},{"id":"GO:0006415","count":4}]},{"hash":"1119983811082101449","title":"Plant secondary cell wall biosynthesis","description":"The top GO terms are dominated by cell wall\u2013related processes, notably plant-type secondary cell wall biogenesis and lignin biosynthetic process, pointing to a cohesive function in building and modifying the plant cell wall. Some other terms (translation, various methylation steps) appear less central, suggesting some noise, but the primary theme is secondary cell wall biosynthesis and lignin formation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0009834","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0006412","count":1},{"id":"GO:1901771","count":1}]},{"hash":"346507559158710959","title":"Photoreceptor development and outer segment organization","description":"This cluster centers on retinal photoreceptor biology, with terms for photoreceptor outer segment organization, retinal rod cell development, and protein localization to photoreceptor segments, plus non-motile cilium assembly. These indicate a coherent theme around photoreceptor/ciliary functions, despite a couple of metabolic-related terms that are less central to this core. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021756","count":1},{"id":"GO:1902855","count":1},{"id":"GO:1903646","count":1},{"id":"GO:0038108","count":1},{"id":"GO:0090526","count":1}]},{"hash":"706596158582105208","title":"Plant Development and Hormone Signaling","description":"The top GO terms cluster around plant-specific developmental processes (floral meristem growth, bract development, multicellular development) and hormone signaling pathways (ethylene and abscisic acid), as well as related processes like wax biosynthesis regulation. While the terms span several aspects, they collectively point to plant development and hormone-regulated regulation as a cohesive theme for this cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051245","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0010451","count":1},{"id":"GO:0009873","count":1}]},{"hash":"1145136366839707143","title":"Ubiquitin-Dependent Protein Degradation and Receptor Turnover","description":"This cluster is dominated by ubiquitin-mediated proteolysis terms (K48-linked ubiquitination, autoubiquitination, ERAD) and the Wnt receptor catabolic process, suggesting a theme of protein quality control and degradation, including turnover of signaling receptors. Some terms (peroxisome import, X-chromosome dosage regulation) are less central but do not override the core degradation-related signals.","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0038018","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0070936","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0016558","count":2}]},{"hash":"154696231844394534","title":"Mitochondrial dynamics and vesicle trafficking","description":"Based on the prominent GO terms, the cluster centers on mitochondrial fission and membrane organization, along with protein targeting to vacuoles and processing in phagocytic vesicles, indicating coordinated mitochondrial dynamics and endomembrane trafficking. Additional terms on apoptosis and cell cycle suggest stress-related regulation and cellular fate decisions, while antibiotic response reflects a broader stress context. Although one term (sensory perception of sound) is less directly related, the mitochondrial/vesicle trafficking theme best represents the core of this cluster.","confidence":"Medium","size":11,"edges":10,"triangles":4,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000266","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0007006","count":4},{"id":"GO:0006623","count":4},{"id":"GO:0007605","count":4}]},{"hash":"2178085201970221354","title":"Stress-Activated Signaling and Oxidative Response","description":"Top GO terms cluster around stress-responsive signaling and protective mechanisms against oxidative and environmental stress (e.g., stress-activated MAPK cascade; responses to hydrogen peroxide, UV-A, heat; negative regulation of ROS metabolism; regulation of amyloid fibril formation). Neuronal transport terms (anterograde axonal protein transport) and estradiol response suggest signaling and transport modulation in stressed cells. Overall, a coherent theme is cellular stress signaling and oxidative stress management.","confidence":"Medium","size":11,"edges":25,"triangles":21,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051403","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0032387","count":3},{"id":"GO:0032355","count":3},{"id":"GO:0099641","count":3}]},{"hash":"1662983443827171346","title":"Immune activation with cytokine signaling and angiogenesis","description":"This cluster is dominated by GO terms related to immune activation and cytokine production (e.g., T cell proliferation, IL-4 production, cytokine regulation) and processes linked to leukocyte migration and vascular remodeling (endothelial cell migration, Rho signaling). While a few terms touch on cytoskeletal localization and development, the strongest common theme is immune activation and inflammatory signaling, with a notable connection to angiogenesis.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":10},{"id":"GO:0001502","count":10},{"id":"GO:0097350","count":10},{"id":"GO:0035372","count":10},{"id":"GO:0043068","count":10}]},{"hash":"920427489307802924","title":"Chromatin-Associated Transcription Regulation","description":"The cluster is dominated by transcription-related terms (GO:0006355) and chromatin binding (GO:0035563), suggesting proteins that regulate gene expression via chromatin interactions. A subset of terms covers metabolism and hormonal responses, which are auxiliary contexts rather than core functions, but do not override the primary signal of transcriptional regulation with chromatin association.","confidence":"Medium","size":11,"edges":27,"triangles":17,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":6},{"id":"GO:0006355","count":6},{"id":"GO:0045654","count":4},{"id":"GO:0035563","count":4},{"id":"GO:0055114","count":4}]},{"hash":"1395420183959682380","title":"Ubiquitin-Dependent Protein Degradation","description":"Top GO signals are dominated by ubiquitination and ubiquitin-dependent protein catabolic processes (K48-linked ubiquitination, autoubiquitination, ERAD). Although a couple terms relate to peroxisome import or X-chromosome regulation, the strongest theme is ubiquitin-mediated proteolysis, suggesting a cluster focused on protein degradation pathways.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038018","count":7},{"id":"GO:0042787","count":7},{"id":"GO:0070936","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0016558","count":7}]},{"hash":"1112228772036095237","title":"Plant phenylpropanoid and flavonoid biosynthesis","description":"The top GO terms center on biosynthesis of anthocyanins, cyanidin glycosides, and lignin, all classic plant phenylpropanoid/flavonoid pathways; additional terms like antibiotic metabolism and xenobiotic glucuronidation appear less coherent with this theme, but the dominant signal is secondary metabolite production in plants.","confidence":"Medium","size":11,"edges":11,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0002175","count":5},{"id":"GO:0009808","count":5},{"id":"GO:0009718","count":5},{"id":"GO:0006711","count":5}]},{"hash":"1255278012684106959","title":"Mitotic chromosome dynamics and spindle assembly","description":"The cluster\u2019s GO terms cluster around mitosis-related processes: kinetochore localization, mitotic spindle establishment/localization, microtubule polymerization, DNA replication-dependent chromatin assembly, and sister chromatid cohesion, pointing to chromosome management and spindle machinery during cell division. A label emphasizing mitotic chromosome dynamics and spindle assembly best represents the shared function of these proteins.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0035048","count":1},{"id":"GO:0034501","count":1},{"id":"GO:0006275","count":1},{"id":"GO:0040001","count":1}]},{"hash":"740489588787658304","title":"Immune activation and cytokine regulation","description":"This cluster is dominated by GO terms related to immune signaling and cytokine production, including T cell proliferation, IL-4 production, and positive regulation of cytokine production, along with neutrophil clearance. Additional terms about endothelial cell migration and Rho signaling reflect the cytoskeletal and migratory context of immune responses. Taken together, the proteins appear to function in orchestrating immune activation and cytokine milieu rather than a single specialized process.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":11},{"id":"GO:0001502","count":11},{"id":"GO:0097350","count":11},{"id":"GO:0035372","count":11},{"id":"GO:0043068","count":11}]},{"hash":"852646772705511202","title":"Plant flavonoid and phenylpropanoid biosynthesis","description":"The top terms cluster around anthocyanin and cyanidin glucoside biosynthesis, lignin metabolism, and flavonoid modifications, which together point to the plant phenylpropanoid pathway and flavonoid production. Some terms (e.g., estrogen catabolic process, xenobiotic glucuronidation) appear less related or are older/obsolete annotations, suggesting possible noise, but the predominant signal is flavonoid/phenylpropanoid biosynthesis in plants.","confidence":"Medium","size":11,"edges":51,"triangles":133,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":5},{"id":"GO:0002175","count":4},{"id":"GO:0009808","count":4},{"id":"GO:0006711","count":4},{"id":"GO:0052697","count":4}]},{"hash":"1686325348055766526","title":"Ribosome Biogenesis and Translation","description":"Cluster centers on the protein synthesis machinery, with strong representation of cytoplasmic and mitochondrial translation, ribosome biogenesis/assembly, and rRNA processing. This points to a cohesive group of ribosome-related proteins involved in making and translating ribosomes. A couple of peripheral terms (antibiotic response, nerve growth factor signaling) are secondary and do not undermine the main theme.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0070126","count":3},{"id":"GO:1901194","count":2},{"id":"GO:0000448","count":2},{"id":"GO:0046677","count":2}]},{"hash":"808714788728562077","title":"T Cell Development and Immune Signaling","description":"The top GO terms include strong signals for T cell biology, notably positive regulation of alpha-beta T cell proliferation and beta selection, pointing to T cell development and immune signaling. Additional terms about VEGF receptor signaling and neutrophil clearance suggest broader immune context, while DNA replication and chromatin assembly-related terms reflect proliferative cell-cycle processes common in developing lymphocytes. Overall, the cluster appears centered on T cell development within an immune signaling framework.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0070926","count":1},{"id":"GO:0006275","count":1},{"id":"GO:0061387","count":1},{"id":"GO:0046641","count":1}]},{"hash":"1579781127640595749","title":"Nitrogen metabolism: ureide/purine catabolism","description":"This cluster is dominated by GO terms tied to nitrogen metabolism, including ureide catabolic process, allantoin assimilation, and purine nucleobase metabolism, along with peptide/protein turnover (proteolysis, peptide catabolic process) and amino acid biosynthesis signals (arginine, lysine). The glucocorticoid response term is a minor outlier. Together, these terms point to nitrogen salvage and amino acid metabolism as the core theme.","confidence":"Medium","size":11,"edges":32,"triangles":59,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010136","count":4},{"id":"GO:0006144","count":4},{"id":"GO:0009442","count":4},{"id":"GO:0006508","count":4},{"id":"GO:0019877","count":4}]},{"hash":"1775946259954233920","title":"Plant chloroplast function and photosynthesis regulation","description":"This cluster is dominated by plant-specific terms related to photosynthesis, chlorophyll biosynthesis, and GA (gibberellin) signaling, which points to chloroplast function and regulation of photosynthetic processes as the core theme. Some terms are more general (protein folding/oligomerization, gluconeogenesis) or oddities (prostate gland development, lead ion response) that may be annotation noise, but the strongest signal ties to chloroplast-associated metabolism and light-driven processes.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":4,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":5},{"id":"GO:0006463","count":4},{"id":"GO:0009938","count":4},{"id":"GO:0030850","count":4},{"id":"GO:1902325","count":4}]},{"hash":"615384191152366901","title":"Endosome-lysosome trafficking and vesicle exocytosis","description":"The top GO terms converge on vesicle movement and membrane organization within the endo-lysosomal system, including endosome-to-lysosome transport, lysosomal membrane dynamics, and regulation of synaptic vesicle exocytosis, with supporting hints from podosome and multivesicular body\u2013related processes. This points to a cohesive theme of intracellular trafficking and lysosome-related pathways across neuronal and secretory contexts.","confidence":"High","size":11,"edges":38,"triangles":51,"max_degree":8,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0060999","count":6},{"id":"GO:1902824","count":5},{"id":"GO:0097212","count":5},{"id":"GO:0033028","count":5},{"id":"GO:0097284","count":5}]},{"hash":"968749898405553779","title":"Immune and ECM remodeling","description":"This cluster combines immune-related processes (T cell cytotoxicity, macrophage apoptosis) with tissue remodeling activities (bone resorption, basement membrane disassembly), suggesting coordinated immune-driven remodeling of the extracellular matrix. Peptide catabolism and catalytic activity regulation further support enzymatic activities in inflammatory remodeling, with some developmental/hormonal context (lung branching, thyroid hormone response) that can intersect these processes.","confidence":"Medium","size":11,"edges":40,"triangles":67,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":8},{"id":"GO:0010813","count":8},{"id":"GO:0010815","count":8},{"id":"GO:0045453","count":8},{"id":"GO:0001913","count":8}]},{"hash":"1468841967925042874","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":1},{"id":"GO:2000344","count":1},{"id":"GO:0016042","count":1},{"id":"GO:0019684","count":1},{"id":"GO:0042773","count":1}]},{"hash":"1025217338281754486","title":"Unknown","description":"The top GO terms span GPCR signaling, cardiac electrical activity, transcription regulation, plant vascular development, exocytosis, cell shape, sumoylation, fungal sporulation membranes, membrane tubulation, and heart rate regulation, with no clear shared function across species or processes. The cluster has no edges or interactions tying these terms together, and there\u2019s no cohesive theme to unify them, so a single biological label isn\u2019t justifiable.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0010222","count":1},{"id":"GO:0045921","count":1}]},{"hash":"1503566866118077509","title":"Calcium-Triggered Transcription Regulators","description":"Based on GO terms, this group centers on calcium ion response and transcriptional regulation (DNA-templated transcription and RNA Pol II\u2013dependent transcription), with several development-related terms implying calcium-regulated gene expression in differentiation. The common theme is calcium-responsive transcription control.","confidence":"Medium","size":11,"edges":52,"triangles":140,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":10},{"id":"GO:0006351","count":9},{"id":"GO:0045944","count":6},{"id":"GO:0032915","count":5},{"id":"GO:0006990","count":5}]},{"hash":"989628625863569006","title":"Isoprenoid biosynthesis","description":"The cluster is dominated by GO terms for biosynthesis of isoprenoid-derived compounds (geranyl/farnesyl/geranylgeranyl diphosphate, monoterpenes, cholesterol, quinones), indicating a cohesive role in isoprenoid and sterol biosynthesis; a couple of general protein-assembly terms are present but secondary.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033386","count":8},{"id":"GO:0051290","count":8},{"id":"GO:0045337","count":8},{"id":"GO:0043693","count":8},{"id":"GO:0015031","count":8}]},{"hash":"446205424928513927","title":"Unknown","description":"The top GO terms are disparate (neuroendocrine differentiation, ribosomal export, iron ion response) with only one gene per term and no network connections, so there is no coherent common function tying the proteins together.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061101","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0010039","count":1}]},{"hash":"1869454218570075575","title":"Transmembrane Transporters","description":"The top GO terms cluster around diverse transmembrane transport activities, including sugar, vitamin, metal ion, nitrate, and xenobiotic transport, as well as neurotransmitter loading into synaptic vesicles, suggesting the proteins are primarily membrane transporters with broad substrate specificity.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0042891","count":2},{"id":"GO:1900754","count":2}]},{"hash":"543720669052583285","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000103","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0050427","count":2}]},{"hash":"1719452088478845602","title":"Steroid hormone biosynthesis and metabolism","description":"The top GO terms cluster around steroid biosynthesis (cortisol, testosterone, brassinosteroids) and related lipid metabolism (omega-oxidation, retinoic acid/vitamin D-related processes) with supporting xenobiotic detoxification pathways. This suggests a cohesive theme of steroid and lipid hormone biosynthesis/metabolism and associated metabolism, justifying the label.","confidence":"High","size":11,"edges":12,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":9},{"id":"GO:0071603","count":9},{"id":"GO:0034651","count":9},{"id":"GO:0070989","count":9},{"id":"GO:0042738","count":9}]},{"hash":"2106330420197017727","title":"Zinc/Cadmium Ion Homeostasis and Detoxification","description":"The cluster centers on metal ion handling, especially zinc and cadmium. Recurrent GO terms include detoxification of zinc ion, response to zinc ion, zinc and cadmium ion transmembrane transport, and cellular detoxification of cadmium ion, with related iron ion homeostasis/transport terms. This points to a cohesive module for metal ion import, transport, and detoxification across membranes. ","confidence":"High","size":11,"edges":19,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010312","count":4},{"id":"GO:0006876","count":4},{"id":"GO:0010043","count":4},{"id":"GO:0032119","count":4},{"id":"GO:0055072","count":4}]},{"hash":"1560352730607752527","title":"ER stress and vesicle trafficking","description":"The cluster is enriched for terms tied to the secretory/endomembrane system: response to endoplasmic reticulum stress, COPII-coated vesicle budding, plasma membrane to endosome transport, endosomal vesicle fusion, and endosome-to-lysosome transport. These collectively point to functions in ER-to-Golgi trafficking and endosomal trafficking, with ruffle assembly suggesting accompanying cytoskeletal dynamics. Although some terms (e.g., division septum assembly, endothelin regulation) are peripheral, the dominant pattern supports a cohesive role in ER stress\u2013linked vesicle trafficking. ","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903206","count":4},{"id":"GO:0034976","count":4},{"id":"GO:1902824","count":3},{"id":"GO:0048227","count":3},{"id":"GO:0097178","count":3}]},{"hash":"428717941428751566","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":13,"triangles":3,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":4},{"id":"GO:0006626","count":4},{"id":"GO:0072321","count":4},{"id":"GO:0051084","count":1},{"id":"GO:0045041","count":1}]},{"hash":"572736362829110954","title":"Ubiquitination and Proteasomal Degradation","description":"Dominant GO terms are ubiquitin-related protein catabolism (ubiquitin-dependent proteolysis, protein ubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process) and histone ubiquitination. This suggests the cluster comprises proteins involved in tagging substrates for degradation by the ubiquitin-proteasome system, including histone modification that can regulate chromatin. Some immune signaling terms (TNF, RIG-I) relate to ubiquitin-mediated regulation. Overall, the cluster centers on ubiquitin tagging and proteasome-mediated turnover.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:1901253","count":5},{"id":"GO:2000620","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0038018","count":5}]},{"hash":"721931204053514266","title":"Arabinogalactan protein glycosylation and cell wall development","description":"The cluster is dominated by GO terms related to arabinogalactan proteins (AGPs), O-linked hydroxyproline glycosylation, and related glycan biosynthesis (e.g., arabinogalactan protein metabolism, poly-N-acetyllactosamine biosynthesis, and specific glycosylation processes). These point to plant cell wall glycoproteins and AGP-related pathways as the core theme, with supporting terms mentioning root hair and seed coat mucilage development that align with plant extracellular matrix biology. Some insect-related terms appear, but they don\u2019t override the AGP/glycosylation-centric signal. Confidence: Medium","confidence":"","size":11,"edges":30,"triangles":23,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0007299","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0048354","count":3},{"id":"GO:0018258","count":3}]},{"hash":"1221710631729842638","title":"Plant oxidative stress response and lignin catabolism","description":"The GO terms cluster around oxidative stress response, oxidant detoxification, and hydrogen peroxide catabolism, plus lignin catabolic processes and plant-type cell wall organization, suggesting proteins involved in plant defense and cell wall remodeling under stress. A few terms point to signaling and protein turnover (phosphorylation, ubiquitin-related processes), while a noisy outlier (wing cell fate specification) is likely irrelevant. Overall, the cluster seems representative of plant stress responses linked to lignin metabolism. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0046274","count":4},{"id":"GO:0042744","count":4},{"id":"GO:0055114","count":4}]},{"hash":"1248502392578120914","title":"Diverse metabolite biosynthesis","description":"The top terms point to biosynthetic processes across diverse metabolite classes (PHB, anthocyanins, waxes, fatty acids/lipids, L-glutamine, glycans), suggesting a unifying theme of metabolite production rather than a single pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0042619","count":7},{"id":"GO:0009718","count":5},{"id":"GO:0006541","count":4},{"id":"GO:0010253","count":4}]},{"hash":"351447861557928554","title":"Chloroplast protein import and photosynthesis","description":"The top GO terms cluster around chloroplast functions, including protein import into the chloroplast stroma, protein import into the mitochondrial matrix (potential dual-targeting), and photosynthesis-related processes such as photosystem I assembly. The strongest cohesive signal is chloroplast biogenesis and photosynthetic machinery, with some mitochondrial terms likely reflecting dual targeting rather than a separate function. This supports a label focused on chloroplast import and photosynthesis as the core theme.","confidence":"Medium","size":11,"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:0000002","count":1},{"id":"GO:0032094","count":1},{"id":"GO:0030150","count":1}]},{"hash":"1517054215789637477","title":"Flavonoid and phenylpropanoid metabolism","description":"The top GO terms cluster around biosynthesis of flavonoids and related compounds (anthocyanin-, cyanidin-3-O-glucoside biosynthesis) and lignin metabolism, plus glucuronidation-based detoxification (xenobiotic and flavonoid glucuronidation) and other metabolic processing. Together these indicate a cohesive theme of secondary metabolite production and modification in plants, with detox pathways linked to those compounds. An outlier term about paranode localization to axon appears unrelated and likely annotation noise. Confidence reflects a solid, but not perfect, linkage to this theme.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":8},{"id":"GO:0002175","count":7},{"id":"GO:0009808","count":7},{"id":"GO:0006711","count":7},{"id":"GO:0052697","count":7}]},{"hash":"706549863608815584","title":"Sphingolipid signaling and metabolism","description":"Based on the top GO terms, most proteins are linked to sphingolipid synthesis and catabolism and to sphingosine-1-phosphate receptor signaling, with accompanying inflammatory regulation (IL-1, TNF pathways) and brain development signals. This suggests a cohesive module centered on sphingolipid-mediated signaling and its roles in inflammation and neural development, rather than a single isolated process.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048146","count":1},{"id":"GO:0046521","count":1},{"id":"GO:2000064","count":1},{"id":"GO:0006954","count":1},{"id":"GO:0010803","count":1}]},{"hash":"1674747954117735905","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009451","count":4},{"id":"GO:0080156","count":4},{"id":"GO:0016554","count":4},{"id":"GO:1905639","count":4},{"id":"GO:0090617","count":4}]},{"hash":"751047165742392817","title":"Developmental transcriptional regulation","description":"The proteins cluster around transcriptional control of development, with GO terms for DNA-templated transcription and regulation of transcription, plus diverse differentiation processes such as somatic embryogenesis, gibberellin response, microgametogenesis, and muscle differentiation. This suggests a coherent module of transcription factors guiding cell fate and growth across developmental contexts, even though the terms span multiple organisms (plants and animals). ","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010262","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0055046","count":1}]},{"hash":"717606634200599699","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":5},{"id":"GO:2000344","count":5},{"id":"GO:0016042","count":5},{"id":"GO:0006491","count":2},{"id":"GO:0006979","count":2}]},{"hash":"1725227413956437110","title":"ER Stress and ER Network Organization","description":"This cluster is dominated by GO terms related to unfolded protein response regulation (IRE1 and PERK pathways) and endoplasmic reticulum tubular network organization, suggesting a shared function in ER stress management and ER morphology. A few development- and organization-related terms appear, but the ER-centered terms provide the strongest common theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903896","count":1},{"id":"GO:0071790","count":1},{"id":"GO:1903371","count":1},{"id":"GO:0051292","count":1},{"id":"GO:1903899","count":1}]},{"hash":"157680067281216228","title":"Cellulose and xylan catabolism","description":"The top GO terms are cellulose catabolic process (3) and xylan catabolic process (2), suggesting a core theme of plant cell wall polysaccharide degradation. The remaining terms are sporadic and less coherent with this core, indicating possible noise or multifunctionality; thus the label focuses on the dominant shared function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0045493","count":2},{"id":"GO:0072327","count":1},{"id":"GO:2000495","count":1},{"id":"GO:0032298","count":1}]},{"hash":"2271713082396405109","title":"Amino acid metabolism and transsulfuration","description":"This cluster centers on amino acid biosynthesis and catabolism, including threonine biosynthesis, transsulfuration, and homocysteine/cysteine-related pathways, with additional links to pyruvate biosynthesis. The presence of insulin response hints suggests metabolic regulation context. Overall, a cohesive theme around amino acid and sulfur amino acid metabolism.","confidence":"Medium","size":10,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042866","count":5},{"id":"GO:0032869","count":5},{"id":"GO:0019499","count":3},{"id":"GO:0009310","count":3},{"id":"GO:0043418","count":3}]},{"hash":"19847954154748109","title":"Vision-related carotenoid and retinoid metabolism","description":"This cluster shows GO terms centered on carotenoids and retinoids (carotene/xanthophyll catabolic, retinol metabolic, retina homeostasis, phototransduction UV), which together suggest a shared function in vision-related pigment turnover. The presence of a few outlier terms like cell division and pinoresinol biosynthesis does not override the dominant vision/metabolism signal, so the label captures the core theme with moderate confidence.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901599","count":3},{"id":"GO:0000920","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0001895","count":1},{"id":"GO:0016121","count":1}]},{"hash":"2248978425054198783","title":"Cell growth, development, and cytoskeletal dynamics","description":"This cluster centers on growth and development processes (anisotropic growth, epithelial proliferation in prostate development) while also tying in cytoskeletal regulation (actin organization via cell adhesion) and nuclear transport and DNA damage response, plus organogenesis events (lung induction, fungiform papilla formation, heart rate regulation). The mix suggests a broad module of cellular organization and developmental signaling rather than a single, specific pathway.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0051211","count":5},{"id":"GO:0060769","count":5},{"id":"GO:0070602","count":5},{"id":"GO:0006607","count":5},{"id":"GO:0060492","count":5}]},{"hash":"1545846644222002653","title":"Embryonic organogenesis and lineage differentiation","description":"The GO terms span multiple developmental processes across different tissues (heart valve development, outflow tract morphogenesis, mesenchyme development) and various lineage differentiations (neural interneuron, floor plate, auditory receptor cell, pancreatic A cell), plus cell-cycle regulation. This pattern points to a broad theme of embryonic tissue morphogenesis and lineage specification rather than a single, specific pathway, justifying the label.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:2000793","count":3},{"id":"GO:2000764","count":3},{"id":"GO:0060375","count":3},{"id":"GO:0060485","count":3},{"id":"GO:0071156","count":3}]},{"hash":"2070967947685139196","title":"Developmental signaling and growth regulation","description":"This cluster centers on regulation of signaling pathways (positive regulation of GTPase activity, serine/threonine kinase activity, protein autophosphorylation) and developmental processes (skin, spinal cord, and multicellular organism development and growth). The convergence on signaling control during development, with some supporting roles in hypoxia response and mRNA transport, suggests proteins that coordinate growth and tissue development rather than a single specialized function.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1506173356556844982","title":"Cytoskeleton and cell cycle regulators","description":"Based on the top GO terms, the proteins frequently participate in cytoskeletal organization and nuclear division: localization to kinetochore and microtubules, negative regulation of CDK activity, and Rho signaling point to cytoskeletal remodeling and cell-cycle control. Additional terms touch on immune and developmental processes (T cell proliferation, neutrophil clearance, cartilage condensation, endothelial migration, cytokine production), which may reflect multifunctional or context-dependent roles of these proteins in signaling networks. Overall, the cluster seems centered on cytoskeletal dynamics and cell cycle regulation with peripheral immune/developmental functions.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":7},{"id":"GO:0045736","count":7},{"id":"GO:0046641","count":6},{"id":"GO:0001502","count":6},{"id":"GO:0097350","count":6}]},{"hash":"915573081578819797","title":"ER-Golgi trafficking and ERAD","description":"The top GO terms are dominated by the ubiquitin-dependent ERAD pathway and vesicle transport between the ER and Golgi (antereograde and retrograde), indicating a cluster of proteins involved in ER quality control and secretory pathway transport. Secondary terms point to related membrane trafficking and turnover processes, with some peripheral links to autophagy and organelle import. Overall, a cohesive theme centers on ER-associated degradation and ER-Golgi trafficking.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0048490","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0016558","count":3},{"id":"GO:0051301","count":3}]},{"hash":"919087398361756662","title":"Unknown","description":"The GO terms span diverse and seemingly unrelated processes, including triglyceride/lipid metabolism, bacterial cell-wall and LPS biosynthesis, cell shape and wall organization, antibiotic response, and various development and immune-related processes across different organisms. There isn\u2019t a clear, cohesive theme tying these proteins to a single function, so a concise, representative label cannot be assigned.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070328","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0009252","count":2}]},{"hash":"1506587690565086227","title":"Embryonic development and translation initiation control","description":"Several terms point to developmental processes (neural tube closure, forebrain and skeletal system development), suggesting a developmental program. The presence of translation initiation-related terms (preinitiation complex formation, translation reinitiation) indicates a layer of protein synthesis regulation, while cell cycle, proliferation, and ER-stress\u2013related apoptosis imply general growth and stress responses. Overall, the cluster seems to center on developmental regulation with links to translation control and cellular stress. ","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001403","count":3}]},{"hash":"456146511679940228","title":"Translation and Transcription Regulation Under Stress","description":"The cluster is enriched for translation-related processes (translation, ribosomal large subunit biogenesis) and transcription regulation (DNA-templated transcription termination/elongation), with accompanying stress-response signals (response to virus, UV-associated translation regulation, p53-mediated DNA damage response). This points to a cohesive module that coordinates gene expression at both transcriptional and translational levels in response to cellular stress.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0009615","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0032784","count":2}]},{"hash":"590874367261444410","title":"Gonad development and reproductive maturation","description":"The cluster shows multiple GO terms tied to gonadal development (including male gonad development), fertilization, vitellogenesis, and estradiol response, plus growth processes\u2014points to a coherent theme of reproductive development and hormone-regulated maturation. Some terms like brain development and transcription-related processes appear as secondary or broader developmental signals, but the core theme is reproduction-related functions.","confidence":"Medium","size":10,"edges":37,"triangles":65,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0008584","count":5},{"id":"GO:0007338","count":5},{"id":"GO:0090230","count":4}]},{"hash":"1535822620238186659","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0044205","count":3},{"id":"GO:0006207","count":3},{"id":"GO:0045892","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009228","count":2}]},{"hash":"692412495364094030","title":"Neural development and glial apoptosis","description":"This cluster is dominated by GO terms related to nervous system development, forebrain development, neuron cellular homeostasis, and glial cell apoptotic processes, suggesting a coherent theme around neural differentiation and glial regulation. A few terms (e.g., L-methionine cycle, melanization defense response, salivary gland histolysis, TGF-beta response) appear but are less central, indicating some noise. Overall, neural development with glial apoptosis is the best-fitting label.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0070050","count":5},{"id":"GO:0030900","count":4},{"id":"GO:0010659","count":4},{"id":"GO:0035006","count":4},{"id":"GO:0033353","count":4}]},{"hash":"2159356158929530704","title":"Chloroplast pigment biosynthesis and protein import","description":"The top GO terms include carotene biosynthetic process and protein import into chloroplast stroma, suggesting plastid-focused metabolism and organelle-targeted protein handling. While there are some mitochondrial-related terms, the chloroplast-associated functions are the most representative of the cluster's themes. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016120","count":1},{"id":"GO:0050881","count":1},{"id":"GO:0031413","count":1},{"id":"GO:0070584","count":1},{"id":"GO:0019216","count":1}]},{"hash":"1821995364025181751","title":"Plant Hormone Signaling and Defense Responses","description":"The top GO terms show strong representation of plant hormone signaling (ACCethylene response, gibberellin signaling, salicylic acid) and defense-related processes (response to chitin, antifungal innate immune regulation), along with differentiation-related terms (atrichoblast, sclerenchyma) and a nutrient-stress cue (boron deprivation). This points to a cohesive cluster of proteins coordinating growth and development through hormone signals while mediating defense against pathogens, with some involvement in epidermal and tissue differentiation. The estrogen term appears minor noise in this plant-focused set.","confidence":"Medium","size":10,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0080169","count":4},{"id":"GO:0009961","count":4},{"id":"GO:0010055","count":4},{"id":"GO:0009751","count":4},{"id":"GO:0009739","count":4}]},{"hash":"41384260614869886","title":"Steroid hormone biosynthesis and metabolism","description":"The cluster is dominated by steroid-related processes: cortisol and testosterone biosynthesis, brassinosteroid biosynthesis, and retinoic acid catabolism, with related pathways in vitamin D response and fatty acid omega-oxidation, plus xenobiotic catabolism. This suggests a core theme of hormone production and processing with accompanying lipid/xenobiotic metabolism. Mammary gland development and endothelial adhesion appear as secondary related processes that can be influenced by hormonal signaling. ","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":4},{"id":"GO:0071603","count":4},{"id":"GO:0034651","count":4},{"id":"GO:0070989","count":4},{"id":"GO:0042738","count":4}]},{"hash":"1308753592093877331","title":"Ubiquitin-Dependent Spindle and Cytokinesis Regulation","description":"The cluster centers on ubiquitin-related processes (protein ubiquitination, K48-linked ubiquitination, and autoubiquitination) and spindle/cytokinesis control (mitotic spindle assembly and orientation checkpoints, septin ring assembly, and negative regulation of septation initiation signaling). This suggests a cohesive role for ubiquitin-mediated proteolysis in regulating spindle dynamics and cytokinesis, with Wnt receptor catabolic process indicating broader degradation pathways as well.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044810","count":4},{"id":"GO:1902364","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0038018","count":4},{"id":"GO:0042787","count":4}]},{"hash":"579629003410494546","title":"Membrane Ion Transport and Homeostasis","description":"The GO terms overwhelmingly emphasize transmembrane transport of Zn2+, Na+, K+, and Cd2+ and intracellular K+ homeostasis, pointing to a cluster of ion transporters/ion channels; other terms are less representative, so the dominant theme is ion transport across membranes.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071577","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0036376","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0030007","count":2}]},{"hash":"1696394640937300363","title":"Nucleolar Transcription and Chromatin Dynamics","description":"The cluster centers on chromatin assembly/heterochromatin at rDNA, transcription regulation and chromatin remodeling (across RNA Pol II/III and RNA-templated transcription), and ribosome biogenesis, all hallmarks of nucleolar transcriptional control and chromatin dynamics. Some terms like apoptotic process and cytokinesis regulation are less central, but the core themes support a nucleolar transcription/chromatin focus.","confidence":"Medium","size":10,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006335","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0051290","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0045815","count":3}]},{"hash":"563177450944192320","title":"Ribosome biogenesis and translation","description":"The top GO terms point strongly to ribosome-related processes: translation, cytoplasmic translation, ribosome biogenesis, LSU-rRNA maturation/export, and snoRNP/snoRNA-related assembly, along with rRNA processing steps. These collectively indicate a cluster focused on ribosome assembly and protein synthesis, with secondary mentions of RNA processing that support the same core function. A few scattered terms (RNA splicing regulation, MAPKKK-related activity) are likely incidental rather than central. ","confidence":"High","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":3},{"id":"GO:0033119","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1296042119629006874","title":"Ubiquitin-Dependent Protein Degradation","description":"The enriched GO terms center on ubiquitination, ERAD, and ubiquitin-dependent proteolysis, indicating a proteostasis/quality-control cluster. Some spindle-assembly related terms may reflect regulation of protein turnover during mitosis, but the dominant signal is ubiquitin-mediated degradation and catabolic processes.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0016567","count":5},{"id":"GO:1901253","count":4},{"id":"GO:0044810","count":4},{"id":"GO:1902364","count":4}]},{"hash":"820425038896667085","title":"Plant terpenoid biosynthesis and gibberellin signaling","description":"This cluster centers on terpenoid biosynthesis (sesquiterpenes, monoterpenes, camphor, geranyl diphosphate) and gibberellin biosynthesis/signaling, with an additional herbivore response term, pointing to a plant terpenoid metabolism and hormone signaling module. A couple of outliers likely reflect annotation noise but do not override the core theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051762","count":2},{"id":"GO:0046211","count":2},{"id":"GO:0009686","count":2},{"id":"GO:0033383","count":2},{"id":"GO:0043693","count":2}]},{"hash":"2008139257326117401","title":"Nuclear gene expression and chromatin regulation","description":"This cluster shows GO terms centered on nuclear processes that control gene expression and genome integrity, including transcription-coupled DNA repair, nuclear mRNA surveillance, and regulation of heterochromatin formation, plus RNA Pol II tethering at the nuclear periphery. While there are also terms related to translation initiation and differentiation, the dominant themes are transcriptional control and chromatin dynamics, with development/proliferation contexts. This suggests a cohesive role in coordinating gene expression at the chromatin and nuclear level.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071033","count":2},{"id":"GO:0090054","count":2},{"id":"GO:0006283","count":2},{"id":"GO:0070196","count":2},{"id":"GO:0090052","count":2}]},{"hash":"2282034692738481732","title":"Bacterial LPS biosynthesis and amino acid metabolism","description":"The cluster is driven by lipopolysaccharide biosynthesis (including core region), along with biosynthetic pathways for histidine and serine, plus related catabolic and transport activities (zinc ion transport). This points to a coherent bacterial envelope\u2013related metabolism theme, with a few unrelated terms likely representing noise.","confidence":"Medium","size":10,"edges":39,"triangles":80,"max_degree":9,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0000105","count":5},{"id":"GO:0006564","count":4},{"id":"GO:0019700","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0009244","count":3}]},{"hash":"1116579434729045536","title":"Oocyte meiosis spindle assembly and ubiquitin-proteasome regulation","description":"The terms strongly point to oocyte maturation, spindle assembly in female meiosis I, and microtubule dynamics, coupled with SCF-dependent ubiquitin-proteasomal protein degradation, suggesting coordinated control of meiotic progression by spindle function and proteolysis. A few neural-development terms appear, but the dominant signal is meiosis-related processes.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":4},{"id":"GO:0046785","count":4},{"id":"GO:0006516","count":4},{"id":"GO:0007057","count":4},{"id":"GO:0070544","count":4}]},{"hash":"612357761332253973","title":"Ubiquitin-Proteasome Regulation of Signaling","description":"Top GO terms point to ubiquitin-dependent protein degradation pathways (ERAD, SCF, protein polyubiquitination, autoubiquitination) that govern signaling and cell proliferation (GTPase activity). Additional stress and hormone-related terms (cadmium response, chitin, glucocorticoid/ABA regulation) are commonly modulated via ubiquitin pathways, supporting a cohesive role in proteostasis and signaling control.","confidence":"High","size":10,"edges":9,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0071276","count":3}]},{"hash":"447124956769017400","title":"Plasma membrane Na+/K+ transport and potassium homeostasis","description":"The top GO terms cluster around exporting/importing Na+ and K+ across the plasma membrane and maintaining intracellular potassium homeostasis, pointing to a functional theme of ion transport regulation at the cell boundary. Other terms (DNA replication, morphogenesis, pain perception, development) appear but are less central, suggesting mixed annotations; thus the label reflects the dominant ion-transport theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0036376","count":2},{"id":"GO:1990573","count":2}]},{"hash":"378799015066755509","title":"Transmembrane Solute Transporters","description":"This cluster centers on transport across membranes for a variety of solutes\u2014ions (Na+, K+, phosphate), metabolites (fucose, vitamins), xenobiotics, and even neurotransmitter loading into synaptic vesicles\u2014indicating a cohesive theme of membrane transport proteins with diverse substrates.","confidence":"High","size":10,"edges":17,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1900754","count":5},{"id":"GO:0015739","count":5},{"id":"GO:0098700","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0035435","count":5}]},{"hash":"301436523673173018","title":"Unknown","description":"The top GO terms are highly diverse, spanning protein assembly, proteasome regulation, development (forebrain), tissue-specific apoptosis (heart, glial), melanization, metabolism (L-methionine cycle), TGF-beta signaling response, salivary gland histolysis, and aging. There is no single coherent function or pathway linking these terms, so a concise, representative label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0070682","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0010659","count":2},{"id":"GO:0035006","count":2}]},{"hash":"590526950374569679","title":"Unknown","description":"The top GO terms span immune signaling (T cell proliferation, cytokine production, neutrophil clearance), development (cartilage condensation), cytoskeletal/trafficking (Rho signaling, microtubule localization), and stress response (cellular response to ethanol), with no single dominant function linking all proteins. There isn\u2019t a cohesive theme to label beyond Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071361","count":7},{"id":"GO:0046641","count":6},{"id":"GO:0001502","count":6},{"id":"GO:0097350","count":6},{"id":"GO:0035372","count":6}]},{"hash":"1128238988349258894","title":"Redox-Linked Metabolic Biosynthesis","description":"The cluster\u2019s top GO terms emphasize multiple biosynthetic processes (retinol, fructose, testosterone, L-ascorbic acid, glutathione) alongside oxidation\u2013reduction (redox) activity, suggesting proteins involved in biosynthesis with redox regulation. Some terms related to stress/regulatory responses (water deprivation, endothelial apoptosis) hint at broader metabolic control. Taken together, the clump appears to center on biosynthetic metabolism with redox context.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042572","count":5},{"id":"GO:0046370","count":5},{"id":"GO:2000353","count":4},{"id":"GO:0044597","count":4}]},{"hash":"1499478394856618225","title":"Regulation of erythrocyte and megakaryocyte differentiation","description":"This cluster is strongly driven by GO terms related to blood cell lineage differentiation, including positive regulation of megakaryocyte differentiation and regulation of erythrocyte differentiation. The presence of these erythroid/megakaryocytic regulatory terms (GO:0045654, GO:0010725, GO:0045648) suggests a shared functional theme centered on hematopoietic lineage control. The accompanying metabolic and immune-related terms seem ancillary rather than defining, though they may reflect broader cellular states. Confidence: High","confidence":"","size":10,"edges":28,"triangles":32,"max_degree":9,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0032496","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0010725","count":4},{"id":"GO:0045648","count":4}]},{"hash":"1012943213543458156","title":"Unknown","description":"The top terms span metabolism, transcription regulation, signaling, vesicle function, and distinct bacterial processes (Type III secretion and flagellar motility), indicating no single unifying function for the cluster.","confidence":"","size":10,"edges":16,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0097053","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0007219","count":3},{"id":"GO:0006353","count":2},{"id":"GO:0042776","count":2}]},{"hash":"1255397429251869811","title":"Fe-S Cluster Biogenesis & Mitochondrial Regulation","description":"These proteins show strong links to iron-sulfur (Fe-S) cluster assembly and transfer, which is central to Fe-S biogenesis and mitochondrial function (GO:0044571, GO:0097428). The mention of mitophagy in response to mitochondrial depolarization further supports a mitochondrial context. Additional, more downstream or context-specific terms (transcription regulation related to iron, circadian rhythm, cytokine production) could reflect broader regulatory roles or secondary associations, but the core theme appears to be Fe-S cluster biogenesis tied to mitochondrial maintenance. Confidence in this label is Medium.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098779","count":2},{"id":"GO:0097428","count":1},{"id":"GO:0044571","count":1},{"id":"GO:0051220","count":1},{"id":"GO:1903026","count":1}]},{"hash":"2067541234008282416","title":"Plant growth and cell wall biosynthesis regulation","description":"The cluster appears to coordinate regulatory control of plant growth and cell-wall\u2013related biosynthesis, as evidenced by GO terms for regulation of chlorophyll biosynthesis, seed growth, lignin biosynthesis, and secondary cell wall biogenesis, plus growth-related regulation of root meristem and leaf senescence. A couple of terms reference telomere/RNA localization and heterochromatin formation, which indicate broader regulatory processes but do not obscure the central plant development/lignin-biosynthesis theme.","confidence":"Medium","size":10,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010380","count":2},{"id":"GO:0080113","count":2},{"id":"GO:1901430","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0010082","count":2}]},{"hash":"1065691925948558354","title":"RNA processing and splicing regulation","description":"The terms are dominated by mRNA splicing via the spliceosome (including alternative splicing and positive regulation of splicing) and other RNA processing terms (modification, stabilization). This suggests the cluster centers on RNA maturation and splicing control, with some related translation initiation associations, but the core theme is mRNA processing/splicing regulation.","confidence":"Medium","size":10,"edges":16,"triangles":3,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0045292","count":5},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0016556","count":3}]},{"hash":"2067688448032004488","title":"Cytoskeleton remodeling and secretion in development","description":"This cluster centers on actin dynamics (stress fiber and lamellipodium assembly), vesicle trafficking (exosomal secretion), and organelle dynamics (mitochondrial fission), with supporting developmental signals (liver development, oligodendrocyte differentiation, multicellular growth) and ubiquitination. The common theme is cytoskeletal remodeling coupled with secretion and organelle dynamics that underpin development and differentiation.","confidence":"Medium","size":10,"edges":10,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0000266","count":3},{"id":"GO:1990182","count":3},{"id":"GO:0051496","count":3},{"id":"GO:0035264","count":3}]},{"hash":"1017132454007294059","title":"Macrophage Activation and Arginine-NO Pathway","description":"The top GO terms show macrophage activation and nitric oxide production in inflammatory response, along with L-arginine catabolic process, indicating a macrophage inflammatory program centered on arginine metabolism to NO. Some transport terms likely reflect amino acid flux supporting this pathway, reinforcing a cohesive theme of macrophage-driven arginine metabolism and NO production.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042116","count":4},{"id":"GO:0006527","count":3},{"id":"GO:0010923","count":3},{"id":"GO:0002537","count":3},{"id":"GO:0070634","count":3}]},{"hash":"2247915140028958121","title":"Immune Activation and Leukocyte Migration","description":"Based on GO terms dominated by immune-related regulation and cell movement, such as positive regulation of alpha-beta T cell proliferation, IL-4 production, cytokine production, neutrophil clearance, and endothelial cell migration, with Rho signaling and microtubule localization supporting cytoskeletal dynamics, the cluster appears to reflect immune activation and leukocyte trafficking.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":9},{"id":"GO:0001502","count":9},{"id":"GO:0097350","count":9},{"id":"GO:0035372","count":9},{"id":"GO:0043068","count":9}]},{"hash":"1650169112509418453","title":"Glycan and membrane lipid biosynthesis","description":"This cluster centers on biosynthetic processes related to glycans and membrane lipids: GPI anchor biosynthesis, glycolipid and phospholipid biosynthesis, glycogen/glucose metabolism, and protein glycosylation in the ER. Even though some terms are obsolete, the recurring theme is the creation of glycan structures and lipid components essential for membrane and glycoprotein formation, with osmotic-stress related terms likely reflecting broader physiological responses. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006506","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0009247","count":2},{"id":"GO:0006006","count":2}]},{"hash":"1852885299228330878","title":"Proteostasis and Immune Signaling Regulators","description":"The proteins cluster around protein turnover (ubiquitination, proteasome assembly) and immune signaling modulation (NOD2 pathway, NF-kappaB sequestration, kinase activity regulation), with additional ties to RNA processing and growth. Environmental response terms (vitamin D, thermoception) suggest broader regulatory roles that intersect signaling and homeostasis. Overall, this group seems to collect regulators of protein fate and innate signaling rather than a single precise function.","confidence":"Medium","size":10,"edges":12,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0033280","count":2},{"id":"GO:0050955","count":2},{"id":"GO:0070682","count":2}]},{"hash":"799309455749971938","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":1},{"id":"GO:0016260","count":1},{"id":"GO:0009228","count":1},{"id":"GO:0070329","count":1},{"id":"GO:0006189","count":1}]},{"hash":"952116608281859866","title":"Broad substrate catabolism and detoxification","description":"The top GO terms point to a collection of catabolic processes (glucuronoside, stilbene, chlorophyll catabolism) and detoxification-related pathways (epoxygenase P450 pathway, cellular oxidant detoxification), with a few miscellaneous steps. This suggests a broad, non-specific set of metabolic breakdown and detox functions rather than a single well-defined pathway, hence a general label that covers diverse substrate catabolism and detoxification fits best.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0019391","count":4},{"id":"GO:0046272","count":4},{"id":"GO:0015996","count":4},{"id":"GO:0019373","count":4}]},{"hash":"1455714777439751083","title":"Cytochrome P450\u2013Mediated Steroid and Xenobiotic Metabolism","description":"The terms cluster around cytochrome P450\u2013driven metabolic processes: epoxygenase activity, oxidative demethylation, omega-oxidation, xenobiotic catabolism, and biosynthesis/turnover of steroids (cortisol, testosterone) as well as retinoic acid and vitamin D pathways. This points to a cohesive theme of P450-catalyzed metabolism rather than a single tissue-specific function.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019373","count":7},{"id":"GO:0030879","count":5},{"id":"GO:0071603","count":5},{"id":"GO:0034651","count":5},{"id":"GO:0070989","count":5}]},{"hash":"826335160474413282","title":"Steroid and lipid metabolism with xenobiotic processing","description":"The top GO terms cluster around steroid biosynthesis (cortisol, testosterone, brassinosteroid) and lipid-related oxidation (omega-oxidation), with related xenobiotic and vitamin-related metabolic processes (retinoic acid, vitamin D). While development terms like mammary gland development and endothelial adhesion appear, the dominant signal is metabolism of steroids, lipids, and foreign compounds, justifying a steroid/lipid metabolism label enriched for xenobiotic processing.","confidence":"Medium","size":10,"edges":24,"triangles":19,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":7},{"id":"GO:0071603","count":7},{"id":"GO:0034651","count":7},{"id":"GO:0070989","count":7},{"id":"GO:0042738","count":7}]},{"hash":"1462855983591037489","title":"Hormone-Regulated Plant Development Transcription","description":"The terms cluster around transcriptional regulation in plants and hormone signaling (ABA and auxin) governing meristem, embryogenesis, flower development, and related developmental processes, suggesting transcription factors coordinating hormone-responsive developmental programs.","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:0006355","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0048507","count":2},{"id":"GO:0010262","count":2}]},{"hash":"1327223422627900389","title":"Unknown","description":"The Top Terms are diverse and only appear once each, spanning xenobiotic transport, circadian regulation, muscle differentiation, germinal center formation, glucosinolate metabolism, renal sodium absorption, viral latency, nervous system development, and ubiquitin-dependent protein degradation. With no shared functional theme or network connectivity among the proteins (no edges/triangles), there is no coherent biological label that captures the cluster. Therefore, Unknown with no confidence is most appropriate.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:2000312","count":1},{"id":"GO:0042752","count":1},{"id":"GO:0035914","count":1},{"id":"GO:0002467","count":1}]},{"hash":"10439704268270797","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":2},{"id":"GO:2000344","count":2},{"id":"GO:0016042","count":2},{"id":"GO:0043085","count":1},{"id":"GO:0035041","count":1}]},{"hash":"985601300640675113","title":"Transport-focused stress-response cluster","description":"The top GO terms are dominated by diverse transmembrane transport activities (sialic acid, vitamin, urate, sodium-dependent organic cation, galactose), suggesting a group enriched for transporter functions. Additional terms point to metabolic regulation (nitrate assimilation, SCF-dependent proteasomal ubiquitin turnover) and stress responses (singlet oxygen, programmed cell death), which often accompany transport regulation. Overall, the strongest common thread is membrane transport, with supportive regulatory and stress-related signals, so the label reflects the primary function with secondary context.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0031571","count":1},{"id":"GO:0000304","count":1},{"id":"GO:0010343","count":1},{"id":"GO:0031146","count":1}]},{"hash":"567570713833740642","title":"T cell Activation and Antigen Presentation","description":"This cluster is driven by immune-related GO terms: T cell proliferation, T cell cytokine production, IL-3 production, and especially MHC class II biosynthetic process, indicating adaptive immune activation and antigen presentation as the core function. While several metal ion transport terms appear, they are less central to the cluster\u2019s main theme. Overall, the immune-related signals support labeling the cluster as T cell activation and antigen presentation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002309","count":2},{"id":"GO:0070627","count":2},{"id":"GO:0071421","count":2},{"id":"GO:0043091","count":2},{"id":"GO:0015690","count":2}]},{"hash":"1914314357040199483","title":"Ubiquinone, Sterol, and Chlorophyll Biosynthesis","description":"This cluster centers on biosynthetic pathways for cofactors and pigments (ubiquinone, sterols, chlorophyll) and hormone biosynthesis (juvenile hormone). While a few terms touch on RNA processing and post-translational modification, the strongest connections are biosynthetic processes, so a label referencing those pathways is appropriate.","confidence":"Medium","size":10,"edges":43,"triangles":105,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0000373","count":2},{"id":"GO:0018027","count":1},{"id":"GO:0014075","count":1}]},{"hash":"490101283806999035","title":"GABAergic Synaptic Transmission and Vesicle Maturation","description":"The dominant GO terms point to neuronal synaptic activity, including neurotransmitter secretion, synaptic vesicle maturation, and regulation of GABAergic transmission, indicating a core function in inhibitory synaptic signaling. Lipid biosynthesis and autophagy-related terms may reflect membrane dynamics, but the central theme remains synaptic vesicle handling and GABAergic signaling.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006646","count":1},{"id":"GO:0046580","count":1},{"id":"GO:1990927","count":1},{"id":"GO:0007269","count":1},{"id":"GO:0046470","count":1}]},{"hash":"692506009603181040","title":"Mitochondrial transport and apoptosis regulation","description":"The terms cluster around transport across mitochondrial membranes (ATP, Mn, heme, CoA, thiosulfate) and mitochondrial-associated processes (fission, apoptotic changes, necroptosis regulation), with metabolic signaling links (insulin/IGF). This points to a mitochondria-centric theme combining transport and cell-death regulation.","confidence":"High","size":10,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":8},{"id":"GO:0061179","count":8},{"id":"GO:1990544","count":8},{"id":"GO:0015886","count":8},{"id":"GO:0090152","count":8}]},{"hash":"635048821439268689","title":"Defense-associated transport and cell wall remodeling","description":"The Top Terms include lipid transport and xenobiotic transmembrane transport, plus defense response to fungus, and several cell wall\u2013related processes (cell wall organization, cellulose catabolic process, peptidoglycan biosynthesis). This points to membrane-embedded transporters that couple substrate movement with cell envelope remodeling and defense, rather than a single isolated pathway. The combination suggests a cohesive theme of transporters involved in defense-related cell wall dynamics.","confidence":"Medium","size":10,"edges":12,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006869","count":3},{"id":"GO:0050832","count":3},{"id":"GO:0010951","count":3},{"id":"GO:0006855","count":1},{"id":"GO:0008360","count":1}]},{"hash":"134068199709470127","title":"Triglyceride catabolism and lipid remodeling","description":"The strongest terms are triglyceride catabolic process, triglyceride mobilization, and triglyceride acyl-chain remodeling, along with phospholipid catabolic processes. This creates a cohesive theme of triglyceride breakdown and lipid remodeling, with endocannabinoid signaling fitting as lipid-based signaling. A few terms like endothelial cell migration are less central but can be associated with lipid-mediated regulation.","confidence":"High","size":10,"edges":21,"triangles":0,"max_degree":6,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0019433","count":8},{"id":"GO:0098869","count":4},{"id":"GO:2000124","count":4},{"id":"GO:2000480","count":4},{"id":"GO:0006642","count":4}]},{"hash":"556184037805378591","title":"Unknown","description":"The top GO terms span immune activation (T cell proliferation, neutrophil clearance), development (cartilage condensation), responses to fungus, cytoskeletal and signaling processes (Rho signaling, microtubule localization), and even neural/vascular functions (linear vestibulo-ocular reflex, endothelial migration). There is no single coherent function tying all terms together, and the cluster has no edges, indicating a heterogeneous set. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":7},{"id":"GO:0001502","count":7},{"id":"GO:0009620","count":7},{"id":"GO:0050929","count":7},{"id":"GO:0097350","count":7}]},{"hash":"496015798042618681","title":"Transmembrane Transporters","description":"The cluster is dominated by GO terms for transmembrane transport of ions and small molecules (potassium, sodium, galactose, sialic acid, urate, vitamins, organic cations, 4-hydroxyphenylacetate), indicating a group of membrane transport proteins with broad substrate specificity. The single behavioral ethanol term appears peripheral and does not define the core function. Edges are absent, consistent with functional similarity rather than protein\u2013protein interaction. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0048149","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0035461","count":2}]},{"hash":"1225435726013718186","title":"Protein acetylation and chromatin regulation","description":"This cluster is dominated by acetylation-related GO terms (N-terminal acetylation, peptidyl-lysine and histone acetylation, N-terminal protein acetylation variants) and chromatin-associated processes (subtelomeric heterochromatin formation, histone modification), suggesting a cohesive theme around protein acetylation and chromatin regulation, with a few metabolic or developmental terms as less central contributors.","confidence":"High","size":10,"edges":41,"triangles":94,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0017198","count":9},{"id":"GO:0006348","count":8},{"id":"GO:0032919","count":8},{"id":"GO:0043967","count":8},{"id":"GO:0018002","count":8}]},{"hash":"229906854736222398","title":"Plant Cell Wall Polysaccharide Biosynthesis and O-Glycosylation","description":"The top GO terms cluster around plant cell wall construction and modification, including secondary cell wall biogenesis, homogalacturonan and glucuronoxylan biosynthesis, mucilage production, and protein O-linked glycosylation (via GalNAc and mannose). This points to a cohesive theme of plant cell wall polysaccharide assembly coupled with protein glycosylation. Some terms like glycogen metabolism or skeletal muscle regeneration appear ancillary or cross-annotated, but they do not outweigh the dominant plant cell wall/glycosylation signal.","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0016266","count":4},{"id":"GO:0009834","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0010192","count":3}]},{"hash":"1718393618638523522","title":"Auxin signaling and shoot apical meristem maintenance","description":"This cluster is dominated by GO terms related to auxin response, auxin-activated signaling, and auxin polar transport, together with maintenance of shoot apical meristem identity, pointing to a core function in auxin-mediated plant development and meristem regulation. Some other terms appear peripheral or incidental.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046620","count":1},{"id":"GO:0009734","count":1},{"id":"GO:0009926","count":1},{"id":"GO:0009733","count":1},{"id":"GO:0006888","count":1}]},{"hash":"784862554079320614","title":"Unknown","description":"The top GO terms are highly diverse (neural crest development, exocytosis regulation, cell shape, nuclear import, sporulation membrane formation, membrane tubulation, heart rate regulation, stress responses, and more), with no unifying biological process evident among the cluster members. Therefore there isn\u2019t a single coherent function to name this group; label as Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014032","count":2},{"id":"GO:0051591","count":2},{"id":"GO:0045921","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0033234","count":1}]},{"hash":"661772395681345243","title":"Fatty acid biosynthesis and vesicle trafficking","description":"The cluster is enriched for fatty acid and sphingolipid biosynthesis and FA elongation (MUFA/PUFA), plus vesicle transport steps (late endosome to vacuole sorting and post-Golgi transport), suggesting roles in membrane lipid production and trafficking. Some development/behavior terms appear but are likely context-specific.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042761","count":1},{"id":"GO:0030148","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0048794","count":1},{"id":"GO:0032511","count":1}]},{"hash":"444466270354297073","title":"Unknown","description":"The top GO terms span meiotic cell cycle, plant meristem transition, neuronal signaling, histone phosphorylation, viral material transport, hydroxyurea response, postsynaptic translation, viral RNA perturbation, miRNA silencing, and filopodium assembly\u2014little to no cohesive function ties these together. With no shared pathway and an edge-free cluster, this set likely reflects heterogeneous signals rather than a single functional module.  ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051321","count":2},{"id":"GO:0010228","count":1},{"id":"GO:0098908","count":1},{"id":"GO:0033129","count":1},{"id":"GO:1901254","count":1}]},{"hash":"453702398758131853","title":"Immune Activation and Cytokine Signaling","description":"Based on the top GO terms, the cluster centers on immune system processes: positive regulation of T cell proliferation, IL-4 production, and cytokine production in immune response, along with neutrophil clearance and cytoskeletal signaling (Rho) that facilitate immune cell movement. Although a couple terms relate to development or microtubule localization, the dominant theme is activation and signaling within the immune system.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":10},{"id":"GO:0001502","count":10},{"id":"GO:0097350","count":10},{"id":"GO:0035372","count":10},{"id":"GO:0043068","count":10}]},{"hash":"720080859516078540","title":"Vesicle trafficking and Golgi transport","description":"The terms point to endomembrane transport\u2014endocytosis, vesicle budding, ER\u2192Golgi and Golgi\u2192vacuole trafficking, retrograde transport to the Golgi, and Golgi localization\u2014indicating proteins involved in vesicle trafficking within the secretory pathway. A few terms denote organismal phenotypes (pigmentation, adult locomotion) and are ancillary, but the core signal is vesicle transport.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016185","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0009615","count":1},{"id":"GO:0006896","count":1},{"id":"GO:0006623","count":1}]},{"hash":"776037539411121443","title":"Growth, Energy Metabolism, and Stress Response","description":"This cluster's top GO terms blend growth-related processes (cell division, DNA replication, rRNA maturation) with energy production (ATP metabolism, regulation of aerobic respiration) and multiple stress-related pathways (antibiotic response, cadmium-associated SCF disassembly, ER-associated misfolded protein catabolic). The convergence of proliferation-associated activities with metabolic and proteostatic stress responses suggests a unit focused on coordinating growth with energy use and stress management, hence the label.","confidence":"Medium","size":9,"edges":24,"triangles":28,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0046677","count":2},{"id":"GO:1990171","count":2}]},{"hash":"1480790398210323954","title":"Cytokinin and Isoprenoid Biosynthesis","description":"The top GO terms are dominated by cytokinin biosynthetic process and positive regulation of IPP biosynthesis via the mevalonate pathway, which together point to a plant isoprenoid/metabolic module linked to cytokinin production. Other terms present (e.g., calcium signaling, NFAT-related signaling, cell adhesion, DNA replication) seem less cohesive with this core theme, likely reflecting background annotations. Confidence: Medium","confidence":"","size":9,"edges":22,"triangles":16,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0061587","count":3},{"id":"GO:0009691","count":3},{"id":"GO:2000002","count":2},{"id":"GO:1900486","count":2},{"id":"GO:1900490","count":2}]},{"hash":"555522645107959172","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0000461","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0046718","count":2}]},{"hash":"896696365168405217","title":"Nucleobase Transport Across Plasma Membrane","description":"The top GO terms are dominated by transport of various nucleobases and related molecules (hypoxanthine, uracil, xanthine, urate, adenine, guanine) across the plasma membrane, suggesting a cohesive function as nucleobase importers or transporters. Although there are a couple of outlier terms (multicellular organism development and snoRNP assembly), the strongest signal across the cluster is nucleobase transport, which provides a clear and concise unifying theme. The absence of network edges doesn\u2019t negate this functional link, since annotations converge on a shared transport role. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:1903825","count":2},{"id":"GO:0035344","count":2},{"id":"GO:0098721","count":2},{"id":"GO:0042906","count":2}]},{"hash":"1386459577246621961","title":"Plant oxidative stress detoxification and metabolite catabolism","description":"This cluster is enriched for oxidative stress-related terms (cellular oxidant detoxification, response to oxidative stress, hydrogen peroxide catabolic process) and includes several plant-specific pigment/metabolite catabolism terms (lignin, stilbene, chlorophyll, glucuronoside). The combined theme suggests proteins involved in detoxifying reactive species while degrading plant metabolites, rather than a single narrow pathway.","confidence":"Medium","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0033617","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0046274","count":1}]},{"hash":"2155216224141241017","title":"ER stress response and protein quality control","description":"This cluster\u2019s top GO terms concentrate on ER stress\u2013related proteostasis: translation initiation regulation under ER stress, chaperone/cofactor\u2013dependent refolding, and misfolded protein transport, indicating a common theme of protein quality control in the secretory pathway. Some development-related terms may be incidental to the set.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":6},{"id":"GO:0051259","count":6},{"id":"GO:0070843","count":6},{"id":"GO:0070389","count":6},{"id":"GO:1900035","count":6}]},{"hash":"1177785239644754188","title":"GA-regulated transcription in plant development","description":"The terms show transcriptional regulation (DNA-templated) combined with plant developmental processes such as seed germination/dormancy, leaf development, root hair growth, and bundle sheath fate, all linked to gibberellin signaling. This points to a cluster of plant transcriptional regulators whose activity and target genes are modulated by GA to drive growth and development. Despite no edges, the GO pattern is coherent around transcription control and GA-responsive development.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0010187","count":1},{"id":"GO:0048366","count":1},{"id":"GO:2000033","count":1}]},{"hash":"553182489163700909","title":"ER Stress and Protein Folding Quality Control","description":"The GO terms emphasize chaperone-assisted refolding, misfolded protein transport, and ER-stress\u2013linked translation, indicating a cohesive role in protein quality control and folding under stress, with a few development-related terms that may be incidental.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":5},{"id":"GO:0051259","count":5},{"id":"GO:0070843","count":5},{"id":"GO:0070389","count":5},{"id":"GO:1900035","count":5}]},{"hash":"2165001534153127531","title":"Ribosome Biogenesis and Translation","description":"Dominant signals are translation and ribosome biogenesis (translation, preribosome assembly, positive regulation of ribosome biogenesis), suggesting the cluster centers on ribosome-related processes. A few DNA-related terms (transcription termination, DNA replication) are present but do not define the main theme.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:1902626","count":2},{"id":"GO:0090070","count":2},{"id":"GO:0006353","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1471607739585884646","title":"Developmental Transcription Regulators","description":"The cluster is dominated by GO terms for DNA-templated transcription and its regulation, with several entries for multicellular organism development, suggesting transcription factors or regulators governing development and cell fate. While there are additional terms related to signaling, immune processes, and apoptosis, the core signal centers on transcriptional control during development, making this label representative of the cluster\u2019s function.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0046677","count":2}]},{"hash":"859584805867029179","title":"Clathrin-mediated endocytosis and vesicle trafficking","description":"The top GO terms are dominated by clathrin-dependent endocytosis, clathrin coat assembly, and synaptic vesicle maturation, with related regulation of endocytosis and receptor signaling (EGFR). This points to a functional theme centered on vesicle formation, internalization, and trafficking, rather than transcriptional control or apoptosis. Thus, the label captures the core function of these proteins, despite a few ancillary terms. ","confidence":"High","size":9,"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:0006915","count":2},{"id":"GO:0098711","count":2},{"id":"GO:2000369","count":2}]},{"hash":"1053164070602317909","title":"ER protein quality control and ER stress response","description":"The dominant GO terms point to endoplasmic reticulum\u2013associated degradation, misfolded protein handling, chaperone-assisted refolding, and stress-induced translation, consistent with ER quality control and the unfolded protein response. Some developmental terms appear incidental.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0000398","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0051259","count":3},{"id":"GO:0070843","count":3}]},{"hash":"914728553509496340","title":"mRNA processing and translation initiation","description":"This cluster is dominated by GO terms related to RNA metabolism and processing (mRNA export, modification, stabilization, splicing, polyadenylation) as well as initiation of translation (eIF4F complex assembly and IRES-dependent initiation). Together they point to a shared role in mRNA maturation and the start of protein synthesis, with a cohesive theme around how RNAs are prepared and translated. Some terms are obsolete, but the core signal remains RNA processing and translation initiation.","confidence":"High","size":9,"edges":16,"triangles":13,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006406","count":5},{"id":"GO:0016556","count":4},{"id":"GO:0048255","count":4},{"id":"GO:0075522","count":4},{"id":"GO:1905663","count":4}]},{"hash":"892065240512875248","title":"Ribosome biogenesis and translation","description":"The protein set is enriched for translation- and ribosome-related terms, including translation, cytoplasmic translation, ribosome biogenesis, ribosomal subunit biogenesis/export, and tRNA modification, pointing to a core function in ribosome assembly and protein synthesis; peripheral terms like iron transport and salt-stress response are less central to the cluster\u2019s primary role.","confidence":"High","size":9,"edges":11,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0015684","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0090529","count":2}]},{"hash":"1622549039169196128","title":"Plant Hormone Signaling and Defense Responses","description":"The set centers on plant-specific processes: gibberellin and ethylene (ACC) signaling, salicylic acid\u2013mediated responses, antifungal innate immunity, and developmental events like atrichoblast differentiation and anthocyanin biosynthesis. Together these terms point to a theme of growth regulation coupled with defense responses in plants; one term (neuronal signaling) appears as an outlier, likely misannotation. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":3},{"id":"GO:0009718","count":3},{"id":"GO:0016575","count":2},{"id":"GO:0080169","count":2},{"id":"GO:0009961","count":2}]},{"hash":"422619683025768933","title":"Unknown","description":"The GO terms include pollination, aluminum cation transport, transcriptional regulation, responses to muscle activity and ethanol, calcium signaling modulation, development, and ER-stress\u2013related apoptosis. This diverse mix lacks a single, coherent function linking the proteins, so a clear, representative label cannot be assigned.","confidence":"","size":9,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009856","count":2},{"id":"GO:0015690","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035994","count":2}]},{"hash":"2157333141140276560","title":"Mitotic cell cycle and growth signaling","description":"The dominant terms point to mitosis and cell division (GO:0000278, GO:0051301) and TORC1 signaling (GO:0038202), indicating a cluster tied to growth control and progression through the cell cycle. Additional regulation of GTPase activity (GO:0043547) supports a broader regulatory network, while mRNA splicing and transport terms (GO:0000398, GO:0051028) suggest concomitant gene expression coordination during division. Overall, the core theme appears to be mitotic cell cycle regulation with growth signaling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0038202","count":2}]},{"hash":"738396347111802448","title":"Signaling pathways regulating cell fate and growth","description":"These proteins appear to participate in several key signaling networks (TGF-beta receptor signaling regulation, canonical Wnt signaling, Hippo signaling) with downstream effects on apoptosis, keratinocyte differentiation, and cell cycle. The common thread is signaling-driven control of cell fate decisions and proliferation. ","confidence":"Medium","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0071353","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0090263","count":2}]},{"hash":"1509973379077248999","title":"Plant growth and cell wall biosynthesis regulation","description":"The top GO terms cluster around plant development and cell wall processes: seed and root meristem growth, leaf senescence, chlorophyll biosynthesis, and notably lignin and secondary cell wall biogenesis. This suggests a functional group of regulators modulating plant growth and cell wall construction. One viral process term appears incidental and not foundational to the cluster\u2019s theme. Overall, the proteins seem linked to growth regulation and lignin/secondary cell wall biosynthesis in plants.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0010380","count":2},{"id":"GO:0080113","count":2},{"id":"GO:1901430","count":2},{"id":"GO:1901347","count":2}]},{"hash":"1293629664679805565","title":"Ubiquitin-Dependent Proteolysis and Inflammatory Signaling","description":"Top GO terms cluster around ubiquitin-mediated protein degradation (K48- and K63-linked ubiquitination, ubiquitin-dependent proteolysis) and inflammatory signaling pathways (TNF signaling, NF-\u03baB activation, JNK cascade), with additional hints of histone modification regulation and receptor turnover. This suggests a cohesive theme of proteostasis intersecting with inflammatory signaling and chromatin regulation. Confidence in this label is High.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":6},{"id":"GO:2000620","count":6},{"id":"GO:0038018","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0033209","count":6}]},{"hash":"2228360171458848557","title":"Epigenetic regulation of immunoglobulin diversification","description":"The GO terms point to histone modifications and chromatin state (H3-K36/K4 methylation, acetylation, heterochromatin formation) together with B cell\u2013specific antibody diversification processes (somatic hypermutation and isotype switching to IgA), indicating a theme of epigenetic control of immunoglobulin gene diversification during B cell maturation.","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010452","count":1},{"id":"GO:0051096","count":1},{"id":"GO:0016446","count":1},{"id":"GO:0048298","count":1},{"id":"GO:0051571","count":1}]},{"hash":"1794085909347766993","title":"Xylem Development and Secondary Cell Wall Biogenesis","description":"This cluster is dominated by GO terms tied to vascular tissue formation and cell wall biosynthesis, including protoxylem development, xylem vessel differentiation, and regulation of secondary cell wall biogenesis, along with transcriptional regulation of DNA-templated processes. The combination suggests a cohesive role in plant vascular development and the transcriptional control underlying it, with some broader developmental terms (callus formation, leaf senescence) reflecting general growth regulation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":3},{"id":"GO:0006355","count":3},{"id":"GO:1990110","count":2},{"id":"GO:1900057","count":2},{"id":"GO:0090059","count":2}]},{"hash":"80909737387734444","title":"Oocyte meiosis and spindle assembly regulators","description":"Most enriched terms point to meiosis/cell-cycle control and spindle assembly in oocytes (SCF\u2013ubiquitin\u2013proteasome\u2013dependent protein catabolic process, oocyte maturation, microtubule polymerization, spindle assembly in female meiosis I), suggesting these proteins function together in meiotic progression and proteolytic regulation; a few neural development terms are present but do not dominate the cluster.","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0046785","count":3},{"id":"GO:0007057","count":3},{"id":"GO:0021678","count":3},{"id":"GO:0006516","count":3}]},{"hash":"255282052178667362","title":"Unknown","description":"The top GO terms include vascular development regulatory processes (negative regulation of VEGF signaling, vasculogenesis, endothelial differentiation), but many other terms indicate disparate metabolic and transport activities, making a single coherent function unlikely.","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1900747","count":4},{"id":"GO:0006124","count":4},{"id":"GO:0007595","count":4},{"id":"GO:2001213","count":4},{"id":"GO:0009399","count":4}]},{"hash":"1506416034737378982","title":"RNA processing and translation initiation","description":"The top GO terms cluster around mRNA maturation and regulation (polyadenylation, spliceosome-mediated splicing, mRNA modification and stabilization) and the assembly of translation initiation machinery (eIF4F complex) as well as IRES-dependent initiation, indicating the proteins are linked to RNA processing and initiation of protein synthesis.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":8},{"id":"GO:0045292","count":8},{"id":"GO:0010610","count":8},{"id":"GO:0016556","count":7},{"id":"GO:0048255","count":7}]},{"hash":"293981382246592406","title":"Folate-one-carbon metabolism and thymidylate biosynthesis","description":"The top GO terms cluster around folate metabolism and one-carbon chemistry (tetrahydrofolate interconversion, folic acid metabolism) and serine biosynthesis/catabolism, feeding into dTMP biosynthesis. This suggests proteins function mainly in supplying one-carbon units for nucleotide synthesis, with some secondary signals related to translation regulation and interferon response. Overall, the core theme is folate/one-carbon metabolism linked to thymidylate production.","confidence":"High","size":9,"edges":23,"triangles":31,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0017148","count":2},{"id":"GO:0006412","count":2},{"id":"GO:1904482","count":1},{"id":"GO:0051289","count":1},{"id":"GO:0006564","count":1}]},{"hash":"2249237547747059147","title":"Ubiquitin-regulated signaling and genome maintenance","description":"The top GO terms point to ubiquitin-dependent regulation across diverse processes: N-end rule\u2013mediated protein turnover, histone ubiquitination, and transcription factor catabolism, alongside immune signaling pathways that rely on ubiquitination (TRIF-dependent TLR signaling and C-type lectin receptor signaling). DNA repair terms (error-free postreplication repair and meiotic DSB formation) suggest involvement of controlled protein turnover in genome maintenance. A few terms (peroxisome matrix import, retinal apoptosis) are less directly connected but can relate to ubiquitin-mediated regulation of protein localization and cell fate. Overall, the cluster centers on ubiquitin-driven regulation of signaling and genome integrity. ","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0035666","count":9},{"id":"GO:0042275","count":9},{"id":"GO:0071596","count":9},{"id":"GO:0010620","count":9},{"id":"GO:0033182","count":9}]},{"hash":"1388314655944949074","title":"Chromatin Organization and Nucleosome Assembly","description":"The cluster is dominated by chromatin-focused processes: nucleosome assembly, heterochromatin organization, and regulation of nucleus size, with additional terms about protein localization to chromatin and histone modifications. These consistent GO terms (e.g., nucleosome assembly, heterochromatin organization, chromatin localization) suggest a coherent theme around chromatin packaging and regulation, with only a few outlier terms such as ER lumen protein retention.","confidence":"High","size":9,"edges":12,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097298","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0016584","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0071169","count":2}]},{"hash":"497038953437564474","title":"Diverse solute transmembrane transporters","description":"Most top GO terms describe transmembrane transport of various solutes (vitamin, xenobiotic, methionine, cobalt ion, glycine betaine, taurine). This suggests a cluster of membrane transporter proteins with broad substrate specificity. A few terms (very long-chain fatty acid catabolic process; response to mercury ion; stem cell proliferation; bacteriocin immunity) are less directly connected and may reflect annotation noise or multifunctionality, but the transport theme dominates.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0015821","count":3},{"id":"GO:0006824","count":3},{"id":"GO:0031460","count":3}]},{"hash":"1881867184921337756","title":"Lymphocyte Activation and Cytokine Signaling","description":"This cluster is dominated by GO terms related to immune signaling and lymphocyte activation, including interleukin-12- and interleukin-1-mediated pathways and T cell/B cell differentiation, suggesting a core theme of immune activation. The translation-related terms are at low counts and likely incidental, not defining the cluster\u2019s main function.","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0006426","count":1},{"id":"GO:0006420","count":1},{"id":"GO:0035722","count":1}]},{"hash":"1690783609146085232","title":"Autophagy and vesicle trafficking regulation","description":"The top GO terms center on autophagy (negative regulation of autophagosome assembly and apoptotic processes) together with intracellular transport and sorting (Golgi retention, endosome to endosome transport, ubiquitin-dependent sorting, and exosomal secretion). This points to a theme of stress-responsive autophagy coupled with regulation of vesicle trafficking and secretion, rather than a single enzymatic function. ","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902902","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0045053","count":4},{"id":"GO:0071454","count":4},{"id":"GO:0043328","count":4}]},{"hash":"874270625551585558","title":"N-terminal methyltransferases in diverse biosynthesis","description":"The top GO terms are dominated by N-terminal peptidyl methylation events (alanine, glycine, serine, trimethylation/dimethylation) and general methylation, with additional biosynthetic processes across various pathways (lipopolysaccharide, daunorubicin, melatonin, lignin, flavonol). This pattern points to a set of methyltransferases acting on diverse biosynthetic routes, giving a cohesive, specific label around N-terminal methylation within biosynthesis.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:1901771","count":2},{"id":"GO:0018012","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0035572","count":2}]},{"hash":"1643073809789166138","title":"LPS core and O-antigen sugar biosynthesis","description":"The top GO terms are dominated by lipopolysaccharide and related sugar biosynthetic processes (O antigen biosynthesis, LPS biosynthetic process, ADP-L-glycero-beta-D-manno-heptose biosynthesis), suggesting the proteins in this cluster participate in bacterial outer membrane component formation. Additional terms for various sugar- and vitamin-related biosynthesis (thiamine, inositol phosphate, galactose metabolism) support a broader theme of carbohydrate metabolism linked to envelope component preparation. Overall, the cluster appears to reflect LPS and associated sugar biosynthesis pathways.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010264","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009243","count":2}]},{"hash":"1600643072582445506","title":"Plant cell wall remodeling and growth","description":"Dominant GO terms point to plant-specific processes: mucilage pectin biosynthesis, cell wall modification, and pectin catabolic process, along with pollen tube growth and lateral root development. These collectively suggest a cluster centered on plant cell wall synthesis/remodeling and growth/differentiation in reproductive and root tissues. A few terms about DNA replication and neural precursor proliferation appear as noisy outliers, but the core theme is plant cell wall\u2013associated growth.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048358","count":2},{"id":"GO:0042545","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0043086","count":1},{"id":"GO:0009860","count":1}]},{"hash":"569695833731083448","title":"Golgi-ER vesicle trafficking and SNARE exocytosis","description":"The cluster shows strong representation of ER-to-Golgi and intra-Golgi vesicle transport, Golgi ribbon formation, and SNARE complex assembly, with components related to exocytic delivery of receptors at synapses. This points to a cohesive role in Golgi- and SNARE-mediated vesicle trafficking and exocytosis, including synaptic receptor delivery and plasticity.","confidence":"High","size":9,"edges":13,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":6},{"id":"GO:0090161","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0006891","count":6},{"id":"GO:0035493","count":5}]},{"hash":"784572220729525605","title":"Gene Expression Regulation and Stress Response","description":"This cluster is enriched for GO terms related to DNA-templated transcription and its regulation, as well as cytoplasmic translational initiation, and various cellular stress responses (amino acid starvation, nitric oxide, ethylene). Together these point to proteins that modulate gene expression at multiple levels and adjust cellular programs under stress, rather than a single specific pathway. A term like oligodendrocyte development is a weaker, possibly off-target annotation, but the dominant theme remains transcriptional and translational control with stress responsiveness.","confidence":"Medium","size":9,"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:0019284","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0043547","count":1}]},{"hash":"1800074015121638004","title":"Bone remodeling and lung branching morphogenesis","description":"The dominant GO terms point to skeletal remodeling (bone resorption, intramembranous ossification) and branching morphogenesis in the lung (epithelial tube branching, lung morphogenesis), supported by basement membrane disassembly and related remodeling processes; regulatory signals like thyroid hormone response and immune/peptide catabolism terms suggest ancillary control layers. Overall, the cluster seems centered on tissue remodeling during bone formation and lung branching morphogenesis.","confidence":"Medium","size":9,"edges":30,"triangles":51,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":6},{"id":"GO:0010813","count":6},{"id":"GO:0010815","count":6},{"id":"GO:0045453","count":6},{"id":"GO:0001913","count":6}]},{"hash":"682321437461818841","title":"Bacterial LPS and O-antigen Biosynthesis","description":"The top GO terms point mainly to lipopolysaccharide biosynthesis, including core region and O-antigen, plus related exopolysaccharide (colanic acid) synthesis. Sugar-nucleotide biosynthesis (GDP-mannose, dTDP-rhamnose) supports glycan assembly, reinforcing a cohesive theme of Gram-negative LPS/glycan production; a few outliers (plant metabolite biosynthesis) are likely annotation noise. Overall, the cluster aligns strongly with bacterial LPS and related polysaccharide biosynthesis.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0030435","count":5},{"id":"GO:0009244","count":4},{"id":"GO:0019673","count":4},{"id":"GO:0019305","count":4}]},{"hash":"1580714956045369963","title":"Proton and Sodium Membrane Transport","description":"The top GO terms are strongly dominated by proton transmembrane transport and sodium ion transmembrane transport, pointing to proteins involved in moving ions across membranes. While a few other terms (e.g., ubiquitination, spindle checkpoint signaling) appear, they are much less represented and do not define the cluster. Thus, the core theme is membrane ion transport, especially for protons and sodium.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015992","count":5},{"id":"GO:0035725","count":5},{"id":"GO:1901253","count":1},{"id":"GO:0044810","count":1},{"id":"GO:1902364","count":1}]},{"hash":"915511861927123271","title":"Plant flavonoid and lignin biosynthesis","description":"The top GO terms cluster around biosynthesis of flavonoids and related pigment compounds (anthocyanin-containing, cyanidin 3-O-glucoside biosynthesis) and lignin metabolism, with supporting terms like flavonoid glucuronidation and related phenylpropanoid processes. This points to a functional group of proteins involved in plant secondary metabolism rather than a single protein complex, despite the disconnected network. The presence of some plant-specific oxidation/modification terms strengthens this interpretation, while a few outliers may reflect broad annotations.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":4},{"id":"GO:0009808","count":4},{"id":"GO:0009718","count":4},{"id":"GO:0006711","count":4},{"id":"GO:0052697","count":4}]},{"hash":"713065567899802974","title":"Plant Growth and Cell Wall Regulation","description":"The GO terms cluster around plant development and growth control, including cytokinin signaling, regulation of secondary cell wall biogenesis and lignin biosynthesis, chlorophyll biosynthesis regulation, seed and root meristem growth, and leaf senescence\u2014all pointing to regulatory roles in plant growth and cell-wall processes rather than a single enzymatic function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009736","count":4},{"id":"GO:1901348","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0010380","count":3},{"id":"GO:0080113","count":3}]},{"hash":"1302494137373245450","title":"Neural development and glial apoptosis","description":"Most terms point to nervous system development (forebrain, nervous system development) and glial cell apoptotic process, suggesting the cluster centers on neural differentiation and programmed cell death in neural/glial contexts. Other terms (TGF-beta signaling, metabolism, and tissue remodeling) are less dominant, likely reflecting broader regulatory roles but do not override the neural-development signal. ","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":5,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":7},{"id":"GO:0010659","count":7},{"id":"GO:0035006","count":7},{"id":"GO:0033353","count":7},{"id":"GO:0071560","count":7}]},{"hash":"1074503597351558776","title":"Neuronal differentiation and axon guidance","description":"Most of the top GO terms point to neural development and differentiation (GABAergic interneuron differentiation, Purkinje cell\u2013granule precursor signaling, spinal cord neuron differentiation) and axon extension, indicating the proteins in this cluster are tied to neural development and axon guidance, with some ancillary developmental processes.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042663","count":3},{"id":"GO:0021892","count":3},{"id":"GO:0030516","count":3},{"id":"GO:0014813","count":3},{"id":"GO:0060928","count":3}]},{"hash":"288305549285753490","title":"Steroid and Lipid Metabolism with Vascular Development","description":"The cluster\u2019s top GO terms center on steroid biosynthesis (cortisol, testosterone), lipid-related processes (omega-oxidation, retinoic acid catabolic, fatty acid oxidation) and xenobiotic metabolism, with a few vascular development terms (retina vasculature, endothelial adhesion). This combination points to a cohesive theme around steroid/lipid and xenobiotic metabolism, with a supporting vascular development context.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061298","count":5},{"id":"GO:0030879","count":3},{"id":"GO:0071603","count":3},{"id":"GO:0034651","count":3},{"id":"GO:0070989","count":3}]},{"hash":"980760245331665982","title":"Protein Processing and Secretory Pathway Regulation","description":"This cluster centers on phosphorylation-related regulation (protein kinase activity and protein phosphorylation) and components of the secretory pathway, including N-glycan processing in the ER, ER-associated degradation, and exocytosis/membrane remodeling. The combination suggests a cohesive theme around how proteins are modified and trafficked through the ER-to-secretory pathway, despite some sporadic terms that may reflect broader regulatory roles or annotation noise.","confidence":"Medium","size":9,"edges":8,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0006468","count":3},{"id":"GO:0006491","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0045921","count":2}]},{"hash":"391063905508671038","title":"COPI-Dependent ER-to-Golgi Trafficking and Secretion","description":"The top GO terms cluster around ER-to-Golgi transport, COPI vesicle budding/coating, Golgi ribbon formation, and regulation of protein exit from the ER, as well as secretion processes (e.g., Wnt). This points to a cohesive role in COPI-mediated trafficking between the ER and Golgi and subsequent protein secretion, with a few development-related terms likely representing broader context. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":2},{"id":"GO:1902003","count":2},{"id":"GO:0001893","count":2},{"id":"GO:0006621","count":2},{"id":"GO:0070863","count":2}]},{"hash":"804272151342821630","title":"Mitotic cell cycle control","description":"The top GO terms strongly emphasize mitosis and G2/M transition regulation, including G2/M transition of the mitotic cell cycle and mitotic G1 cell size control checkpoint signaling, pointing to a cohesive theme of cell cycle control and progression. A few terms pertain to differentiation, viral transcription, or DNA integration, which are less central to the core theme and may reflect broader or multifunctional roles of the proteins. Overall, the cluster appears best described by mitotic cell cycle regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0033598","count":1},{"id":"GO:0030857","count":1},{"id":"GO:0010389","count":1},{"id":"GO:0000086","count":1}]},{"hash":"313472804998829075","title":"Oocyte meiosis and spindle assembly proteins","description":"The top GO terms emphasize oocyte maturation, spindle assembly in female meiosis I, and SCF-ubiquitin\u2013proteasome\u2013dependent protein catabolism, along with microtubule polymerization. Together they point to proteins that coordinate meiosis progression and spindle dynamics in oocytes, with ubiquitin-mediated degradation regulating cell-cycle timing. While a few broader developmental terms appear, the core signal is meiosis/spindle-related.","confidence":"High","size":9,"edges":32,"triangles":58,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0001556","count":6},{"id":"GO:0046785","count":6},{"id":"GO:0006516","count":6},{"id":"GO:0007057","count":6}]},{"hash":"171316421851638450","title":"Flowering timing and floral development","description":"The GO terms show a clear signal for plant reproductive development: inflorescence development, short-day photoperiodism, and regulation of transition from vegetative to reproductive phase, plus flower development and multicellular organism development. A few terms (e.g., sperm capacitation, acetylcholine metabolism, mitochondrial protein import) seem unrelated and may reflect annotation noise, but the dominant theme is flowering timing and floral development.","confidence":"Medium","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0048240","count":1},{"id":"GO:0010229","count":1},{"id":"GO:0048575","count":1},{"id":"GO:0042755","count":1}]},{"hash":"583420876716594619","title":"Ubiquitin-mediated proteolysis and spindle checkpoint","description":"Based on the top GO terms, the cluster is dominated by ubiquitin-related processes: ubiquitin-dependent protein catabolic process, K48- and K6-linked ubiquitination, and autoubiquitination, pointing to proteasomal degradation and ubiquitin signaling. Additional terms reference histone catabolic processes and cell cycle control via the mitotic spindle assembly checkpoint, suggesting co-involvement in chromatin regulation and chromosome segregation. The convergence of ubiquitin-dependent catabolism with spindle checkpoint signaling supports a cohesive label centered on ubiquitin-mediated protein turnover and cell-cycle regulation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0070936","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0085020","count":4}]},{"hash":"1711437433263914088","title":"Regulated Xylem Differentiation and Vascular Development","description":"Top GO terms are dominated by transcriptional regulation (regulation of DNA-templated transcription, DNA-templated transcription) and vascular development signals (protoxylem development, xylem vessel differentiation, secondary cell wall biogenesis). While some terms touch on callus formation and senescence, the strongest and most recurrent theme is controlled xylem differentiation and vascular tissue formation in plants, suggesting the proteins act as transcriptional regulators of vascular development. High","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:1990110","count":2},{"id":"GO:1900057","count":2},{"id":"GO:0090059","count":2},{"id":"GO:1904250","count":2}]},{"hash":"884394145275492402","title":"Neural development and synaptic function","description":"The cluster is dominated by neural-related terms: synapse organization, learning, neuroblast differentiation, and regulation of synaptic transmission, all pointing to neuronal development and synaptic activity. Supporting terms like cholesterol biosynthesis align with neuronal membrane biology, while broad stress-related responses (glucocorticoid, xenobiotic, and folic acid responses) suggest adaptive signaling in neural contexts. A few outliers (cellulose catabolic process, obsolete cocaine metabolic process) likely reflect annotation noise rather than core biology.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050808","count":5},{"id":"GO:0030245","count":5},{"id":"GO:0007612","count":5},{"id":"GO:0032223","count":5},{"id":"GO:0050783","count":5}]},{"hash":"975517291380229287","title":"Developmental signaling and morphogenesis","description":"Top GO terms include imaginal disc-derived leg morphogenesis, BMP secretion, Rac signaling regulation, dendritic spine modification, and ER unfolded protein response regulation. Together they point to a cluster involved in signaling pathways that drive tissue morphogenesis and patterning, with effects on cytoskeletal dynamics, neuron structure, and morphogen secretion. Some terms are obsolete or represent broad cellular processes, but the dominant theme remains developmental signaling linked to morphogenesis.","confidence":"Medium","size":9,"edges":11,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046856","count":1},{"id":"GO:1904425","count":1},{"id":"GO:0007480","count":1},{"id":"GO:0035021","count":1},{"id":"GO:0008272","count":1}]},{"hash":"1270074440407114363","title":"Phenylpropanoid and Flavonoid Biosynthesis","description":"Most terms point to biosynthesis and modification of phenylpropanoid-derived compounds: lignin, anthocyanins, cyanidin glucoside, and flavonoid glucuronidation. A few terms (paranode axon localization, estrogen catabolism, antibiotic metabolism) appear unrelated or cross-annotated, likely reflecting background noise or broader xenobiotic metabolism, but the dominant signal supports a phenylpropanoid/flavonoid theme.","confidence":"Medium","size":9,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":7},{"id":"GO:0009808","count":7},{"id":"GO:0009718","count":7},{"id":"GO:0006711","count":7},{"id":"GO:0052697","count":7}]},{"hash":"1311921360469588042","title":"RNA modification and methylation","description":"This cluster has several RNA-centric GO terms like tRNA wobble uridine modification, tRNA methylation, RNA guanine-N7 methylation, rRNA modification, and 7-methylguanosine mRNA capping, plus related protein methylation (peptidyl-arginine methylation). Although a few terms (antibiotic biosynthetic process, nodulation) seem less related, the strongest shared theme is RNA modification and methylation pathways, implying a cohesive functional focus despite the lack of detected interactions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0046690","count":5},{"id":"GO:0002098","count":5},{"id":"GO:0019919","count":5},{"id":"GO:0009877","count":5}]},{"hash":"826879794627490618","title":"Plant organellar RNA editing and processing","description":"The top GO terms center on RNA modification and editing in mitochondria and chloroplasts, including mitochondrial mRNA processing, cytidine-to-uridine editing, chloroplast RNA modification, and plastid transcription. This points to a cluster of proteins involved in organellar RNA processing/editing in plants, with related signals to plastid-nucleus communication and seed-related development.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":3},{"id":"GO:0009451","count":3},{"id":"GO:0016554","count":3},{"id":"GO:0080156","count":3},{"id":"GO:1905639","count":3}]},{"hash":"1182495369412891858","title":"Plant growth and biosynthesis regulation","description":"This cluster\u2019s top GO terms center on regulatory processes in plants (regulation of chlorophyll biosynthesis, seed growth, lignin/cell wall biosynthesis, leaf senescence, and root meristem growth), suggesting a cohesive theme of controlling developmental and metabolic pathways. A few terms related to telomere/nuclear processes are broader and less tightly linked, but the dominant pattern points to plant growth and biosynthesis regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010380","count":1},{"id":"GO:0080113","count":1},{"id":"GO:1901430","count":1},{"id":"GO:1901347","count":1},{"id":"GO:0010082","count":1}]},{"hash":"1158922451140194537","title":"Viral Entry and Genome Integration","description":"The proteins are annotated with GO terms about viral penetration into the host nucleus, DNA transposition, retrotransposition, DNA integration, and proviral latency, indicating a theme of genetic material moving into/within the host genome. Additional terms on symbiont entry and host apoptosis, and cell-cycle processes like mitotic spindle assembly, suggest the involvement of host manipulation during infection or transposition. Together these terms point to a function cluster centered on genome integration and mobile genetic element activity driven by viral or symbiont interactions.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075732","count":1},{"id":"GO:0006313","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0032197","count":1},{"id":"GO:0015074","count":1}]},{"hash":"881413302188533165","title":"Embryonic neural development and vesicle trafficking","description":"This cluster\u2019s top GO terms are strongly biased toward neural development events (spinal cord development, neural tube closure, embryonic organ development) suggesting a role in early neural tissue formation. The presence of COPII-coated vesicle budding points to active secretory pathway function, which would be important for delivering signaling and structural proteins during development. Some terms are broader cellular processes (ribosomal biogenesis, kinase activity regulation) that can appear across many proteins, but the neural development signals are the most distinctive linkage.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090114","count":3},{"id":"GO:0031505","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0051441","count":2}]},{"hash":"1348286188749747553","title":"DNA replication and chromatin regulation","description":"This set centers on DNA replication components (DNA unwinding, primer synthesis, DNA topology changes) and associated chromatin dynamics (subtelomeric heterochromatin formation, histone exchange). The presence of SOS response and hypoxia-related terms suggests stress-related genome maintenance. Together they indicate a theme of DNA replication coupled with chromatin regulation and genome stability under cellular stress.","confidence":"Medium","size":8,"edges":17,"triangles":14,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":3},{"id":"GO:0006269","count":2},{"id":"GO:0006268","count":2},{"id":"GO:0006265","count":2},{"id":"GO:0000184","count":2}]},{"hash":"607233353197941956","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1453436317910455316","title":"Gametogenesis and meiosis","description":"The top GO terms cluster around germline development and meiotic processes (spermatid development, reciprocal meiotic recombination, oocyte karyosome formation, germarium-derived oocyte fate determination), with supporting roles for cell cycle and DNA replication, and translation. A secondary, less central signal is response to antibiotic, but the dominant theme is gamete formation and meiosis.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006260","count":2}]},{"hash":"501887587534859661","title":"Unknown","description":"The GO terms span neural development and synaptic activity (nervous system development, Schwann cell development, excitatory postsynaptic potential) as well as cell cycle and DNA replication (DNA replication, G1/S transition, kinetochore localization, meiotic cell cycle) and other unrelated processes (B cell receptor signaling, response to cocaine, skeletal muscle development). This lack of a cohesive, shared function across the cluster suggests no single representative theme, so the label Unknown with None confidence.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0007399","count":6},{"id":"GO:0050853","count":6},{"id":"GO:0034501","count":6},{"id":"GO:0051321","count":6}]},{"hash":"2034686107293201737","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0034316","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0016567","count":2}]},{"hash":"2137031047991506579","title":"Developmental immune and cell-cycle signaling","description":"The proteins show a mix of immune-regulatory terms (cytokine production, T cell proliferation, neutrophil clearance), development-related processes (cartilage condensation, endothelial cell migration), plus core cell-cycle and cytoskeletal elements (DNA replication, Rho signaling, microtubule localization). This suggests a broad coordination between development, immune signaling, and cell proliferation rather than a single, narrow function.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0046641","count":6},{"id":"GO:0001502","count":6},{"id":"GO:0097350","count":6},{"id":"GO:0035372","count":6}]},{"hash":"1793448906544571229","title":"Plant photoperiodic flowering and far-red signaling","description":"The top GO terms point to plant light perception and flowering control in response to day length (far-red signaling, short-day/long-day photoperiodism, and flowering regulation). The presence of a phosphorelay signaling term supports a two-component signaling role often involved in light and circadian responses. Obsolete histone acetylation terms appear as noise rather than core function, so the dominant theme is photoperiodic signaling linked to flowering control.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010018","count":2},{"id":"GO:0043970","count":1},{"id":"GO:0070868","count":1},{"id":"GO:0043971","count":1},{"id":"GO:0044154","count":1}]},{"hash":"122759116145195328","title":"Ribosome Biogenesis and mRNA Processing","description":"The cluster is enriched for terms related to ribosome assembly (ribosome biogenesis, small subunit biogenesis) and multiple aspects of mRNA metabolism (export, modification, stabilization), plus translation initiation complex assembly, pointing to a cohesive role in ribosome production and mRNA handling for translation.","confidence":"High","size":8,"edges":9,"triangles":4,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006406","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0016556","count":3}]},{"hash":"1765114958150584936","title":"Unknown","description":"The GO terms are divergent\u2014developmental (forebrain, nervous system), apoptotic processes in multiple tissues, defense and signaling responses, metabolism, and even obsolete terms\u2014giving no single cohesive function to the eight proteins.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0010659","count":2},{"id":"GO:0035006","count":2},{"id":"GO:0033353","count":2},{"id":"GO:0071560","count":2}]},{"hash":"1007703830416696584","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0051083","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0060174","count":1},{"id":"GO:0033234","count":1}]},{"hash":"405548348741553251","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010087","count":1},{"id":"GO:1904751","count":1},{"id":"GO:0000389","count":1},{"id":"GO:0000494","count":1},{"id":"GO:0051096","count":1}]},{"hash":"485222027563964167","title":"Vertebrate neural tube and forebrain development","description":"The top GO terms overwhelmingly point to neural development and early embryogenesis in vertebrates, including neural tube development, neural tube closure, and forebrain development, with supporting signals in mesoderm formation and neural patterning via hedgehog pathway regulation. A concurrent set of terms about DNA replication and mitotic cell cycle suggests the proliferative phase accompanying development. Some terms like parathyroid hormone response are less central but do not override the dominant neural-development theme, so the cluster best labeled as vertebrate neural tube and forebrain development. ","confidence":"High","size":8,"edges":2,"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:1901621","count":4},{"id":"GO:0001707","count":4},{"id":"GO:0071374","count":4}]},{"hash":"2156688201537196542","title":"Heavy Metal Transport and Detoxification","description":"Top GO terms cluster around metal ion transport (mercury, cadmium, copper, zinc), detoxification of mercury, copper homeostasis, and related metal ion regulation, suggesting a functional theme of cellular metal handling and detoxification despite sparse connectivity. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015694","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0046689","count":1}]},{"hash":"2201216337577816796","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:2000825","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0007049","count":1}]},{"hash":"867810769384611290","title":"Retinoid and fatty acid metabolism","description":"The GO terms cluster around metabolism of retinol, fatty acids (biosynthesis and omega-oxidation), prostaglandins, and aldehydes/formaldehyde, with associated redox processes and a broader xenobiotic/drug-response context. This points to a cohesive theme of processing small molecules and lipids through oxidation-reduction pathways, rather than a single narrow function. ","confidence":"Medium","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042572","count":7},{"id":"GO:0006068","count":6},{"id":"GO:0006069","count":6},{"id":"GO:0006633","count":5},{"id":"GO:0010430","count":5}]},{"hash":"34447434992368541","title":"Unknown","description":"The GO terms span disparate developmental processes across different tissues and organisms (facial nerve and spinal cord morphogenesis, shoot apical meristem maintenance, oocyte fate, polarity specification), plus unrelated tasks like rRNA maturation and miRNA regulation. With no clear shared function or pathway and zero edges linking the terms, there isn\u2019t a coherent theme to name a specific cluster function. Confidence in a meaningful single label is therefore None. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021610","count":1},{"id":"GO:0007294","count":1},{"id":"GO:0010216","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0021965","count":1}]},{"hash":"665621728023764975","title":"Unknown","description":"The GO terms in this cluster cover mammalian lactation and several vascular development regulators (negative regulation of VEGF signaling, vasculogenesis, endothelial differentiation) alongside a diverse set of metabolic and transport processes (ferredoxin metabolism, nitrogen fixation, sodium ion transport, ATP synthesis/coupled electron transport, xanthine/phenylacetate catabolism). There isn\u2019t a single coherent theme or pathway that links these functions; the vascular-related terms are only a subset of unrelated metabolic annotations. Given this lack of a unifying function, the cluster is best labeled Unknown. ","confidence":"","size":8,"edges":8,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007595","count":3},{"id":"GO:1900747","count":2},{"id":"GO:0006124","count":2},{"id":"GO:2001213","count":2},{"id":"GO:0009399","count":2}]},{"hash":"1923373337374156167","title":"Translation initiation machinery and mRNA export","description":"This cluster is dominated by GO terms related to translation initiation, preinitiation complex formation, reinitiation, and regulation of initiation, with an additional term for mRNA export from the nucleus. While a few secondary terms touch on chromatin assembly and cell division, the core theme is translation initiation and related RNA processing, making this label representative of the cluster\u2019s function.","confidence":"High","size":8,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0006446","count":3}]},{"hash":"1776461889913452143","title":"Transcription and Ribosome Biogenesis","description":"Top GO terms show transcription by RNA polymerases I, II, and III, including tRNA transcription by Pol III, RNA-templated transcription, and transcription elongation/termination by Pol III, plus ribosome biogenesis and snRNA capping. Together these terms point to a cluster enriched in components of the transcriptional machinery and ribosome assembly. Some plant-related terms appear (negative regulation of leaf senescence, stem cell maintenance) but they are peripheral to the core transcription/biogenesis theme, so a label focused on transcription and ribosome biogenesis is most representative and concise.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902455","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0006366","count":1}]},{"hash":"2225277169960588956","title":"Plant transcriptional regulation and development","description":"The top GO terms cluster around regulation of DNA-templated transcription and DNA-templated transcription, plus multicellular organism development, with plant-specific signals such as abscisic acid signaling and cutin biosynthesis. While there are also general cellular processes (splicing, ribosomal export), the dominant theme is regulation of gene expression linked to plant development and signaling. Therefore, this cluster can be labeled as a plant transcriptional regulation and development module.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0000398","count":1}]},{"hash":"2089823512822923263","title":"Developmental and immune signaling regulation","description":"The top GO terms cluster around modulation of development-related processes (cartilage condensation, Wnt signaling regulation, transcription) and immune-related activities (T cell proliferation, neutrophil clearance), along with apoptosis and proliferation control and cellular localization processes. This mix suggests a broad regulatory cluster influencing both developmental signaling and immune cell dynamics, rather than a single, cohesive pathway or function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043065","count":7},{"id":"GO:0008285","count":7},{"id":"GO:0016477","count":7},{"id":"GO:0090090","count":7},{"id":"GO:0046826","count":7}]},{"hash":"2055440243350170723","title":"Cell Cycle Regulation in Regenerating Tissues","description":"The cluster\u2019s dominant GO terms center on G1/S and G2/M cell cycle control (transitions, CDK activity) together with tissue proliferation signals such as liver regeneration and mammary epithelial proliferation, indicating a shared role in regulating cell division during tissue regeneration. Some unrelated terms (early viral transcription, Leydig differentiation) appear but are less representative of the core theme.","confidence":"Medium","size":8,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097421","count":4},{"id":"GO:0000083","count":3},{"id":"GO:0033598","count":3},{"id":"GO:0030857","count":3},{"id":"GO:0010389","count":3}]},{"hash":"2258914977887977833","title":"Nucleotide salvage and amino acid metabolism","description":"This cluster is dominated by nucleotide salvage and catabolic processes (UMP salvage, purine ribonucleoside salvage, inosine/guanosine catabolism) and by L-glutamine metabolism, with additional signals for autophagy and proteolysis indicating cellular turnover. The inclusion of cobalamin biosynthesis and urate biosynthesis broadens the metabolic context, but the strongest common theme remains nucleotide salvage and amino acid metabolism alongside turnover mechanisms.","confidence":"Medium","size":8,"edges":19,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0006914","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0006148","count":1}]},{"hash":"1554082086965028041","title":"Membrane trafficking and dynamics regulation","description":"This cluster is dominated by terms tied to membrane processes: exocytosis regulation, membrane tubulation, and membrane formation, indicating control of membrane dynamics and vesicle trafficking. Additional terms about nuclear import and signaling appear ancillary, but the membrane-centric terms support this theme.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045921","count":4},{"id":"GO:0008360","count":4},{"id":"GO:0033234","count":4},{"id":"GO:0032120","count":4},{"id":"GO:1903525","count":4}]},{"hash":"466006018265212315","title":"Tissue development and lipid signaling","description":"The cluster includes several developmental terms across tissues (CNS development, retina vasculature morphogenesis, osteoblast differentiation, multicellular growth) alongside lipid mediator pathways (prostaglandin biosynthesis, linoleic acid metabolism), suggesting a module centered on tissue growth and lipid-based signaling rather than a single precise function.","confidence":"Medium","size":8,"edges":18,"triangles":15,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":4},{"id":"GO:0014810","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0045669","count":3},{"id":"GO:0061299","count":3}]},{"hash":"982040448946608359","title":"Immune Activation and Cytokine Signaling","description":"The predominant GO terms point to adaptive and innate immune functions \u2014 T cell proliferation, IL-4 production, and cytokine production regulation \u2014 with neutrophil clearance and endothelial cell migration suggesting immune cell trafficking. Additional terms refer to cytoskeletal and signaling processes (Rho signaling, microtubule localization) that support immune cell activation and movement. Overall, the proteins appear to form a cluster centered on immune response initiation and cytokine signaling.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":8},{"id":"GO:0001502","count":8},{"id":"GO:0097350","count":8},{"id":"GO:0035372","count":8},{"id":"GO:0043068","count":8}]},{"hash":"21663237101572816","title":"Multisubstrate Transmembrane Transporters","description":"The top GO terms are all transporter-related, covering diverse substrates (sialic acid, galactose, urate, nitrate, potassium, organic cations) and vesicle loading, which together point to a family of membrane transport proteins with broad specificity.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0015747","count":2},{"id":"GO:0070715","count":2},{"id":"GO:0015757","count":2}]},{"hash":"141616974434160250","title":"Protein Homeostasis and Organelle Trafficking","description":"The cluster centers on processes related to protein handling and trafficking, including ER-Golgi transport, general protein processing, proteolysis, SCF complex dynamics under stress, and mitochondrial inner-m membrane protein insertion, all of which point to cellular proteostasis and organelle-focused protein management. The estradiol response and T cell homeostasis appear more as context-specific signaling or downstream effects rather than core cluster functions, so they do not dominate the theme. Overall, the group seems tied to maintaining protein quality and coordinating intracellular trafficking and energy-related protein functions.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0016485","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0032355","count":2}]},{"hash":"2179431889825842608","title":"Amino acid biosynthesis and central carbon metabolism","description":"The cluster is dominated by GO terms for amino acid biosynthesis (tryptophan, threonine, leucine-related catabolism, glutamate) and core carbon metabolism (glycolysis, gluconeogenesis), suggesting a group of proteins involved in amino acid production and energy metabolism. Some development-related terms appear but are likely incidental annotations; the metabolic terms provide a cohesive theme.","confidence":"Medium","size":8,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000162","count":3},{"id":"GO:0009088","count":2},{"id":"GO:0021983","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0006094","count":2}]},{"hash":"50876315090379854","title":"Fatty acid biosynthesis and transport","description":"This cluster emphasizes fatty acid biosynthetic processes and fatty acid transport, with multiple GO terms pointing to fatty acid biosynthesis (GO:0006633) and long/medium-chain fatty acid import/transport. Additional lipid-related terms such as bile acid and menaquinone biosynthesis support a broader lipid metabolism theme, suggesting the proteins participate in lipid synthesis and handling rather than unrelated processes.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":6},{"id":"GO:0010124","count":6},{"id":"GO:0006633","count":5},{"id":"GO:0019427","count":5},{"id":"GO:0008206","count":5}]},{"hash":"1436939808939133379","title":"Chromatin Organization and Nucleosome Assembly","description":"The top GO terms cluster around chromatin biology: localization to chromatin, nucleosome assembly, heterochromatin organization, and histone modification-related processes. This points to proteins involved in maintaining chromatin structure and nucleosome dynamics in the nucleus. A few obsolete terms and one outlier (vitellogenesis) likely reflect annotation history rather than a true functional outlier for this cluster.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":2},{"id":"GO:0097298","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0016584","count":1},{"id":"GO:0080182","count":1}]},{"hash":"1057244402113021160","title":"Membrane Ion Transport and Homeostasis","description":"The cluster\u2019s top GO terms center on transport across membranes for ions and osmolytes (chloride, cobalt, methionine, glycine betaine, taurine) and associated changes in cellular ion balance (intracellular pH elevation, membrane hyperpolarization). This points to a shared function in maintaining ion gradients and osmotic/charge homeostasis, with sperm capacitation reflecting ion flux involvement and the fatty acid catabolic term representing a supporting energy context. Overall, the dominant theme is membrane transport and ionic regulation.","confidence":"Medium","size":8,"edges":11,"triangles":6,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051454","count":4},{"id":"GO:1902476","count":4},{"id":"GO:0048240","count":4},{"id":"GO:0015821","count":3},{"id":"GO:0036249","count":3}]},{"hash":"977457099226130365","title":"Endomembrane Vesicle Trafficking","description":"The cluster centers on intracellular transport of vesicles among the endomembrane system components (ER, Golgi, endosomes, lysosome) and gaps to the plasma membrane, including recycling pathways and vacuole targeting. Terms like ER-to-Golgi transport, endosome-to-Golgi/late endosome transport, vesicle fusion with Golgi, and endocytic recycling indicate a cohesive vesicular trafficking theme, with ruffle assembly hinting at endocytosis dynamics. This supports a focused label on vesicle trafficking within the endomembrane network.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":2},{"id":"GO:0045022","count":2},{"id":"GO:1903078","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0034498","count":2}]},{"hash":"1776168667015665614","title":"Unknown","description":"The top terms span transcription regulation, protein complex formation, lipid transport, immune defense, cell junctions, cytoskeletal dynamics, and immune cell activity, indicating several disparate cellular processes rather than one cohesive function. There isn\u2019t a single clear theme to bind these proteins into a specific label.","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006869","count":1},{"id":"GO:0050832","count":1}]},{"hash":"1876057503498091593","title":"Unknown","description":"Top terms span immune responses, circadian rhythm, renal development/absorption, plant gravitropism, and ubiquitin-mediated proteolysis, with no clear unifying function across the proteins. This heterogeneity suggests no coherent cluster theme can be assigned.","confidence":"","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000312","count":1},{"id":"GO:0042092","count":1},{"id":"GO:0042748","count":1},{"id":"GO:0032764","count":1},{"id":"GO:0002467","count":1}]},{"hash":"1716662531479455191","title":"RNA processing and translation initiation","description":"The cluster shows enrichment for mRNA modification, splicing, stabilization, and polyadenylation, plus translation initiation terms (IRES-dependent initiation and eIF4F complex assembly), suggesting proteins involved in RNA maturation and initiation of protein synthesis. Some terms are obsolete or unrelated (nitrate assimilation, blastocyst formation), but the core pattern points to RNA metabolism and translation control.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0048255","count":1},{"id":"GO:0075522","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1454013995464934503","title":"Stress-Activated MAPK and Redox Response","description":"The proteins in this cluster prominently feature stress-responsive signaling (MAPK cascade) and redox-related processes (responses to hydrogen peroxide, ROS metabolism), along with UV-A and estradiol-related signaling and regulatory controls on transport and epithelial-mesenchymal dynamics. This combination suggests a cohesive module centered on sensing and mitigating stress while coordinating intracellular transport and remodeling.","confidence":"Medium","size":8,"edges":10,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010719","count":2},{"id":"GO:0051403","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0032387","count":1},{"id":"GO:0032355","count":1}]},{"hash":"573227251374689119","title":"Plant Hormone Signaling and Growth Regulation","description":"The terms show responses to plant hormones (salicylic acid, gibberellin), defense-related signals (chitin), and several growth/regulatory processes (seed growth, root meristem growth, chlorophyll biosynthesis, lignin/cell wall regulation). This points to a coordinating role in hormone signaling with growth and defense, rather than a single pathway, supporting the label Plant Hormone Signaling and Growth Regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0010200","count":2},{"id":"GO:0010380","count":1},{"id":"GO:0080113","count":1}]},{"hash":"1007967345220467166","title":"Viral entry and proviral latency","description":"The most represented GO terms are about viral penetration into the host nucleus, DNA integration, and establishment of integrated proviral latency, which together point to viral genome integration and latency as the central theme. Other terms reference host-symbiont interactions and calcium signaling, which may reflect viral manipulation of host pathways. Overall, the cluster seems best described by viral entry and proviral latency.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0075732","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0075713","count":2}]},{"hash":"2114074602912324107","title":"Diverse solute transporters","description":"The top GO terms cluster around membrane transport of a variety of substrates (methionine, glycine betaine, cobalt ions, taurine, vitamins, carbohydrates), suggesting a group of proteins functioning as diverse solute transporters. While a few outlier terms appear (e.g., stem cell proliferation, mercury response, fatty acid catabolism), the common thread is transport across membranes for multiple substrates.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015821","count":1},{"id":"GO:0031460","count":1},{"id":"GO:0006824","count":1},{"id":"GO:0015734","count":1},{"id":"GO:0042760","count":1}]},{"hash":"1969356892701432291","title":"TLR signaling and macrophage activation","description":"Proteins show enrichment for Toll-like receptor pathways (TLR8 signaling and MyD88-independent signaling), regulation of cytokine production, macrophage activation, and antimicrobial/ antiviral responses, indicating a cohesive innate immune response driven by TLR signaling in macrophages.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":6},{"id":"GO:0050707","count":6},{"id":"GO:0034158","count":6},{"id":"GO:0002756","count":6},{"id":"GO:1900155","count":6}]},{"hash":"1654325084861133416","title":"RNA processing and translation with stress response","description":"This cluster centers on RNA metabolism and protein synthesis, highlighted by intron splicing (Group I/II) and tRNA methylation, alongside translation. The presence of stress-related terms (response to antibiotic, cycloheximide, and general stress) suggests coordinated regulation of RNA processing and translation under stress. Some terms like cobalamin biosynthesis and far-red light response are more peripheral but do not override the core RNA/translation theme.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0002940","count":1},{"id":"GO:0000372","count":1}]},{"hash":"1190504513782117349","title":"Golgi- and Synaptic Vesicle Trafficking","description":"The top GO terms cluster around Golgi-related vesicle trafficking (ER-to-Golgi transport, intra-Golgi transport, Golgi ribbon formation, Golgi-to-vacuole transport) and SNARE complex assembly. The presence of exocytic insertion of neurotransmitter receptors and links to long-term potentiation point to neuronal vesicle fusion at synapses, suggesting these proteins coordinate Golgi-based sorting and SNARE-driven fusion in neurons.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":6},{"id":"GO:0090161","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0006891","count":5},{"id":"GO:0035493","count":4}]},{"hash":"414620033779131307","title":"Fungal cell wall polysaccharide biosynthesis","description":"The top GO terms center on biosynthesis and organization of cell wall glycans (GDP-mannose, cell wall mannoprotein biosynthesis, slime layer polysaccharide biosynthesis) and on cell morphogenesis, suggesting proteins involved in constructing or remodeling fungal cell walls and their extracellular glycans. While a few terms reference broader glycan pathways, the dominant theme is cell wall\u2013related glycan production.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":3},{"id":"GO:0009298","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0005978","count":3}]},{"hash":"900104057346663715","title":"Plant cell wall biosynthesis and remodeling","description":"The cluster shows strong enrichment for plant-type cell wall biogenesis and modification, including xyloglucan and xylan metabolic processes, and root hair development, pointing to proteins involved in cell wall synthesis/remodeling in plants. Some terms are obsolete, but the dominant signal is plant cell wall polysaccharide biosynthesis.","confidence":"Medium","size":8,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0006627","count":1},{"id":"GO:0000746","count":1},{"id":"GO:0010411","count":1},{"id":"GO:0009827","count":1}]},{"hash":"1276235855571216288","title":"Male reproductive development and androgen signaling","description":"In this cluster, several prominent GO terms point to male reproductive biology and hormone signaling: prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly. These suggest that the proteins may function together in androgen-dependent development and signaling pathways relevant to male reproductive tissues. The other terms (e.g., cilium-related processes and gluconeogenesis regulation) are less cohesive with this theme, implying some functional noise but not overriding the core reproductive/hormonal signal.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1903646","count":4},{"id":"GO:0090526","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0030850","count":4},{"id":"GO:0046661","count":4}]},{"hash":"826773451841911980","title":"Steroid and lipid metabolism","description":"This cluster centers on lipid- and hormone-related metabolism, including prostaglandin biosynthesis, steroid hormones (cortisol, testosterone), retinoic acid, and vitamin D signaling, plus fatty acid omega-oxidation and xenobiotic catabolism. While some GO terms touch on development and cell adhesion, these likely reflect downstream effects of lipid hormones on mammary gland and endothelial biology, supporting a cohesive lipid/hormone theme.","confidence":"Medium","size":8,"edges":21,"triangles":27,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":7},{"id":"GO:0030879","count":6},{"id":"GO:0071603","count":6},{"id":"GO:0034651","count":6},{"id":"GO:0070989","count":6}]},{"hash":"936281556125915089","title":"Cytokinin-regulated plant growth and lignin biosynthesis","description":"The top GO terms point to cytokinin-activated signaling and regulation of diverse plant developmental and metabolic processes, including chlorophyll biosynthesis, seed and root meristem growth, leaf senescence, and lignin/secondary cell wall biosynthesis. Together they suggest a coherent theme of regulatory control over plant growth and cell wall formation, with cytokinin signaling as a central axis. Some other terms about RNA/telomere localization regulation appear peripheral to this core theme. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009736","count":4},{"id":"GO:0010380","count":3},{"id":"GO:0080113","count":3},{"id":"GO:1901430","count":3},{"id":"GO:1901347","count":3}]},{"hash":"2305672598420496778","title":"Salicylic acid\u2013mediated plant defense signaling","description":"The cluster is dominated by defense-related GO terms and a salicylic acid\u2013mediated signaling pathway, indicating a plant immune response module. Terms like 'defense response', 'response to biotic stimulus', and 'salicylic acid mediated signaling pathway' point to SA-dependent defense; 'regulation of defense response to fungus' supports fungal pathogen resistance. A pollen tube reception term suggests plant-specific signaling contexts but the overall pattern centers on immune signaling rather than developmental processes.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010483","count":1},{"id":"GO:0009607","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0009863","count":1},{"id":"GO:1900150","count":1}]},{"hash":"2191562011976962928","title":"Plant development and phenylpropanoid metabolism","description":"The Top Terms cluster centers on plant-specific developmental processes (leaf development, nectar secretion) and metabolism of phenylpropanoids (lignin, flavonoids, hydroxycinnamate conjugates, cutin), with supporting ideas of carbohydrate transport (sucrose/fructose) and auxin-related regulation. This suggests a cohesive theme of growth/development coupled with secondary metabolism and structural biopolymer biosynthesis in plants. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048366","count":1},{"id":"GO:0010252","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0080088","count":1},{"id":"GO:0009809","count":1}]},{"hash":"975302918535114889","title":"Plant light signaling and growth regulation","description":"The top GO terms cluster around light sensing and signaling (far-red/red light phototransduction and signaling), regulation of circadian rhythm, and downstream growth/development processes (chlorophyll biosynthesis, seed growth, root meristem growth, and cell wall/lignin biosynthesis), indicating a cohesive plant light-responsive growth program.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006313","count":2},{"id":"GO:0042753","count":2},{"id":"GO:0009585","count":2},{"id":"GO:0010018","count":2}]},{"hash":"506438096603850456","title":"Unknown","description":"The GO terms cover a broad and diverse set of processes including limb development, chromatin regulation, vitamin D response, sensory thermosensation, proteasome assembly, cytokinesis-related membrane addition, NF-kappaB signaling, NOD2 signaling, and Golgi-to-plasma membrane transport, with no single cohesive function or pathway emerging to unify the cluster.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060174","count":1},{"id":"GO:0035563","count":1},{"id":"GO:0033280","count":1},{"id":"GO:0050955","count":1},{"id":"GO:0070682","count":1}]},{"hash":"338118428948782580","title":"Floral nectar secretion and sugar transport","description":"The strongest terms point to nectar secretion (GO:0071836) and carbohydrate movement, including sucrose transport (GO:0015770) and fructose export from vacuole to cytoplasm (GO:1902334), which together define nectar production and sugar flux in floral tissues. Other terms touch on plant development and signaling (auxin regulation, cell wall loosening, reproduction) but are less central to the cluster\u2019s core theme. Confidence: Medium","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":2},{"id":"GO:0015770","count":1},{"id":"GO:0010930","count":1},{"id":"GO:0071836","count":1},{"id":"GO:1902334","count":1}]},{"hash":"1434325914044816310","title":"Meiosis I Spindle Assembly and Oocyte Maturation","description":"The top GO terms converge on meiotic spindle dynamics and oocyte maturation (microtubule polymerization; spindle assembly in female meiosis I; oocyte maturation) and on proteostasis and cell-cycle regulation (SCF-dependent ubiquitin-mediated proteolysis; negative regulation of cell proliferation). While there are a few neural-development terms in the list, the strongest signal is female meiosis/oocyte development and associated protein degradation pathways, suggesting a cluster of proteins functioning in meiotic progression and oocyte maturation, with linked cell-cycle control. Medium","confidence":"","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046785","count":7},{"id":"GO:0007057","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0021678","count":7},{"id":"GO:0006516","count":7}]},{"hash":"1741300649430827835","title":"Viral life cycle and genome integration","description":"These proteins appear linked to viral infection and genome integration processes, including virion assembly, entry into the host nucleus, DNA integration, proviral latency, and viral release; retrotransposition aligns with genome mobility relevant to provirus formation. A minor association with RNA turnover via miRNA catabolism is noted. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075732","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0006313","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0006508","count":1}]},{"hash":"1910395933510295555","title":"Bacterial LPS and O-antigen biosynthesis","description":"Top GO terms are dominated by lipopolysaccharide biosynthetic processes (LPS core, O antigen, UDP-rhamnose) along with related carbohydrate metabolism, indicating proteins function together in assembling LPS components in Gram-negative bacteria. Secondary terms like galactose and acetoin catabolic processes suggest broader metabolism but do not override the main LPS biosynthesis theme.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0009243","count":3},{"id":"GO:0019388","count":3}]},{"hash":"497143849595472598","title":"ER-Glycoprotein Maturation and Secretion","description":"This cluster centers on ER-based processing: protein retention in the ER lumen, dolichol-linked glycosylation, and protein transport, pointing to maturation and trafficking of secreted/glycosylated proteins. The inclusion of innate immune signaling and T cell\u2013related terms suggests these mature proteins participate in immune responses, aligning the theme with ER-dependent secretion of immune mediators.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":2},{"id":"GO:0002369","count":2},{"id":"GO:0010204","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0070231","count":2}]},{"hash":"2272044943139827160","title":"Plant oxidative stress response and lignin remodeling","description":"The top terms cluster around oxidative stress mitigation (response to oxidative stress, oxidant detoxification, hydrogen peroxide catabolic process) and plant-specific cell wall remodeling (plant-type cell wall organization, lignin catabolic process), suggesting a theme of cell wall modification under oxidative stress in plants. Some terms (e.g., CXCL2 production) appear mismatched and may be annotation noise, but the dominant plant-related processes support this label.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:1904209","count":1},{"id":"GO:0071307","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0006979","count":1}]},{"hash":"1119530238301335826","title":"Unknown","description":"The GO terms associated with this cluster are highly diverse, including DNA repair, telomere maintenance, calcium-mediated signaling, multiple developmental processes (placenta, liver, embryonic digestive tract), aging, and immune signaling (B and T cell pathways). With only single-term representations and no connections between them (edges and triangles are zero), there is no cohesive, interpretable function linking the proteins. Therefore a clear, specific label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":1},{"id":"GO:0000723","count":1},{"id":"GO:0050850","count":1},{"id":"GO:0001890","count":1},{"id":"GO:0048566","count":1}]},{"hash":"12230629659485663","title":"Histone and protein acetylation for chromatin regulation","description":"The set includes multiple acetylation-related GO terms (histone H4 acetylation, N-terminal acetylation, peptidyl-lysine acetylation, propionylation) and a term on subtelomeric heterochromatin formation, suggesting a common theme of acetylation-driven chromatin modification and gene regulation. Some terms (leaf formation, ectoine biosynthesis) seem less directly connected and may be noise, but the dominant signal points to chromatin-associated acetylation.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":7},{"id":"GO:0032919","count":7},{"id":"GO:0043967","count":7},{"id":"GO:0018002","count":7},{"id":"GO:0045150","count":7}]},{"hash":"542907300132611275","title":"Innate Antimicrobial Defense and Proteolysis","description":"The cluster includes GO terms for defense against oomycetes, fungus, and bacteria, plus killing of cells of another organism and positive regulation of antibacterial peptide production, pointing to innate immune responses. Proteolysis and protein catabolic process terms may reflect proteolytic enzymes involved in defense; a signaling term (response to cGMP) is present, while a couple of unrelated terms (renin-angiotensin regulation, amyloid precursor protein biosynthesis) appear as noise. Overall, the dominant theme is antimicrobial defense and related proteolysis.","confidence":"Medium","size":8,"edges":10,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0002229","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0042742","count":1},{"id":"GO:0031640","count":1},{"id":"GO:0002803","count":1}]},{"hash":"368201531960709481","title":"Unknown","description":"The top terms are a mix of DNA damage response and chromatin-related processes, hormone response, hypoxia, neuronal development, immune isotype switching, and sebaceous gland proliferation, with no clear single pathway or function tying them together. The cluster also has no edges or clear interaction structure, suggesting disparate proteins rather than a coherent unit, so a specific functional label cannot be justified.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043516","count":1},{"id":"GO:0035441","count":1},{"id":"GO:0010424","count":1},{"id":"GO:0071549","count":1},{"id":"GO:0048387","count":1}]},{"hash":"1388812914891812636","title":"Chloroplast movement and amino acid catabolism","description":"The cluster features strong chloroplast photorelocation signals (chloroplast accumulation and chloroplast avoidance movement) along with several amino-acid catabolic processes (phenylalanine and tyrosine) and xenobiotic catabolism, pointing to plant-specific chloroplast dynamics tied to metabolic remodeling. While there are also general gene-expression terms (regulation of transcription and translation), these appear less central to the main theme. Therefore, the name captures the dominant chloroplast movement/metabolic theme of the cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006417","count":1},{"id":"GO:0042256","count":1},{"id":"GO:0009904","count":1},{"id":"GO:0009903","count":1},{"id":"GO:0006559","count":1}]},{"hash":"1043405910495352397","title":"Plant Development and Auxin Signaling","description":"These proteins cluster around plant developmental processes and hormone signaling: meristem development, leaf vascular pattern formation, longitudinal axis specification, auxin-activated signaling, and DNA-templated transcription regulation. The presence of fruit dehiscence and auxin response supports a cohesive theme of auxin-regulated growth and tissue patterning in plants, with transcriptional control as a common mechanism. A minor note is DNA transposition, which may reflect broader chromatin-related activity but does not override the dominant developmental signal.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006313","count":1},{"id":"GO:0090305","count":1},{"id":"GO:0048507","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0009733","count":1}]},{"hash":"252190321031803480","title":"Developmental transcriptional regulation and morphogenesis","description":"The cluster is dominated by GO terms tied to DNA-templated transcription (transcriptional regulation) and developmental morphogenesis. Terms such as embryonic cell shape regulation, trophoblast giant cell differentiation, and mammary duct terminal end bud growth point to development and tissue patterning, while plasminogen activation and macrophage chemotaxis regulation suggest related remodeling and immune interactions. Overall, the common thread is transcriptional control of developmental processes and tissue morphogenesis rather than a single biochemical pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0010758","count":1},{"id":"GO:0016476","count":1},{"id":"GO:0060707","count":1}]},{"hash":"1325601069784750060","title":"Immune signaling and cellular stress responses","description":"The terms include IL-6 production and isotype switching, pointing to immune signaling, alongside cadmium/ROS responses, protein refolding, and telomere maintenance, suggesting broader cellular stress and genome maintenance processes; together they imply a cluster centered on immune-related signaling intertwined with stress responses rather than a single pathway.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1904871","count":7},{"id":"GO:2000778","count":7},{"id":"GO:1901998","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0048291","count":7}]},{"hash":"2168414261618508886","title":"Unfolded protein response and chaperone activity","description":"The cluster is dominated by GO terms related to dealing with misfolded or unfolded proteins (cellular response to unfolded protein, protein targeting to membranes for cotranslational translocation, and chaperone/cofactor\u2013dependent refolding). This points to a protein quality-control network activated during ER stress and folding load. Some terms (DNA replication, karyogamy) are less aligned but do not overwhelm the folding/stress theme, so the primary interpretation is protein folding stress response.","confidence":"Medium","size":7,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":6},{"id":"GO:1900035","count":4},{"id":"GO:0016226","count":4},{"id":"GO:1903751","count":4},{"id":"GO:1903382","count":4}]},{"hash":"1389478958424634034","title":"Fungal mating and sporulation membrane remodeling","description":"This cluster centers on processes tied to fungal mating (karyogamy during conjugation) and sporulation (prospore/ascospore membrane formation), along with membrane remodeling activities (exocytosis, membrane tubulation) and protein localization to extracellular regions. While some terms are broader (transcription regulation, signaling), the strongest signals point to membrane-associated events in the fungal life cycle's mating and sporulation stages.","confidence":"Medium","size":7,"edges":10,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0007165","count":3},{"id":"GO:0045921","count":2},{"id":"GO:0008360","count":2}]},{"hash":"1043896394510689155","title":"Plant RNA processing and ribosome biogenesis","description":"The cluster is dominated by GO terms related to nuclear RNA processing and ribosome biogenesis, including regulation of spliceosome activity, ribosomal small subunit assembly, and RNase MRP\u2011dependent mRNA decay, with supporting terms on chromosome condensation and rRNA export; a couple of plant development terms likely reflect context-specific roles but do not outweigh the core RNA-processing/ribosome synthesis signal.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":2},{"id":"GO:0090506","count":2},{"id":"GO:2000032","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0031581","count":2}]},{"hash":"1367992126226867871","title":"Plant oxidative stress response and lignin metabolism","description":"The cluster shows enrichment for oxidative stress response and detoxification (GO:0006979, GO:0098869, GO:0042744), plus hydrogen peroxide catabolic process, and includes plant-specific processes such as lignin catabolic process and plant-type cell wall organization, pointing to a coordinated plant redox and cell wall remodeling function. A couple of low-frequency terms (viral translation initiation/termination, follicle cell development) are likely noise.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0046274","count":3},{"id":"GO:0042744","count":3},{"id":"GO:0055114","count":3}]},{"hash":"21528871842499194","title":"RNA splicing and translation initiation","description":"This cluster shows enrichment for mRNA splicing (GO:0006376, GO:0000380), mRNA stability and modification (GO:0010610, GO:0016556, GO:0048255), and components involved in translation initiation (GO:0097010, GO:0075522). The combination points to proteins coordinating RNA processing and the initiation of translation, with hints of RNA remodeling via helicase activity. This cohesive theme supports labeling as RNA splicing and translation initiation.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":1},{"id":"GO:0048255","count":1},{"id":"GO:0075522","count":1}]},{"hash":"1413725136465288325","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0071031","count":2},{"id":"GO:1901253","count":1}]},{"hash":"1963216111297138441","title":"Ribosome biogenesis and ER-Golgi trafficking","description":"The top GO terms cluster around ribosome biogenesis and regulation of translational initiation, indicating a function in protein synthesis. Additional terms point to the secretory pathway, specifically vesicle transport between the ER and Golgi and related GTPase activity, suggesting coordination between ribosome production and protein trafficking. Some terms also touch on general growth-related processes like cell division, but the core themes are ribosome assembly and ER-Golgi trafficking.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006890","count":2}]},{"hash":"1079747480415812111","title":"RNA metabolism and translation control","description":"The GO terms cluster around mRNA processing and regulation: mRNA stability, translation, modification, stabilization, and initiation complex assembly, with additional splicing and polyadenylation aspects. This suggests a coherent theme of RNA metabolism tightly linked to translational control, including stress responses and viral initiation contexts, despite some outliers like blastocyst formation. ","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0016556","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1981203853228420653","title":"Unknown","description":"The cluster\u2019s top GO terms span ubiquitin-dependent ERAD and proteolysis-related processes alongside diverse areas like cell division and mRNA splicing, with little coherent functional convergence. Because there isn\u2019t a single, representative function tying the terms together, a specific label cannot be confidently assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000398","count":2},{"id":"GO:1901621","count":1},{"id":"GO:0051259","count":1}]},{"hash":"1380558325327650492","title":"Nuclear transport and mitotic regulation","description":"The proteins cluster around core nuclear processes tied to cell cycle control and mitosis: G1/S transition, spindle organization, ubiquitin-dependent protein turnover, and nuclear import/localization. While there are a few metabolic terms present, the strongest signal is a cohesive network governing nuclear function during division, justifying a label focused on nuclear transport and mitotic regulation.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":3},{"id":"GO:0033132","count":3},{"id":"GO:0090526","count":3},{"id":"GO:1901181","count":2},{"id":"GO:0035080","count":2}]},{"hash":"583357433200328574","title":"Light-regulated circadian transcription","description":"GO terms center on phototransduction and far-red light signaling, combined with regulation of DNA-templated transcription and positive regulation of circadian rhythm, indicating a cluster focused on light-triggered transcriptional control and circadian regulation; metabolic terms appear secondary.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009585","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0042753","count":1},{"id":"GO:0010018","count":1},{"id":"GO:0042758","count":1}]},{"hash":"1266374005789123876","title":"Postsynaptic signaling regulation","description":"The dominant terms point to synaptic function and postsynaptic organization (PSD assembly, regulation of synaptic vesicle clustering, and tyrosine dephosphorylation), with signaling moderation (PI3K/AKT) and redox balance. A few terms pertain to cell cycle processes, suggesting multi-function proteins, but the core theme appears to be neuronal synaptic regulation.","confidence":"Medium","size":7,"edges":16,"triangles":15,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0051898","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0035335","count":2},{"id":"GO:2000808","count":2}]},{"hash":"2290537581717009323","title":"Nuclear RNA processing and proteasome-dependent cell cycle control","description":"Top GO terms indicate nuclear RNA processing (spliceosome assembly) and ubiquitin-proteasome\u2013dependent protein degradation, together with cell-cycle transitions (G2/M, exit from mitosis) and nuclear localization; the cluster likely represents nuclear regulation of RNA processing and proteostasis during cell cycle.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0010265","count":1},{"id":"GO:0000086","count":1},{"id":"GO:0051457","count":1}]},{"hash":"1793821824850517209","title":"Central carbon metabolism","description":"Most of the top GO terms describe carbohydrate and energy metabolism (glucose metabolism, TCA cycle, regulation of pyruvate decarboxylation to acetyl-CoA, glyoxylate/inositol/oxalate catabolic processes). A couple terms about pyramidal neuron and cerebellar cortex development are present but less represented, so they are likely incidental. The cluster is best described as central carbon metabolism and energy production.","confidence":"High","size":7,"edges":15,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0021860","count":2},{"id":"GO:0033611","count":2},{"id":"GO:0021695","count":2}]},{"hash":"502874187702060372","title":"Innate immune signaling regulators","description":"The cluster shows enrichment for regulatory roles in antiviral innate signaling (negative regulation of RIG-I and MDA-5 pathways, negative regulation of interferon production), as well as modulation of complement activation and dendritic cell chemotaxis, with additional links to PI3K/AKT signaling. This pattern points to a cohesive function in modulating innate immune responses rather than a single metabolic process, justifying a label focused on innate immune signaling regulation.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0070131","count":1},{"id":"GO:0039536","count":1},{"id":"GO:0035042","count":1},{"id":"GO:0051897","count":1}]},{"hash":"361467152994248411","title":"Spliceosome and RNA Processing Complex","description":"This cluster centers on RNA splicing and processing, with multiple GO terms for spliceosome-mediated mRNA splicing, spliceosomal complex assembly, and general mRNA processing, plus rRNA processing steps and transcription termination, pointing to a coherent RNA maturation module.","confidence":"High","size":7,"edges":13,"triangles":10,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0000464","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0006378","count":2}]},{"hash":"454927044195257060","title":"Unknown","description":"The top GO terms span apoptotic processes, tissue development (salivary gland, cornification), circadian rhythm, estradiol response, nutrient signaling, immune/proliferation regulation, and bone-related processes. There is no single cohesive function uniting these terms across the seven proteins, so a confident, specific label cannot be assigned.","confidence":"","size":7,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":1},{"id":"GO:0030502","count":1},{"id":"GO:0070268","count":1},{"id":"GO:0042747","count":1},{"id":"GO:0031667","count":1}]},{"hash":"1031890900319495991","title":"Negative regulation of diverse cellular processes","description":"The top GO terms are dominated by negative regulation terms across multiple processes (ion channel activity, autophagy, proteasome degradation, mitochondrial fusion, gene expression); a few items like PML body organization are related to cellular regulation at the nuclear level. This pattern suggests the proteins in this cluster function to suppress or modulate diverse cellular pathways rather than participate in a single, cohesive process.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:1903071","count":4},{"id":"GO:1902260","count":4},{"id":"GO:0010216","count":4},{"id":"GO:0045648","count":4},{"id":"GO:1901097","count":4}]},{"hash":"1580735862912691934","title":"Large subunit ribosome biogenesis","description":"Dominant signals are LSU rRNA maturation, large subunit preribosome assembly, and ribosomal large subunit biogenesis, pointing to a ribosome biogenesis/assembly cluster with translation as a secondary tie-in. Some unrelated terms (DNA repair, cell cycle) are present but are less informative.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0006412","count":1}]},{"hash":"1742702223648672761","title":"DNA replication and SOS repair cluster","description":"The top GO terms emphasize DNA replication, SOS response, cell division, and nucleotide-excision repair, indicating a cohesive theme of genome maintenance and replication under stress. Although there are some unrelated terms (transport and Golgi retention), the dominant signals point to DNA maintenance and damage response pathways.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0009432","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0000733","count":4},{"id":"GO:0019079","count":4}]},{"hash":"1735132774355973470","title":"Ubiquitin modification and deubiquitination","description":"The top terms show a clear enrichment for protein ubiquitination and multiple linkage-specific deubiquitination activities (K29, K63, K33), pointing to ubiquitin signaling as the core theme of this cluster. There are a couple of RNA processing terms (splicing regulation and chloroplast mRNA modification) that are less representative, but do not outweigh the dominant ubiquitin-related signals. Overall, the proteins in this cluster are best described as involved in ubiquitin modification and deubiquitination processes.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0035523","count":1},{"id":"GO:1900871","count":1},{"id":"GO:0006977","count":1},{"id":"GO:0070536","count":1}]},{"hash":"664902180287659168","title":"Diverse biosynthetic and metabolic processes","description":"The top terms are varied biosynthesis and metabolism-related processes (anthocyanin, sterol, antibiotic, UDP-rhamnose, lipopolysaccharide core, long-chain fatty-acyl-CoA, and L-glutamine metabolism), suggesting these proteins participate in multiple biosynthetic pathways rather than a single one. Some cell cycle/division terms appear but the dominant signal is broad biosynthesis, matching a loosely connected metabolic cluster with minimal interactions.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":4},{"id":"GO:0016126","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0017000","count":3}]},{"hash":"585987182941274793","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":9,"triangles":3,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006270","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0044205","count":2}]},{"hash":"2098175802805742102","title":"Unknown","description":"Top GO terms span very different biological contexts, including plant development (microgametogenesis, somatic embryogenesis), insect cell differentiation (R7 cell differentiation), and metabolism of several plant and fungal polysaccharides (chitin, cellulose, xylan, L-arabinose). Additional terms reference autophagy-related vesicle trafficking and DNA integration. The terms do not converge on a single coherent function or pathway, so no specific, representative label can be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055046","count":1},{"id":"GO:0045466","count":1},{"id":"GO:0010262","count":1},{"id":"GO:0006032","count":1},{"id":"GO:0030245","count":1}]},{"hash":"1970333215679802191","title":"Developmental differentiation and morphogenesis","description":"These terms cluster around embryonic development and tissue specification across multiple lineages: mesenchyme development, floor plate and heart valve morphogenesis, neuronal and sensory cell differentiation, and regulatory control of differentiation and the cell cycle. The common thread is developmental patterning and morphogenesis across diverse tissues, rather than a single pathway, so a general label for developmental differentiation and morphogenesis fits best.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":6},{"id":"GO:0060766","count":6},{"id":"GO:2000793","count":5},{"id":"GO:2000764","count":5},{"id":"GO:0060375","count":5}]},{"hash":"703642734031626722","title":"Developmental transcription regulation","description":"The cluster is enriched for transcription-related GO terms (RNA polymerase II transcription, DNA-templated transcription) alongside numerous development-related terms (heart valve and mesenchyme development, floor plate, cortical interneuron differentiation, auditory receptor fate), suggesting proteins that coordinate gene expression during developmental processes rather than a single tissue-specific function.","confidence":"Medium","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:0006351","count":2},{"id":"GO:2000793","count":1},{"id":"GO:2000764","count":1},{"id":"GO:0060375","count":1}]},{"hash":"510436674127524052","title":"Regulators of Signaling and Membrane Dynamics","description":"The top GO terms describe regulatory roles across various cellular processes, including negative regulation of protein kinase activity, regulation of exocytosis and membrane tubulation, cell shape regulation, and membrane-associated functions like nuclear import and sporulation membrane formation. This suggests a cluster of proteins that broadly modulate signaling and membrane dynamics rather than a single, cohesive pathway. Given the diversity and lack of a tightly connected process, the label reflects a general regulatory function in signaling and membrane processes.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0045921","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0033234","count":2},{"id":"GO:0032120","count":2}]},{"hash":"2295768125706821327","title":"Transcription Regulation and RNA Processing","description":"Dominant GO terms point to regulation of transcription and RNA processing/splicing (transcription regulation, spliceosomal disassembly, RNA splicing, and mRNA processing), with a couple of muscle proliferation notes that are related to gene expression programs. Overall, the cluster centers on transcriptional control and RNA maturation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0031062","count":1},{"id":"GO:0014842","count":1},{"id":"GO:0032091","count":1},{"id":"GO:0000390","count":1}]},{"hash":"665978952270590794","title":"Ubiquitin-Proteasome Mediated Cell Cycle Control","description":"The cluster is dominated by GO terms tied to ubiquitin-dependent degradation (SCF-dependent proteasomal ubiquitin-protein catabolic processes and positive regulation of protein polyubiquitination) and cell cycle machinery (spindle assembly, microtubule polymerization, mitotic G1 DNA damage checkpoint, and regulation of DNA replication initiation), suggesting a cohesive role in proteostasis coupled to cell-cycle progression. Some terms also reflect stress responses (arsenic, cadmium), circadian rhythm regulation, and general protein turnover, but these appear secondary to the core theme of ubiquitin-driven cell-cycle regulation.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042752","count":5},{"id":"GO:0046785","count":5},{"id":"GO:0007057","count":5},{"id":"GO:0030174","count":5},{"id":"GO:0042787","count":5}]},{"hash":"1012552507681154921","title":"Nervous system development","description":"Dominant terms such as forebrain development, nervous system development, and glial cell apoptotic process point to a neural development theme; while there are a few unrelated terms (e.g., L-methionine cycle), the overall signal is that these proteins cluster around neural development and glial-related apoptosis.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0010659","count":3},{"id":"GO:0035006","count":3},{"id":"GO:0033353","count":3},{"id":"GO:0071560","count":3}]},{"hash":"1621602168810116034","title":"Neural tube and craniofacial development","description":"Dominant GO terms point to embryonic neural development and craniofacial/skeletal morphogenesis (neural tube closure, forebrain development, embryonic cranial skeleton morphogenesis, skeletal system development). Housekeeping processes like DNA-templated transcription and DNA replication are present but do not define the cluster\u2019s primary function. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0048701","count":3}]},{"hash":"857297763435277962","title":"RNA Processing and Translation Initiation","description":"These proteins cluster around RNA metabolism and protein synthesis control: regulation of mRNA stability under stress, mRNA modification and stabilization, alternative splicing via the spliceosome, and assembly of the eIF4F translation initiation complex (including IRES-dependent initiation). The mix of mRNA processing and translation initiation terms suggests a cohesive function in RNA maturation and regulation of translation, especially under stress.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":7},{"id":"GO:0016556","count":6},{"id":"GO:0048255","count":6},{"id":"GO:0075522","count":6},{"id":"GO:1905663","count":6}]},{"hash":"657907939872957639","title":"Steroid Hormone Biosynthesis and Xenobiotic Metabolism","description":"This cluster centers on steroid biosynthesis (cortisol, testosterone, brassinosteroids) and related metabolic/detoxification pathways (xenobiotic catabolic process, fatty acid omega-oxidation, retinoic acid/vitamin D responses). While a few terms touch development or adhesion, the strongest recurring signal is steroid and lipid/xenobiotic metabolism, suggesting a cohesive metabolic role for the proteins.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":2},{"id":"GO:0071603","count":2},{"id":"GO:0034651","count":2},{"id":"GO:0070989","count":2},{"id":"GO:0042738","count":2}]},{"hash":"1910013821428574685","title":"Plant development and cell wall remodeling","description":"The cluster includes GO terms tied to plant growth and reproduction (meristem transition, flower phyllotaxis, microsporogenesis) as well as cell wall-related processes (cell wall organization, pectin and alginate metabolism). It also contains general cellular processes like photosystem I electron transport, translation (valyl-tRNA aminoacylation), and ER stress response, which are common in plant cells. Taken together, the terms point to a cohesive theme of plant development coupled with cell wall biosynthesis/remodeling, despite the diversity of specific processes. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009773","count":1},{"id":"GO:0006438","count":1},{"id":"GO:0030968","count":1},{"id":"GO:0010228","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1686549441815063963","title":"Innate Immune Signaling and Inflammation","description":"The cluster is enriched for innate immune processes, with MyD88-independent Toll-like receptor signaling, response to fungus, neutrophil clearance, and alpha-beta T cell proliferation indicating immune activation and signaling. Additional terms like Rho signaling, microtubule localization, and programmed cell death reflect broader signaling cross-talk and cell fate decisions; a few developmental/metabolic terms appear, but the dominant theme is immune signaling and inflammation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0008286","count":7},{"id":"GO:0046641","count":6},{"id":"GO:0001502","count":6},{"id":"GO:0009620","count":6},{"id":"GO:0097350","count":6}]},{"hash":"659011319600448926","title":"Mitotic cell cycle and DNA replication","description":"Dominant terms are DNA replication and mitotic cell cycle, indicating a cell-division\u2013focused cluster. Other terms relate to cytoskeletal signaling and immune modulation, which can accompany division or development.","confidence":"High","size":7,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0046641","count":5},{"id":"GO:0001502","count":5},{"id":"GO:0097350","count":5}]},{"hash":"402166988138950622","title":"Unknown","description":"The top GO terms span immune signaling (TLR and lectin pathways), DNA repair, ubiquitin-dependent protein turnover and histone modification, transcription factor regulation, meiotic DSB formation, and peroxisome protein import, with no single cohesive function dominating the cluster. The diversity suggests no specific shared function to name, and several terms are even marked obsolete, so the appropriate label is Unknown with no confidence.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0035666","count":7},{"id":"GO:0042275","count":7},{"id":"GO:0071596","count":7},{"id":"GO:0010620","count":7},{"id":"GO:0033182","count":7}]},{"hash":"2064862041612250183","title":"Central energy metabolism and oxidative stress response","description":"Top terms cluster around glycolysis, the TCA cycle, and lactate fermentation, with additional hints of redox and xenobiotic stress responses. This combination indicates a group of proteins focused on core energy production and oxidative stress management, rather than a specific developmental or signaling function. Therefore the label captures the shared theme of central metabolism coupled with redox response.","confidence":"High","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":5},{"id":"GO:0006099","count":5},{"id":"GO:0006096","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0080093","count":3}]},{"hash":"2137364104105960528","title":"Unknown","description":"The GO terms are highly diverse, spanning redox-related metabolism (oxidation-reduction, redox homeostasis) and various biosynthetic and regulatory processes (glutamate, lipoate, guanine, auxin; chromatin binding regulation; corticosterone response). With no edges and a small, scattered set of annotations across different contexts, there is no cohesive common function tying the proteins together. Therefore this cluster cannot be confidently labeled with a single representative function.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0045654","count":5},{"id":"GO:0035563","count":5},{"id":"GO:0097054","count":5},{"id":"GO:0009106","count":5}]},{"hash":"1905430896362075770","title":"Fatty acid biosynthesis and transport","description":"The top GO terms point to fatty acid biosynthesis (GO:0006633) and lipid handling, including long-chain fatty acid import (GO:0044539) and medium-chain fatty acid transport (GO:0001579). This suggests a cluster centered on lipid metabolism, particularly synthesis and cellular transport of fatty acids, with some additional metabolite biosynthesis signals. The diversity of terms prevents a narrower single-pathway label, so a broad lipid metabolism label best captures the cluster\u2019s main function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902987","count":2},{"id":"GO:0009718","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006633","count":1},{"id":"GO:0010124","count":1}]},{"hash":"2300883324882685801","title":"Mitochondrial metabolism and autophagy regulation","description":"The top GO terms point to mitochondrial-focused processes (mitochondrial translation, fatty acid catabolism) together with autophagy/mitophagy-related terms (autophagy, negative regulation of mitophagy). This suggests a cluster of proteins involved in mitochondrial metabolism and its quality control via autophagy. Some terms (e.g., nylon catabolic process) may be annotation noise or peripheral to the main theme. ","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007029","count":2},{"id":"GO:0009062","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0019876","count":2},{"id":"GO:0070681","count":2}]},{"hash":"1972675258442465663","title":"Neural development and glial apoptosis","description":"Based on the top GO terms, the strongest and most recurring signals are forebrain development, nervous system development, and glial cell apoptotic process, which point to a coherent theme of neural development and regulation of glial cell fate. Other terms like cellular response to TGF-beta and L-methionine cycle provide contextual signaling and metabolism, but do not override the central neural-development focus. Therefore, this cluster is best labeled as Neural development and glial apoptosis. ","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":6},{"id":"GO:0010659","count":6},{"id":"GO:0035006","count":6},{"id":"GO:0033353","count":6},{"id":"GO:0071560","count":6}]},{"hash":"2104133354241739247","title":"Plant cytokinin signaling and floral development","description":"The GO terms are centered on plant development and hormone signaling, including cytokinin-activated signaling, flower and anther development, and regulation of vegetative phase change, suggesting these proteins participate in plant growth and flowering control. Some terms like sporulation and bacterial motility appear, which may reflect annotation noise or cross-species references, but the core theme is plant developmental signaling. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":2},{"id":"GO:0009908","count":2},{"id":"GO:0048653","count":2},{"id":"GO:0010321","count":2},{"id":"GO:0006935","count":1}]},{"hash":"1264864997817090575","title":"Plant secondary metabolism and cell-wall biosynthesis","description":"This cluster centers on plant-specific biosynthetic processes such as lignin, cutin, and flavonoid production, alongside related plant development/ Hormone processes (auxin homeostasis, pollination). The common thread appears to be plant metabolic pathways contributing to cell-wall components and protective metabolites, with some supporting developmental signals. Confidence: Medium","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0080088","count":1},{"id":"GO:0009809","count":1},{"id":"GO:0009963","count":1}]},{"hash":"986898190728776545","title":"Golgi nucleotide-sugar transport and glycosylation","description":"This cluster centers on transmembrane transport of sugar nucleotides into the Golgi lumen (UDP-glucose, GDP-fucose) and related glycosylation processes (O-linked and N-glycan fucosylation). Additional terms for transmembrane transport of triose phosphates and phosphoglycerates support a broader Golgi transporter context. Plant-specific terms like root hair and lateral root development may reflect downstream roles of glycosylation in development. Overall, the link is Golgi-based sugar transport and glycosylation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015786","count":1},{"id":"GO:0080147","count":1},{"id":"GO:1990536","count":1},{"id":"GO:0036066","count":1},{"id":"GO:0035436","count":1}]},{"hash":"366873634507576509","title":"Membrane Transporters","description":"The cluster is driven by diverse transmembrane transport functions: vitamin, xenobiotic, sialic acid, urate, galactose, sodium-dependent organic cation transport, and related solute transfers, plus a vesicular neurotransmitter loading term. This combination strongly suggests a group of membrane transporter proteins that move a variety of small molecules across membranes.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0015739","count":1},{"id":"GO:0015747","count":1}]},{"hash":"1621905267246903729","title":"Arabinogalactan protein\u2013driven plant cell wall biosynthesis","description":"The top terms concentrate on plant-specific processes: plant-type secondary cell wall biogenesis, root hair development, seed coat mucilage biosynthesis, arabinogalactan protein metabolism, and hydroxyproline glycosylation. Together they point to Arabinogalactan Protein (AGP)\u2013mediated glycoprotein production and cell wall assembly in plants. Some non-plant terms appear but are likely annotation noise; the dominant signal supports AGP-related cell wall biosynthesis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0007299","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0048354","count":2},{"id":"GO:0018258","count":2}]},{"hash":"1464674421410852582","title":"Transmembrane Transporters","description":"The top GO terms are dominated by transmembrane transport activities (sialic acid, vitamin, galactose, ion, xenobiotic transport, and neurotransmitter loading into synaptic vesicles), indicating these proteins primarily function as carriers or channels moving substrates across membranes; a few terms (e.g., nitrate assimilation) may reflect associated transport roles or linked metabolic processes.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0015739","count":6},{"id":"GO:0035461","count":6},{"id":"GO:0015757","count":6},{"id":"GO:0042891","count":6},{"id":"GO:1900754","count":6}]},{"hash":"565660822393876387","title":"mRNA decay and P-body assembly","description":"This cluster is dominated by terms related to post-transcriptional mRNA regulation, including deadenylation-dependent decay, decapping, P-body assembly, and miRNA-mediated silencing, indicating a functional grouping around mRNA turnover and translational repression, with a minor outlier term for phosphatidylcholine catabolism. ","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034638","count":2},{"id":"GO:0043928","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0045944","count":1}]},{"hash":"635723697964633120","title":"SCF-Mediated Ubiquitin-Proteasome Degradation","description":"This cluster is characterized by GO terms centered on ubiquitin-dependent proteolysis and SCF complex activity, including SCF-dependent proteasomal degradation and SCF complex assembly. The presence of ubiquitination-related processes, along with meiotic cell cycle regulation terms and receptor turnover (e.g., Wnt receptor catabolic process), all point to proteolytic control of protein levels via the ubiquitin-proteasome system, with SCF ligases playing a key role. Confidence reflects a cohesive link to ubiquitin-mediated degradation as the unifying theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0051759","count":5},{"id":"GO:1902104","count":5},{"id":"GO:0030433","count":5}]},{"hash":"711862953739387407","title":"Detoxification and Xenobiotic Metabolism","description":"The GO terms are dominated by responses to toxic substances and cellular oxidant detoxification, with several catabolic processes for lipids and conjugates, suggesting a cluster centered on detoxification and related metabolism rather than a single specific pathway. Some terms may reflect peripheral processes, but the detox theme is strongest.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0019391","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0055114","count":2}]},{"hash":"408989262863364109","title":"Muscle development and calcium signaling with transcriptional regulation","description":"Several GO terms emphasize muscle biology (positive regulation of skeletal muscle cell differentiation) and calcium signaling (cellular response to calcium ion), with transcriptional control (transcription by RNA polymerase II) tying these together. The presence of locomotor rhythm supports a muscle-function theme, while nutrient-responsive transcription and TGF-beta production reflect broader developmental signaling. Some terms relate to stress or development axes, which may be secondary. Overall, the cluster appears to center on muscle development coordinated by calcium signaling and transcriptional regulation.","confidence":"Medium","size":7,"edges":14,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":3},{"id":"GO:0071277","count":3},{"id":"GO:2001016","count":2},{"id":"GO:1990442","count":2},{"id":"GO:0010691","count":2}]},{"hash":"562691431121444147","title":"Steroid Hormone Biosynthesis and Metabolism","description":"The cluster is dominated by GO terms tied to steroid production and processing, including cortisol and testosterone biosynthesis and brassinosteroid biosynthesis, along with related metabolic and catabolic processes (retinoic acid, vitamin D response, omega-oxidation, xenobiotic catabolism). While terms like mammary gland development and endothelial adhesion reflect tissue contexts where hormones act, the central, shared theme is steroid biosynthesis and metabolism. ","confidence":"High","size":7,"edges":10,"triangles":6,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":6},{"id":"GO:0071603","count":6},{"id":"GO:0034651","count":6},{"id":"GO:0070989","count":6},{"id":"GO:0042738","count":6}]},{"hash":"739957951467359375","title":"GPI-anchored membrane protein processing and trafficking","description":"This cluster centers on membrane-associated protein handling: GPI anchor biosynthesis, proteolysis of membrane proteins at ectodomain and intracellular domains, ER-to-cytosol retrograde transport, ER exit and surface localization. The inclusion of regulators of calcineurin-NFAT signaling and immune response suggests calcium-dependent signaling outputs tied to membrane processing and trafficking. A few terms like pseudohyphal growth may reflect broader regulatory contexts, but the dominant theme is membrane protein processing and trafficking.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0006509","count":1},{"id":"GO:0051533","count":1},{"id":"GO:1904211","count":1},{"id":"GO:0070886","count":1}]},{"hash":"129931974022488286","title":"Vesicle trafficking and SNARE-mediated exocytosis","description":"The terms point to vesicle transport and fusion steps across Golgi, vacuole, and plasma membrane, including SNARE complex assembly and Golgi ribbon formation, plus exocytic insertion of receptors and neurotransmitter secretion. This suggests a coherent cluster centered on vesicle trafficking and exocytotic machinery, with related secretory regulation in neural and immune contexts.","confidence":"High","size":7,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0033194","count":2},{"id":"GO:0035493","count":2},{"id":"GO:0051024","count":2}]},{"hash":"1985099222103121486","title":"Neuronal spine morphogenesis and synaptic vesicle trafficking","description":"The top GO terms point to neuron-specific processes: regulation of dendritic spine morphogenesis and development, hippocampus development, and regulation of synaptic vesicle exocytosis, supported by membrane trafficking (Golgi to plasma membrane transport) and cytoskeletal remodeling (ruffle assembly). Mitochondrion inheritance aligns with energy needs in developing synapses. Although a couple terms seem less related (e.g., mating projection growth), the dominant signal is neuronal spine formation and synaptic function. ","confidence":"High","size":7,"edges":11,"triangles":2,"max_degree":4,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0097178","count":4},{"id":"GO:0000001","count":4},{"id":"GO:0061001","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0043001","count":4}]},{"hash":"2257548430797343604","title":"Post-transcriptional mRNA processing and translation","description":"The top GO terms cluster around mRNA processing (modification, stabilization, alternative and cis-splicing via spliceosome, polyadenylation) and translation initiation (IRES-dependent initiation, EIF4F complex assembly). This points to a cohesive functional module coordinating RNA maturation with translation initiation, which fits the protein set well. Some obsolete terms appear, but the core theme is consistent.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0075522","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0006378","count":2}]},{"hash":"1319379520899924994","title":"Unknown","description":"The top GO terms span plant development (stomatal morphogenesis), endocrine processing (insulin processing, renin secretion), signaling (peptide pheromone maturation), embryonic patterning (zygotic axis determination), and cholesterol transport via receptor-mediated endocytosis, with some obsolete terms. These represent disparate biological contexts across kingdoms and do not indicate a single cohesive function for the cluster, so no specific, representative label can be assigned beyond Unknown.","confidence":"","size":7,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010103","count":3},{"id":"GO:0030070","count":3},{"id":"GO:0007323","count":3},{"id":"GO:0032805","count":3},{"id":"GO:0032804","count":3}]},{"hash":"269230480666936735","title":"Unknown","description":"The top GO terms span diverse processes (DNA replication, glycogen metabolism, mevalonate/isoprenoid biosynthesis, calcium signaling and NFAT activation, inflammatory regulation, cell adhesion, and lung development) with no clear, single biological function linking the proteins. This heterogeneity suggests the cluster does not reflect a coherent, shared role, making a specific functional label uncertain.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000002","count":1},{"id":"GO:1900486","count":1},{"id":"GO:1900490","count":1},{"id":"GO:0050728","count":1},{"id":"GO:0005513","count":1}]},{"hash":"849865773128781333","title":"Triglyceride metabolism and synapse organization","description":"The top GO terms are dominated by triglyceride catabolic processes, triglyceride mobilization, and phospholipid catabolism/remodeling, suggesting a lipid metabolism emphasis. A subset of terms touches on inhibitory synapse assembly and presynaptic organization (neurexin clustering), implying these proteins may function at the interface of lipid remodeling and synaptic membrane assembly in neurons. Overall, the label reflects a lipid-centric cluster with a possible neuronal synaptic context.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":4},{"id":"GO:2000480","count":3},{"id":"GO:0006642","count":3},{"id":"GO:0046338","count":3},{"id":"GO:0034638","count":3}]},{"hash":"2126375673010024986","title":"Seed dormancy and shoot system development regulation","description":"The GO terms include seed dormancy regulation, germination inhibition, and brassinosteroid signaling, alongside shoot/leaf development and radial patterning, pointing to a developmental regulatory module in plants that ties seed fate to early shoot growth. The starch and maltose catabolic terms suggest energy mobilization to support such growth. Together these terms imply a brassinosteroid-regulated program coordinating seed dormancy with subsequent shoot system development.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005983","count":1},{"id":"GO:0048831","count":1},{"id":"GO:0000024","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0009742","count":1}]},{"hash":"1556514073404747917","title":"Neuronal GPCR-cAMP Signaling and Vesicle Fusion","description":"The cluster shows a core theme around G protein-coupled receptor (GPCR) signaling and cAMP pathways, including an adenylate cyclase-inhibiting GPCR signal and cAMP-related regulation terms, plus neuronal context such as forebrain neuron development and response to electrical stimulus, and vesicle fusion, suggesting involvement in neuronal signaling and neurotransmitter release. Some terms are marked obsolete or broad (e.g., cell cycle, pigmentation), indicating possible annotation noise, but the overarching pattern points to GPCR-cAMP\u2013driven neuronal signaling and vesicle trafficking.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0031684","count":1},{"id":"GO:0021884","count":1},{"id":"GO:0007193","count":1},{"id":"GO:0043950","count":1}]},{"hash":"2043089721425130951","title":"Vacuolar amino acid transporters","description":"Most terms point to transmembrane transport of amino acids into the vacuole (and some export), including L-tyrosine, L-glutamate, L-arginine, L-histidine, and L-asparagine, plus general ion/molecule transport. This suggests a cluster of proteins functioning as vacuolar amino acid transporters. A few terms (lateral root morphogenesis, intron splicing) and obsolete entries are less connected and likely annotation noise, but do not dominate the set.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010102","count":1},{"id":"GO:0000373","count":1},{"id":"GO:0090514","count":1},{"id":"GO:1901481","count":1},{"id":"GO:0090518","count":1}]},{"hash":"1700578664781346329","title":"Hematopoietic stress response and immune signaling","description":"This cluster blends immune-related processes (positive regulation of IL-6 production; isotype switching to IgG) with stress and survival pathways (apoptotic regulation in bone marrow, cadmium response, ROS regulation, protein refolding, telomere maintenance). The common thread appears to be stress- and immune-related functions in hematopoietic cells rather than a single cohesive pathway, justifying a label that reflects both aspects.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1904871","count":3},{"id":"GO:2000778","count":3},{"id":"GO:1901998","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0048291","count":3}]},{"hash":"2210652340244596136","title":"Immune Defense, Coagulation, and Angiogenesis","description":"The GO terms show a coherent theme around immune defense (defense response to Gram-positive bacteria, complement activation) and hemostasis-related processes (positive regulation of blood coagulation) along with vascular remodeling (positive regulation of angiogenesis, smooth muscle cell migration). While some terms reflect general cellular processes (DNA replication, transcription regulation), the strongest signals tie to immune/coagulation and vascular changes, justifying this combined label.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071333","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0045766","count":2}]},{"hash":"2137678671170890079","title":"Neural Development","description":"The top GO terms are dominated by nervous system development, neural tube closure, forebrain development, and dendrite morphogenesis, indicating a cluster of proteins involved in neural development. While terms for DNA replication, repair, transcription, and the cell cycle appear, the neural development terms are most frequent and define the cluster's likely function.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0001843","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0006281","count":6},{"id":"GO:0048813","count":6}]},{"hash":"944763279017770791","title":"ER Stress Response and Protein Folding","description":"The cluster's GO terms predominantly point to ER-associated protein handling, unfolded protein response, and SRP-dependent targeting to the membrane, indicating a role in protein quality control and stress response; a few terms are unrelated (DNA replication, hematopoietic differentiation), but the central signal is ER stress/protein folding.","confidence":"High","size":6,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:1900035","count":2},{"id":"GO:0016226","count":2},{"id":"GO:1903751","count":2},{"id":"GO:1903382","count":2}]},{"hash":"39565905881017821","title":"Pollen-wall lipid and flavonoid biosynthesis","description":"The proteins show strong representation of fatty acid biosynthesis and long-chain fatty-acyl-CoA metabolism, plus sporopollenin, chalcone, and flavonoid biosynthetic processes. This combination points to processes involved in pollen-wall construction (sporopollenin) supported by lipid and phenolic metabolite pathways, with flavonoids and chalcones as typical phenylpropanoid-derived components. The cluster likely reflects coordinated biosynthesis for pollen wall formation and related secondary metabolites.","confidence":"High","size":6,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":3},{"id":"GO:0035336","count":3},{"id":"GO:0080110","count":3},{"id":"GO:0031148","count":3},{"id":"GO:0071770","count":3}]},{"hash":"686792837976138705","title":"Plant Development and Hormone-Regulated Transcription","description":"The GO terms show enrichment for DNA-templated transcription regulation along with plant developmental processes (floral meristem growth, bract development, multicellular organism development) and hormone signaling (abscisic acid and ethylene). This pattern suggests a set of transcriptional regulators coordinating growth, epidermal features like cutin and wax biosynthesis, and hormone responses typical of plant development. The label captures the core theme across these terms.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0010451","count":1},{"id":"GO:0009873","count":1},{"id":"GO:0010432","count":1},{"id":"GO:0007275","count":1}]},{"hash":"2050862225256377838","title":"Nuclear transcription and chromatin organization","description":"The cluster shows a pattern dominated by nuclear processes: DNA-templated transcription, transcription preinitiation complex assembly, nucleosome assembly, and pericentric heterochromatin formation, pointing to roles in transcription initiation and chromatin packaging. Some vesicle trafficking terms and rRNA processing terms are present but appear less representative of the core theme. This suggests the proteins collectively participate in gene expression regulation and chromatin organization more than in cytosolic trafficking.","confidence":"Medium","size":6,"edges":9,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000469","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0048280","count":1},{"id":"GO:0048279","count":1},{"id":"GO:0016320","count":1}]},{"hash":"979265496461718226","title":"Glycan and cell wall biosynthesis","description":"The top GO terms cluster around carbohydrate biosynthesis and cell surface components (GDP-mannose, UDP-glucose, LPS, lipid A) and include cell wall organization and mannoprotein biosynthesis. This suggests a common function in producing and assembling cell-surface glycans and cell-wall polysaccharides across species.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":2},{"id":"GO:0009298","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0000032","count":2}]},{"hash":"1115444923182284233","title":"Steroid Hormone Biosynthesis and Xenobiotic Metabolism","description":"The top GO terms strongly point to steroid biosynthesis (cortisol, testosterone) and related metabolic processes (fatty acid omega-oxidation, xenobiotic catabolic process, oxidative demethylation). While some developmental terms appear, the core signal is metabolic and endocrine rather than purely developmental, suggesting a cluster of proteins involved in steroidogenesis and detox/lipid metabolism.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061298","count":4},{"id":"GO:0030879","count":3},{"id":"GO:0071603","count":3},{"id":"GO:0034651","count":3},{"id":"GO:0070989","count":3}]},{"hash":"483097090462499988","title":"Endosomal Trafficking and Vesicle Sorting","description":"This cluster centers on GO terms for endocytosis and endosome-mediated transport to the Golgi and vacuole, including multivesicular body sorting; together they point to a cohesive set of proteins involved in endomembrane trafficking and cargo sorting within the endocytic pathway.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0006623","count":1}]},{"hash":"2180557837836613184","title":"DNA Replication Machinery","description":"Most of the prominent GO terms here are directly tied to DNA replication and genome maintenance (primer synthesis, DNA unwinding, topological changes). The additional terms (hypoxia response, UV protection, embryonic development, nonsense-mediated decay, hair cell differentiation, MDA-5 signaling) appear to be broader or incidental annotations, possibly reflecting multifunctional proteins or cross-annotation. Overall, the cluster is best described by a replication-centric theme with some ancillary functions.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":3},{"id":"GO:0006269","count":2},{"id":"GO:0032508","count":2},{"id":"GO:0009650","count":2},{"id":"GO:0006268","count":2}]},{"hash":"1639443840656096686","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1904571","count":2},{"id":"GO:0000492","count":2},{"id":"GO:0000470","count":2},{"id":"GO:0000185","count":2},{"id":"GO:0031120","count":2}]},{"hash":"660683777084723867","title":"Plastid rRNA maturation and ribosome biogenesis","description":"The strongest GO terms are maturation of 5.8S rRNA and maturation of LSU rRNA from tricistronic rRNA transcript, which points to ribosome biogenesis in plastids/chloroplasts. The presence of a plastid-related term (light-independent chlorophyll biosynthetic process) further supports a plastid context. While a few other terms are unrelated noise, the dominant theme is plastid rRNA processing and ribosome assembly.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0070940","count":2},{"id":"GO:0006935","count":1},{"id":"GO:0018027","count":1}]},{"hash":"388459767374470142","title":"Plant energy metabolism and metal detox","description":"The GO terms point to organellar energy production (mitochondrial complex I/II assembly, photosynthesis and photosystem II O2-evolving complex assembly) and organellar gene expression (rRNA methylation). They also include plant-specific signals (response to cytokinin) and metal handling/detoxification (mercury, cadmium transport; copper transfer). Taken together, this suggests a cluster of plant proteins involved in energy metabolism in organelles and metal homeostasis/detox. ","confidence":"Medium","size":6,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":2},{"id":"GO:0070475","count":1},{"id":"GO:0032981","count":1},{"id":"GO:0009735","count":1},{"id":"GO:0015979","count":1}]},{"hash":"1109946861938374280","title":"Unknown","description":"The GO terms are scattered across immune-related processes (innate immune response, neutrophil clearance) and broader cellular roles (DNA repair, protein ubiquitination, microtubule localization, vitamin D response). There isn\u2019t a single coherent function that ties all six proteins together, so the set appears heterogeneous rather than representing a specific pathway. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035372","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0051092","count":2}]},{"hash":"1821403555767574658","title":"Steroid and lipid metabolism","description":"The top GO terms cluster around biosynthesis and catabolic processes for steroids and lipid-related pathways (cortisol and testosterone biosynthesis, fatty acid omega-oxidation, retinoic acid catabolic, vitamin D response, xenobiotic metabolism), suggesting a cohesive theme of steroid/hormone and lipid metabolism. Some terms like mammary gland development and endothelial adhesion appear peripheral and may reflect tissue context rather than core function. The absence of network edges supports a loosely connected set of metabolic functions rather than a single interaction module.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":2},{"id":"GO:0071603","count":2},{"id":"GO:0034651","count":2},{"id":"GO:0070989","count":2},{"id":"GO:0042738","count":2}]},{"hash":"1142811094567474691","title":"Microtubule-driven mitosis and neural transport","description":"The top GO terms center on microtubule-based processes (minus-end directed sliding, centrosome separation, mitotic spindle orientation) plus aspects of neuronal transport and tissue architecture (dendritic transport, adherens junction maintenance, cerebellar structure organization). This points to a set of proteins coordinating cytoskeletal dynamics for cell division and for intracellular transport in neural and epithelial contexts, hence the chosen label. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000911","count":6},{"id":"GO:0098971","count":6},{"id":"GO:0021685","count":6},{"id":"GO:0021693","count":6},{"id":"GO:0045218","count":6}]},{"hash":"1277088152413212046","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms tied to ribosome assembly and protein synthesis, including translation, maturation of LSU rRNA, ribosome biogenesis, and cytoplasmic translation initiation\u2014covering initiation complex formation and both initiation and its regulation. These terms collectively point to a group of proteins involved in ribosome production and control of translation rather than unrelated processes.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000463","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0000055","count":1},{"id":"GO:1901857","count":1}]},{"hash":"613564948156159735","title":"Bacterial lipid and steroid metabolism","description":"This cluster shows several terms tied to lipid biosynthesis and metabolism (mycolic acid biosynthesis, fatty acid elongation, retinol metabolism) and steroid-related processes (testosterone biosynthetic, androgen metabolic/catabolic). While sporulation and regulation of transcription appear less directly linked, the dominant signal is lipid and steroid metabolic pathways in bacteria, potentially including Actinobacteria. Confidence: Medium","confidence":"","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030435","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0045150","count":3},{"id":"GO:0042572","count":3},{"id":"GO:0061370","count":3}]},{"hash":"174171493770984288","title":"Unknown","description":"Top GO terms span several distinct metabolic processes (anthocyanin biosynthesis; allantoin, ureide, purine nucleobase catabolism; oxalate and lignin metabolism) as well as plasmodesmata-mediated transport and paranode localization, with no clear unifying function. The lack of edges and the diverse annotations suggest the cluster does not represent a single, coherent biological role.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":3},{"id":"GO:0010136","count":2},{"id":"GO:0000256","count":2},{"id":"GO:0033609","count":2},{"id":"GO:0017000","count":2}]},{"hash":"609028489597277524","title":"Stress-Linked Organelle Protein Import and Metabolism","description":"The GO terms cluster around stress responses (oxidative stress, cadmium stress) and energy-related processes, including peroxisomal matrix protein import, mitochondrial inner membrane protein insertion, ATP metabolism, and regulation of aerobic respiration, with DNA replication/cell division suggesting a stress-linked link to the cell cycle.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1990171","count":2}]},{"hash":"164362204234112700","title":"Methylation-linked biosynthesis of small molecules","description":"The prominent GO terms center on methylation (protein methylation and general methylation) and various biosynthetic processes (cobalamin, antibiotics, coumarin, lignin), suggesting the proteins participate in methylation-driven biosynthesis of small-molecule metabolites rather than a single, specific pathway.","confidence":"Medium","size":6,"edges":10,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":4},{"id":"GO:0006479","count":3},{"id":"GO:0032259","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006584","count":2}]},{"hash":"772674293251039691","title":"Neural development and synaptic regulation","description":"The top GO terms point to neural development and synaptic function, including synapse organization, learning, neuroblast differentiation, and negative regulation of cholinergic synaptic transmission, which together suggest a cluster of proteins involved in neuronal development and synaptic signaling. Some terms (e.g., cellulose catabolic process, cocaine metabolic process, cholesterol biosynthetic process) appear ancillary or anomalous, but the core themes align with neural differentiation and synaptic regulation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":3},{"id":"GO:0050808","count":3},{"id":"GO:0030245","count":3},{"id":"GO:0007612","count":3},{"id":"GO:0032223","count":3}]},{"hash":"2144863001077940923","title":"Mitochondrial dynamics and apoptosis","description":"The top terms center on mitochondrial functions (mitochondrial translation and regulation of mitochondrial fusion) and apoptosis, with additional signals from DNA-templated transcription and signaling pathways, suggesting a theme of mitochondrial-nuclear coordination in cell fate.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006915","count":1},{"id":"GO:0032543","count":1},{"id":"GO:0015074","count":1},{"id":"GO:1901253","count":1}]},{"hash":"32512718645027873","title":"Organic Compound Metabolism and Detoxification","description":"The Top Terms point to diverse catabolic and metabolic processes acting on various organic molecules (stilbene, chlorophyll, uracil) and to detoxification/oxidation-reduction activities (P450 epoxygenase pathway, cellular oxidant detoxification). The presence of antibiotic biosynthetic and depalmitoylation processes further supports a general metabolic/processing role rather than a single, cohesive pathway. Overall, this cluster seems to group proteins involved in broad metabolism and detoxification of organic compounds.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0046272","count":2},{"id":"GO:0015996","count":2},{"id":"GO:0019373","count":2}]},{"hash":"484354276472765464","title":"Steroid hormone biosynthesis and metabolism","description":"GO terms cluster around steroid biosynthesis and hormone-related metabolism (cortisol, testosterone, retinoic acid/catabolic processes, vitamin D response, and brassinosteroid biosynthesis). Additional terms reflect lipid/xenobiotic oxidation and development that are frequently hormone-regulated, supporting a cohesive theme of steroid hormone production and related metabolic pathways.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":3},{"id":"GO:0071603","count":3},{"id":"GO:0034651","count":3},{"id":"GO:0070989","count":3},{"id":"GO:0042738","count":3}]},{"hash":"2017487466067594778","title":"Protein acetylation","description":"The top GO terms are dominated by various acetylation processes (N-terminal acetylation, peptidyl-lysine/glutamate acetylation, and histone H4 acetylation) with a chromatin-associated term (subtelomeric heterochromatin formation) suggesting a shared theme around acetylation and chromatin regulation. Some other terms like leaf formation or ectoine biosynthesis seem unrelated and may reflect annotation noise. Overall, the cluster appears to center on acetylation-related functions, including histone-related modifications, rather than a single narrowly defined pathway.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":2},{"id":"GO:0032919","count":2},{"id":"GO:0043967","count":2},{"id":"GO:0018002","count":2},{"id":"GO:0045150","count":2}]},{"hash":"163055835655014175","title":"Plant Development and Hormone Signaling Regulation","description":"These proteins cluster around plant-specific development and hormone-responsive pathways, including floral meristem growth, bract development, and general multicellular development, alongside ethylene- and abscisic acid-activated signaling and transcriptional regulation. The mix of developmental processes, hormone signaling, wax biosynthesis regulation, and transcription/kinase activity modulation suggests a module coordinating organ formation and defense through transcriptional control and signaling networks.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010432","count":2}]},{"hash":"1690545283262425428","title":"NF-kappaB and JNK pathway regulators","description":"Genes appear to regulate JNK cascade and NF-kappaB activation, with linked ubiquitination and histone modification processes suggesting coordinated signaling and transcriptional regulation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000620","count":2},{"id":"GO:0036205","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0007250","count":2},{"id":"GO:0070512","count":2}]},{"hash":"97685181294136676","title":"One-carbon and amino acid metabolism","description":"The top GO terms point to amino acid biosynthesis and one-carbon metabolism, including the L-methionine cycle, L-serine biosynthesis, formate catabolism, and dicarboxylic acid metabolism, with supporting references to vitamin B6 (pyridoxine) biosynthesis and polyamine (spermine) catabolism. Despite some obsolete terms and an outlier adipogenesis term, the central theme ties to metabolic pathways involved in amino acid turnover and one-carbon flux.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0034720","count":2},{"id":"GO:0046208","count":2},{"id":"GO:0043648","count":2},{"id":"GO:0033353","count":2}]},{"hash":"1936078551510950594","title":"Unknown","description":"The GO terms are highly diverse, spanning peptide methylation, chlorophyll/juvenile hormone/antibiotic biosynthesis, cellular senescence, and stress responses, with no clear shared function or interaction pattern to tie the proteins into a coherent theme.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":1},{"id":"GO:0014075","count":1},{"id":"GO:0036068","count":1},{"id":"GO:0035572","count":1},{"id":"GO:0046690","count":1}]},{"hash":"1043297317397393196","title":"Plant Hormone Signaling and Defense Responses","description":"The top GO terms cluster around plant hormone signaling (gibberellin, salicylic acid, ACC/ethylene) and immune responses (chitin sensing, antifungal defense), with associated epidermal differentiation processes (atrichoblast, sclerenchyma), suggesting a module linking growth regulation with plant innate immunity.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080169","count":4},{"id":"GO:0009961","count":4},{"id":"GO:0010055","count":4},{"id":"GO:0009751","count":4},{"id":"GO:0009739","count":4}]},{"hash":"1836741620906719954","title":"Ubiquitin-dependent transcription regulation","description":"This cluster is characterized by GO terms tied to protein ubiquitination and degradation, including the N-end rule pathway and histone ubiquitination, as well as transcription factor catabolism. Together these point to a common theme: ubiquitin-mediated control of transcription through targeted protein turnover. Several terms in the list relate to immune signaling and DNA repair as potential ancillary roles or background associations, so the dominant signal remains ubiquitin-dependent transcription regulation rather than a single defined pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0035666","count":6},{"id":"GO:0042275","count":6},{"id":"GO:0071596","count":6},{"id":"GO:0010620","count":6},{"id":"GO:0033182","count":6}]},{"hash":"1999620980805015045","title":"Unknown","description":"The top GO terms are highly diverse and show no single, shared function. They span exocytosis regulation, membrane remodeling, nuclear import, toxin response, astrocyte activation, heart rate regulation, sporulation membrane formation, and adenylate cyclase signaling, making it unclear what common biological role ties these proteins together.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045921","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0033234","count":1},{"id":"GO:0032120","count":1},{"id":"GO:1903525","count":1}]},{"hash":"1495500669490792796","title":"Ciliogenesis and photoreceptor organization","description":"This cluster is best described by ciliogenesis and photoreceptor organization, given the repeated emphasis on regulation of non-motile cilium assembly and photoreceptor cell outer segment organization. Some other GO terms touch on broad tissue development and immune responses, which are less cohesive with the core ciliary/sensory signal, but the cilium/photoreceptor theme is the strongest.","confidence":"Medium","size":6,"edges":7,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070389","count":4},{"id":"GO:0035457","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0009938","count":4},{"id":"GO:0003283","count":4}]},{"hash":"1939701351687017162","title":"Innate Immunity and Neurobehavioral Signaling","description":"The top GO terms show strong enrichment for innate immune responses to lipopolysaccharide and bacteria, dsRNA sensing, and interferon-beta production, indicating a core immune function. Several terms also relate to neural development and behavior (axonogenesis, synapse assembly, dopamine response, pain behavior), suggesting the cluster links immune signaling to neurobehavioral processes. Confidence: Medium","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051965","count":6},{"id":"GO:0045087","count":6},{"id":"GO:0071222","count":6},{"id":"GO:0050830","count":6},{"id":"GO:0061368","count":6}]},{"hash":"584891044254893015","title":"Immune Activation and Transcriptional Regulation","description":"The cluster features terms tied to innate immune response, T cell proliferation, neutrophil clearance, and programmed cell death, along with DNA-templated transcription and transcriptional regulation, suggesting a group of proteins involved in immune signaling and gene expression control. Some microtubule localization and cartilage-related terms are peripheral, but the dominant theme is immune activation and transcriptional control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035372","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051436","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0051092","count":3}]},{"hash":"2220691447846278148","title":"Translation initiation and mRNA processing regulation","description":"The cluster is enriched for terms related to regulation of translational initiation, assembly of the eIF4F complex, mRNA modification and stabilization, and alternative splicing, suggesting a cohesive role in post-transcriptional gene expression control, including translation initiation and mRNA maturation processes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006446","count":4},{"id":"GO:0016556","count":3},{"id":"GO:0048255","count":3},{"id":"GO:0075522","count":3},{"id":"GO:1905663","count":3}]},{"hash":"856947145994410735","title":"Amino acid biosynthesis and metabolism","description":"The top GO terms point to amino acid-related pathways (glutamine, glutamate, phenylalanine) and central carbon metabolism (TCA), with some transcription activity present but not dominant. The cluster appears to reflect proteins involved in amino acid biosynthesis and metabolism, plus related metabolic processes; some terms are obsolete, which lowers cohesion. ","confidence":"Medium","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0019551","count":3},{"id":"GO:0006541","count":2},{"id":"GO:0019552","count":2}]},{"hash":"494567371696211941","title":"Vitamin and antioxidant biosynthesis","description":"The cluster shows multiple biosynthetic processes for small molecules, especially vitamins (retinol/retinal, L-ascorbic acid) and antioxidants (glutathione), along with a steroid biosynthesis term (testosterone). The presence of these related metabolic processes suggests a theme of vitamin/steroid and redox metabolism, though some signaling and stress-related terms are also present, indicating multifunctionality or pleiotropy.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":5},{"id":"GO:0042574","count":5},{"id":"GO:2000353","count":4},{"id":"GO:0044597","count":4},{"id":"GO:0009414","count":4}]},{"hash":"377355930155501382","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning plant secondary metabolism (lignin, anthocyanin biosynthesis), animal/human metabolism (estrogen catabolism), broad xenobiotic and antibiotic metabolism, a neuronal localization term, and several obsolete terms, with little overlap linking them into a single coherent function. The single edge and lack of a unifying theme support labeling this cluster as Unknown.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009718","count":3},{"id":"GO:0097171","count":2},{"id":"GO:0002175","count":2},{"id":"GO:0009808","count":2}]},{"hash":"775831446861597915","title":"Vesicle trafficking and cytoskeletal regulation","description":"This cluster centers on processes tied to moving and secreting vesicles and remodeling the cytoskeleton: neurotransmitter secretion, calcium-regulated lysosome exocytosis, and actin-driven structures like dendritic spines and podosomes, plus mating projection growth. Lipid biosynthesis terms likely reflect membrane supply for vesicles, and Ras signaling modulation fits into the broader signaling context that controls trafficking and morphology. Overall, the shared thread is vesicle dynamics coupled with cytoskeletal remodeling in neuronal and immune contexts.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0031384","count":6},{"id":"GO:0010796","count":6},{"id":"GO:0060999","count":5},{"id":"GO:0071803","count":5},{"id":"GO:0006646","count":5}]},{"hash":"499743456083149422","title":"Cholinergic signaling with oxidative stress response","description":"These proteins appear linked to cholinergic synaptic signaling and oxidative stress responses, including ethanol response, ROS metabolism, and hydrogen peroxide\u2013mediated programmed cell death, with additional hints from serotonin uptake regulation and ion transporter activity, pointing to a neural-stress signaling module.","confidence":"Medium","size":6,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":4},{"id":"GO:0006979","count":4},{"id":"GO:0036245","count":3},{"id":"GO:0007271","count":3},{"id":"GO:0060192","count":3}]},{"hash":"2090043076591038646","title":"Unknown","description":"The top GO terms span many tissues and processes (neural differentiation, heart development, muscle satellite cell commitment, root development, meiosis, vitamin A metabolism, etc.) with no single cohesive function linking the proteins. As a result, there isn\u2019t a specific, representative theme to name the cluster beyond a broad developmental/differentiation context.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042663","count":1},{"id":"GO:0021892","count":1},{"id":"GO:0080022","count":1},{"id":"GO:0030516","count":1},{"id":"GO:0014813","count":1}]},{"hash":"1617555639600471853","title":"Plant innate immunity and hypersensitive response","description":"These terms converge on plant immune defense against bacteria and the hypersensitive response, including innate signaling; the negative regulation term adds a regulatory nuance, but the cluster clearly represents plant innate immunity/HR activity.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034051","count":1},{"id":"GO:0009816","count":1},{"id":"GO:0009626","count":1},{"id":"GO:0010204","count":1}]},{"hash":"538863514263568402","title":"Transmembrane transporters","description":"The cluster\u2019s top GO terms are dominated by various membrane transport activities (sialic acid, vitamin, urate, organic cation, galactose, potassium, nitrate assimilation, etc.) and neurotransmitter loading, indicating proteins that move solutes across membranes rather than performing catalytic or structural roles. The shared theme across substrates and transport directions supports a single functional category: membrane transporters.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":5},{"id":"GO:0035461","count":5},{"id":"GO:0015747","count":5},{"id":"GO:0070715","count":5},{"id":"GO:0015757","count":5}]},{"hash":"759789232459858408","title":"Unknown","description":"The top GO terms are highly diverse, spanning mitochondrial import and membrane permeability, triglyceride biosynthesis regulation, cell cycle control, zinc response, tRNA surveillance, NF-kappaB signaling, and spindle checkpoint signaling. This lack of a single cohesive functional theme (and even presence of obsolete terms) makes it unclear what a representative, specific label would be. Confidence: None","confidence":"","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":3},{"id":"GO:0010867","count":3},{"id":"GO:2000134","count":3},{"id":"GO:1903740","count":3},{"id":"GO:0046902","count":3}]},{"hash":"704262656370680016","title":"Diverse Organic Compound Catabolism","description":"This cluster is enriched for catabolic and detoxification activities across a range of organic substrates, including glucuronosides, stilbenes, and chlorophyll, with P450-related oxidation and cellular oxidant detoxification terms. While some GO terms (antibiotic biosynthesis, C-terminal demethylation) are less obviously catabolic, they still fit within broader metabolic processing of organic molecules, suggesting a cohesive theme of diverse organic compound metabolism.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019391","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0015996","count":2},{"id":"GO:0019373","count":2}]},{"hash":"218811733777934025","title":"Proteolysis and Tissue Remodeling","description":"The top GO terms include peptide catabolism (neuropeptide and bradykinin), regulation of catalytic activity, and remodeling processes (bone resorption, basement membrane disassembly), plus immune and developmental remodeling (T cell cytotoxicity, macrophage apoptosis, lung branching). Together, they suggest a common theme of proteolysis-driven remodeling across tissues.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":6},{"id":"GO:0010813","count":6},{"id":"GO:0010815","count":6},{"id":"GO:0045453","count":6},{"id":"GO:0001913","count":6}]},{"hash":"1101025585527448453","title":"Ubiquitin-dependent regulation of transcription and signaling","description":"The top GO terms are dominated by ubiquitin-related processes (N-end rule\u2013mediated proteolysis, histone ubiquitination, transcription factor turnover, and DNA repair), suggesting a common theme of ubiquitin-dependent regulation of transcription and chromatin. Additional terms point to innate immune signaling and genome maintenance, which are often governed by ubiquitin-mediated regulation. Thus, the cluster likely reflects proteins involved in ubiquitin-dependent control of transcriptional activity and signaling pathways.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0035666","count":5},{"id":"GO:0042275","count":5},{"id":"GO:0071596","count":5},{"id":"GO:0010620","count":5},{"id":"GO:0033182","count":5}]},{"hash":"531918824171036284","title":"Unknown","description":"This cluster lacks a single cohesive biological theme: terms range from proteolysis and protein catabolic processes to plant defense (systemic acquired resistance, antibacterial peptide production) and even plant cell wall breakdown (xylan catabolic process), plus signaling and vascular regulation (cGMP response, renin\u2013angiotensin). The heterogeneity and sparse connectivity suggest no clear, unified function for the group.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006627","count":1},{"id":"GO:0000746","count":1},{"id":"GO:0002803","count":1},{"id":"GO:0030163","count":1},{"id":"GO:0070305","count":1}]},{"hash":"1033532740554785819","title":"Pollination and seed/embryo development","description":"The main GO terms center on pollination, pollen tube development, seed development, and embryo development, pointing to plant reproductive processes. Aluminum cation transport is present but appears peripheral to the dominant reproductive themes. Given the strong representation of reproductive development terms, this cluster is best described as a module of plant reproductive development associated with fertilization and seed formation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009856","count":1},{"id":"GO:0015690","count":1},{"id":"GO:0048868","count":1},{"id":"GO:0048316","count":1},{"id":"GO:0009790","count":1}]},{"hash":"1784416125182495496","title":"Microbial biosynthesis and metabolism","description":"Top GO terms indicate a bias toward biosynthetic and metabolic processes common in microbes, including antibiotic biosynthesis, sporulation, mycolic acid and LPS core biosynthesis, GDP-mannose metabolism, and acetoin catabolism. Some terms (retinol and testosterone biosynthesis) appear as outliers or noisy annotations, but the prevailing pattern is microbial biosynthetic activity. The absence of edges suggests this cluster groups proteins by functional annotations rather than direct interactions, supporting a high-level label around biosynthesis and metabolism in microbes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0045150","count":1},{"id":"GO:0042572","count":1}]},{"hash":"1425692467298774431","title":"Embryonic organogenesis and cell fate specification","description":"This cluster includes proteins associated with developmental patterning and lineage specification across several tissues, notably cardiac morphogenesis (heart valve development, outflow tract morphogenesis, cardioblast migration), mesenchyme development, floor plate formation, and neural and pancreatic cell fate decisions (GABAergic interneurons, auditory receptor fate, pancreatic A cells). The common thread is embryonic tissue morphogenesis and differentiation, with some alignment to cell cycle regulation in proliferative progenitors.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000793","count":4},{"id":"GO:2000764","count":4},{"id":"GO:0060375","count":4},{"id":"GO:0060485","count":4},{"id":"GO:0071156","count":4}]},{"hash":"103748986347799175","title":"Neural and cardiac development regulators","description":"The cluster shows enrichment for neural differentiation (astrocyte, GABAergic interneuron, auditory receptor fate) and cardiac/mesenchymal morphogenesis (heart valve development, mesenchyme development), plus transcriptional regulation and cell-cycle control, suggesting broad developmental regulatory roles across neural and cardiac lineages rather than a single pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048712","count":4},{"id":"GO:2001038","count":4},{"id":"GO:0006366","count":4},{"id":"GO:2000793","count":3},{"id":"GO:2000764","count":3}]},{"hash":"1456232017360165973","title":"Unknown","description":"The top GO terms span diverse biosynthetic and modification processes (lipid/sterol, mycolic acid, chlorophyll, juvenile hormone) plus unrelated responses and modifications, showing no cohesive single function for the cluster. Confidence in a unifying theme is therefore None.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016126","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0018027","count":1},{"id":"GO:0014075","count":1},{"id":"GO:0036068","count":1}]},{"hash":"879033126322168787","title":"Plant transcriptional regulation and development","description":"Top GO terms indicate regulation and execution of DNA-templated transcription, plus several plant-specific developmental processes (floral meristem growth, bract development, multicellular organism development) and hormone/signaling pathways (ethylene, ABA). Also includes DNA repair and response to ionizing radiation, suggesting a link to stress-induced transcriptional control. Taken together, the cluster appears to group plant proteins that regulate transcription during development and integrate stress/hormone signals.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010212","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0010451","count":1}]},{"hash":"542696006404047412","title":"Anthocyanin biosynthesis and lignin metabolism","description":"The top GO terms cluster around flavonoid/anthocyanin production (anthocyanin-containing compound biosynthesis, cyanidin 3-O-glucoside biosynthesis) and lignin metabolism, with related flavonoid modifications. This points to a cohesive phenylpropanoid pathway theme rather than unrelated processes.","confidence":"High","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":5},{"id":"GO:0002175","count":4},{"id":"GO:0009808","count":4},{"id":"GO:0006711","count":4},{"id":"GO:0052697","count":4}]},{"hash":"1606450761646729783","title":"Xylem development and hormone-responsive transcription","description":"This cluster centers on vascular development in plants, with terms pointing to protoxylem development and xylem vessel differentiation, and links to transcriptional regulation and secondary cell wall biogenesis. The presence of hormone-related responses (salicylic acid and gibberellin) and developmental processes like callus formation and leaf senescence suggests transcription factors governing xylem formation under hormonal cues. Together, these indicate a cohesive theme of transcriptional regulation driving xylem development in hormones\u2019 presence.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:1901348","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2}]},{"hash":"862273855303934504","title":"Steroid and retinoid metabolism","description":"The cluster centers on biosynthesis and metabolism of steroid hormones (cortisol, testosterone) and lipid-derived signals (retinoic acid), with related vitamin D responses and steroid-like pathways (brassinosteroids in plants). Additional terms include xenobiotic catabolism and omega-oxidation, which are commonly linked to detoxification enzymes that also process lipid hormones. A few terms (mammary gland development, endothelial adhesion) are less directly connected, but the dominant theme is steroid/retinoid metabolism and associated detoxification processes.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":6},{"id":"GO:0071603","count":6},{"id":"GO:0034651","count":6},{"id":"GO:0070989","count":6},{"id":"GO:0042738","count":6}]},{"hash":"1548548524481351040","title":"Chemical stimulus response and metabolism","description":"Predominant GO terms center on responses to chemical stimuli ( xenobiotic, alkaloid, glucocorticoid, gibberellin) and various metabolic processes (cholesterol biosynthesis, cellulose catabolism), plus regulatory aspects like receptor recycling. Although the terms span diverse contexts, the common thread is chemicals-responsive signaling intertwined with metabolism.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0006695","count":3},{"id":"GO:0051384","count":3},{"id":"GO:0009939","count":3},{"id":"GO:0043279","count":3}]},{"hash":"1889829034110292298","title":"Photosynthesis and respiration energy metabolism proteins","description":"Most Top Terms cluster around energy metabolism: photosynthesis, photosystem II stabilization, mitochondrial electron transport, aerobic respiration, and proton transmembrane transport, suggesting the proteins contribute to cellular energy production. A handful of brain-development GO terms appear, likely annotation noise or cross-species associations, not indicating a unified brain-specific function for this cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0006950","count":1},{"id":"GO:0042549","count":1},{"id":"GO:0021794","count":1},{"id":"GO:0021860","count":1}]},{"hash":"57129655770600715","title":"Unknown","description":"The top GO terms span immune response, development in several tissues, apoptosis, metabolism, and proteolysis, with no single coherent theme tying them together. The absence of shared pathway connections and the diverse tissue associations make it unclear what specific function unites these proteins, so a precise, representative label cannot be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0010659","count":3},{"id":"GO:0035006","count":3}]},{"hash":"942145061160588083","title":"Rac/Rho-mediated dendritic spine morphogenesis","description":"The dominant GO terms point to Rac and Rho GTPase signaling driving actin cytoskeleton remodeling, lamellipodium and ruffle formation, and positive regulation of dendritic spine development and morphogenesis, all essential for neuronal spine formation. The presence of Golgi to plasma membrane transport hints at trafficking involved in membrane remodeling, and hippocampus development supports a neural context for these processes, together indicating a cluster centered on neuronal actin-driven spine morphogenesis regulated by Rac/Rho pathways.","confidence":"High","size":6,"edges":10,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016601","count":2},{"id":"GO:0045792","count":2},{"id":"GO:0043001","count":2},{"id":"GO:0097178","count":2},{"id":"GO:0060999","count":2}]},{"hash":"1449121894018994313","title":"Peroxisome biogenesis and dynamics","description":"The GO terms cluster around peroxisomal processes: inheritance, protein import into peroxisome membranes, ER-dependent peroxisome organization, membrane biogenesis, and fission, plus ER-to-peroxisome trafficking. This suggests proteins involved in peroxisome assembly, maintenance, and division, with a few ancillary terms (e.g., stabilization) and one unrelated term likely representing noise. Confidence is High.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045033","count":1},{"id":"GO:0045046","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0032581","count":1},{"id":"GO:0072321","count":1}]},{"hash":"74234997640396473","title":"Ubiquitin-Proteasome\u2013Mediated Cell Cycle Control","description":"The cluster is dominated by GO terms for ubiquitin-dependent proteolysis (SCF-dependent and general proteasomal degradation) and cell-cycle\u2013related processes (spindle assembly in meiosis, DNA replication initiation regulation, and G1 DNA damage checkpoint signaling). Microtubule polymerization and circadian rhythm regulation align with degradation-based control of cytoskeletal dynamics and timing, while stress responses to cadmium/arsenic reflect proteostasis-related signaling. Collectively, these terms point to coordinated protein turnover governing cell cycle progression and spindle function.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0042752","count":3},{"id":"GO:0046785","count":3},{"id":"GO:0007057","count":3},{"id":"GO:0030174","count":3}]},{"hash":"266178988971817708","title":"Ubiquitin-Proteasome-Mediated Cell Cycle Regulation","description":"This cluster centers on ubiquitin-dependent proteolysis (SCF-dependent pathways) linked to cell cycle control, including spindle assembly in meiosis and DNA replication initiation regulation, with related DNA damage signaling. Additional terms for circadian regulation and heavy-metal responses may reflect broader stress signaling connected to ubiquitin pathways, but the dominant theme is proteolysis governing cell-cycle processes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0042752","count":1},{"id":"GO:0046785","count":1},{"id":"GO:0007057","count":1},{"id":"GO:0030174","count":1}]},{"hash":"1276020177784559154","title":"Unknown","description":"The top GO terms span membrane remodeling, nuclear transport, signaling, and stress/immune responses with no single cohesive function evident, so a specific, representative label is not reliably deduced.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045921","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0033234","count":1},{"id":"GO:0032120","count":1},{"id":"GO:1903525","count":1}]},{"hash":"1268241939222463510","title":"Diverse Biosynthetic Pathways","description":"The top GO terms show multiple, disparate biosynthetic processes (anthocyanin, poly-hydroxybutyrate, mycolic acid, retinol, and steroid-related biosynthesis) along with a few regulatory and catabolic terms, indicating no single cohesive function for the cluster. The common theme is metabolism across different pathways, so a label like \u201cDiverse Biosynthetic Pathways\u201d captures the overall tendency without over-committing to a specific pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009718","count":3},{"id":"GO:0042619","count":3},{"id":"GO:1902987","count":2},{"id":"GO:0045150","count":2}]},{"hash":"1438358737987038909","title":"Unknown","description":"The Top Terms span transcriptional regulation (DNA-templated transcription, miRNA transcription/processing), chromatin dynamics (nucleosome disassembly), DNA recombination (DNA strand invasion), developmental regulation (organ boundary specification), and environmental responses (response to deep water) with one term related to biofilm adhesion. There is no single cohesive biological theme tying these terms together across all proteins, so a specific functional label isn\u2019t supported.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900189","count":1},{"id":"GO:0005987","count":1},{"id":"GO:0006337","count":1},{"id":"GO:1902895","count":1},{"id":"GO:0042148","count":1}]},{"hash":"1525427383707938914","title":"Cell cycle regulation and ubiquitination","description":"The GO terms cluster around control of the cell cycle (G2/M transition, exit from mitosis) and ubiquitin-mediated processes (SCF complex assembly, polyubiquitination), with additional links to apoptosis regulation and transcription, suggesting a coherent role in regulating cell cycle progression via ubiquitin ligase pathways.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0060544","count":1}]},{"hash":"1372591680685538677","title":"Innate immune signaling and regulation","description":"This cluster centers on innate immune sensing and signaling pathways: response to fungus, MyD88-independent TLR signaling, cytokine-mediated signaling, and negative regulation of chemokine signaling and JAK-STAT\u2013mediated pathways. These terms together point to a shared theme of immune detection and regulation. Some terms (vestibuloocular reflex, bone trabecula formation, and a peptide cross-linking term) are less directly related, possibly reflecting broader roles of immune signaling in neural and skeletal contexts or annotation noise, but the dominant pattern is innate immune signaling and inflammatory control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":6},{"id":"GO:0050929","count":6},{"id":"GO:0060007","count":6},{"id":"GO:0002756","count":6},{"id":"GO:0019221","count":6}]},{"hash":"2190413674140378369","title":"Endosomal trafficking and autophagy regulation","description":"This cluster centers on endocytic/secretory vesicle trafficking (endosome to lysosome transport, plasma membrane to endosome transport, COPII-coated vesicle budding, endosomal vesicle fusion) and autophagosome assembly, with actin-driven membrane remodeling (ruffle assembly) supporting these processes. A couple of terms (neuron fate determination, division septum assembly) are less directly related, but the dominant theme is vesicle trafficking and membrane dynamics.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:1902824","count":6},{"id":"GO:0048227","count":6},{"id":"GO:0097178","count":6},{"id":"GO:0003100","count":6},{"id":"GO:0090114","count":6}]},{"hash":"1657607328577924435","title":"Plant nitrate and peptide transporters","description":"The GO terms are dominated by nitrate assimilation and transmembrane transport of nitrates and peptides (oligopeptides, dipeptides), with a few other nutrient transport terms, plus hormone-related signaling (auxin, gibberellin) typical of plant nutrient regulation. This suggests a cohesive group of plant membrane transport proteins specializing in nitrate and peptide nutrients, possibly including NRT and peptide transporter families.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":5},{"id":"GO:0010336","count":4},{"id":"GO:0035672","count":4},{"id":"GO:0080055","count":4},{"id":"GO:0009635","count":4}]},{"hash":"1095109227291057142","title":"Bacterial aromatic amino acid catabolism and xenobiotic detox","description":"The cluster shows strong signals for catabolism of phenylalanine and tyrosine, xenobiotic and glutathione metabolism, antibiotic response, and enterobactin biosynthesis, suggesting a bacterial module for aromatic compound breakdown and detoxification under stress. A potentially noisy term about transcription by RNA polymerase II is noted, but the core theme is aromatic amino acid catabolism and detox pathways.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006559","count":4},{"id":"GO:0006572","count":4},{"id":"GO:0006357","count":3},{"id":"GO:0019243","count":3},{"id":"GO:0055114","count":3}]},{"hash":"810896590457666834","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":1},{"id":"GO:2000344","count":1},{"id":"GO:0016042","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0009451","count":1}]},{"hash":"768743481282129330","title":"Cell Cycle and Chromosome Maintenance","description":"Top GO terms indicate DNA replication, CENP-A chromatin assembly, and cell division, with microtubule severing tying into spindle dynamics, all pointing to chromosome maintenance during the cell cycle. While other terms touch on ribosome maturation or vesicle transport, the dominant signals cluster around nuclear processes essential for mitosis and genome integrity.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0051301","count":2}]},{"hash":"742847900653146840","title":"Nuclear snoRNP and telomerase assembly","description":"The top GO terms cluster around box H/ACA snoRNP assembly, snoRNA-guided pseudouridylation, and telomerase holoenzyme assembly/localization, indicating a shared theme of nuclear RNA processing and ribonucleoprotein assembly. While there is a distant hint of ribosome biogenesis and nuclear export processes, the dominant signal is snoRNP/telomerase\u2013related functions in the nucleus.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1905323","count":1},{"id":"GO:0031120","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000493","count":1}]},{"hash":"1521220866766857349","title":"Broad-Spectrum Solute Transporters","description":"Most top GO terms describe transport across membranes for a variety of substrates (methionine, glycine betaine, cobalt ions, taurine, vitamins, carbohydrates). This indicates the proteins cluster as transporters or transporter-associated components with broad substrate specificity. A few terms pertain to unrelated processes (fatty acid catabolism, mercury response, bacteriocin immunity) that may be peripheral or noisy; however, the dominant signal is membrane transport. ","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0015821","count":4},{"id":"GO:0031460","count":4},{"id":"GO:0006824","count":4},{"id":"GO:0015734","count":4},{"id":"GO:0042760","count":4}]},{"hash":"1151511193422117325","title":"ER Tubular Network Organization","description":"Top GO terms are dominated by ER tubular network formation and membrane organization, with ER-dependent peroxisome organization also represented, suggesting a shared role in shaping ER morphology and related organelle interactions. While neural development terms appear, they seem secondary to the ER-centric theme. Overall, the cluster appears focused on endoplasmic reticulum tubular network organization.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032581","count":1},{"id":"GO:0071788","count":1},{"id":"GO:2000172","count":1},{"id":"GO:0006694","count":1},{"id":"GO:0060317","count":1}]},{"hash":"416557640303828396","title":"Exocytosis and membrane trafficking regulation","description":"The strongest GO terms center on exocytosis, vesicle and membrane dynamics, and localization to the extracellular region, suggesting a secretory/membrane-trafficking function for the cluster; a few terms (nuclear import, heart rate) appear tangential, but do not dominate the theme.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0045921","count":5},{"id":"GO:0008360","count":5},{"id":"GO:0033234","count":5},{"id":"GO:0030916","count":5},{"id":"GO:0035592","count":5}]},{"hash":"1003284933090961683","title":"Oocyte mRNA localization and translation regulation","description":"This cluster centers on RNA processing and translation control, with terms for spliceosome assembly, mRNA modification and stabilization, and translation initiation (including eIF4F assembly and IRES-dependent initiation). The presence of oocyte-specific terms like pole plasm oskar mRNA localization and axis specification suggests a coherent theme of regulated mRNA metabolism and translation during oogenesis, making this a concise and representative label.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000244","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0048255","count":1},{"id":"GO:0060213","count":1},{"id":"GO:0075522","count":1}]},{"hash":"1819126112000588965","title":"DNA replication/repair and meiotic recombination proteins","description":"The GO terms are dominated by DNA replication, recombination, and repair, with several meiotic-related terms (reciprocal meiotic recombination, oocyte karyosome formation) suggesting a meiotic genome-maintenance theme; translation and xenobiotic response are present but less prominent. This points to a cluster of proteins involved in genome maintenance and meiotic processes, with some broader housekeeping roles.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0051260","count":2}]},{"hash":"2233543852246412914","title":"Energy metabolism and nutrient signaling","description":"The top GO terms are dominated by energy-related processes (ATP biosynthesis, glycolysis, pyruvate biosynthesis) and nutrient/stress responses (response to nutrient, insulin stimulus, heat), suggesting a cluster centered on cellular energy production and nutrient signaling, with some ancillary terms like antibiotic biosynthesis that may reflect broader metabolic capabilities in this set.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006754","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0061621","count":1},{"id":"GO:0007584","count":1}]},{"hash":"2304326328294831059","title":"Purine Nucleotide Metabolism and Salvage","description":"The top GO terms are centered on purine nucleotide metabolism and salvage (AMP salvage, purine ribonucleotide interconversion, ADP biosynthetic process, nucleoside monophosphate phosphorylation, CDP biosynthetic process, ITP metabolic process), suggesting a cohesive function in generating and interconverting purine nucleotides. There are also brain and liver development terms and DNA-templated transcription, but these appear secondary to the core metabolic theme rather than defining the cluster\u2019s main role.","confidence":"High","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":4},{"id":"GO:0015951","count":3},{"id":"GO:0001889","count":3},{"id":"GO:0046705","count":3},{"id":"GO:0046940","count":3}]},{"hash":"2244839223271459644","title":"Cell Wall and Polysaccharide Biosynthesis","description":"Based on the top GO terms, these proteins cluster around cell wall/morphogenesis and polysaccharide biosynthesis, including GDP-mannose biosynthesis, cell wall mannoprotein biosynthetic process, slime layer polysaccharide biosynthesis, LPS biosynthesis, and related envelope assembly processes. The repeated emphasis on cell wall organization and extracellular polysaccharide production suggests a shared function in building or remodeling the cell envelope, rather than cytosolic metabolic pathways. Despite no reported edges within the cluster, the GO term coherence supports a cohesive envelope biosynthesis theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":3},{"id":"GO:0009298","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0005978","count":3}]},{"hash":"1681363699004621655","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":1},{"id":"GO:0034476","count":1},{"id":"GO:1901917","count":1},{"id":"GO:0071033","count":1},{"id":"GO:0000973","count":1}]},{"hash":"1238041743719666492","title":"Lung development and calcium signaling with adhesion","description":"The top GO terms point to lung morphogenesis (GO:0030324), cell-cell adhesion (GO:0098609), and calcium/calcineurin\u2013NFAT signaling (GO:0005513, GO:0051533), suggesting a module involved in lung development guided by calcium-dependent signaling and cell adhesion. While others like DNA replication and glycogen metabolism appear, they are less central to this core theme. Overall, the data support a developmental signaling cluster focused on lung formation with calcium-mediated adhesion, hence medium confidence.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000002","count":5},{"id":"GO:1900486","count":5},{"id":"GO:1900490","count":5},{"id":"GO:0050728","count":5},{"id":"GO:0005513","count":5}]},{"hash":"1725997877492978720","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048254","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0000494","count":1},{"id":"GO:0006356","count":1},{"id":"GO:0008033","count":1}]},{"hash":"73129424912547819","title":"Viral life cycle components","description":"GO terms in this cluster are dominated by viral processes: virion assembly, viral release from host cell, and viral budding via the ESCRT pathway, along with proviral latency and DNA integration. While some terms touch on host processes, the viral-related annotations are distinctive, suggesting these proteins cluster around steps of the viral life cycle and proviral maintenance. Therefore, the label reflects a cohesive viral life-cycle orientation with strong supporting terms.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0070124","count":1},{"id":"GO:0051245","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0019068","count":1}]},{"hash":"399200744835707837","title":"RNA Splicing and Stress Granule Regulation","description":"The terms converge on post-transcriptional RNA regulation: spliceosome-driven splicing and its upregulation, mRNA stability/modification, and stress-granule localization. This suggests the proteins function together in RNA processing and stress-responsive mRNA handling, consistent with a cohesive RNA metabolism module.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0010610","count":3},{"id":"GO:0000398","count":3},{"id":"GO:1903608","count":3}]},{"hash":"2159550034233089898","title":"Mitochondrial metabolism and apoptosis","description":"The cluster\u2019s top GO terms point mainly to mitochondrial function\u2014mitochondrial translation, redox homeostasis, and membrane potential\u2014turther reinforced by the apoptotic process term. While some terms touch on hematopoietic differentiation and neurotransmitter regulation, these are less central to the shared theme. Overall, the proteins seem to cluster around mitochondrial metabolism and cell fate decisions.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0045648","count":1},{"id":"GO:0042391","count":1}]},{"hash":"1522017126634765486","title":"Nucleotide metabolism and tRNA editing","description":"GO terms indicate a coherence around nucleotide/nucleoside metabolism and RNA editing/deamination (e.g., tRNA wobble A-to-I editing, cytidine deamination, deoxycytidine catabolic, uridine biosynthesis, cytosine/guanine metabolism, UMP salvage). While some terms like riboflavin/nitrile biosynthesis and antibiotic response appear, the dominant signals are nucleotide-modifying and recycling activities, justifying a label centered on nucleotide metabolism and RNA editing. Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002100","count":3},{"id":"GO:0009972","count":3},{"id":"GO:0006217","count":3},{"id":"GO:0046109","count":3},{"id":"GO:0019858","count":3}]},{"hash":"304963172753310817","title":"Neural development and embryogenesis","description":"The top GO terms are centered on neural development and embryogenesis (spinal cord development, neural tube closure, neuron projection development, embryonic organ development), indicating a cohesive theme around neural formation during embryonic stages. Some terms are broader cellular processes (e.g., ribosomal biogenesis, multicellular organism growth) but do not override the dominant neural-development signal.","confidence":"Medium","size":5,"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:0051441","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0001843","count":2}]},{"hash":"45334494120709415","title":"ER Stress and Protein Folding Quality Control","description":"The top GO terms cluster around misfolded protein handling, chaperone-dependent refolding, and ER stress\u2013related translation initiation, suggesting a shared role in ER-associated protein quality control; while a few terms touch on development or obsolete annotations, the strongest signal is ER folding and processing.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":1},{"id":"GO:0051259","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0070389","count":1},{"id":"GO:1900035","count":1}]},{"hash":"2070878885705699450","title":"ER stress\u2013linked protein folding and quality control","description":"The terms point to protein folding/refolding (chaperone-dependent and misfolded protein transport) and translation initiation in response to ER stress, with some emphasis on protein oligomerization and heat response; together these suggest a cluster centered on cellular protein quality control under stress, particularly ER stress, rather than a single developmental signaling module, though a mesoderm-related term hints at broader developmental context.","confidence":"Medium","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1901621","count":5},{"id":"GO:0051259","count":5},{"id":"GO:0070843","count":5},{"id":"GO:0070389","count":5},{"id":"GO:1900035","count":5}]},{"hash":"692926515332028634","title":"RNA splicing and quality-control under stress","description":"The top GO terms cluster around RNA processing and surveillance (splicing regulation, tRNA surveillance, exon ligation, RNA-protein interactions) with additional links to stress responses (cold, stress granule localization). Although a couple terms touch DNA replication and protein targeting, the dominant signal is RNA metabolism and quality control mechanisms, particularly under cellular stress, supporting this label.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0006605","count":3},{"id":"GO:0006269","count":3},{"id":"GO:0071038","count":3}]},{"hash":"107878217515999316","title":"RNA processing and translation regulation","description":"This cluster centers on post-transcriptional control: splicing regulation via the spliceosome, alternative splicing, RNA modification and stabilization, ncRNA-mediated gene silencing, and translation initiation factors, together pointing to RNA processing and translation control of gene expression.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0016556","count":4},{"id":"GO:0048255","count":4},{"id":"GO:0075522","count":4}]},{"hash":"7872191086640405","title":"RNA processing and stress granule localization","description":"Based on the GO terms, the proteins cluster around RNA metabolism and quality control (TRAMP tRNA surveillance, RNA exon ligation, RNA-protein cross-linking) and stress-related localization (cytoplasmic stress granules, cold response). While some DNA-repair terms appear, the strongest, cohesive signal is RNA processing and stress-granule dynamics, suggesting a role in RNA quality control under stress.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006605","count":1},{"id":"GO:0006269","count":1},{"id":"GO:0071038","count":1},{"id":"GO:0070417","count":1},{"id":"GO:1903608","count":1}]},{"hash":"1791218697211914034","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":2},{"id":"GO:0009451","count":2},{"id":"GO:0016554","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0070129","count":2}]},{"hash":"360560992488554384","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":1},{"id":"GO:0009451","count":1},{"id":"GO:0016554","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0070129","count":1}]},{"hash":"2006971347140817749","title":"Embryogenesis and RNA processing","description":"The Top Terms show strong signals for embryonic development (spinal cord development, neural tube closure, embryonic organ development) alongside RNA processing and ribosome biogenesis (spliceosome-mediated mRNA splicing and large subunit biogenesis), suggesting a theme where RNA processing and protein synthesis support embryonic development, even without detected protein\u2013protein interactions. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0016226","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0042273","count":1}]},{"hash":"1769249491077389136","title":"Unknown","description":"The terms are highly diverse, spanning cell migration and exocytosis, DNA replication/transcription, development, plant hormone signaling, and vesicle transport, with no clear single pathway connecting them. This suggests no cohesive theme for the cluster, or possible annotation noise.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1565013000452379222","title":"Migration and cytoskeletal signaling","description":"The top GO terms center on promoting cell movement (fibroblasts, endothelial cells) and cytoskeletal regulation (Rho signaling, microtubule localization), indicating a core theme of regulated cell migration and cytoskeletal dynamics. Additional terms touch development and immune-related signaling, which are related processes in migratory and signaling pathways. Overall, these proteins likely participate in pathways coordinating movement and cytoskeletal control rather than a single static function.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0010763","count":3},{"id":"GO:0032435","count":3},{"id":"GO:0046641","count":2},{"id":"GO:0001502","count":2}]},{"hash":"593562988830848091","title":"Unknown","description":"The top terms span a highly diverse set of processes (cell migration; telomere maintenance and capping; mRNA processing; regulation of CDK activity; fat cell differentiation; response to muscle stretch; fungal cell wall biosynthesis; division septum assembly). With no edge connections and only sparse, heterogeneous functional annotations, there is no clear shared function linking these proteins as a cohesive cluster. Therefore, Unknown with no confident representative function.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0045736","count":2}]},{"hash":"122508318885639381","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006189","count":3},{"id":"GO:0006353","count":2},{"id":"GO:0042417","count":2}]},{"hash":"290220595253787816","title":"Translation Machinery and Hypusination","description":"Most of the top GO terms describe core protein synthesis steps (translation, translational initiation/elongation/termination, and frameshifting) and the hypusine biosynthetic process that modifies eIF5A to promote elongation. This coherence suggests the cluster reflects components of the translation machinery and a key post-translational modification pathway, despite a couple of outliers like DNA transposon-related terms which may reflect annotation noise or incidental overlap.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0032197","count":1},{"id":"GO:0034050","count":1},{"id":"GO:0008612","count":1},{"id":"GO:0045905","count":1}]},{"hash":"2208319395702593072","title":"Stress-Activated MAPK Signaling and Oxidative Stress Response","description":"The cluster centers on stress response pathways, notably the stress-activated MAPK cascade, responses to oxidative stress (H2O2, ROS), heat and UV stress, and proteostasis-related regulation, with additional hints of hormone signaling (estradiol) and intracellular/axonal transport adjustments\u2014all pointing to a cohesive stress-response proteome.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051403","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0032387","count":3},{"id":"GO:0032355","count":3},{"id":"GO:0099641","count":3}]},{"hash":"697030828566220378","title":"Plant oxidative stress response and lignin metabolism","description":"Based on the most represented GO terms (response to oxidative stress, cellular oxidant detoxification, hydrogen peroxide catabolic process) and plant-specific processes (plant-type cell wall organization, lignin catabolic process), the proteins in this cluster appear to participate in defense against reactive oxygen species and remodeling of the cell wall via lignin metabolism, i.e., a plant oxidative stress response coupled to cell wall modification.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006979","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0046274","count":3},{"id":"GO:0042744","count":3},{"id":"GO:0055114","count":3}]},{"hash":"1562690707009867057","title":"Bacterial biosynthesis and metal transport","description":"This cluster centers on biosynthetic processes such as LPS, antibiotic, serine, and sialic acid biosynthesis, together with metal ion transport (copper and cadmium); the terms point to bacterial metabolism and transport capabilities rather than a single shared pathway, with dephosphorylation and P450-related reactions as additional but less cohesive themes.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0019373","count":2},{"id":"GO:0006825","count":2}]},{"hash":"346832316147065813","title":"Golgi Vesicle Trafficking and Protein Sorting","description":"This cluster is enriched for GO terms related to Golgi retention, ER-to-Golgi transport, inter-Golgi vesicle traffic, vesicle-mediated transport, and lysosome targeting, indicating a cohesive set of proteins involved in Golgi trafficking and cargo sorting.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0048219","count":2},{"id":"GO:0031954","count":1}]},{"hash":"415058046156058726","title":"Transcription Regulation and tRNA Modification","description":"The dominant GO terms point to transcriptional control (DNA-templated transcription; negative regulation of transcription by RNA polymerase II) and tRNA modification (tRNA methylation; tRNA wobble uridine modification). While a few terms refer to lipopolysaccharide response or biosynthetic processes in other organisms, the strongest shared function among the cluster members appears to be involvement in gene expression regulation at both the level of transcription and tRNA modification.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0032496","count":3},{"id":"GO:0042135","count":3},{"id":"GO:0042420","count":3},{"id":"GO:0009809","count":2}]},{"hash":"1601848747864568832","title":"Unknown","description":"The GO terms span multiple distinct themes (amino acid biosynthesis, metal ion transport, xenobiotic/stilbene catabolism, cytochrome P450 pathways, hormone response, lipid dephosphorylation, and LPS biosynthesis), with no single shared function uniting the proteins. Therefore a confident, specific label cannot be assigned.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":3},{"id":"GO:0071577","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0019373","count":3},{"id":"GO:0033574","count":3}]},{"hash":"10189238180621947","title":"Immune signaling and cadherin-mediated adhesion regulation","description":"These proteins show enrichment for immune signaling terms (positive regulation of Toll-like receptor 3 signaling and establishment of T cell polarity) and cell adhesion (positive regulation of cadherin-mediated cell\u2013cell adhesion, regulation of adhesion molecule production). PKC signaling also ties into these pathways, and podocyte development underscores cadherin-associated adhesion in specialized kidney cells. Together, they point to a theme of coordinating immune signaling with cell\u2013cell adhesion regulation.","confidence":"Medium","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045861","count":4},{"id":"GO:0070528","count":4},{"id":"GO:0060355","count":4},{"id":"GO:0045541","count":4},{"id":"GO:0070584","count":4}]},{"hash":"1679343403264576294","title":"Unknown","description":"The top GO terms point to several unrelated processes (nervous system and forebrain development, glial and cardiac apoptotic processes, TGF-beta response, melanization defense, methionine cycle, salivary gland histolysis) and even obsolete terms. With no clear shared function or interaction among proteins, and no edges linking them, there is no coherent theme to define a meaningful label. Therefore Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0010659","count":3},{"id":"GO:0035006","count":3},{"id":"GO:0033353","count":3},{"id":"GO:0071560","count":3}]},{"hash":"1030142168748192538","title":"Unknown","description":"The top GO terms span amino acid biosynthesis, cardiac hypertrophy regulation, ionotropic glutamate signaling, metal ion transport, pheromone-induced fusion, nitric oxide signaling, membrane potential stabilization, stilbene catabolism, and calcineurin-NFAT regulation. This broad, heterogeneous mix does not reveal a single cohesive biological function or pathway for the cluster, making a specific, representative label difficult.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":2},{"id":"GO:1903243","count":2},{"id":"GO:0035235","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0000749","count":2}]},{"hash":"209824465158966573","title":"Steroid Hormone and Xenobiotic Metabolism","description":"The cluster is enriched for steroid hormone biosynthesis (cortisol, testosterone) and lipid/retinoid-related signaling (retinoic acid, vitamin D response), plus xenobiotic catabolic and oxidative demethylation processes. This suggests a common theme of hormone-related metabolism and detoxification, with some tissue-development terms as potential secondary roles.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":3},{"id":"GO:0030879","count":2},{"id":"GO:0071603","count":2},{"id":"GO:0034651","count":2},{"id":"GO:0070989","count":2}]},{"hash":"1156560200206997240","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050427","count":3},{"id":"GO:0006068","count":3},{"id":"GO:0006478","count":3},{"id":"GO:0006044","count":3},{"id":"GO:0030573","count":3}]},{"hash":"470122569492300391","title":"Gametogenesis and chromatin remodeling","description":"These proteins appear linked to reproductive development (spermatid development, sperm DNA condensation, vitellogenesis) and chromatin-associated processes (DNA replication-dependent chromatin assembly, histone methylation regulation, transcription preinitiation complex assembly). The overlap suggests a theme around gametogenesis with chromatin remodeling and transcription control.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":5},{"id":"GO:1900446","count":4},{"id":"GO:0090230","count":4},{"id":"GO:0007296","count":4},{"id":"GO:0031639","count":4}]},{"hash":"1922976948568663740","title":"Ubiquitination and Protein Degradation","description":"The top GO terms cluster around ubiquitination (protein ubiquitination; ubiquitin-dependent protein catabolic process; histone ubiquitination) and related proteolytic/receptor degradation processes (Wnt receptor catabolic process; histone catabolic process). Additional terms connect to signaling regulation (TNF-mediated signaling, JNK cascade, RIG-I pathway), supporting a theme of ubiquitin-driven protein modification and degradation as the common function. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":2},{"id":"GO:2000620","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1426024117294561561","title":"Unknown","description":"The top terms are highly diverse, including chromatin remodeling, DNA methylation, several developmental processes (megakaryocyte differentiation, limb bud formation, otic vesicle formation), and hormone responses (salicylic acid, gibberellin). This mix across different biological contexts provides no single unifying function for the cluster, so a cohesive label isn\u2019t supported.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045654","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0009751","count":2}]},{"hash":"564644064717237312","title":"Vertebrate development and cell fate specification","description":"The top GO terms point to developmental and differentiation processes across multiple tissues (somites, interneurons, AV node, endodermal fate, muscle satellite cells) along with general growth. This suggests a theme of developmental programs rather than a single molecular function. Although edges are absent in the network data, the shared emphasis on development supports this label as representative of the cluster. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":2},{"id":"GO:0072756","count":1},{"id":"GO:0061053","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0042663","count":1}]},{"hash":"1915281726129849709","title":"Proteasome-Driven Antigen Presentation & Immune Signaling","description":"GO terms cluster around proteasome assembly and ubiquitin-dependent protein turnover, plus antigen processing and MHC class I presentation, with immune signaling pathways (TNF, T cell receptor) indicating a link between proteostasis and immune activation.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006521","count":4},{"id":"GO:0080129","count":4},{"id":"GO:0061418","count":4},{"id":"GO:0010950","count":4},{"id":"GO:0031146","count":4}]},{"hash":"2253829088468818513","title":"Proteostasis and degradation regulation","description":"The proteins appear enriched for terms governing protein quality control, including ubiquitin-proteasome\u2013related regulation, autophagy maturation, aggresome assembly, and sumoylation, with additional links to ER stress and mitochondrial dynamics. This points to a cohesive theme of maintaining protein homeostasis and regulated degradation under stress.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":5},{"id":"GO:0010216","count":5},{"id":"GO:0045648","count":5},{"id":"GO:1901097","count":5},{"id":"GO:1901799","count":5}]},{"hash":"960633178342059924","title":"Plant Hormone Signaling and Defense","description":"The GO terms center on responses to salicylic acid, gibberellin, and the ethylene precursor ACC, plus chitin and antifungal defense, with some developmental differentiation (atrichoblast, sclerenchyma) and autophagy. Together they suggest a theme of hormone-regulated signaling linked to plant defense and some growth/differentiation processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2},{"id":"GO:0080169","count":1},{"id":"GO:0009961","count":1},{"id":"GO:0010055","count":1}]},{"hash":"740002295621797431","title":"Immune activation and cell proliferation","description":"The cluster combines immune-related processes (positive regulation of T cell proliferation, cytokine production, neutrophil clearance) with DNA replication, suggesting involvement in immune signaling alongside cell growth/division. Supporting terms for cytoskeletal dynamics (Rho signaling, microtubule localization) and developmental processes (cartilage condensation, endothelial migration) imply coordinated movement and maturation during immune responses and tissue development. Overall, a theme of immune activation linked to proliferation and cytoskeletal regulation fits best.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0046641","count":4},{"id":"GO:0001502","count":4},{"id":"GO:0097350","count":4},{"id":"GO:0035372","count":4}]},{"hash":"121971426707394478","title":"Autophagy Assembly and Stress-Responsive Cell Fate","description":"These proteins cluster around autophagy-related processes: autophagosome assembly, phagophore assembly site localization, and cytoplasm-to-vacuole targeting (Cvt) pathway, with nucleophagy and responses to nitrogen starvation. Additional terms linking to leaf senescence and programmed cell death fit autophagy's role in stress adaptation and developmental cell fate decisions, suggesting a cohesive theme of autophagy machinery and its regulation under stress. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":2},{"id":"GO:0032258","count":1},{"id":"GO:0010150","count":1},{"id":"GO:0034497","count":1},{"id":"GO:2001237","count":1}]},{"hash":"1592295715212804193","title":"Unknown","description":"The top GO terms include translation and maturation of SSU-rRNA, indicating ribosome-related processes, but also oxylipin biosynthesis terms, which are lipid metabolic pathways. The mix suggests no single cohesive function for the cluster, implying the proteins are not functionally cohesive.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0031408","count":1},{"id":"GO:1902609","count":1}]},{"hash":"1098415704404238134","title":"Amino acid biosynthesis and related metabolism","description":"The top GO terms are dominated by amino acid biosynthetic processes\u2014aromatic amino acid biosynthesis, chorismate biosynthesis, and histidine biosynthesis\u2014indicating a core theme around amino acid production. Additional terms for glucose-6-phosphate metabolism and glucose homeostasis suggest these proteins participate in broader central metabolism. The presence of several non-metabolic response terms likely reflects annotation noise, but the strongest signal centers on amino acid biosynthesis, supporting this label with moderate confidence.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009073","count":1},{"id":"GO:0009423","count":1},{"id":"GO:0000105","count":1},{"id":"GO:0051156","count":1},{"id":"GO:0051024","count":1}]},{"hash":"2050619016831044817","title":"Fatty acid and acyl-CoA metabolism","description":"The terms cluster around lipid biosynthesis and acyl-CoA metabolism (palmitic acid biosynthesis; medium- and long-chain fatty-acyl-CoA biosynthesis and catabolism; acyl-CoA metabolic process), with a hint of regulation of fatty acid biosynthesis.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900535","count":2},{"id":"GO:0009239","count":2},{"id":"GO:0051792","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0045717","count":2}]},{"hash":"1374887661939582762","title":"Unknown","description":"The top GO terms point to two different biological themes: transcription-related processes (DNA-templated transcription, transcription initiation, regulation) often linked to developmental programs like sporulation (GO:0030435) and heat response (GO:0009408); and amino acid transport into the vacuole (tyrosine, arginine, histidine, glutamate-related terms, etc.), which is a nutrient uptake process. The divergence suggests these proteins do not share a single, cohesive function, so the cluster cannot be confidently assigned to a specific biological process.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0001123","count":1}]},{"hash":"896096341142224266","title":"Translation machinery and translational regulation","description":"This cluster is dominated by translation-related GO terms: general translation (GO:0006412), regulation of translational fidelity (GO:0006450), positive regulation of translational elongation (GO:0045901), and selenocysteine incorporation (GO:0001514), indicating a coherent theme around the translation apparatus and its control, including specialized translation. A few terms such as glial cell proliferation and cell division appear, which may reflect broader cellular proliferation contexts or annotation noise, but do not override the main translation-centric signal. Therefore, the cluster most plausibly represents components involved in translation and its regulation.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006450","count":1},{"id":"GO:0014009","count":1},{"id":"GO:1901001","count":1},{"id":"GO:0044376","count":1}]},{"hash":"246226682885612695","title":"Histone acetylation and chromatin regulation","description":"GO terms are dominated by acetylation-related chromatin modifications (histone H4 acetylation, peptidyl-lysine acetylation, N-terminal acetylation) and subtelomeric heterochromatin formation, pointing to a chromatin-regulation cluster driven by acetylation. Some metabolic acetylation processes appear as secondary links, but the central theme remains chromatin modification via acetylation.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":5},{"id":"GO:0032919","count":5},{"id":"GO:0043967","count":5},{"id":"GO:0018002","count":5},{"id":"GO:0045150","count":5}]},{"hash":"432510639715633857","title":"Multi-tissue developmental differentiation","description":"These terms point to differentiation and morphogenesis across diverse tissues and stages, from early embryonic formation (primitive streak) to organ-specific differentiation (neuronal, pancreatic, ear, uterine, gonadal, vascular, floral). The lack of a single dominant process suggests a broad developmental theme rather than a specific function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021902","count":2},{"id":"GO:0072107","count":2},{"id":"GO:0003309","count":2},{"id":"GO:0042472","count":2},{"id":"GO:0060037","count":2}]},{"hash":"1681444507712500752","title":"Biosynthesis of lipids, steroids, and antibiotics","description":"The top GO terms cluster around biosynthetic processes for lipids and lipid-containing molecules (lipopolysaccharide, mycolic acid, retinol metabolism) as well as steroid/androgen biosynthesis and antibiotic biosynthesis. Although one term concerns transcription regulation, the shared theme is generation of diverse biosynthetic products, particularly lipids and steroid-related compounds, rather than a single, narrow pathway. This suggests a general biosynthesis-focused cluster.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0009103","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0042572","count":2}]},{"hash":"309878050575769489","title":"Embryonic development and cell fate specification","description":"The proteins appear linked to broad developmental processes across tissues, with emphasis on heart morphogenesis (valve development, outflow tract morphogenesis, cardioblast migration) and mesenchyme formation, plus various lineage specifications (neural floor plate, GABAergic interneurons, auditory and pancreatic cell fates) and cell-cycle regulation. This points to a shared role in embryonic tissue morphogenesis and lineage determination, rather than a single pathway.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:2000793","count":5},{"id":"GO:2000764","count":5},{"id":"GO:0060375","count":5},{"id":"GO:0060485","count":5},{"id":"GO:0071156","count":5}]},{"hash":"1860550729319616691","title":"Mitochondrial energy metabolism and redox regulation","description":"The top GO terms are dominated by mitochondrial-associated processes: aerobic electron transport chain, lipoate metabolic process, glycerol-3-phosphate catabolic process, and removal of superoxide radicals, pointing to energy production and oxidative stress handling. Some other terms reflect broader metabolic or regulatory activities, but the strongest cohesive signal is mitochondrial metabolism and redox balance, justifying this label.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002097","count":5},{"id":"GO:0019646","count":5},{"id":"GO:0045654","count":5},{"id":"GO:0035563","count":5},{"id":"GO:0055114","count":5}]},{"hash":"336193495637450746","title":"Chaperone-Mediated Protein Folding and Steroid Receptor Assembly","description":"The top GO terms point to chaperone-dependent refolding and chaperone-mediated protein folding, with steroid hormone receptor complex assembly also highlighted, which often requires chaperones like HSP90. Other terms touch on cilium/photoreceptor organization and development, which can be linked to chaperone roles in specialized cellular contexts. Overall, the cluster most plausibly reflects proteins involved in chaperone-assisted folding and maturation of signaling receptors, rather than a single tissue-specific process.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0070389","count":3},{"id":"GO:0006463","count":3},{"id":"GO:0009938","count":3},{"id":"GO:0030850","count":3},{"id":"GO:0060613","count":3}]},{"hash":"307775127861954475","title":"Unknown","description":"The top GO terms span very different biological areas (plant pigment and lignin metabolism, bacterial PHB biosynthesis and sporulation, neuron axon localization, and various xenobiotic/estrogen/antibiotic metabolic processes), with several obsolete annotations, giving no coherent shared function for the cluster. Therefore no specific representative label can be assigned.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009718","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0002175","count":1}]},{"hash":"1811559525645268254","title":"Unknown","description":"The terms are scattered across transcription, neural development, circadian rhythm, signaling, stress responses, and apoptosis with no single cohesive function tying the proteins together. Because of this lack of a clear shared theme, a meaningful label cannot be assigned beyond Unknown.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":2},{"id":"GO:1990442","count":1},{"id":"GO:0010691","count":1},{"id":"GO:0045475","count":1},{"id":"GO:0032915","count":1}]},{"hash":"1730728676395455608","title":"Regulation of plant growth and development","description":"These GO terms cluster around regulatory processes in plants, including regulation of chlorophyll biosynthesis, seed growth, lignin and secondary cell wall biosynthesis, and root meristem growth, as well as leaf senescence. The mix of positive and negative regulation terms suggests a broader regulatory module controlling plant development and metabolism, rather than a single enzyme or pathway. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010380","count":2},{"id":"GO:0080113","count":2},{"id":"GO:1901430","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0010082","count":2}]},{"hash":"1675394081641778176","title":"Plant secondary metabolite biosynthesis","description":"The terms point to plant-specific biosynthetic pathways such as lignin and flavonol biosynthesis, plus melatonin and oxalate metabolism, which together indicate production of diverse plant metabolites. The plasmodesmata-mediated transport term suggests intercellular movement of these metabolites, consistent with plant tissues. Some N-terminal methylation terms may reflect regulatory/modification enzymes linked to these pathways. Although daunorubicin biosynthesis is unusual for plants, the overall pattern centers on biosynthesis of small-molecule plant metabolites and their intercellular handling. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010497","count":1},{"id":"GO:0033609","count":1},{"id":"GO:1901771","count":1},{"id":"GO:0018012","count":1},{"id":"GO:0018013","count":1}]},{"hash":"858981012976479688","title":"Regulation of Plant Growth and Cell Wall Biosynthesis","description":"The top GO terms point to regulatory control over plant developmental processes and biosynthetic pathways, including chlorophyll biosynthesis, seed growth, lignin/syringal biosynthesis, and secondary cell wall biogenesis, along with growth-related processes like root meristem activity and leaf senescence. This suggests a cohesive cluster of proteins involved in modulating plant growth and cell-wall\u2013associated metabolism, with some broader chromatin-related terms that may reflect general gene regulation in plants. Overall, a plant growth and cell-wall regulation theme fits best.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010380","count":2},{"id":"GO:0080113","count":2},{"id":"GO:1901430","count":2},{"id":"GO:1901347","count":2},{"id":"GO:0010082","count":2}]},{"hash":"1600053608583256843","title":"Fungal sphingolipid and ergosterol metabolism","description":"These proteins appear to participate in membrane lipid biosynthesis, as indicated by strong enrichment for sphingolipid metabolism (mannosyl-inositol phosphorylceramide metabolic process) and ergosterol biosynthesis regulation, along with related lipid biosynthetic processes. While a few annotations are broader or cross-species, the combination of sphingolipid and ergosterol terms points to fungal membrane lipid metabolism as the core theme.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0006636","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0032443","count":3}]},{"hash":"1360214254897393020","title":"Ubiquitin-Proteasome Regulation of Circadian and Cell Cycle","description":"The cluster shows strong enrichment for ubiquitin-dependent protein catabolic processes, including SCF-dependent pathways, and positive regulation of polyubiquitination, pointing to proteostasis control via the ubiquitin-proteasome system. The presence of circadian rhythm regulation and mitotic DNA damage checkpoint signaling suggests turnover of clock and cell-cycle regulators is a central theme, with additional signals related to metal-induced stress responses. A concise label capturing ubiquitin-mediated regulation with circadian and cell-cycle relevance fits best.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0042752","count":3},{"id":"GO:0030174","count":3},{"id":"GO:0046685","count":3}]},{"hash":"1157060639551946557","title":"Meiosis spindle assembly and proteasomal degradation","description":"The top terms cluster around ubiquitin-proteasome\u2013dependent protein catabolism, microtubule polymerization, and spindle assembly in female meiosis I, plus oocyte maturation. These collectively suggest a function in meiotic progression and spindle dynamics regulated by proteolysis. Some neural-development terms appear as noise but do not override the main meiotic/microtubule theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0046785","count":2},{"id":"GO:0007057","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0021678","count":2}]},{"hash":"2243370991371856103","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0060192","count":1},{"id":"GO:1901206","count":1},{"id":"GO:0044205","count":1}]},{"hash":"173320836769605223","title":"Pexophagy and cold stress response","description":"The top GO terms point to autophagy of peroxisomes (pexophagy) and response to freezing, suggesting a theme centered on peroxisome turnover under cold stress; transport is generic and less defining for the cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006810","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0050826","count":1}]},{"hash":"919783442950201173","title":"ER stress response and protein folding regulation","description":"This cluster is dominated by GO terms pointing to ER-associated protein quality control: misfolded protein transport, chaperone-dependent protein refolding, and translation initiation in response to ER stress. Together these indicate a coherent theme of folding regulation and stress-responsive control to prevent accumulation of misfolded proteins. Some terms (mesoderm formation, parathyroid hormone stimulus) are less central and may reflect broader roles, but the core signal centers on ER stress\u2013related protein folding and quality control.","confidence":"High","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:0051259","count":3},{"id":"GO:0070843","count":3},{"id":"GO:0070389","count":3}]},{"hash":"624719420566428268","title":"Ubiquitin-Dependent Proteolysis (SCF/Proteasome)","description":"This cluster is enriched for GO terms related to ubiquitin-dependent protein catabolism, particularly SCF-dependent ubiquitination feeding into proteasomal degradation. This strongly suggests involvement in regulated protein turnover. Additional terms point to cell-cycle and cytoskeletal processes that can be affected by proteolysis (e.g., spindle checkpoint signaling, septin ring assembly). Overall, the common theme is targeted degradation of proteins by the ubiquitin-proteasome system.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0031146","count":3},{"id":"GO:1901253","count":2},{"id":"GO:0044810","count":2},{"id":"GO:1902364","count":2}]},{"hash":"708926045996318291","title":"Flower development and epidermal cuticle biosynthesis","description":"This cluster is dominated by terms tied to flower and bract development (floral meristem growth, bract development, multicellular organism development) and transcriptional regulation, alongside signaling pathways (ethylene, abscisic acid) and regulation of cutin and wax biosynthesis. Together, these terms point to proteins involved in flower development with coordinated control of epidermal lipid barrier formation (cuticle). ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010451","count":2},{"id":"GO:0009873","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010432","count":2},{"id":"GO:0007275","count":2}]},{"hash":"2114803801124696310","title":"Secondary cell wall biosynthesis and sclerenchyma differentiation","description":"Top terms indicate glucuronoxylan biosynthesis and plant-type secondary cell wall biogenesis, with a clear signal of sclerenchyma cell differentiation. Additional hormone response (gibberellin, salicylic acid, ethylene precursor ACC) and antifungal innate immune regulation terms are present but act as supportive regulatory context rather than core functions. This points to a cohesive theme of cell wall construction and differentiation in plant tissue, particularly sclerenchyma.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010417","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0080169","count":1},{"id":"GO:0009961","count":1},{"id":"GO:0010055","count":1}]},{"hash":"321612772347856001","title":"Antiviral ubiquitin-proteasome signaling","description":"This cluster is dominated by GO terms linking ubiquitin-dependent proteolysis (SCF-dependent proteasomal ubiquitin-mediated protein degradation) with innate antiviral responses (defense against virus, innate immune response) and signaling pathways (RIG-I regulation, NF-kappaB activation, JNK regulation), suggesting a coherent theme of ubiquitin-proteasome\u2013mediated modulation of antiviral signaling and immune responses.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0042787","count":3},{"id":"GO:2000620","count":2}]},{"hash":"776328698423426460","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms for ubiquitin-mediated proteolysis, including K48- and K6-linked ubiquitination, autoubiquitination, and histone catabolism. These themes reflect targeted protein turnover and chromatin regulation by ubiquitin, with some ancillary links to TNF signaling and transport regulation, but the unifying motif is proteostasis through ubiquitination.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0036205","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0085020","count":3}]},{"hash":"787393091795366966","title":"Ubiquitin-Proteasome Mediated Proteolysis","description":"The top GO terms are dominated by ubiquitination and proteasomal degradation processes (SCF-dependent ubiquitin-proteasome pathway and protein polyubiquitination), with proteolysis also present. Other terms such as retina development or viral entry are likely less representative noise given the small cluster size, so the core theme centers on protein tagging and degradation via the ubiquitin-proteasome system.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060041","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000209","count":2},{"id":"GO:1903704","count":1}]},{"hash":"1506255383789834401","title":"Plant development and hormone signaling","description":"This cluster shows strong signals for plant-specific growth and tissue-differentiation processes, including endosperm regulation, flower and lateral root development, phloem/xylem histogenesis, and responses to hormones like auxin and ethylene (auxin biosynthesis, ethylene response) as well as growth responses such as shade avoidance and gravitropism. While fatty acid biosynthesis is a general metabolic term present, the predominant theme centers on plant development and hormone-mediated growth. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":2},{"id":"GO:0055114","count":2},{"id":"GO:2000014","count":2},{"id":"GO:0009641","count":1},{"id":"GO:0009684","count":1}]},{"hash":"294526395015107598","title":"Lipid and Carbohydrate Biosynthesis","description":"The terms center on biosynthetic processes for lipids and carbohydrate-derived structures (mycolic acid, LPS core, GDP-mannose, dTDP-rhamnose) as well as steroid-related lipid metabolism (testosterone/androgen). While there are outliers (acetoin catabolism, transcription regulation), the dominant pattern points to lipid and carbohydrate biosynthesis pathways, making the label plausible though not perfectly tight due to term diversity. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0009244","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0071768","count":2}]},{"hash":"485219807552240344","title":"ER targeting and ERAD","description":"The top GO terms are dominated by processes of SRP-dependent cotranslational targeting to the membrane, ER-to-cytosol retrograde transport (ERAD), and post-translational targeting to membranes. This points to a cluster of proteins involved in directing nascent and processed proteins to the ER membrane, monitoring quality, and routing them for degradation when needed, with a broader tie to membrane trafficking. A few immune-defense terms appear but are likely secondary annotations; the core theme is ER-focused protein targeting and quality control.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0000060","count":1}]},{"hash":"362603942088703393","title":"Unknown","description":"The enriched GO terms span diverse processes from plant metabolism (lignin and anthocyanin biosynthesis) to xenobiotic/drug metabolism (glucuronidation, antibiotic metabolism) and even a neural-specific localization (paranode region of axon), with estrogen catabolic activity also present. This mixture suggests no single cohesive function tying the proteins together, so the cluster is best labeled Unknown with no confidence in a representative function.","confidence":"","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":4},{"id":"GO:0009808","count":4},{"id":"GO:0009718","count":4},{"id":"GO:0006711","count":4},{"id":"GO:0052697","count":4}]},{"hash":"1462643006530961286","title":"Unknown","description":"The GO terms cover a wide range of distinct metabolic and post-translational processes (polyhydroxybutyrate biosynthesis, stilbene and chlorophyll catabolism, glucuronoside and phospholipid remodeling, P450 epoxygenase pathway, antibiotic biosynthesis, and protein demethylation), with no clear shared function among the proteins.","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:0019391","count":1},{"id":"GO:0046272","count":1},{"id":"GO:0015996","count":1}]},{"hash":"305729610769077805","title":"Prokaryotic transcription-translation machinery and metabolism","description":"The top GO terms include translation, SSU-rRNA maturation, and transcription regulation, pointing to core bacterial gene expression processes. The additional metabolic terms (retinol and androgen metabolism, acetoin catabolism, mycolic acid biosynthesis) suggest associated metabolic activities rather than a single cohesive pathway. This fits a label about bacterial expression machinery with diverse metabolism, but the link is weak due to dispersion of terms.","confidence":"Low","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0045150","count":1},{"id":"GO:0042572","count":1}]},{"hash":"1078008914902769540","title":"Embryonic morphogenesis and patterning","description":"The top GO terms point to embryonic development and tissue morphogenesis across multiple lineages (palate, mesoderm, left/right patterning, placenta, hair follicle, cartilage, EMT in endocardial cushion formation), with one DNA repair term seeming incidental. This coherently suggests a cluster involved in embryonic development and morphogenesis rather than a single specialized pathway. ","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":1},{"id":"GO:0060707","count":1},{"id":"GO:0007498","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0010957","count":1}]},{"hash":"1600947594800015285","title":"Sphingolipid Transport and Metabolism","description":"The top GO terms cluster around glycosphingolipid/glycosphingolipid metabolic processes and ceramide/ceramide phosphate transport (e.g., ER to Golgi ceramide transport, glycosphingolipid metabolic process), complemented by general transmembrane transport terms (organic cation, polyol, ammonium). This pattern points to a set of membrane transport proteins dedicated to sphingolipid handling and related metabolism, with possible ties to defense signaling. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046836","count":1},{"id":"GO:0015695","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0015791","count":1},{"id":"GO:0009751","count":1}]},{"hash":"2015802308396448709","title":"RNA stability and translation regulation","description":"This cluster centers on post-transcriptional control: mRNA stability/modification/stabilization, alternative splicing, and initiation of translation (including eIF4F assembly and IRES-dependent initiation), all pointing to coordinated RNA metabolism and translational control, especially under stress.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":5},{"id":"GO:0016556","count":4},{"id":"GO:0048255","count":4},{"id":"GO:0075522","count":4},{"id":"GO:1905663","count":4}]},{"hash":"662016365834228507","title":"Membrane dynamics and trafficking regulation","description":"Top GO terms point to processes involving membranes and cargo movement, including positive regulation of exocytosis, regulation of membrane tubulation, and prospore membrane formation, which together suggest membrane biogenesis and trafficking as a core theme. Additional terms about cell shape, nuclear import, and adenylate cyclase activation support a broader membrane-associated signaling/transport context. Some terms (methylmercury response, astrocyte activation) are less central and reflect broader stress or activation states. Overall, the cluster seems to center on membrane dynamics and related signaling.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045921","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0033234","count":2},{"id":"GO:0032120","count":2},{"id":"GO:1903525","count":2}]},{"hash":"1294653210540791682","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072344","count":1},{"id":"GO:0018937","count":1},{"id":"GO:1990116","count":1},{"id":"GO:1902167","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1097614475442958066","title":"Sphingolipid Signaling and Phospholipid Metabolism","description":"This cluster shows strong enrichment for sphingolipid-related terms (regulation of sphingolipid signaling, sphinganine-1-phosphate metabolism) and phospholipid metabolism (phospholipid dephosphorylation, phospholipid catabolic and glycerolipid biosynthesis processes), suggesting a lipid signaling/remodeling theme rather than a single transport function.","confidence":"High","size":5,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902068","count":3},{"id":"GO:0044329","count":3},{"id":"GO:0015760","count":3},{"id":"GO:0044330","count":3},{"id":"GO:0046839","count":3}]},{"hash":"1681526394075529304","title":"Unknown","description":"The top terms are a mix of animal sensory development (olfactory learning, retina development) and plant development/process terms (plant-type cell wall biogenesis, xylem/phloem pattern formation) plus cytoskeleton organization, giving no clear, cohesive theme across all proteins. This makes a single intuitive label unreliable.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008355","count":1},{"id":"GO:0060041","count":1},{"id":"GO:0007010","count":1},{"id":"GO:0009832","count":1},{"id":"GO:0010051","count":1}]},{"hash":"1833034754590991673","title":"Negative Regulation of Cellular Processes","description":"The top GO terms are dominated by multiple instances of negative regulation across diverse cellular processes (e.g., autophagosome maturation, action potential, mitochondrial fusion, proteasomal degradation, transcription regulation), with a related note on PML body organization. This pattern points to a shared theme of downregulation or modulation of various cellular activities rather than a single, cohesive pathway, justifying a label focused on negative regulation across processes.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":4},{"id":"GO:1902260","count":4},{"id":"GO:0010216","count":4},{"id":"GO:0045648","count":4},{"id":"GO:1901097","count":4}]},{"hash":"6414028974866598","title":"Light-Responsive Photosynthesis Proteins","description":"The GO terms cluster around light sensing and responses (red/blue/UV-A light, low/high light, nonphotochemical quenching) and photosynthesis/PSI light harvesting, with a note on chlorophyll-related biosynthesis, suggesting proteins involved in photoprotection and light-driven photosynthesis.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010196","count":3},{"id":"GO:0010218","count":2},{"id":"GO:0010114","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0009645","count":2}]},{"hash":"1822651602661391734","title":"Proteostasis and ER Stress Response","description":"The top GO terms cluster around protein quality control: misfolded protein transport, chaperone-dependent refolding, and translation initiation regulation in response to ER stress, along with related proteostasis processes like oligomerization. Although there are a couple of developmental terms (mesoderm formation, Hedgehog pathway regulation) present, the dominant signal is proteostasis and ER stress\u2013mediated transcription/translation regulation, suggesting the proteins function together in maintaining protein homeostasis under stress.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901621","count":2},{"id":"GO:0051259","count":2},{"id":"GO:0070843","count":2},{"id":"GO:0070389","count":2},{"id":"GO:1900035","count":2}]},{"hash":"741552651476559462","title":"Mitotic cell cycle regulation","description":"The term distribution is dominated by mitosis-related terms (mitotic sister chromatid separation, mitotic cell cycle, mitotic cytokinesis), indicating proteins involved in controlling cell division. Additional terms point to related regulatory layers (protein methylation, ubiquitin-dependent ERAD, nuclear import, GTPase activity, apoptotic regulation, mitochondrial calcium signaling), consistent with coordinated cell-cycle progression and checkpoints.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006479","count":2},{"id":"GO:0051306","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000281","count":2}]},{"hash":"331515799004953628","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001253","count":1},{"id":"GO:0031440","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0006362","count":1}]},{"hash":"29856040149132420","title":"Unknown","description":"The GO terms are scattered across development (spinal cord development, neural tube closure, multicellular growth) and cellular processes (protein import, ribosome biogenesis, vesicle trafficking) with no clear shared function or interaction, so a cohesive label is not apparent.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0017038","count":1},{"id":"GO:0051441","count":1},{"id":"GO:0075522","count":1}]},{"hash":"1224541520244519623","title":"Ribosome biogenesis and growth","description":"The GO terms show prominent ribosome biogenesis (including large subunit biogenesis) signals along with cell division and organismal growth terms; a few development-related terms may be incidental. This points to a theme centered on ribosome production and related growth processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0035264","count":2},{"id":"GO:0021510","count":2}]},{"hash":"1674410472554231300","title":"Nuclear RNA Processing and Ribosome Biogenesis","description":"The top GO terms cluster around nuclear functions such as ribosomal large subunit biogenesis, mRNA export from the nucleus, and RNA processing steps, with a nod to DNA replication. Although several terms are obsolete, the common theme appears to be nucleus\u2011based RNA metabolism and ribosome assembly, justifying a label focused on these processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072711","count":1},{"id":"GO:0017038","count":1},{"id":"GO:1990120","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0010501","count":1}]},{"hash":"2292124408992309460","title":"RNA and protein methylation","description":"This cluster is dominated by GO terms related to methylation across RNA and proteins, including 2-methylguanosine metabolic process, rRNA guanine-N7-methylation, tRNA methylation, 7-methylguanosine cap, and protein methylation. Although a couple terms are obsolete, the prevailing theme points to methyltransferase activity and methylation pathways that modify RNA molecules and proteins, suggesting these proteins function in methylation/modification processes. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080180","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0032775","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0006479","count":1}]},{"hash":"488924028192322277","title":"Neurodevelopment and apoptotic regulation","description":"The top GO terms cluster around neural development (forebrain development, neural tube closure) and apoptotic processes in neural and glial cells (glial cell apoptotic process, neuron apoptotic process, regulation of apoptotic signaling, apoptotic DNA fragmentation), with some terms touching on TGF-beta signaling and cell division. The combination suggests a theme of neurodevelopmental control paired with programmed cell death, rather than a single purely metabolic or structural function. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0001843","count":2},{"id":"GO:2001235","count":2},{"id":"GO:0030900","count":2},{"id":"GO:1902510","count":2}]},{"hash":"1546811502122847484","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0031442","count":1},{"id":"GO:0048574","count":1},{"id":"GO:0048571","count":1}]},{"hash":"480205712363305137","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042797","count":3},{"id":"GO:0031440","count":3},{"id":"GO:0045899","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001172","count":3}]},{"hash":"478460422112355506","title":"RNA splicing and mRNA export machinery","description":"The top GO terms center on spliceosome-mediated splicing and mRNA export (positive regulation of mRNA splicing via spliceosome, spliceosomal complex disassembly, poly(A)+ mRNA export from nucleus), with supporting signals from ncRNA-mediated silencing and ribosomal biogenesis, indicating a cohesive theme of RNA processing and nuclear mRNA trafficking.","confidence":"High","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0000390","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0017038","count":3},{"id":"GO:1990120","count":3}]},{"hash":"1446757599367172886","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042797","count":1}]},{"hash":"621482804182642300","title":"RNA pseudouridylation and translation","description":"The top GO terms include translation and enzymes making pseudouridine in tRNA/rRNA, suggesting RNA modification linked to protein synthesis as the cluster\u2019s core function, despite some unrelated metabolic terms.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0006784","count":1},{"id":"GO:2001059","count":1}]},{"hash":"2018505781739823114","title":"Viral entry, uncoating, and release","description":"The top GO terms are dominated by steps in the viral life cycle: uncoating of virus, fusion of the viral membrane with the host membrane, and viral release from the host cell, along with at least one term about activation of viral genome replication by the host. While a couple terms seem unrelated (e.g., plant sepal formation, some obsolete regulatory terms), the overall cluster evidence points to processes governing viral infection stages. This makes a concise label of viral entry/uncoating/release representative of the dominant function in this cluster, with some noise from incidental annotations.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019061","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0010849","count":1},{"id":"GO:0071492","count":1}]},{"hash":"721847070444999548","title":"Flavonoid and lignan biosynthesis and transport","description":"This cluster is enriched for GO terms related to plant phenylpropanoid metabolism, including anthocyanin-containing compound biosynthesis and flavonoid transport from ER to vacuole, as well as secoisolariciresinol lignan biosynthesis and related catabolism. Together, these terms point to roles in the biosynthesis and trafficking of plant polyphenols (flavonoids and lignans). Some unrelated terms appear, but the dominant signal supports a plant secondary metabolite biosynthesis/function theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":2},{"id":"GO:1901098","count":1},{"id":"GO:1901525","count":1},{"id":"GO:1903415","count":1},{"id":"GO:0032435","count":1}]},{"hash":"1764209281355415513","title":"mRNA processing and translation initiation","description":"The top GO terms cluster around post-transcriptional mRNA maturation (polyadenylation, splicing, stabilization, modification) and initiation of translation (eIF4F complex assembly, IRES-dependent initiation). Despite a few unrelated or obsolete terms, the dominant signal is RNA processing and the start of translation, suggesting proteins involved in mRNA maturation and translation initiation.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0016556","count":3},{"id":"GO:0048255","count":3},{"id":"GO:0075522","count":3},{"id":"GO:1905663","count":3}]},{"hash":"942581971400309655","title":"Autophagy and Inflammation Regulation","description":"Top GO terms emphasize autophagy and inflammatory responses, including autophagy (GO:0006914) and inflammatory response (GO:0006954), with an indication of acute inflammatory activation. Additional terms relate to modulation of ubiquitin-protein transferase activity and protein sumoylation, which are connected to signaling and protein turnover that intersect autophagy and immune signaling. A metabolic note appears as L-glutamine metabolic process, which can support immune cell function and autophagic processes. Overall, the cluster appears to be centered on the interface between autophagy and inflammatory regulation, rather than a single isolated function.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"autophagy","top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:2001268","count":3},{"id":"GO:0033234","count":3},{"id":"GO:0060081","count":3},{"id":"GO:1903178","count":3}]},{"hash":"1524718528452103792","title":"Neural development and apoptosis regulation","description":"The top GO terms point to neural development (neural tube closure, forebrain development) and apoptosis regulation (positive regulation of apoptotic signaling, glial cell apoptotic process, regulation of apoptotic DNA fragmentation), suggesting the cluster centers on neural development with associated apoptosis control. While there are also terms related to cell division and microtubule dynamics, the predominant signal reflects neural development coupled with programmed cell death pathways.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0001843","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2001235","count":2}]},{"hash":"65998597702747050","title":"Virus Entry and Release","description":"This cluster is dominated by viral lifecycle terms: uncoating of virus, fusion of viral membrane with host, viral release from host cell, and host-mediated activation of viral genome replication, pointing to steps of virus-host interaction during infection. A few terms like protein folding and sepal formation appear as noise or misannotations, but the core theme remains viral entry, genome activation, and egress.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019061","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0010849","count":1},{"id":"GO:0071492","count":1}]},{"hash":"2029165544373212129","title":"ER stress response and COPII vesicle trafficking","description":"Top terms are dominated by the endoplasmic reticulum unfolded protein response, COPII-coated vesicle budding, and ER localization, with calcium homeostasis linked to ER function. These collectively point to a cohesive theme of ER stress signaling and ER-to-Golgi trafficking, suggesting the cluster represents ER-based protein handling and transport rather than other cellular processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0044828","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0090114","count":1}]},{"hash":"1769624283188708439","title":"Neural development and transcription regulation","description":"The cluster\u2019s top GO terms are centered on DNA-templated transcription and neural development, including spinal cord development and neural tube closure, pointing to a set of proteins involved in transcriptional control during neural development. Other terms indicate broader developmental processes, with some housekeeping-related terms present, but the dominant signal is neural development and transcriptional regulation.","confidence":"High","size":4,"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:0035264","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0051441","count":1}]},{"hash":"415273534485367511","title":"Unknown","description":"The GO terms span immune signaling (IL-12/IL-13, Th2 differentiation), angiogenesis, host\u2013symbiont interactions, fungal cell wall regulation, neuronal synaptic processes, and lipid biosynthesis. There is no single cohesive function uniting these terms, and there are no edges among the proteins, so a unified, specific label is not apparent.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904385","count":1},{"id":"GO:2000667","count":1},{"id":"GO:0060237","count":1},{"id":"GO:0043536","count":1},{"id":"GO:0032615","count":1}]},{"hash":"1173971327169265108","title":"Unknown","description":"The top terms are spread across very different processes, including GPCR signaling, various metabolic biosynthesis pathways (isoprenoid farnesyl diphosphate, IPP via MEP/mevalonate), carbohydrate phosphorylation, amino acid metabolism (homoserine, methionine), and even transcriptional regulation by galactose, with several entries marked obsolete. There isn\u2019t a single cohesive function or pathway that ties these proteins together, so a concise, representative label isn\u2019t well-supported.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007200","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0043448","count":1},{"id":"GO:0000435","count":1},{"id":"GO:0010142","count":1}]},{"hash":"982405855248320134","title":"Meiosis and Cytokinesis","description":"The GO terms for this cluster are dominated by meiotic and cytokinetic processes (meiosis I/II cytokinesis, male meiosis cytokinesis, actomyosin contractile ring contraction, and cell plate assembly), suggesting a shared function in cell division during meiosis. There are a couple of outlier terms (pinoresinol biosynthetic process, cerebral cortex development) that are less cohesive with the main theme, but the core signal points to cytokinesis linked to meiosis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901599","count":1},{"id":"GO:0000919","count":1},{"id":"GO:0048137","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0007110","count":1}]},{"hash":"1648087925666678548","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042797","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0006386","count":1}]},{"hash":"737469436597133880","title":"ERAD and mitochondrial fusion regulation","description":"The cluster\u2019s GO terms cluster around ER-associated protein processes (sumoylation, ubiquitin-dependent ERAD, tail-anchored ER membrane insertion) and mitochondrial dynamics (negative and positive regulation of mitochondrial fusion), suggesting a theme of coordinating protein quality control at the ER with mitochondrial fusion regulation. Translation appears as a broad cellular process present in the set, and some terms are obsolete, but the core signal points to ERAD-related quality control linked to mitochondrial dynamics. Overall, this label captures the dominant functions represented.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:1901097","count":2},{"id":"GO:0010637","count":2},{"id":"GO:1902283","count":2},{"id":"GO:0006412","count":2}]},{"hash":"126903336095010542","title":"Lipid and small-molecule metabolism","description":"The top GO terms point to a mix of lipid-related pathways (fatty acid biosynthesis, fatty acid omega-oxidation, prostaglandin metabolism, retinol metabolism) along with catabolic processes for ethanol, formaldehyde, and galactose, plus a redox/oxidation-reduction theme. This pattern suggests a general cluster of metabolic transformation of lipids and other small molecules rather than a single precise function.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006633","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0010430","count":2},{"id":"GO:0006068","count":2}]},{"hash":"1429723950211625017","title":"Transcriptional regulation of shoot formation in plants","description":"Top GO terms indicate regulation of DNA-templated transcription and regulation of secondary shoot formation, suggesting these proteins act as transcriptional regulators influencing shoot development. The combination implies a coherent theme around transcriptional control linked to shoot formation in plants, supporting this label.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:2000032","count":4},{"id":"GO:0006355","count":4}]},{"hash":"234246449284664675","title":"mRNA processing and translation initiation","description":"The top GO terms center on post-transcriptional regulation: mRNA modification, stabilization, and splicing, with translation initiation components like eIF4F complex assembly and IRES-dependent initiation. This suggests the cluster represents proteins involved in mRNA maturation and the initiation of translation. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0048255","count":1},{"id":"GO:0075522","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0006378","count":1}]},{"hash":"1311301890584025535","title":"Nuclear RNA Processing and Ribosome Biogenesis","description":"This cluster centers on nuclear RNA maturation and export, plus assembly of ribosomal subunits and nuclear protein import, suggesting a role in preparing RNA and ribosome components for expression. Some terms (e.g., embryonic development and innate immune signaling) may reflect broader associations or noise, but the core signals point to nuclear RNA handling and ribosome assembly. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0017038","count":3},{"id":"GO:1990120","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0048568","count":3}]},{"hash":"1656122829645121775","title":"Amino acid biosynthesis and transsulfuration","description":"This cluster is driven by several GO terms tied to amino acid production and related metabolism: 2-oxobutyrate and pyruvate biosynthesis, and specific biosynthetic processes for serine (D-serine), threonine, isoleucine, and cysteine via transsulfuration. Although a couple of obsolete terms appear, the dominant theme centers on amino acid biosynthesis and interconversion, suggesting the proteins collaborate in amino acid metabolism rather than a single signaling or structural role. The appearance of a morphine-response term is likely incidental to annotation noise rather than central function.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046360","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0018871","count":2},{"id":"GO:0070179","count":2},{"id":"GO:0070689","count":2}]},{"hash":"475744918463648422","title":"Splicing and stimulus-driven differentiation","description":"This cluster centers on RNA processing terms (spliceosome-mediated mRNA splicing and polyadenylation) and includes signaling-related and differentiation terms (p38 MAPK cascade, responses to glucocorticoid and EGF, and differentiation processes like monocyte, T follicular helper cell differentiation, and proepicardium development), suggesting a link between RNA processing and stimulus-responsive differentiation pathways.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0071385","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0045657","count":2}]},{"hash":"484871656371794514","title":"Neural development and apoptosis signaling","description":"This cluster shows a coherent theme of nervous system development (nervous system development, forebrain development, neural tube closure) together with apoptotic regulation (glial cell apoptotic process, positive regulation of apoptotic signaling, regulation of apoptotic DNA fragmentation) and TGF-beta\u2013related signaling, suggesting proteins involved in neural formation with controlled cell death. Some unrelated terms like pigmentation or SREBP signaling may reflect broader developmental or metabolic links, but the dominant pattern is neural development coupled with apoptosis regulation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0001843","count":2}]},{"hash":"649370188981506566","title":"RNA processing and transcription regulation","description":"The top GO terms point to RNA biology and transcription control, with multiple terms on RNA-templated transcription, transcription termination, transcription antitermination, nuclear mRNA surveillance, TRAMP-dependent tRNA surveillance, and translation. These collectively suggest a cluster focused on RNA metabolism and gene expression regulation, despite a few outlier terms that are less representative.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0001172","count":3},{"id":"GO:0006353","count":2},{"id":"GO:0071038","count":2},{"id":"GO:0010590","count":2}]},{"hash":"313479419387044256","title":"Ubiquitin-Proteasome Regulation","description":"Based on the top GO terms, most proteins in this cluster relate to ubiquitination (GO:0016567) and proteasome regulatory particle assembly, suggesting involvement in protein turnover and regulated degradation. Other terms (vitamin D response, thermoception, oligodendrocyte differentiation, dendrite development, and kinase activity regulation) are less central but may reflect broader signaling roles. Overall, the dominant theme is ubiquitin-proteasome\u2013mediated regulation of protein life cycle and signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0033280","count":3},{"id":"GO:0050955","count":2},{"id":"GO:0070682","count":2},{"id":"GO:0007253","count":2}]},{"hash":"1238065622637755001","title":"Microtubule-Driven Mitosis and Transport","description":"The top GO terms center on microtubule dynamics: spindle assembly, centrosome separation, and chromosome recapture during mitosis, along with minus-end directed microtubule sliding, and motor-driven anterograde transport along microtubules. Additional terms reference structural organization in neural tissues and adherens junctions, which can relate to cytoskeletal organization and polarity. Overall, the cluster appears to reflect microtubule-based processes governing cell division and intracellular transport, with some involvement in neural tissue structure. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0000911","count":1},{"id":"GO:0098971","count":1},{"id":"GO:0021685","count":1},{"id":"GO:0021693","count":1}]},{"hash":"908474251487314961","title":"Plant development and hormone signaling","description":"The top GO terms center on flower and anther development, vegetative phase changes, and differentiation events, with additional links to hormone signaling (gibberellin/GA and salicylic acid) and regulation of GA signaling. A related term on antifungal innate immune response regulation suggests a link to defense, indicating a cluster of proteins involved in coordinating plant growth, development, hormone signaling, and immune responses. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009908","count":1},{"id":"GO:0048653","count":1},{"id":"GO:0010321","count":1},{"id":"GO:0080169","count":1},{"id":"GO:0009961","count":1}]},{"hash":"1576193426623957184","title":"Innate and Adaptive Immune Signaling","description":"This cluster shows multiple immune-related GO terms: innate responses to fungus and MyD88-independent TLR signaling, neutrophil clearance, and adaptive T cell proliferation, suggesting a common theme of immune activation and regulation. A few terms about cartilage/bone development and endothelial migration appear less central and may reflect broader signaling cross-talk or annotation noise. Overall, label captures the dominant immune-focused function of this cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":3},{"id":"GO:0001502","count":3},{"id":"GO:0009620","count":3},{"id":"GO:0097350","count":3},{"id":"GO:0035372","count":3}]},{"hash":"442584359001838148","title":"Cartilage and airway morphogenesis","description":"The top GO terms cluster around developmental processes such as cartilage condensation, trachea formation, and epithelial proliferation in lung morphogenesis, suggesting a theme of cartilage/airway development. Supporting cellular machinery terms (microtubule localization, Golgi inheritance, Rho signaling) fit morphogenesis but are secondary. A few immune-related terms appear, but the dominant signal points to respiratory tract and cartilage development.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001502","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0043536","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0002741","count":2}]},{"hash":"1916438837780618874","title":"Immune activation and cytokine production","description":"This cluster centers on immune signaling and regulation, highlighted by positive regulation of T cell proliferation, interleukin-4 production, and broader cytokine production in immune responses. Additional terms point to immune cell movement and trafficking (endothelial migration, Rho signaling, microtubule localization) and neutrophil clearance, suggesting a theme of immune activation coupled with cell migration. A couple of outliers (e.g., cartilage condensation) may reflect broader developmental contexts or annotation noise, but the dominant signal is immune activation and cytokine-mediated regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046641","count":2},{"id":"GO:0001502","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0043068","count":2}]},{"hash":"23374019936690318","title":"Immune cytokine signaling and endothelial migration","description":"The cluster's top GO terms cluster around immune signaling (alpha-beta T cell proliferation, cytokine production, interleukin-4 production, neutrophil clearance) and processes driving endothelial cell migration, supported by Rho-mediated signaling and cytoskeletal associations. While a term like cartilage condensation or microtubule localization adds breadth, the shared theme appears to be immune-driven signaling linked to cell movement and vascular remodeling.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":4},{"id":"GO:0001502","count":4},{"id":"GO:0097350","count":4},{"id":"GO:0035372","count":4},{"id":"GO:0043068","count":4}]},{"hash":"1064929321891807201","title":"Neural development and brain metabolism","description":"This cluster is driven by GO terms linked to forebrain and nucleus accumbens development, plus several brain-related metabolic processes (retinol, GABA, ethanol), suggesting a theme of neural development coupled with neural metabolism. Some terms are less coherent (embryonic gut, endothelial proliferation), but the core signal points to brain development and metabolic activity.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":4},{"id":"GO:0042572","count":4},{"id":"GO:0001936","count":4},{"id":"GO:0006068","count":4},{"id":"GO:0009450","count":4}]},{"hash":"2171183585968307926","title":"Bacterial exopolysaccharide biosynthesis","description":"This cluster centers on glycan biosynthesis and cell surface components, including alginic acid biosynthesis, UDP-glucose/UDP-glucuronate biosynthetic pathways, glycosaminoglycan biosynthesis, and enterobacterial common antigen biosynthesis, all pointing to extracellular polysaccharide production and cell envelope assembly. A related term about cell envelope stress supports envelope-associated functions, though one term (gastrulation) appears unrelated noise. Overall, the theme is exopolysaccharide and envelope glycan biosynthesis.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042121","count":2},{"id":"GO:0014823","count":2},{"id":"GO:0046168","count":2},{"id":"GO:0036460","count":2},{"id":"GO:0045454","count":2}]},{"hash":"1758609668206686257","title":"Mitochondrial Stress Response and Proteostasis","description":"The GO terms show oxidative stress response, cadmium stress adaptation, and energy metabolism (ATP, aerobic respiration) alongside protein quality control processes (mitochondrial protein insertion, proteasome assembly, misfolded protein degradation, ribosome/translation-related assembly). This points to a cluster of proteins involved in managing cellular stress, maintaining mitochondrial function, and preserving proteome integrity, rather than a single linear pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":2},{"id":"GO:1990171","count":1},{"id":"GO:0032979","count":1},{"id":"GO:1903715","count":1},{"id":"GO:0046034","count":1}]},{"hash":"1789383931742253755","title":"Unknown","description":"The GO terms span innate immune signaling (TRIF-dependent TLR and C-type lectin receptor pathways), DNA repair and chromatin regulation (postreplication repair, meiosis DSB formation, histone ubiquitination), transcription factor turnover (N-end rule pathway, TF catabolism), and even peroxisome import, with no clear single functional theme tying all four proteins together. Because of this diversity, a concise, representative label cannot be confidently assigned.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0035666","count":4},{"id":"GO:0042275","count":4},{"id":"GO:0071596","count":4},{"id":"GO:0010620","count":4},{"id":"GO:0033182","count":4}]},{"hash":"1431821163594307611","title":"Translation Machinery and RNA Processing","description":"This cluster is dominated by GO terms tied to protein synthesis and RNA processing, including mitochondrial translation elongation, translational elongation and termination, selenocysteine incorporation, and diphthamide modification of histidine (linked to EF2 function). The presence of spliceosomal tri-snRNP assembly reinforces an RNA-processing connection, suggesting these proteins broadly participate in gene expression at the translation and RNA-processing levels.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014009","count":2},{"id":"GO:0017183","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0002244","count":2},{"id":"GO:0000244","count":2}]},{"hash":"722242180730519726","title":"Unknown","description":"The GO terms span nervous system development, glial and cardiac apoptosis, immune/metabolic processes, and tissue remodeling, with no clear single function tying them together and no edges among proteins. This makes it hard to assign a coherent, representative label beyond Unknown. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":1},{"id":"GO:0010659","count":1},{"id":"GO:0035006","count":1},{"id":"GO:0033353","count":1},{"id":"GO:0071560","count":1}]},{"hash":"1024389675575518907","title":"Oocyte Meiosis: Spindle Assembly & Ubiquitin Degradation","description":"The dominant GO terms point to meiotic spindle formation and microtubule dynamics in oocytes (microtubule polymerization; spindle assembly in female meiosis I) together with ubiquitin-dependent proteolysis (ubiquitin-dependent and SCF-dependent proteasomal degradation). This combination suggests proteins coordinating meiotic progression through spindle organization and timely protein turnover. Some developmental terms (oocyte maturation, neural tube initiation) can reflect broader developmental roles but do not override the core meiotic/proteolysis theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046785","count":3},{"id":"GO:0007057","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0021678","count":3}]},{"hash":"425493637475462700","title":"Glycolysis and gluconeogenesis","description":"The top GO terms highlight canonical glycolysis and gluconeogenesis, pointing to central carbon metabolism. Additional carbohydrate catabolic processes (glucarate, galactonate, mandelate) reinforce a carbohydrate metabolism theme, while other terms (cell wall organization, menaquinone biosynthesis) appear as broader metabolic context. Overall, the cluster seems centered on energy production through carbohydrate metabolism rather than a single specialized function. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":3},{"id":"GO:0019394","count":2},{"id":"GO:0034194","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0071555","count":2}]},{"hash":"638142866391110486","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"Top GO terms center on ubiquitination and proteasomal degradation (e.g., ubiquitin-dependent protein catabolic process; SCF-dependent proteasomal ubiquitin-dependent protein catabolic process), with related terms involving receptor downregulation and cell cycle-related regulation (spindle checkpoint signaling). This pattern strongly suggests a cluster devoted to regulated protein turnover via the ubiquitin-proteasome system, influencing signaling and mitosis. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0031146","count":2},{"id":"GO:1901253","count":2},{"id":"GO:0044810","count":2},{"id":"GO:1902364","count":2}]},{"hash":"740488328703892581","title":"Developmental transcriptional regulation","description":"The terms center on DNA-templated transcription and its regulation, with many entries tied to developmental processes such as leaf morphogenesis, axis polarity, and germ cell development (oocyte and spermatid formation). This suggests proteins involved in controlling gene expression during development, even though terms span plant and animal contexts. Confidence: Medium","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:2000032","count":1},{"id":"GO:0009965","count":1},{"id":"GO:0045962","count":1},{"id":"GO:0006355","count":1}]},{"hash":"468333760579302160","title":"Plant light-sensing and photosynthesis","description":"The GO terms cluster around responses to multiple light wavelengths (red, far-red, blue, UV-A) and light intensity, plus photosynthesis and light-harvesting processes (PSI) and nonphotochemical quenching, with a note on phytol biosynthesis regulation. This suggests a cohesive theme of light perception and photosynthetic regulation in plants.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010218","count":2},{"id":"GO:0010114","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0009645","count":2},{"id":"GO:0071486","count":2}]},{"hash":"1981488037709027440","title":"Unknown","description":"The GO terms span metabolism (propylene and thymidine catabolism, antibiotic metabolism), energy/mitochondrial processes (aerobic electron transport chain, membrane potential), oxidative stress response (response to menadione), and nuclear/regulatory processes (chromatin binding, differentiation regulation), with no clear shared function among the proteins. The lack of edges/triangles and heterogeneous terms suggest no cohesive cluster function to label confidently.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042208","count":2},{"id":"GO:0016999","count":2},{"id":"GO:0030259","count":2},{"id":"GO:0006214","count":1},{"id":"GO:0036245","count":1}]},{"hash":"269036548589094500","title":"Unknown","description":"Top terms span DNA damage regulation, mevalonate/isoprenoid metabolism, calcium signaling/NFAT, inflammatory response, cell adhesion, DNA replication, glycogen metabolism, and lung development, indicating no single cohesive function for the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000002","count":1},{"id":"GO:1900486","count":1},{"id":"GO:1900490","count":1},{"id":"GO:0050728","count":1},{"id":"GO:0005513","count":1}]},{"hash":"886676474701910631","title":"Meiosis I spindle assembly in oocytes","description":"This cluster is dominated by GO terms for spindle assembly in female meiosis I, oocyte maturation, and microtubule polymerization, indicating proteins involved in meiotic spindle formation and oocyte development; ubiquitin-proteasome\u2013related terms support cell-cycle regulation during meiosis.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007057","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0051436","count":4},{"id":"GO:0001556","count":4}]},{"hash":"91503096018484676","title":"Multi-tissue Development and Protein Processing","description":"The top GO terms point to development across several tissues (spermatid, keratinocyte, hippocampus, substantia nigra) and processes like keratinization, Golgi localization, protein complex formation, deubiquitination, TOR signaling, and regulation of apoptosis. This suggests involvement in general developmental and cellular-regulatory pathways rather than a single tissue-specific function, so the label should reflect both broad developmental roles and protein-processing/regulatory activity.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":2},{"id":"GO:0003334","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0031424","count":2},{"id":"GO:0051683","count":2}]},{"hash":"180586502614158041","title":"Diverse Substrate Membrane Transporters","description":"Top GO terms point to transport across membranes for many substrates (sialic acid, vitamin, urate, organic cations, galactose, 4-hydroxyphenylacetate, nitrate, potassium, neurotransmitter loading), suggesting a broad collection of transport proteins rather than a single pathway. This justifies a label capturing the common function of membrane transport across diverse substrates.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0035461","count":1},{"id":"GO:0015747","count":1},{"id":"GO:0070715","count":1},{"id":"GO:0015757","count":1}]},{"hash":"1280516292708059344","title":"DNA repair and translesion synthesis","description":"This cluster is dominated by GO terms tied to DNA damage response and repair, notably error-free translesion synthesis and nucleotide-excision repair, plus DNA biosynthetic processes and gap filling. While a few other terms seem ancillary, the core shared function across the terms is DNA repair/maintenance during replication stress, guiding the label to reflect that theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0006297","count":2},{"id":"GO:1990171","count":1},{"id":"GO:0032979","count":1}]},{"hash":"2229809188230522533","title":"Chloroplast translation & ribosome maturation","description":"The top terms center on translation and maturation of ribosomal RNA, with chloroplast fission indicating organelle biogenesis; together they suggest a focus on chloroplast ribosome assembly and protein synthesis, with a couple of ancillary processes (transcription antitermination and stress response) as secondary associations.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0010020","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0006950","count":1}]},{"hash":"1052010229983292831","title":"Plant Hormone Signaling and Defense Responses","description":"The GO terms cluster around plant hormone signaling (gibberellin and salicylic acid), stress responses to fungi (chitin) and antifungal immunity, and epidermal/tissue differentiation (atrichoblast, sclerenchyma), suggesting a cohesive theme of growth regulation linked to defense and tissue differentiation in plants.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045648","count":2},{"id":"GO:0080169","count":2},{"id":"GO:0009961","count":2},{"id":"GO:0010055","count":2},{"id":"GO:0009751","count":2}]},{"hash":"875379280711009848","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006306","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0042417","count":1},{"id":"GO:0044205","count":1}]},{"hash":"2082374513689774910","title":"Ubiquitination and deubiquitination in cell cycle control","description":"The cluster centers on ubiquitin signaling, featuring multiple deubiquitination activities (K29-, K63-, K33-linked) and ubiquitination, tied to regulation of the cell cycle and DNA damage response. A few terms about chloroplast mRNA modification and vitamin B1 response are present but less connected to the core theme, suggesting the primary function is ubiquitin-mediated control of cell cycle progression.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0035523","count":1},{"id":"GO:1900871","count":1},{"id":"GO:0006977","count":1},{"id":"GO:0070536","count":1}]},{"hash":"704036304338227788","title":"RNA Processing and Translation Initiation","description":"This cluster is enriched for RNA-focused processes: formation of the translation preinitiation complex and IRES-dependent translation initiation point to translation initiation, while spliceosomal conformational changes relate to RNA processing. The other terms (exosomal secretion, mitochondrial fission, and various deubiquitination activities) are less coherent with the core theme, suggesting possible multifunctional entries. Overall, the prominent signal is in RNA processing and translation initiation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010950","count":1},{"id":"GO:0045471","count":1},{"id":"GO:0051726","count":1},{"id":"GO:0075522","count":1},{"id":"GO:0035871","count":1}]},{"hash":"1357155127926055437","title":"Cytokinin signaling and plant growth regulation","description":"This cluster is dominated by GO terms for cytokinin-activated signaling and broad regulation of growth-related processes in plants, including chlorophyll biosynthesis, root meristem growth, seed growth, leaf senescence, and cell wall/lignin biosynthesis, suggesting a coherent regulatory role in plant development.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":3},{"id":"GO:0010380","count":1},{"id":"GO:0080113","count":1},{"id":"GO:1901430","count":1},{"id":"GO:1901347","count":1}]},{"hash":"2296163993306336638","title":"Plant hormone signaling and fungal defense","description":"The proteins show enrichment for plant hormone responses (gibberellin, salicylic acid, ethylene precursor) alongside defense-related terms (chitin response, antifungal immune regulation), with additional development/differentiation terms (atrichoblast, sclerenchyma). This suggests a cluster centered on how hormone signaling modulates growth and immune responses in plants.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080169","count":2},{"id":"GO:0009961","count":2},{"id":"GO:0010055","count":2},{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2}]},{"hash":"1883744387060317692","title":"Embryonic organogenesis and tissue differentiation","description":"This cluster\u2019s top GO terms cover heart development (valve and morphogenesis), mesenchyme development, and multiple tissue-lineage differentiations (neural interneuron differentiation, floor plate, auditory receptor fate, pancreatic A cell fate) alongside cell-cycle regulation. The common theme is broad embryonic tissue formation and lineage specification across several organ systems, rather than a single pathway, so a high-level label of embryonic organogenesis and tissue differentiation is appropriate.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000793","count":3},{"id":"GO:2000764","count":3},{"id":"GO:0060375","count":3},{"id":"GO:0060485","count":3},{"id":"GO:0071156","count":3}]},{"hash":"633591267069890562","title":"Plant growth and development regulation","description":"This cluster centers on GO terms describing regulation across multiple plant growth and metabolic processes (chlorophyll biosynthesis, seed growth, lignin and secondary cell wall biosynthesis, root meristem growth, leaf senescence, etc.), suggesting the proteins mainly act as regulators of diverse plant developmental pathways rather than executing a single process.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0010380","count":3},{"id":"GO:0080113","count":3},{"id":"GO:1901430","count":3},{"id":"GO:1901347","count":3},{"id":"GO:0010082","count":3}]},{"hash":"1485103709914048018","title":"Mitochondrial tRNA and rRNA Methylation","description":"Most terms indicate RNA methylation/modification processes, notably mitochondrial tRNA methylation, tRNA N1-guanine methylation, and rRNA methylation, along with wybutosine biosynthesis. This points to RNA maturation/modification pathways centered on mitochondria and translation-related RNAs.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070901","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0002939","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2235125829485132201","title":"Unknown","description":"The GO terms span oxidation-reduction, amine metabolism, various biosynthetic and post-translational modification processes, and stress responses across plants, bacteria, and insects, with no clear shared function. Because there is no coherent theme and no connections between the proteins, this cluster should be labeled Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0030416","count":2},{"id":"GO:0018027","count":1},{"id":"GO:0014075","count":1},{"id":"GO:0036068","count":1}]},{"hash":"865331329377406190","title":"Protein peptidyl methylation","description":"The top GO terms cluster around various peptidyl methylation processes (lysine, arginine, serine) and general methylation, suggesting a cohesive function in post-translational modification by methyl groups, despite a few unrelated biosynthetic terms.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":1},{"id":"GO:0014075","count":1},{"id":"GO:0036068","count":1},{"id":"GO:0035572","count":1},{"id":"GO:0046690","count":1}]},{"hash":"859362306372805263","title":"Spermatogenesis and chromatin packaging","description":"The GO terms cluster around sperm development (spermatid development, sperm DNA condensation) and chromatin-related processes (pericentric heterochromatin formation, DNA replication-dependent chromatin assembly, transcription preinitiation complex regulation), suggesting a focus on germ cell differentiation and chromatin organization during spermatogenesis, despite some outliers. ","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900446","count":4},{"id":"GO:0090230","count":4},{"id":"GO:0007296","count":4},{"id":"GO:0031639","count":4},{"id":"GO:0035264","count":4}]},{"hash":"1293012151534752652","title":"Male germline meiosis and spermatogenesis","description":"The top GO terms are dominated by male germline development and meiotic processes (spermatocyte division, male meiosis chromosome condensation/segregation, male germ-line cyst formation, stem cell population maintenance), indicating a cluster focused on germline development and meiosis. Some terms (neural differentiation, fear behavior) are outliers or broader cellular processes, but the core theme remains germline meiosis.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045665","count":1},{"id":"GO:0048137","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0001662","count":1},{"id":"GO:0019827","count":1}]},{"hash":"1791390588826003314","title":"Ubiquitin-dependent protein degradation","description":"Dominant GO terms center on tagging proteins for destruction via ubiquitin (ubiquitin-dependent protein catabolic process, various ubiquitination types, autoubiquitination) and histone catabolic processes, suggesting a module of proteins involved in ubiquitin-proteasome\u2013mediated proteolysis. Secondary terms (TNF signaling regulation, spindle-associated processes) are less central to the core function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0036205","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0051865","count":3},{"id":"GO:1903265","count":3}]},{"hash":"766937371802887372","title":"Plant development and hormone-defense signaling","description":"The top GO terms cluster around key plant developmental processes (flower and anther development, vegetative phase change, atrichoblast differentiation) and hormone-related responses (gibberellin, salicylic acid) along with a defense/immune association (antifungal response) and a boron-responsive note. This points to a cohesive theme of growth and development modulated by hormone signaling with defense involvement, despite no observed network edges. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009908","count":1},{"id":"GO:0048653","count":1},{"id":"GO:0010321","count":1},{"id":"GO:0080169","count":1},{"id":"GO:0009961","count":1}]},{"hash":"2251756172745539336","title":"Fungal ammonium transport and nitrogen metabolism","description":"This cluster is dominated by GO terms related to ammonium transport (including transepithelial and methylammonium transport) and nitrogen utilization/metabolism, suggesting a shared function in nitrogen handling, particularly in fungi under nutrient limitation. The presence of growth responses to nutrient limitation (pseudohyphal and invasive growth) supports a context of nutrient-stress adaptation. The box C/D snoRNP assembly term appears less connected, but the strongest signals point to nitrogen/ammonium transport and metabolism in a fungal setting.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000492","count":1},{"id":"GO:0072488","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0060586","count":1}]},{"hash":"2231904324975631303","title":"Ubiquitin-Driven NF-\u03baB/JNK Signaling","description":"The top GO terms cluster around ubiquitin-dependent protein modification and proteolysis (K48/K63 ubiquitination, autoubiquitination) and inflammatory signaling (TNF-mediated signaling, NF-\u03baB-inducing kinase activation) plus JNK cascade regulation, suggesting a common function in ubiquitin-regulated inflammatory signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":2},{"id":"GO:2000620","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0033209","count":2},{"id":"GO:0070535","count":2}]},{"hash":"295655605057567521","title":"Vacuolar trafficking and ion transport","description":"This cluster centers on vacuolar processes (vacuolar organization, targeting to vacuole, acidification) and membrane/ion transport (proton and sodium translocation, proton-motive force-driven ATP synthesis) with a note on copper ion homeostasis. Together these terms suggest a cohesive role in vacuolar maintenance and associated ion transport functions across membranes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017196","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0015991","count":1}]},{"hash":"2004212281070640781","title":"Cytoplasmic protein folding and quality control","description":"The top GO terms center on cytoplasmic protein folding (GO:0006457), chaperone-mediated complex assembly (GO:0051131), and ubiquitin-proteasome\u2013mediated quality control (GO:0071629), indicating a proteostasis/chaperone-focused cluster. Additional terms about tubulin/microtubule organization suggest some cytoskeletal associations, but the core signal is chaperone activity and protein quality control in the cytoplasm. Transcription-related and amino acid catabolic terms appear ancillary or incidental to a small set of annotations. Overall, the most representative theme is cytoplasmic protein folding and quality control.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071629","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0051131","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0043622","count":1}]},{"hash":"1028149862539753504","title":"Plant Hormone Signaling and Development","description":"The terms cluster around plant hormone signaling pathways (cytokinin, ABA, gibberellin) together with developmental processes (flower development, cell differentiation) and defense responses (response to biotic stimulus, defense). This suggests proteins involved in hormone-regulated signaling that coordinate growth, development, and defense in plants, with nodulation as an additional developmental process. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009607","count":1},{"id":"GO:0080163","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0043086","count":1}]},{"hash":"574422610743473966","title":"Ubiquitin-Dependent Receptor Turnover in Development","description":"This cluster shows enrichment for ubiquitin-dependent protein catabolic processes and receptor-related catabolic processes (e.g., Wnt receptor catabolic process) along with developmental signaling terms (multicellular organism development, TNF signaling). The common thread appears to be regulation of signaling via ubiquitin-mediated degradation of receptors, linking protein turnover to developmental pathways.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903215","count":2},{"id":"GO:0045676","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0007275","count":2},{"id":"GO:1901253","count":2}]},{"hash":"1843020698032420188","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071044","count":1},{"id":"GO:0071037","count":1},{"id":"GO:0000973","count":1},{"id":"GO:0032066","count":1},{"id":"GO:0090503","count":1}]},{"hash":"1744472929059512156","title":"Nucleotide salvage and nucleoside catabolism","description":"The dominant GO terms converge on salvage and breakdown of nucleotides and nucleosides (uridine, inosine, cytidine, guanosine, purine/pyrimidine bases) and related interconversions, with NAD/Nicotinamide riboside salvage also listed. Together, these terms point to a cohesive function focused on nucleotide salvage and nucleoside catabolism/ metabolism, with occasional RNA turnover reference. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":2},{"id":"GO:0034356","count":1},{"id":"GO:0019358","count":1},{"id":"GO:0015949","count":1},{"id":"GO:0006218","count":1}]},{"hash":"797623105162177256","title":"Mevalonate/Lipid Biosynthesis","description":"The cluster shows strong ties to lipid metabolism and isoprenoid biosynthesis, with terms for lipid A biosynthetic process and the mevalonate pathway (isopentenyl diphosphate biosynthesis). While some regulatory terms appear, the dominant theme is lipid/isoprenoid metabolism, which best anchors the cluster\u2019s function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":2},{"id":"GO:0055114","count":2},{"id":"GO:2000002","count":1},{"id":"GO:1900486","count":1},{"id":"GO:1900490","count":1}]},{"hash":"2044881404318481940","title":"Brain and neural development","description":"The top GO terms are dominated by neural/brain development (forebrain development, neural tube closure, brain development) within multicellular organism development, with supporting signals like TGF-beta response and apoptosis. This suggests the proteins share a role in CNS formation and neural differentiation, making this label representative though not exclusively specific given some broader terms.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0030900","count":2},{"id":"GO:0010659","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0034349","count":2}]},{"hash":"1471521079409000600","title":"Glycan Biosynthesis and ECM Components","description":"Most of the top GO terms are biosynthetic processes for glycans and proteoglycans (xyloglucan, xylogalacturonan, arabinan, fucose, heparan sulfate proteoglycan biosynthesis), pointing to extracellular matrix (ECM) component formation. A smaller subset relates to development signaling (BMP pathway, endoderm development, embryonic skeletal joint development), which can be linked to ECM-mediated signaling during development. Overall, the cluster appears to reflect glycan/ECM biosynthesis and its role in development rather than a single enzyme pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010398","count":2},{"id":"GO:0009863","count":2},{"id":"GO:0008101","count":2},{"id":"GO:0072498","count":2},{"id":"GO:0009969","count":2}]},{"hash":"62540388513910110","title":"Glycan Biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for glycans and proteoglycans\u2014xylogalacturonan, xyloglucan, arabinan, and biosynthesis of heparan sulfate/heparin proteoglycans\u2014pointing to a core theme of glycan assembly and extracellular matrix components. Developmental and signaling terms (BMP signaling, salicylic acid signaling, endoderm development) are present but less represented, suggesting they are secondary associations within this small cluster. Overall, the shared function appears to be glycan/proteoglycan biosynthesis. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":2},{"id":"GO:0010398","count":1},{"id":"GO:0009863","count":1},{"id":"GO:0008101","count":1},{"id":"GO:0072498","count":1}]},{"hash":"2017712777880477989","title":"Adaptive immune activation and cytokine production","description":"The cluster shows strong enrichment for immune-related terms, notably positive regulation of T cell proliferation, interleukin-4 production, and cytokine production in immune responses, as well as neutrophil clearance. While there are a few unrelated terms (e.g., cartilage condensation, endothelial migration) the dominant signal centers on adaptive immune activation and cytokine regulation, with supporting links to signaling and cytoskeletal organization.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046641","count":2},{"id":"GO:0001502","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0043068","count":2}]},{"hash":"226566553285211837","title":"Neural development and embryogenesis","description":"Dominant signal is neural development and embryogenesis (spinal cord development, neural tube closure, neuron projection development, embryonic organ development, multicellular organism growth), with a few general terms related to cellular trafficking and growth.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0051441","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0001843","count":1}]},{"hash":"2281005302678417663","title":"Meiosis and DNA Repair","description":"The cluster\u2019s GO terms are dominated by meiotic processes and DNA maintenance (reciprocal meiotic recombination, meiotic mismatch repair, meiotic heteroduplex formation, mismatch repair, telomerase holoenzyme complex assembly), suggesting genome maintenance and meiotic function. While terms like chemotaxis, placenta development, and protein folding appear, they are not as representative, so the core signal points to meiotic DNA repair activities.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007131","count":1},{"id":"GO:0006935","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0001890","count":1}]},{"hash":"270446761431399114","title":"mRNA processing and translation initiation","description":"The proteins in this cluster are linked to multiple aspects of RNA maturation and control of translation, including mRNA modification and stabilization, spliceosome-mediated splicing (both alternative and cis-splicing), polyadenylation, and assembly of translation initiation machinery (eIF4F) with IRES-dependent initiation. This combination points to a cohesive theme of post-transcriptional RNA processing coupled to initiation of translation, rather than a single enzymatic activity. ","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016556","count":1},{"id":"GO:0048255","count":1},{"id":"GO:0075522","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0006378","count":1}]},{"hash":"1263378770293974891","title":"ER protein processing linked to T cell signaling","description":"The GO terms indicate ER lumen protein retention/transport alongside T cell\u2013related immune processes (cytokine production, apoptosis) and innate immune signaling, suggesting these proteins cluster around ER-associated protein handling with T cell immune function.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":1},{"id":"GO:0002369","count":1},{"id":"GO:0010204","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0070231","count":1}]},{"hash":"741064528541950167","title":"Amino acid and small molecule transport","description":"The GO terms cluster around transport across membranes, especially amino acids and related small molecules (ornithine, lysine, GABA, D-serine, ammonium) with transepithelial transport and import across membranes, indicating a transporter-focused group. Additional terms on arginine catabolism and nitric oxide production align with related metabolic pathways tied to these transport processes. Overall, a cohesive theme of amino acid and small-molecule transport.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006527","count":1},{"id":"GO:0010923","count":1},{"id":"GO:0002537","count":1},{"id":"GO:0070634","count":1},{"id":"GO:0006884","count":1}]},{"hash":"858764071406484452","title":"Plant lignan and anthocyanin biosynthesis","description":"Top terms cluster around lignan biosynthesis (secoisolariciresinol, lariciresinol, pinoresinol) and anthocyanin biosynthesis, both part of the plant phenylpropanoid pathway. This suggests the proteins participate in plant secondary metabolism focused on producing lignans and anthocyanins. Some other terms relate to general sugar-nucleotide metabolism or related processes that can support glycosylation or precursor supply, but the dominant theme is lignan and anthocyanin biosynthesis. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0080028","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0009244","count":1},{"id":"GO:1902135","count":1}]},{"hash":"470806569207663198","title":"Nuclear transport and telomere tethering","description":"The top GO terms are dominated by nuclear import/export and RNA transport (tRNA export, mRNA transport, NLS-bearing protein import) along with telomere-associated genome organization (telomere tethering, chromatin silencing near telomeres, localization to the nuclear periphery). This points to a coherent theme of nuclear trafficking and perinuclear genome maintenance, with a few peripheral terms (innate immune signaling, hematopoiesis) likely representing broader cellular contexts or annotation noise. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006409","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0035392","count":2},{"id":"GO:0036228","count":2},{"id":"GO:0035080","count":2}]},{"hash":"1404763095571171863","title":"Immune signaling and cellular stress responses","description":"The top GO terms point to immune-related activities (positive regulation of IL-6 production, isotype switching to IgG) alongside broad cellular stress and survival processes (protein refolding, cadmium response, ROS regulation, telomere maintenance, cell division). This suggests the cluster reflects immune signaling coupled with general stress resilience rather than a single unified function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904871","count":3},{"id":"GO:2000778","count":3},{"id":"GO:1901998","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0048291","count":3}]},{"hash":"538956134090854664","title":"Nuclear transport and pore organization","description":"This cluster centers on nuclear transport and nuclear pore dynamics: import into nucleus (NLS-bearing proteins, regulation of import), RNA export from the nucleus, nuclear pore organization, and mitotic nuclear membrane disassembly. The presence of protein\u2013protein interaction terms (heterotrimerization, homooligomerization) supports complexes that assemble or function at the nuclear pore or envelope, consistent with a cohesive nuclear transport module.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007077","count":1},{"id":"GO:0006999","count":1},{"id":"GO:0036228","count":1},{"id":"GO:0070208","count":1},{"id":"GO:0051260","count":1}]},{"hash":"1256137340267313076","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0006353","count":3},{"id":"GO:0042417","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0045892","count":3}]},{"hash":"1914889105878878315","title":"Unknown","description":"The Top Terms are highly heterogeneous: chromatin organization and translation suggest nuclear roles, while collagen catabolic processes imply extracellular matrix remodeling, and cell-cycle regulation/ubiquitin ligase activity point to signaling and protein quality control. The presence of obsolete terms and lack of a single cohesive function make it difficult to assign a specific, representative label to this cluster.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034396","count":2},{"id":"GO:0030574","count":2},{"id":"GO:0034724","count":2},{"id":"GO:0035551","count":2},{"id":"GO:0050821","count":1}]},{"hash":"325117389909128080","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090615","count":1},{"id":"GO:0009451","count":1},{"id":"GO:0016554","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0070129","count":1}]},{"hash":"605470278489245136","title":"Nucleolar ribosome biogenesis and rRNA processing","description":"The top terms point to nuclear/nucleolar activities: protein import into the nucleus, maturation of SSU-rRNA, and ribosomal large subunit biogenesis, plus mRNA export. Taken together, these terms suggest a cluster of proteins involved in ribosome assembly and RNA processing in the nucleolus.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0017038","count":3},{"id":"GO:1990120","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0010501","count":3},{"id":"GO:1904570","count":3}]},{"hash":"1387043261215612878","title":"Calcium-NFAT Signaling in Lung Development","description":"The cluster centers on calcium-related functions (detection of calcium ion) and the calcineurin-NFAT signaling cascade, with negative regulation of inflammatory response and cell\u2013cell adhesion supporting a tissue-context role in lung development. While metabolism-related terms (mevalonate pathway) and DNA replication appear, they are less tightly connected to the core calcium/NFAT theme, so the label captures the most coherent functional thread.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000002","count":3},{"id":"GO:1900486","count":3},{"id":"GO:1900490","count":3},{"id":"GO:0050728","count":3},{"id":"GO:0005513","count":3}]},{"hash":"230157729897221291","title":"Embryonic neural development & ER-Golgi trafficking","description":"These proteins are annotated with neural development terms (spinal cord development, neural tube closure, embryonic organ development) and with secretory pathway processes (ER exit, COPII vesicle budding, vesicle-mediated transport), suggesting a link between embryonic morphogenesis and intracellular protein trafficking. The absence of observed interactions in the network supports a labeling based on shared functional annotations rather than connectivity. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070863","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0021510","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0001843","count":1}]},{"hash":"1115154570350935960","title":"RNA Processing & Spliceosome Assembly","description":"This cluster\u2019s top GO terms cluster around RNA processing: maturation of 5S rRNA, mRNA splicing via the spliceosome, and spliceosomal snRNP assembly, which suggests a shared role in RNA maturation/splicing. Some other terms (metabolic and plant-specific development) may reflect annotation noise or multi-function proteins, but the RNA-processing signals are the strongest link.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000481","count":1},{"id":"GO:0045585","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0010588","count":1}]},{"hash":"1572445529021645665","title":"Cap-dependent Translation Initiation Regulation","description":"The cluster is dominated by terms related to the regulation and assembly of the eIF4F cap-binding complex and translation initiation (e.g., positive regulation of eIF4F complex assembly, polysome/mRNA cap binding). Although a few terms are obsolete or divergent, the prevalent theme points to control of translation initiation via cap-dependent mechanisms.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1905537","count":2},{"id":"GO:1905606","count":2},{"id":"GO:1905696","count":2},{"id":"GO:1905618","count":2},{"id":"GO:1905612","count":2}]},{"hash":"1676838650370693964","title":"Unknown","description":"The top GO terms span metabolism (glycolysis, fatty acid oxidation, carnitine metabolism), hypoxia response, development/remodeling (epithelial differentiation, angiogenesis regulation, plasminogen activation), and even RNA processing, with no single unifying function that ties all three proteins together. Therefore a concise, representative label cannot be determined with confidence.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019619","count":1},{"id":"GO:0060702","count":1},{"id":"GO:0071456","count":1},{"id":"GO:0030855","count":1},{"id":"GO:0031639","count":1}]},{"hash":"873898559527732693","title":"Unknown","description":"The GO terms are highly diverse, spanning nucleotide metabolism and catabolic processes, apoptosis, chitin metabolism and cuticle development, and several immune/developmental terms, with no single cohesive function linking the proteins. There are no edges or a clear shared pathway to base a specific label on.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901069","count":1},{"id":"GO:0009117","count":1},{"id":"GO:0046085","count":1},{"id":"GO:0009158","count":1},{"id":"GO:0006915","count":1}]},{"hash":"2245009193907308506","title":"Cofactor Biosynthesis","description":"Top GO terms cluster around biosynthetic processes for various cofactors and cofactors-related modifications (queuosine, thiamine, lipoate, molybdopterin, menaquinone, biotin; plus protein lipoylation and rRNA base methylation), suggesting the proteins participate in cofactor biosynthesis or assembly.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008616","count":2},{"id":"GO:0042426","count":2},{"id":"GO:0009228","count":1},{"id":"GO:0009107","count":1},{"id":"GO:0006777","count":1}]},{"hash":"1585890258602876816","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":1},{"id":"GO:0097309","count":1},{"id":"GO:0039520","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1544872957205765394","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000350","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0000389","count":1}]},{"hash":"582003277429037967","title":"Proteostasis and RNA Processing","description":"These proteins show enrichment for mRNA splicing via spliceosome, ubiquitin-dependent protein degradation, and autophagy, along with ribosome biogenesis and endosomal-lysosomal transport. Together, the terms suggest a cluster centered on cellular protein quality control and RNA processing pathways, rather than a single specialized function. The developmental terms may reflect broader roles in multicellular organisms or could be incidental with this small set.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0006914","count":1}]},{"hash":"46688780485427972","title":"Unknown","description":"The GO terms are highly diverse, spanning plant reproductive development (double fertilization, carpel identity, fruit abscission), immune/germinal center processes, hematopoietic proliferation, platelet formation, vascular and cartilage/vascular smooth muscle differentiation, and amyloid-beta clearance. There is no clear shared function tying these terms together, so a coherent label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080155","count":1},{"id":"GO:0002634","count":1},{"id":"GO:0071864","count":1},{"id":"GO:0060532","count":1},{"id":"GO:0001197","count":1}]},{"hash":"2148965589657479873","title":"Proteostasis regulation and organelle organization","description":"The terms cluster around regulation of protein turnover (ER-associated ubiquitin-dependent degradation and autophagy) and cellular organization (cytoplasmic microtubule organization and nuclear body organization), with several obsolete terms and outliers. This suggests a cohesive theme of proteostasis coupled with organelle dynamics rather than a single specific pathway.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":3},{"id":"GO:1902260","count":3},{"id":"GO:0010216","count":3},{"id":"GO:0045648","count":3},{"id":"GO:1901097","count":3}]},{"hash":"985012117545616264","title":"Transcriptional Regulation and Stem Cell Maintenance","description":"This cluster centers on regulation of DNA-templated transcription and somatic stem cell maintenance, with accompanying themes of development (proepicardium) and RNA processing (mRNA modification and stabilization), plus responses to growth signals (EGF) and hormones (glucocorticoid). The unifying thread appears to be control of gene expression during development and stem cell maintenance.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043486","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0035019","count":1},{"id":"GO:0071385","count":1},{"id":"GO:0071364","count":1}]},{"hash":"1841480382696641967","title":"Unknown","description":"The GO terms span immune signaling, plant development, and protein turnover with no single cohesive function tying the proteins together, so there isn\u2019t a clear label beyond Unknown. ","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006956","count":1},{"id":"GO:0015995","count":1},{"id":"GO:0006471","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0043248","count":1}]},{"hash":"1808129980860067120","title":"Diverse Biosynthetic Processes","description":"The terms indicate involvement in a wide range of biosynthetic pathways (fatty acids, flavonoids/chalcones, sporopollenin, DIF-1, cell wall components, resorcinol, serine, LPS core), spanning different organisms. There isn\u2019t a single cohesive process shared by all terms, just a broad theme of biosynthesis, so a general label is most appropriate.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":1},{"id":"GO:0035336","count":1},{"id":"GO:0080110","count":1},{"id":"GO:0031148","count":1},{"id":"GO:0071770","count":1}]},{"hash":"2109933415715507011","title":"Plant Development and Cuticle/Wax Regulation","description":"This cluster\u2019s GO terms cluster around plant development (floral meristem growth, bract development, multicellular organism development) and cuticle biosynthesis (wax and cutin) with hormone signaling (ABA and ethylene) and transcription regulation. The combination suggests proteins involved in coordinating floral development with cuticle formation and hormone-guided gene expression, rather than a single tight biochemical pathway. Confidence: Medium","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010451","count":1},{"id":"GO:0009873","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0010432","count":1},{"id":"GO:0007275","count":1}]},{"hash":"1956397591092657653","title":"Plant secondary metabolism and cell-wall biosynthesis","description":"The top terms are dominated by plant-specific biosynthetic processes (lignin, cutin, flavonoids, auxin-related homeostasis), suggesting a cluster of enzymes involved in producing plant secondary metabolites and cell-wall components. Some unrelated or obsolete terms are present, but the core signal points to plant metabolic pathways rather than single-protein activities.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010252","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0080088","count":1},{"id":"GO:0009809","count":1},{"id":"GO:0009963","count":1}]},{"hash":"757228614896555080","title":"Light-responsive transcription and DNA processes","description":"The GO terms point to a theme where light signaling (far-red phototransduction and far-red signaling) intersects with transcriptional regulation (regulation of DNA-templated transcription, circadian rhythm regulation) and DNA-related processes (DNA integration, DNA transposition), suggesting a cluster of proteins involved in light-regulated gene expression and DNA remodeling. Some terms (immune regulation and centrosome localization) appear less connected, so the connection is not perfect, but the core motif is light-influenced transcription/DNA activity.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0045347","count":1},{"id":"GO:1904780","count":1},{"id":"GO:0000289","count":1}]},{"hash":"418272868073567323","title":"Protein quality control","description":"The terms cluster around ubiquitin-proteasome\u2013dependent degradation, autophagy regulation, aggresome assembly, sumoylation, and stress-related pathways (ER stress, mitochondrial dynamics), all pointing to a proteostasis or protein quality-control module.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":3},{"id":"GO:0010216","count":3},{"id":"GO:0045648","count":3},{"id":"GO:1901097","count":3},{"id":"GO:1901799","count":3}]},{"hash":"2196509561668882434","title":"Regulation of secondary shoot formation","description":"The top GO terms point to plant-specific regulation of secondary shoot formation and general transcriptional regulation. Together they suggest proteins that act as transcriptional regulators controlling shoot development in plants, particularly lateral/secondary shoots. The cluster is small but coherently tied to plant development via transcriptional control.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:2000032","count":3},{"id":"GO:0006355","count":3}]},{"hash":"1147794038325248914","title":"Ribosome biogenesis and translation regulation","description":"The GO terms cluster around core ribosome biology and multiple facets of translation, including biogenesis, assembly/disassembly, preinitiation complex formation, initiation/reinitiation, and translation regulation and fidelity.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0002192","count":1},{"id":"GO:0002188","count":1},{"id":"GO:1990145","count":1}]},{"hash":"2133604953712763369","title":"Unknown","description":"The GO terms span plant developmental processes (flower and anther development, vegetative phase change) and diverse transport/metabolic processes (various transports, fatty acid catabolism, mercury response). With only three proteins and no connections between them, there isn\u2019t a clear, single function tying the cluster together, so a specific label isn\u2019t justifiable. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009908","count":1},{"id":"GO:0048653","count":1},{"id":"GO:0010321","count":1},{"id":"GO:0015821","count":1},{"id":"GO:0031460","count":1}]},{"hash":"1528798345030781773","title":"Microtubule Organization and Ubiquitin Regulation","description":"The top GO term is microtubule cytoskeleton organization, suggesting a core microtubule-related function. The other terms point to ubiquitin-dependent processes (ERAD, deubiquitination) and regulation of autophagy and organelle dynamics, indicating a theme of cytoskeleton-associated control of protein turnover and trafficking via ubiquitin systems. Some terms are obsolete, but the shared signal supports a microtubule-centered role linked to ubiquitin-mediated regulation.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000226","count":2},{"id":"GO:1903094","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2000157","count":2},{"id":"GO:0001827","count":1}]},{"hash":"1260071042078529224","title":"Golgi organization and retrograde transport","description":"The top GO terms point to Golgi apparatus organization (GO:0007030) and retrograde vesicle transport within the Golgi (GO:0000301), indicating the proteins cluster around Golgi trafficking and maintenance functions. With a small set of proteins and direct association to these Golgi-related processes, the label accurately reflects the cluster\u2019s shared role.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007030","count":1},{"id":"GO:0000301","count":1}]},{"hash":"1399438208967468332","title":"T cell activation and cytokine production","description":"The top GO terms cluster around immune activation, including positive regulation of alpha-beta T cell proliferation, interleukin-4 production, and positive regulation of cytokine production in immune response. Additional terms reference neutrophil clearance, programmed cell death, and immune signaling, indicating a cohesive theme of immune activation and cytokine regulation. The presence of Rho signaling and microtubule localization suggests cytoskeletal changes accompanying immune cell migration and activation, reinforcing this immune-centric interpretation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046641","count":3},{"id":"GO:0001502","count":3},{"id":"GO:0097350","count":3},{"id":"GO:0035372","count":3},{"id":"GO:0043068","count":3}]},{"hash":"1441174209907284322","title":"ER Stress and Protein Folding","description":"The top GO terms are dominated by endoplasmic reticulum unfolded protein response and protein folding, indicating the cluster centers on ER quality control and stress response. While other terms touch on development, signaling, or reproduction, the strongest common thread is involvement in managing misfolded proteins and maintaining ER function.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"protein folding","top_go_terms":[{"id":"GO:0030968","count":3},{"id":"GO:0006457","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0048387","count":3},{"id":"GO:2000510","count":3}]},{"hash":"30038919782963760","title":"Nucleotide biosynthesis and salvage","description":"This cluster\u2019s top GO terms cluster around nucleotide metabolism and energy-related biosynthesis: CDP biosynthesis, purine ribonucleotide interconversion, ADP and AMP biosynthesis, nucleoside monophosphate phosphorylation, and AMP salvage, with additional ties to coenzyme A biosynthesis and ITP metabolism. Development terms for liver and brain appear but are likely incidental annotations rather than core functions of the cluster. Overall, the proteins seem linked by nucleotide metabolism and salvage pathways.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046705","count":3},{"id":"GO:0015951","count":3},{"id":"GO:0001889","count":3},{"id":"GO:0046940","count":3},{"id":"GO:0046939","count":3}]},{"hash":"94529748990808175","title":"Ribosome Biogenesis and Translation","description":"This cluster centers on translation-related GO terms (translation, cytoplasmic translation), ribosome biogenesis and export (ribosomal small/large subunit biogenesis/export), and tRNA modification, indicating a shared function in ribosome assembly and protein synthesis; the other terms (antibiotic response, stress regulation, cell division) appear as related or secondary processes tied to ribosome function and stress adaptation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090529","count":2}]},{"hash":"1905471205484548444","title":"Glial Metabolic Redox Balance","description":"The GO terms point to central carbon metabolism and redox biology (TCA cycle, isocitrate metabolism, NADPH regeneration, NADP+ biosynthesis) and an oxidative stress response, suggesting a metabolic program that supports glial cell function. The included terms about negative regulation of glial proliferation/migration and MMP secretion further imply a regulatory, glia-focused context in which metabolism and redox state influence cell behavior and extracellular remodeling.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060253","count":1},{"id":"GO:0006740","count":1},{"id":"GO:1903976","count":1},{"id":"GO:0006102","count":1},{"id":"GO:1904465","count":1}]},{"hash":"747963303361234388","title":"Bacterial Sporulation and Motility Signaling","description":"In this cluster, the dominant GO terms point to bacterial developmental processes, including sporulation and its regulation, as well as chemotaxis and flagellum-dependent motility. There are also signals related to phosphorelay systems and general transcription, suggesting a coordinated bacterial response that links movement, development, and environmental sensing. The mix reflects a bacterial-focused functional theme rather than a single, unified plant or animal pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0042173","count":1}]},{"hash":"1569326171468296575","title":"Gametogenesis Chromatin Remodeling","description":"The terms emphasize chromatin assembly and histone exchange, plus sperm-related processes like spermatid development and sperm DNA condensation, with estradiol/vitellogenesis hints suggesting hormonal regulation of gamete formation; together they point to chromatin remodeling during gametogenesis.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900446","count":2},{"id":"GO:0090230","count":2},{"id":"GO:0071392","count":2},{"id":"GO:0043486","count":2},{"id":"GO:0007296","count":2}]},{"hash":"1336670799697902508","title":"Unknown","description":"The listed GO terms span metabolism, autophagy, cell migration, immune signaling, neurochemical response, and development, with no clear shared function among the proteins, so a cohesive descriptive label cannot be assigned.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":1},{"id":"GO:1901097","count":1},{"id":"GO:0010596","count":1},{"id":"GO:0009620","count":1},{"id":"GO:0050929","count":1}]},{"hash":"402947837624329642","title":"Endosomal Vesicle Trafficking","description":"The top GO terms cluster around endosome transport and vesicle formation, including endosome-to-lysosome transport, plasma membrane to endosome transport, endosomal vesicle fusion, and COPII-coated vesicle budding. Additional terms suggest actin-driven membrane remodeling (ruffle assembly) and autophagy regulation, all fitting a cohesive theme of intracellular vesicular trafficking through endosomal pathways and lysosomal degradation. Together, these indicate proteins involved in endosomal sorting and vesicle trafficking rather than a single static function.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:1902824","count":3},{"id":"GO:0048227","count":3},{"id":"GO:0097178","count":3},{"id":"GO:0003100","count":3},{"id":"GO:0090114","count":3}]},{"hash":"1420765061194350276","title":"Immune signaling and cell adhesion regulation","description":"The top GO terms point to regulation of signaling pathways (PKC signaling, TLR3 signaling, T cell polarity) and processes governing cell\u2013cell adhesion (cadherin-mediated adhesion), with additional emphasis on proteolysis and lipid localization. This suggests the proteins act as regulators of immune or intercellular signaling networks and adhesion rather than a single biochemical activity. Thus, a label centered on immune signaling and cell adhesion regulation captures the common theme among the terms.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045861","count":3},{"id":"GO:0070528","count":3},{"id":"GO:0060355","count":3},{"id":"GO:0045541","count":3},{"id":"GO:0070584","count":3}]},{"hash":"290814363582086339","title":"Unknown","description":"The GO terms are highly diverse, spanning chemotaxis, transcription, metabolism, ion transport, neuronal signaling, and pheromone response, with no single shared function linking the proteins. The lack of apparent functional cohesion (0 edges, 0 triangles) suggests these proteins do not form a cohesive module, so a clear label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006564","count":1},{"id":"GO:1903243","count":1},{"id":"GO:0035235","count":1}]},{"hash":"2123584286434471810","title":"Endocytosis and endosome transport","description":"The top GO terms indicate vesicle trafficking centered on endocytosis and endosome-to-lysosome routes, including endocytosis, plasma membrane to endosome transport, endosomal vesicle fusion, and COPII-coated vesicle budding. Together these suggest a cluster enriched for endocytic uptake and endosome maturation processes. A couple of terms (DNA integration, neuron fate determination) appear less connected and may reflect annotation noise, but the dominant signal supports endocytic vesicle trafficking.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":2},{"id":"GO:0006858","count":1},{"id":"GO:0015074","count":1},{"id":"GO:1902824","count":1},{"id":"GO:0048227","count":1}]},{"hash":"2246149880086387123","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0014070","count":2},{"id":"GO:0034244","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0072711","count":1},{"id":"GO:0017038","count":1}]},{"hash":"954244437148933740","title":"RNA processing and translation initiation","description":"These proteins are linked to RNA metabolism and translation control\u2014miRNA processing, mRNA modification and stabilization, alternative splicing, and initiation of translation (including IRES-dependent and eIF4F complex assembly). Blastocyst formation may reflect developmental contexts requiring translational regulation; DNA integration appears incidental.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010587","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0048255","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1185827543167547327","title":"Apoptosis and intracellular trafficking","description":"The GO terms cluster around apoptotic processes and mitochondrial fragmentation, alongside several trafficking-related terms (protein retention in Golgi, endocytic recycling, receptor internalization), suggesting a theme of stress-induced cell death coupled with intracellular transport. Even though there are no edges, these shared functions form a coherent high-level label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":1},{"id":"GO:0098884","count":1},{"id":"GO:1901001","count":1},{"id":"GO:1901741","count":1},{"id":"GO:0043653","count":1}]},{"hash":"1698866306086901286","title":"Ubiquitin-like modification and autophagy","description":"Top terms emphasize ubiquitin-like conjugation (neddylation, ufmylation, urmylation) and autophagy pathways (CVT, mitophagy), indicating a common function in ubiquitin-like signaling and autophagy processes. Other terms are less represented, so the overarching theme is autophagy-related protein modification.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051726","count":2},{"id":"GO:0045116","count":2},{"id":"GO:0032258","count":1},{"id":"GO:1990592","count":1},{"id":"GO:0032447","count":1}]},{"hash":"1118901677434508424","title":"GABAergic Synaptic Signaling and Endocytosis","description":"The top GO terms cluster around neuronal communication and vesicle trafficking, including GABAergic synaptic transmission, postsynaptic receptor internalization, ephrin receptor signaling, and endocytic recycling. These collectively suggest a function in synaptic signaling and receptor/vesicle trafficking, with some unrelated terms likely representing broader or incidental annotations.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060047","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0048013","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0051932","count":2}]},{"hash":"528178445919718958","title":"GPI-anchor and lipid biosynthesis","description":"The top GO terms point to GPI anchor biosynthesis and a suite of lipid/glycan-related biosynthetic processes (glycolipids, phospholipids, phosphatidylinositol, glucose/glycogen), suggesting a cluster focused on membrane lipid and glycoprotein assembly. Some osmotic stress terms are present but secondary, indicating osmotic response rather than primary function. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0009414","count":2},{"id":"GO:0009247","count":2},{"id":"GO:0046488","count":2},{"id":"GO:0006006","count":2}]},{"hash":"1114886196771301539","title":"Plant cell wall biosynthesis and pollen germination","description":"The top GO terms center on plant cell wall construction and organization (cellulose biosynthetic process, primary/secondary cell wall biogenesis, cell wall organization, cell plate assembly) along with pollen germination, indicating a cohesive function in wall biosynthesis linked to pollen development; UDP-glucose metabolism and rhamnogalacturonan I side chain metabolism support polysaccharide production for walls.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010400","count":2},{"id":"GO:0000919","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0006011","count":2},{"id":"GO:0009833","count":2}]},{"hash":"1015112805079813083","title":"Peptide Catabolism and Tissue Remodeling","description":"This cluster centers on catabolic processes of peptides (neuropeptides and bradykinin) and remodeling-related activities (basement membrane disassembly, bone resorption). It also includes immune-related processes (T cell cytotoxicity, macrophage apoptosis) and hormonal responsiveness (thyroid hormone stimulus), which together point to coordinated peptide processing and extracellular/tissue remodeling in immune and developmental contexts.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":2},{"id":"GO:0010813","count":2},{"id":"GO:0010815","count":2},{"id":"GO:0045453","count":2},{"id":"GO:0001913","count":2}]},{"hash":"1369465836677354294","title":"Viral entry, uncoating, and release","description":"The GO terms are dominated by steps in the viral life cycle\u2014uncoating, fusion of viral and host membranes, viral release, and host-mediated activation of viral replication\u2014suggesting a cluster focused on virus entry and egress. A few terms (e.g., protein folding, sepal formation) appear incidental noise, but the core theme is viral infection processes.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019061","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0010849","count":1},{"id":"GO:0071492","count":1}]},{"hash":"1035542863614287023","title":"ERAD and Proteasome-Mediated Proteostasis","description":"The top terms highlight ER-associated degradation (ERAD) and ubiquitin-dependent proteolysis, including maintenance of unfolded proteins in ERAD and proteasomal protein catabolic processes. While a few terms are unrelated or obsolete, the dominant theme points to protein quality control via the ERAD-UPS-proteasome axis, with some related notes on autophagy and turnover. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1904378","count":2},{"id":"GO:1903071","count":1},{"id":"GO:1902260","count":1},{"id":"GO:0010216","count":1},{"id":"GO:0045648","count":1}]},{"hash":"765122848399388574","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":1},{"id":"GO:0042773","count":1},{"id":"GO:0060192","count":1},{"id":"GO:1901206","count":1},{"id":"GO:0044205","count":1}]},{"hash":"442377222771947140","title":"Neuro-Epidermal Development Signaling","description":"This cluster centers on developmental processes in both neural and epidermal tissues: keratinocyte development, epidermal cell division regulation, neuron migration, and substantia nigra development, supported by signaling and cell-cycle pathways (CDK activity regulation, glucocorticoid/nuclear receptor signaling). While there are some general trafficking and DNA-damage\u2013response terms, the dominant theme is cross-tissue development and signaling. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006605","count":3},{"id":"GO:0003334","count":3},{"id":"GO:0006977","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0000079","count":3}]},{"hash":"289845566422325359","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":3},{"id":"GO:0010265","count":3},{"id":"GO:0044810","count":3},{"id":"GO:1902364","count":3},{"id":"GO:2000620","count":3}]},{"hash":"982995148176269110","title":"RNA processing and gene silencing","description":"The GO terms show a clear focus on RNA metabolism and regulation (rRNA processing; primary miRNA processing; regulation of miRNA metabolism; post-transcriptional gene silencing by regulatory ncRNA and by mRNA cleavage). Adenosine-to-inosine RNA editing also appears, reinforcing the RNA-processing theme. A few morphogenesis terms are present but appear incidental and do not define the cluster. Altogether, the dominant signal is RNA processing and gene silencing.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006382","count":2},{"id":"GO:0021610","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0021965","count":1},{"id":"GO:2000628","count":1}]},{"hash":"830384779404341265","title":"Unknown","description":"The top GO terms are too diverse to define a single coherent function for this cluster, spanning amino acid biosynthesis, ion transport and membrane potential, neurotransmitter signaling, pheromone-induced conjugation, and various regulatory pathways. With no edges and only a few shared term counts, there isn\u2019t a unifying biological role that ties the proteins together, so Unknown is appropriate.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":2},{"id":"GO:1903243","count":2},{"id":"GO:0035235","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0000749","count":2}]},{"hash":"660172335486805570","title":"Endomembrane trafficking and protein localization","description":"This cluster centers on vesicle-mediated transport within the secretory pathway\u2014ER to Golgi, Golgi to endosomes, endosome to Golgi, and recycling\u2014along with protein localization to the plasma membrane. Although a single cell-cycle term appears, the dominant pattern is intracellular trafficking and membrane targeting, suggesting the proteins work together in endomembrane transport and localization processes.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0045022","count":2},{"id":"GO:1903078","count":2}]},{"hash":"2297198025617948348","title":"Unknown","description":"The GO terms are heterogeneous, spanning fungal sphingolipid and sterol metabolism, general lipid biosynthesis, nitrogen metabolism, and tissue-specific differentiation, with no clear shared function linking the three proteins. The absence of edges further suggests there is no coherent cluster theme to name precisely.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:0006636","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0000001","count":3}]},{"hash":"1784770683840583900","title":"Oxidative stress and xenobiotic response","description":"Top GO terms indicate redox and stress responses (oxidation-reduction, hydroperoxide, xenobiotic, UV protection), with a few development/EC terms that may reflect downstream signaling noise; since there are no edges, the cluster likely groups by shared stress-response functions rather than physical interactions.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0010269","count":2},{"id":"GO:0042493","count":2},{"id":"GO:2000179","count":2},{"id":"GO:0042345","count":1}]},{"hash":"25313813968900889","title":"Unknown","description":"The terms are highly diverse and largely unconnected, with only single annotations and no edges linking the proteins, making it impossible to infer a shared biological function. Examples span redox response, protein refolding, interferon signaling, steroid receptor assembly, and various plant/animal developmental terms, suggesting annotation noise rather than a coherent cluster. Therefore, this cluster is labeled Unknown with no clear confidence.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051775","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0035457","count":1},{"id":"GO:0006463","count":1},{"id":"GO:0009938","count":1}]},{"hash":"1964836900678541990","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":1},{"id":"GO:0052704","count":1},{"id":"GO:0006751","count":1},{"id":"GO:0009116","count":1},{"id":"GO:0052699","count":1}]},{"hash":"2001483057375952924","title":"Plant hormone signaling and defense responses","description":"The terms cluster around plant hormone responses (salicylic acid, gibberellin, 1-aminocyclopropane-1-carboxylic acid) and immune/defense processes (chitin response, antifungal innate immune regulation), suggesting a theme of hormone-mediated signaling coordinating defense. Developmental differentiation terms also appear, hinting at stress-related growth adjustments, which fits a cohesive plant stress signaling/defense theme.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0080169","count":1},{"id":"GO:0009961","count":1},{"id":"GO:0010055","count":1},{"id":"GO:0009751","count":1},{"id":"GO:0009739","count":1}]},{"hash":"1449210673667188752","title":"Plant growth and defense signaling","description":"The GO terms cluster around plant-specific processes: responses to hormones (gibberellin, salicylic acid, ethylene precursor), fungal/chitin defense (response to chitin, antifungal immunity), and differentiation of plant tissues (atrichoblast, sclerenchyma). Although one term about spinal cord differentiation appears, the dominant theme is plant growth regulation coupled with innate immune responses, justifying this label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080169","count":2},{"id":"GO:0009961","count":2},{"id":"GO:0010055","count":2},{"id":"GO:0009751","count":2},{"id":"GO:0009739","count":2}]},{"hash":"7826078155708987","title":"Plant flavonoid and lignin biosynthesis","description":"Dominant terms point to plant phenylpropanoid metabolism, including lignin biosynthesis (GO:0009808) and anthocyanin/cyanidin biosynthesis (GO:0009718, GO:0033485), with supporting flavonoid glucuronidation/xenobiotic metabolism annotations; one neuronal paranode localization term appears as an outlier.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002175","count":3},{"id":"GO:0009808","count":3},{"id":"GO:0009718","count":3},{"id":"GO:0006711","count":3},{"id":"GO:0052697","count":3}]},{"hash":"716019847265415465","title":"Mitotic spindle assembly and cell cycle control","description":"GO terms point to mitosis and cell division (mitotic cell cycle, chromosome segregation, spindle assembly, microtubule polymerization) and to regulated proteolysis (SCF-dependent ubiquitin-proteasome pathways, degradation of cell-cycle proteins), with a minor reference to circadian rhythm regulation. Together these terms suggest a cluster of proteins involved in mitotic progression and its proteolytic control.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":1},{"id":"GO:0007059","count":1},{"id":"GO:0031110","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0042752","count":1}]},{"hash":"1200573855683511382","title":"Spindle Checkpoint and Protein Degradation","description":"The top GO terms cluster around mitotic spindle assembly and orientation checkpoint signaling, septin ring assembly, and ubiquitin-dependent protein catabolic processes, indicating a theme of cell division regulation coupled with protein turnover; a few terms (TNF signaling, Wnt catabolism) may reflect broader signaling connections but do not override the core spindle/ubiquitin signals.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901253","count":2},{"id":"GO:0044810","count":2},{"id":"GO:1902364","count":2},{"id":"GO:2000620","count":2},{"id":"GO:0038018","count":2}]},{"hash":"1624278619611821896","title":"Unknown","description":"The GO terms are heterogeneous: DNA integration, translation, and responses to antibiotics (including cycloheximide) do not converge on a single clear function. With no edges and only individual terms represented, there isn\u2019t a cohesive theme tying the proteins together. Confidence: None.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1}]},{"hash":"2199546482409940601","title":"Embryonic development and morphogenesis","description":"The GO terms cluster around embryonic development, placental and organ morphogenesis, EMT, left-right patterning, and endocrine system development, suggesting a shared theme of developmental differentiation and tissue formation. A couple of plant-specific auxin terms appear among the top terms, which may reflect annotation noise rather than a true functional convergences; overall the terms point to developmental processes rather than a single pathway. Confidence in this labeling is medium due to the mixture of terms and small cluster size.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":2},{"id":"GO:0009733","count":2},{"id":"GO:0060707","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0060536","count":1}]},{"hash":"16896670007892195","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048366","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0000398","count":1}]},{"hash":"2267834667627394928","title":"Proteasomal ubiquitination and antiviral defense","description":"It clusters around ubiquitin-dependent proteolysis (SCF-dependent and polyubiquitination) and antiviral/innate immune responses, suggesting a primary role in ubiquitin-mediated protein degradation linked to antiviral defense. A few other terms (circadian rhythm, microtubule polymerization, meiosis spindle assembly, DNA replication regulation, arsenic response) are less represented.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2}]},{"hash":"2087866752306229850","title":"Bacterial chemotaxis and sporulation signaling","description":"The cluster features GO terms tied to motility (chemotaxis and flagellum-dependent movement), signal transduction (phosphorelay systems), and sporulation regulation, suggesting bacterial proteins that sense environmental cues and coordinate movement with developmental decisions like sporulation. Although there are some plant-related terms, the strongest signal is bacterial regulatory activity linking sensing to sporulation and motility. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0042173","count":1}]},{"hash":"1728794243043963715","title":"ER Targeting and Protein Translocation","description":"Based on the GO terms, the cluster centers on targeting and translocation of proteins to/through the ER and membranes (SRP-dependent cotranslational targeting to ER, post-translational membrane targeting, and ER-to-cytosol retrograde transport) along with ERAD-related activity, indicating a cohesive theme of ER-associated protein targeting and quality control. Some plant-specific signaling terms are present but do not drive the core function of the cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0000060","count":1}]},{"hash":"181929565318395038","title":"Mitochondrial transporters","description":"The top GO terms are dominated by transport across mitochondrial membranes (mitochondrial ATP, CoA, manganese, heme, thiosulfate), with additional hints of mitochondrial-related apoptosis regulation. This points to a cohesive theme of mitochondrial transport/metabolic processes, justifying a label focused on mitochondrial transporters.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":2},{"id":"GO:0061179","count":2},{"id":"GO:1990544","count":2},{"id":"GO:0015886","count":2},{"id":"GO:0090152","count":2}]},{"hash":"908045332028089590","title":"Unknown","description":"The associated GO terms are diverse and span several unrelated processes (pseudohyphal growth regulation, urmylation, tyrosine dephosphorylation, mitotic M phase, tRNA seleno-modification, molybdopterin cofactor biosynthesis, redox homeostasis, transsulfuration, etc.), with no clear shared function or network among the three proteins, and no observed edges to suggest a cohesive cluster function.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000220","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0000087","count":1},{"id":"GO:0070329","count":1}]},{"hash":"1840015883589659984","title":"Oocyte maturation and meiotic spindle assembly","description":"This cluster is dominated by GO terms related to oocyte maturation, spindle assembly in female meiosis I, and microtubule polymerization, pointing to a shared function in meiotic progression and spindle organization in oocytes. While a few terms touch on broader cell-cycle processes, the strongest signals are meiosis- and spindle-related, supporting a label for oocyte maturation and meiotic spindle assembly.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001556","count":1},{"id":"GO:0046785","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0007057","count":1},{"id":"GO:0070544","count":1}]},{"hash":"660487386060052248","title":"Platelet Activation Signaling","description":"The GO terms point to platelet-related regulation and signaling, including positive regulation of platelet activation, protein secretion by platelets, and integrin activation, alongside PKC signaling and cytoskeletal localization. Although a few terms are unrelated (e.g., planar polarity), the strongest signal centers on platelet activation and associated signaling pathways, suggesting this cluster represents platelet activation/adhesion processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090163","count":1},{"id":"GO:0034242","count":1},{"id":"GO:0070528","count":1},{"id":"GO:0060134","count":1},{"id":"GO:0033625","count":1}]},{"hash":"144298172255132770","title":"Unknown","description":"The three proteins carry divergent GO terms (response to karrikin, flavonoid biosynthetic process, and DNA integration) and there are no connecting edges or shared enriched functions, so there is no coherent common function to label the cluster with.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080167","count":1},{"id":"GO:0009813","count":1},{"id":"GO:0015074","count":1}]},{"hash":"221426923639683716","title":"Hypoxia-Driven Metabolism and Angiogenesis Regulation","description":"These proteins co-occur with GO terms for cellular response to hypoxia, glycolytic process, plasminogen activation, and negative regulation of angiogenesis, plus epithelial differentiation. The overlap suggests a unit focused on adapting to low oxygen through metabolic reprogramming (glycolysis) and tissue remodeling while suppressing new blood vessel formation. Overall, the dominant theme is hypoxia-driven metabolic reprogramming and angiogenesis control.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":3},{"id":"GO:0030855","count":3},{"id":"GO:0031639","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0016525","count":3}]},{"hash":"1307127994251704236","title":"ER Stress Response and COPII Vesicle Budding","description":"The top GO terms point to endoplasmic reticulum unfolded protein response, ER localization, COPII-coated vesicle budding, and ER calcium homeostasis, all suggesting proteins that function in ER stress signaling and ER-to-Golgi trafficking. Some virus-host interaction terms appear but are likely contextual rather than core to the cluster. Overall, the cluster appears cohesive around ER stress and vesicle trafficking.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0044828","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0090114","count":1}]},{"hash":"2245076713854664880","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0015074","count":1}]},{"hash":"626943243260008376","title":"Cell wall biosynthesis and related metabolism","description":"The cluster is dominated by GO terms tied to cell wall biology\u2014cell wall organization, cell wall polysaccharide biosynthesis, and arabinan biosynthesis\u2014alongside a broader mix of metabolic processes (methanol, lactate, L-ascorbic acid, alkaloids, cytokinins) and cell shape regulation. This suggests a best-effort theme around cell wall biogenesis with accompanying metabolism, but the presence of diverse, non-wall-specific terms makes the overall linkage modest. ","confidence":"Low","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0015945","count":3},{"id":"GO:0009820","count":3},{"id":"GO:1903457","count":3}]},{"hash":"2018128808093993175","title":"Synaptic vesicle trafficking and GABAergic transmission","description":"The top GO terms point to synaptic vesicle maturation, neurotransmitter secretion, and GABAergic regulation, indicating a core role in neuronal vesicle cycling and synaptic transmission. Supporting terms about membrane lipid biosynthesis and autophagosome-related vesicle processes suggest related vesicle formation and exocytosis activities, though the strongest signal is synaptic vesicle\u2013related functions.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006646","count":3},{"id":"GO:0046580","count":3},{"id":"GO:1990927","count":3},{"id":"GO:0007269","count":3},{"id":"GO:0046470","count":3}]},{"hash":"371423334350120278","title":"Mitochondrial Energy Metabolism","description":"The top GO terms are dominated by mitochondrial processes\u2014assembly of respiratory chain complex IV, proton transmembrane transport, and ATP synthesis-coupled electron transport\u2014pointing to oxidative phosphorylation as the shared function. Although a few differentiation-related terms appear, they are less representative of the cluster, making energy metabolism the most coherent label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0042774","count":1},{"id":"GO:0042747","count":1},{"id":"GO:0042663","count":1}]},{"hash":"1846302122884847603","title":"Sphingolipid Transport and Metabolism","description":"This cluster centers on lipid transport and processing, with strong hits for ceramide and glycosphingolipid trafficking (ER to Golgi ceramide transport; ceramide transport; glycosphingolipid metabolic process; glycolipid transport), pointing to sphingolipid trafficking as the core function. The presence of defense-related terms (defense response to bacterium, response to salicylic acid) can reflect sphingolipid signaling roles in plant immunity, reinforcing the thematic link to sphingolipid transport/metabolism.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046836","count":1},{"id":"GO:0015695","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0015791","count":1},{"id":"GO:0009751","count":1}]},{"hash":"275682436508810954","title":"Steroid Hormone Biosynthesis and Metabolism","description":"The cluster shows GO terms centered on biosynthesis and catabolism of steroids and related lipid hormones (cortisol, testosterone, brassinosteroid), along with processes like fatty acid omega-oxidation, retinoic acid and vitamin D responses, and xenobiotic metabolism. These collectively suggest a theme of hormone-related lipid metabolism and sensing, even though a couple terms pertain to developmental or adhesion processes that can be downstream hormone effects. Confidence: Medium","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030879","count":1},{"id":"GO:0071603","count":1},{"id":"GO:0034651","count":1},{"id":"GO:0070989","count":1},{"id":"GO:0042738","count":1}]},{"hash":"564253702062689588","title":"SNARE-Mediated Exocytosis","description":"The GO terms point strongly to vesicle trafficking and membrane fusion, especially SNARE complex assembly (GO:0035493) and exocytic events such as vesicle fusion with the Golgi (GO:0048280), cortical granule exocytosis (GO:0060471), and exocytic insertion of neurotransmitter receptors (GO:0098967). Other terms related to secretion (norepinephrine release) and general exocytosis align with a core role in vesicle-mediated release. A single sporulation-related term is less consistent with the main theme but does not override the dominant exocytic/trafficking signal. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":1},{"id":"GO:0048280","count":1},{"id":"GO:0060471","count":1},{"id":"GO:0031321","count":1},{"id":"GO:0033194","count":1}]},{"hash":"764065545851496968","title":"Unknown","description":"The top GO terms are a mix of amino-acid catabolic processes and various cellular responses to chemicals (antibiotics, histamine, azide, copper starvation), plus an obsolete oxidation-reduction term and unrelated protoxylem development. There is no clear, cohesive biological theme tying these terms together across the protein set, so a specific, representative label is not justifiable.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019607","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0071420","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0090059","count":1}]},{"hash":"1167526817476016578","title":"Acetylation and chromatin modification","description":"Top GO terms are dominated by acetylation-related processes (N-terminal acetylation, histone H4/H3 acetylation, peptidyl-lysine acetylation) and a chromatin-related term (subtelomeric heterochromatin formation), indicating a cluster of proteins involved in acetylation-driven chromatin regulation. Some outliers reference metabolic or non-chromatin roles (acetoin and ectoine biosynthesis, leaf formation), but the shared theme is acetylation-mediated modification and chromatin dynamics.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":3},{"id":"GO:0032919","count":3},{"id":"GO:0043967","count":3},{"id":"GO:0018002","count":3},{"id":"GO:0045150","count":3}]},{"hash":"552617498348325280","title":"Nuclear Transcription Regulators","description":"The dominant GO term is DNA-templated transcription (GO:0006351) with a related term positive regulation of DNA binding, suggesting these proteins function in transcription regulation within the nucleus. Other terms are sparse or obsolete (e.g., ER transport, protein repair), which may reflect multifunctional or poorly resolved annotations rather than a shared pathway. Based on the strongest signal, the cluster best fits transcription-regulation proteins.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1903206","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0030091","count":1}]},{"hash":"2286171942373137611","title":"Unknown","description":"There is no shared GO term enrichment, no edges, and no apparent functional link among the proteins, so no coherent theme can be inferred from this cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"55385218027298884","title":"Meiosis and Gametophyte Development","description":"The GO terms link core meiotic processes (double-strand break repair and reciprocal meiotic recombination) with plant reproductive development (embryo sac and pollen development), suggesting proteins involved in meiosis and both female and male gametophyte formation in plants.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006302","count":1},{"id":"GO:0009553","count":1},{"id":"GO:0007131","count":1},{"id":"GO:0009555","count":1}]}]