[{"hash":"626547785340081065","title":"Acetylation-Centered Metabolic and Translation Cluster","description":"The top GO terms indicate a focus on acetylation events (N-terminal propionylation, peptidyl-lysine N6-acetylation, spermine acetylation, obsolete N-terminal serine acetylation) alongside metabolic processes (acetoin catabolic, mycothiol biosynthesis, arginine biosynthesis) and translation. This suggests a cluster tied to protein acetylation and related metabolism/translation contexts, with a few chromatin-related terms that may reflect broader regulatory roles or annotation noise. ","confidence":"Medium","size":29,"edges":25,"triangles":12,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":5},{"id":"GO:0010125","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0006526","count":4},{"id":"GO:0061606","count":4}]},{"hash":"1459605826018860830","title":"Biosynthesis and redox homeostasis","description":"The top GO terms point to multiple biosynthetic pathways (sterol, ubiquinone, polyhydroxybutyrate, antibiotic biosynthesis) and cell redox balance, suggesting a metabolic cluster focused on building essential biomolecules and maintaining redox state. A few terms (splicing, neural proliferation) seem outliers or annotation noise; overall the shared theme is biosynthetic metabolism with redox regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":3},{"id":"GO:1901006","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0006744","count":3}]},{"hash":"504165724147212049","title":"Photosynthesis-linked energy metabolism and translation regulation","description":"The cluster centers on energy production processes (photosynthesis, mitochondrial ETC, anaerobic respiration) and pigment/porphyrin biosynthesis (heme), complemented by nitrogen metabolism and folate metabolism, along with signals of translation and its negative regulation. This suggests a cohesive module combining energy metabolism with some translational control, likely in photosynthetic or nitrogen-fixing microbes. ","confidence":"Medium","size":29,"edges":391,"triangles":3279,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006120","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0015979","count":2}]},{"hash":"33536607113971712","title":"Proliferation signaling and translation initiation","description":"Proteins in this cluster are enriched for terms tied to cell proliferation and signaling (mitotic cell cycle; positive regulation of cell population proliferation; positive regulation of GTPase activity; positive regulation of serine/threonine kinase activity and autophosphorylation) along with gene expression processes (mRNA transport; formation of translation preinitiation complex). This suggests a cohesive theme where growth signals coordinate cell division with the initiation of protein synthesis, though there are some terms that reflect broader cellular processes. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0051028","count":4},{"id":"GO:0031954","count":4},{"id":"GO:0071902","count":4}]},{"hash":"424509724438267993","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009738","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0015979","count":2}]},{"hash":"1468992417516680867","title":"Glutathione-mediated redox detoxification and xenobiotic response","description":"The top GO terms converge on redox biology and detoxification: oxidation-reduction processes, cellular oxidant detoxification, and glutathione metabolic process, plus responses to toxic and xenobiotic substances (ethanol, xenobiotics). Although aging and growth terms appear, the dominant theme is defense against oxidative stress and chemical challenge via glutathione-dependent pathways, which best captures the cluster's shared function.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1642717943240742558","title":"Muscle and heart transcriptional regulation","description":"Top GO terms point to DNA-templated transcription and positive regulation of transcription by RNA polymerase II, coupled with muscle lineage development (myotube cell development) and heart development. Chromatin-related processes (nucleosome assembly, histone modification) and signaling aspects (dexamethasone response, regulation of protein kinase activity) suggest a transcription-centric program coordinating muscle/heart development with chromatin dynamics and hormonal signaling.","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0014904","count":2},{"id":"GO:0006334","count":2}]},{"hash":"2024954586468154442","title":"Mitotic cell cycle and ubiquitin-mediated degradation","description":"The top GO terms point to mitosis (cell division, metaphase/anaphase transition) and APC/C-dependent/ubiquitin\u2011mediated proteolysis (including K11-linked ubiquitination), indicating a cohesive cluster of mitotic regulators and proteolysis machinery. Minor terms like habituation or macroautophagy are less representative.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007091","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0070979","count":2}]},{"hash":"858985801665774519","title":"Unknown","description":"The top GO terms reflect a mix of membrane transport (xenobiotic transmembrane transport; ER to Golgi vesicle transport), photosynthesis-related processes (photosynthesis; photosystem II stabilization), stress and signaling responses (response to lead ion; unfolded protein response; response to morphine; glucocorticoid signaling), and chromatin regulation (histone dephosphorylation; negative regulation of chromatin binding). There is no single cohesive function linking these processes, and the entries likely represent a heterogeneous set of proteins or annotations, making it unclear how these proteins function together as a single cluster.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:0015979","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0010288","count":2},{"id":"GO:0006986","count":2}]},{"hash":"2163378845628979533","title":"ER Protein Quality Control and ERAD","description":"The terms cluster around endoplasmic reticulum quality control: cellular response to unfolded proteins, retrograde transport from ER to cytosol, protein retention in the ER lumen, and ER-associated degradation pathways, plus N-glycan processing toward lysosome. A few terms (DNA-templated transcription, liver development) appear tangential, but the dominant theme is ER homeostasis and glycoprotein handling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0034620","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1904153","count":1},{"id":"GO:0030970","count":1}]},{"hash":"2169325729271576768","title":"Vesicle trafficking and exocytosis regulation","description":"The top terms point to membrane trafficking processes: negative regulation of SNARE complex assembly, exocytosis, pinocytosis, and related GTPase activity, suggesting a cluster centered on vesicle fusion and endocytosis regulation. While there are some off-target terms (e.g., Wnt signaling, mRNA processing), the strongest signal is vesicle trafficking, making this an appropriate, specific label.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0048549","count":3}]},{"hash":"1768542702446506905","title":"Mitochondrial translation and protein maturation","description":"The top terms are strongly centered on translation (GO:0006412) and mitochondria-related processing (rRNA import into mitochondrion; N-terminal protein amino acid modification; co-translational protein modification), pointing to ribosome activity and mitochondrial protein maturation. The other terms reflect broader catabolic metabolism, but they do not cohesively define a single pathway; the strongest signal is mitochondrial translation and associated protein processing, which is why this label is most representative. ","confidence":"Medium","size":28,"edges":372,"triangles":3124,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0043448","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0015996","count":2}]},{"hash":"1626829341508550917","title":"Virus infection and host response","description":"Based on the prominence of virion assembly, viral life cycle, host-mediated activation of viral genome replication, and leukocyte migration, the cluster centers on viral infection processes and host immune interactions. While a couple terms (e.g., sepal formation) appear unrelated and may reflect annotation noise, the overall pattern clearly points to virus-host interactions and the viral life cycle.","confidence":"High","size":28,"edges":69,"triangles":58,"max_degree":12,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":9},{"id":"GO:0030260","count":6},{"id":"GO:0050900","count":6},{"id":"GO:0010849","count":6},{"id":"GO:0000413","count":6}]},{"hash":"343165737397224406","title":"Mitochondrial/Chloroplast energy metabolism and cofactor biosynthesis","description":"This cluster pulls together processes tied to organelle energy production and redox balance, including mitochondrial electron transport (NADH to ubiquinone), heme and ubiquinone biosynthesis, sterol biosynthesis, and chloroplast-related protein import. While a few terms like tRNA wobble modification and xenobiotic response are also present, the dominant theme is energy metabolism and the biosynthesis of redox cofactors within mitochondria and chloroplasts, suggesting a cohesive functional module around organellar metabolism.","confidence":"High","size":28,"edges":113,"triangles":153,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0045037","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0055114","count":2}]},{"hash":"249806077455120594","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":6,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0000466","count":5},{"id":"GO:0048568","count":5},{"id":"GO:0000472","count":5}]},{"hash":"229833753523945772","title":"Developmental gene regulation and differentiation","description":"The cluster includes GO terms centered on transcription (DNA-templated transcription) and histone modification (epigenetic regulation), plus development-associated processes (brain development, male gonad development, osteoblast differentiation) and related growth and RNA transport. This suggests a cohesive theme of gene expression control guiding developmental differentiation across tissues, rather than a single specialized pathway.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043966","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0007338","count":5},{"id":"GO:0001649","count":5}]},{"hash":"1953860042085406796","title":"Innate antiviral immunity and ER stress","description":"The top GO terms point to innate immune defense against viruses (innate immune response, defense response to virus) and broader pathogen defense (defense response to Gram-positive bacteria), with supportive links to transcriptional regulation (DNA-templated transcription) and ER-associated processes (protein folding in ER, ubiquitin-dependent ERAD) and redox balance. The \u201csingle fertilization\u201d term seems incidental. Overall, this cluster is best described as innate antiviral immunity with connected ER stress/quality-control aspects.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0016032","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0006469","count":2}]},{"hash":"2104935714959826892","title":"Bacterial antibiotic biosynthesis and response","description":"Proteins in this cluster are enriched for antibiotic biosynthetic process and response to antibiotic, with additional bacterial-typical transcription-related terms (DNA-templated transcription, polycistronic mRNA processing). Some terms are obsolete, but the overarching theme points to a gene set involved in antibiotic production and associated stress/detoxification responses in bacteria. A few outlier terms (e.g., cilium assembly, axis elongation) do not define the cluster\u2019s core function, which remains antibiotic biosynthesis and response.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0016575","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1706638813406821221","title":"Ubiquitin-Proteasome Regulation and NF-kB Signaling","description":"The top GO terms cluster around ubiquitination (K63-, K48-, K6-linked) and autoubiquitination, plus SCF-dependent proteasomal degradation and ERAD, indicating a group of proteins involved in tagging substrates for destruction. The presence of NF-kB signaling regulation and peroxisomal protein import suggests additional regulatory and recycling roles (e.g., peroxisome receptor ubiquitination), but the core theme is ubiquitin-mediated proteolysis and its signaling connections.","confidence":"High","size":28,"edges":168,"triangles":532,"max_degree":25,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0070534","count":12},{"id":"GO:0051865","count":12},{"id":"GO:0030433","count":12},{"id":"GO:0051301","count":11},{"id":"GO:0031146","count":11}]},{"hash":"636027938084947013","title":"Regulated GTPase/kinase signaling and axonogenesis","description":"The top GO terms cluster around modulation of signaling pathways (positive regulation of GTPase activity, regulation of kinase activity, guanylate cyclase activity) and neural development (axonogenesis), suggesting a theme of signaling regulation tied to neuronal differentiation. Other terms ( xenobiotic response, nuclear import, differentiation in other tissues) indicate broader regulatory roles, making the overall function plausible but somewhat heterogeneous. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006607","count":2}]},{"hash":"98047708381415743","title":"Growth signaling and translation control","description":"This cluster centers on nutrient/growth sensing and the regulation of protein synthesis and ribosome biogenesis, as evidenced by terms for TORC1 signaling, nutrient response, translation initiation, mRNA transport, and rRNA maturation. While a couple of terms touch cytoskeletal or chromatin aspects, the dominant theme is growth signaling coupled to translation machinery and ribosome assembly.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0070262","count":2}]},{"hash":"552391162227418789","title":"Oxidative Stress Detoxification and Innate Defense","description":"This cluster is dominated by GO terms for oxidative-reduction processes, cellular oxidant detoxification, and innate immune response, indicating proteins that participate in managing oxidative stress and defending against pathogens. While other terms (antibiotic biosynthesis, morphine response, and transcription regulation) are present, they are less aligned with the core redox/immune theme, likely representing ancillary roles or annotation noise. Overall, the cluster seems best described as a redox-balanced defense module.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0043278","count":3},{"id":"GO:0006888","count":3}]},{"hash":"1916001185490904521","title":"LPS Core Biosynthesis and Envelope Assembly","description":"This cluster centers on lipopolysaccharide biosynthesis, especially core region and the ADP-L-glycero-beta-D-manno-heptose pathway, pointing to LPS core assembly in Gram-negative bacteria. Other terms (antibiotic response, copper transport, Ca2+ homeostasis) likely reflect envelope stress and metal homeostasis linked to the outer membrane.","confidence":"High","size":27,"edges":28,"triangles":6,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0009103","count":5},{"id":"GO:0030091","count":4},{"id":"GO:0097171","count":4},{"id":"GO:0009244","count":4}]},{"hash":"1398816442015126739","title":"DNA-Templated Transcription and Cell Cycle Regulation","description":"Dominated by transcription-related terms and cell cycle terms, with ER transport and ER stress terms suggesting coordination between transcription control, cell division, and protein handling in the secretory pathway.","confidence":"High","size":27,"edges":25,"triangles":4,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0010738","count":4},{"id":"GO:0000186","count":4}]},{"hash":"2081639275625607643","title":"Stress Response and Chromatin Regulation","description":"The cluster centers on diverse stress-related responses (to ethanol, antibiotics, starvation, estradiol) and includes regulation of the cell cycle together with deubiquitinase activities (histone H2A K63-linked and protein K11-linked), suggesting coordination between stress sensing and chromatin-mediated gene regulation. This combination points to a cohesive theme of stress response linked to chromatin modification and cell-cycle control.","confidence":"Medium","size":27,"edges":12,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0051726","count":3},{"id":"GO:0045471","count":3},{"id":"GO:0070537","count":3},{"id":"GO:0035871","count":3}]},{"hash":"650360948904506840","title":"GTPase-driven cell migration and epithelial polarity","description":"The cluster shows strong signals for cell migration, establishment of epithelial cell polarity, and positive regulation of GTPase activity, suggesting a set of proteins coordinating cytoskeletal remodeling and directional movement via small GTPases. Additional terms related to temperature stress and apoptosis exist but do not outweigh the core theme of motility and polarity regulation, making this a coherent functional cluster. ","confidence":"High","size":27,"edges":81,"triangles":3,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0050821","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0009409","count":2}]},{"hash":"447867985000372261","title":"Neural development and EMT","description":"This cluster shows a bias toward neural development terms (substantia nigra development; Schwann cell development) and epithelial-to-mesenchymal transition, which together point to neural differentiation and neural crest\u2013like EMT processes. Additional related terms like branching in blood vessel morphogenesis and GTPase signaling support a developmental remodeling theme. Some outliers (lipid A biosynthesis, plant ABA signaling, hydrogen peroxide response) may reflect annotation noise rather than a cohesive functional core. ","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0009245","count":3},{"id":"GO:0035562","count":2},{"id":"GO:0001837","count":2}]},{"hash":"1830809728983483080","title":"Developmental biology and cell cycle","description":"The top GO terms show a clear emphasis on development (heart development, Schwann cell development, embryonic cranial skeleton morphogenesis) alongside core cellular processes (DNA replication, DNA-templated transcription, mitotic centrosome separation) indicating a cluster of proteins involved in developmental regulation intertwined with cell cycle and gene expression. The abscisic acid signaling term likely represents cross-annotation noise. Overall, the theme centers on development with supporting cell-cycle activities.","confidence":"Medium","size":27,"edges":184,"triangles":624,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007100","count":11},{"id":"GO:0043065","count":10},{"id":"GO:0006260","count":9},{"id":"GO:0048701","count":9},{"id":"GO:0006351","count":9}]},{"hash":"1980634549174553957","title":"Chromatin Remodeling and Transcription Initiation","description":"The top GO terms cluster around chromatin biology and transcription initiation: RNA polymerase II preinitiation complex assembly, chromatin remodeling, heterochromatin formation, histone H2A deubiquitination, and telomere protection, indicating a nuclear chromatin regulation module that facilitates transcription initiation. Plant-specific signals (osmotic stress, ethylene response, flavonoid/lignin biosynthesis) may reflect broader transcriptional regulation contexts but do not override the central chromatin-focused theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":3},{"id":"GO:0000183","count":2},{"id":"GO:0043044","count":2},{"id":"GO:1900386","count":2},{"id":"GO:0006970","count":2}]},{"hash":"1531811649841538005","title":"Chromatin Regulation and Transcription","description":"These terms cluster around DNA-templated transcription, nucleosome assembly, and DNA methylation/heterochromatin regulation, with additional hints of nuclear protein folding support for transcription complexes; the obsolete terms likely reflect legacy annotations but do not change the shared chromatin/transcription theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0010424","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0090309","count":2}]},{"hash":"228564645255362569","title":"Photosynthesis and flagellar motility","description":"The top terms show strong enrichment for photosynthesis and photosystem I/II-related electron transport, paired with bacterial-type flagellum-dependent motility and flagellum assembly, indicating a cluster of proteins involved in photosynthetic energy generation in bacteria as well as components of the flagellar motility apparatus. Additional metabolic terms (TCA cycle, choline catabolism) support energy metabolism but the core theme is photosynthetic energy production coupled with motility. ","confidence":"High","size":27,"edges":218,"triangles":872,"max_degree":24,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0015979","count":4},{"id":"GO:0071973","count":2},{"id":"GO:0009773","count":2},{"id":"GO:0008616","count":2}]},{"hash":"1749491358146331225","title":"Histone methylation and cell cycle regulation","description":"The cluster shows strong signals for histone lysine methylation (e.g., H3-K36 methylation; monomethylation/dimethylation) and transcriptional regulation, coupled with multiple mitotic/meiotic cell-cycle terms (mitotic cell cycle, spindle assembly, centrosome duplication, meiotic cell cycle). This pattern suggests a chromatin-modifying module that coordinates chromatin state with cell division. Some terms like heart development and visual learning may be unrelated noise or pleiotropic annotations, but the core theme is chromatin modification linked to cell cycle control.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0010452","count":2},{"id":"GO:0018026","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0008542","count":2}]},{"hash":"1788044505143701014","title":"Hormone signaling and metabolic stress responses","description":"Most prominently, the cluster includes hormone-related response terms (thyroid hormone, retinoic acid receptor signaling) and metabolic processes (norepinephrine metabolism, bile acid biosynthesis), with several stress-related terms (water deprivation, methylglyoxal). This suggests a theme around hormonal signaling coupled to metabolism and stress adaptation, hence the label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0009414","count":2},{"id":"GO:0097066","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0048385","count":1}]},{"hash":"1856429889308968025","title":"Cardiac development and endothelial angiogenesis","description":"This cluster shows enrichment for heart-related processes such as cardiac morphogenesis, SA node signaling, and Notch signaling in the developing heart, along with endothelial differentiation and sprouting angiogenesis, suggesting a module coordinating heart formation with vascular development, supported by actin assembly and transcriptional activity.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0003213","count":2},{"id":"GO:1903589","count":2},{"id":"GO:0051017","count":2}]},{"hash":"1752920628433837985","title":"Mitochondrial Redox Balance and Organelle Maintenance","description":"Based on GO terms enriched in the cluster, several terms point to redox biology and mitochondrial-related processes (cellular response to oxidative stress; redox homeostasis; intracellular iron ion homeostasis; protein import into mitochondrial intermembrane space). Additional terms touch on autophagy regulation, vacuolar fusion, and microtubule dynamics, consistent with organelle maintenance and trafficking. A single palmitoylation term suggests membrane-associated modulation, but the dominant theme is mitochondrial redox balance and organelle quality control, supporting a label centered on mitochondria and stress responses. The sebaceous gland development term is likely an outlier or annotation noise.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018230","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0016242","count":1},{"id":"GO:0045454","count":1}]},{"hash":"255648500053301056","title":"Plant developmental transcriptional regulation","description":"The cluster is characterized by GO terms centered on DNA-templated transcription and its regulation, along with multicellular and seed development, mRNA transport, and plant-specific processes (wax biosynthesis, phyllotactic patterning). The inclusion of response to chitin and defense-related regulation suggests integration of transcriptional control with defense signaling in plants. Overall, it reflects transcriptional regulators involved in plant development and associated defense responses.","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:0010200","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0051028","count":3}]},{"hash":"1353458293671138121","title":"Steroid biosynthesis and mitochondrial energy metabolism","description":"The GO terms point to steroidogenesis and signaling (terpenoid biosynthetic process, steroid hormone receptor complex assembly, prostate gland development, male sex differentiation) alongside mitochondrial energy pathways (oxidative phosphorylation, aerobic electron transport chain, proton transmembrane transport). This combination suggests a coherent theme around steroid biosynthesis/signaling coupled with mitochondrial energy metabolism, rather than unrelated processes. ","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0071357","count":2},{"id":"GO:0006463","count":2}]},{"hash":"1457857227210961225","title":"Nuclear Transport and Chromatin Maintenance with Autophagy","description":"The cluster combines nuclear-related processes (NLS-dependent protein import, chromatin assembly, heterochromatin formation) with autophagy-related and vacuolar processes (microautophagy, vacuole fusion). This pattern suggests proteins involved in nuclear regulation that may intersect with vesicle/vacuole and autophagy pathways, with some involvement in RNA transport and signaling. While the mix is broad, the strongest common thread centers on nuclear transport and chromatin maintenance, with supportive autophagy links.","confidence":"Low","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":3},{"id":"GO:2000012","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0043065","count":2}]},{"hash":"359226374266606564","title":"TORC1 Signaling and Cell Cycle Regulation","description":"This cluster centers on TORC1 signaling, GTPase activity regulation, mitotic processes and cell cycle control (mitotic spindle assembly, negative regulation of G0 to G1), together with transcriptional and chromatin regulatory functions (DNA-templated transcription, histone H4-K16 acetylation, mRNA transport). The combination suggests a cohesive growth- and gene-expression\u2013regulatory module linking signaling to cell division and chromatin state, with an immune defense term likely representing annotation noise or shared signaling pathways.","confidence":"Medium","size":26,"edges":10,"triangles":3,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0038202","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0070262","count":6},{"id":"GO:0051301","count":6}]},{"hash":"2268914502295217248","title":"Translation and mRNA turnover with proliferation signals","description":"This cluster is dominated by translation-related GO terms (translation, translational initiation/termination, cytoplasmic translation, positive regulation of translation, and selenocysteine incorporation) and mRNA decay (deadenylation-dependent decay), with additional cell-cycle/proliferation terms (cell division, glial cell proliferation). The combination suggests a module centered on protein synthesis and its post-transcriptional regulation, potentially linked to proliferative states in glial or other cells. The appearance of an antibiotic response may reflect general stress responses that intersect with translation control rather than a direct antibiotic-specific pathway.","confidence":"Medium","size":26,"edges":33,"triangles":9,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0046677","count":7},{"id":"GO:0006412","count":6},{"id":"GO:0001514","count":6},{"id":"GO:0000288","count":6}]},{"hash":"2145216122487940187","title":"Stress-Responsive Growth and Cell Cycle Signaling","description":"The top terms point to cellular stress responses (cadmium, hypoxia) combined with growth and division signaling (TORC1, mitotic cell cycle, GTPase regulation), plus related trafficking and protein organization processes. This suggests a cluster centered on how stress signals influence growth control and cell cycle progression, with supporting roles from mRNA transport and vesicle trafficking. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":6},{"id":"GO:0071456","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0051301","count":6}]},{"hash":"575825846165042158","title":"Unknown","description":"The top GO terms are scattered across innate immunity, virus defense, metabolism, cell cycle, and even chloroplast-related processes, with many obsolete terms present. There is no single cohesive function linking the cluster, and the connectivity (edges/triangles) is zero, so a specific, representative label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051348","count":2},{"id":"GO:0006478","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0051607","count":2}]},{"hash":"1903472686288541551","title":"Neuroimmune Innate Signaling and Inflammation","description":"This cluster centers on innate immune receptor signaling, including toll-like receptor pathways (TLR2 and MyD88-independent signaling), regulation of dendritic cell cytokine production, and promotion of inflammatory responses, indicating a cohesive immune activation theme. The inclusion of terms related to myelination and dopamine-related cellular responses suggests neuroimmune interactions in the nervous system, possibly microglial or glial context.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0006469","count":5},{"id":"GO:0042552","count":5},{"id":"GO:0002730","count":4},{"id":"GO:0007186","count":4}]},{"hash":"1025612691322147822","title":"Developmental transcriptional regulation","description":"The dominant terms are DNA-templated transcription and its regulation, paired with multiple developmental processes (multicellular development, nervous system development, spermatid development, seed development). Plant-specific signaling (ABA-activated pathway) and defense responses also appear, implying transcriptional control of development across species, with some stress-responsive roles. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009738","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0000278","count":2}]},{"hash":"413067859225266548","title":"Strigolactone biosynthesis and shoot development","description":"The cluster includes GO terms for strigolactone biosynthesis (GO:1901601) and secondary shoot formation (GO:0010223), indicating a link to plant hormone production that regulates shoot branching and development. Additional terms point to broader metabolic and catabolic activities (lipids, glucuronosides), suggesting general cellular metabolism in these proteins. While there are some unrelated annotations, the strongest signal is the plant-specific strigolactone pathway and shoot development, making this a concise and representative label for the cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":4},{"id":"GO:0019433","count":4},{"id":"GO:0019260","count":3},{"id":"GO:0010223","count":3},{"id":"GO:0006660","count":3}]},{"hash":"2233524556570335942","title":"Developmental signaling and Golgi vesicle trafficking","description":"The top terms point to multicellular development across tissues like skin, spinal cord, heart (SA node), and vasculature, indicating a developmental biology theme. Intersecting terms include intra-Golgi vesicle transport, GTPase activity regulation, and protein homooligomerization, suggesting involvement in vesicle trafficking and signaling during development. This combination best captures the cluster\u2019s likely functional scope without overreaching to a single precise pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006891","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0007275","count":2}]},{"hash":"670087473451072275","title":"DNA repair and nucleotide catabolism","description":"The GO terms indicate a blend of DNA maintenance (DNA repair, DNA-templated transcription, and positive regulation of double-strand break repair) with several nucleotide- and cofactor-related catabolic processes (diadenosine tetraphosphate, nucleobase-containing molecules, CoA, IDP, folic acid). This pattern suggests a cluster of proteins involved in genome integrity plus nucleotide metabolism or salvage pathways. The link across repair and catabolic processes supports a cohesive theme around maintaining DNA and nucleotide balance rather than a single isolated pathway.","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0015967","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0006351","count":3},{"id":"GO:2000233","count":2},{"id":"GO:2000781","count":2}]},{"hash":"1729338757735271246","title":"Metabolic biosynthesis and detoxification","description":"This cluster centers on biosynthetic and catabolic processes (antibiotic and biotin biosynthesis; uracil and 1,2-dichloroethane catabolism), along with detoxification and redox-related activities (cellular oxidant detoxification; oxidation-reduction process; response to toxic substances) and nutrient utilization (nitrogen utilization). While some terms like secondary shoot formation and endocannabinoid signaling regulation are broader GO associations, the dominant pattern points to metabolism and detox pathways rather than a single specialized function. Therefore, the label reflects the main theme of the cluster.","confidence":"Medium","size":26,"edges":28,"triangles":1,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0006212","count":7},{"id":"GO:0098869","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0009102","count":7}]},{"hash":"1476787368447381230","title":"Mitochondrial import and inner-membrane dynamics","description":"The top GO terms cluster around mitochondrial targeting, insertion into the inner mitochondrial membrane, and positive regulation of mitochondrial fission, suggesting a theme of mitochondrial protein import/assembly and dynamics. Some terms are obsolete and a few stress-response terms are peripheral, but the strongest signals point to mitochondrial biogenesis and morphology. ","confidence":"Medium","size":25,"edges":12,"triangles":10,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":4},{"id":"GO:0072321","count":2},{"id":"GO:0045039","count":2},{"id":"GO:0001300","count":1},{"id":"GO:0014850","count":1}]},{"hash":"1668696976639349597","title":"Translation Machinery and Ribosome Biogenesis","description":"The top GO terms cluster around protein synthesis and ribosome biology: cytoplasmic and mitochondrial translation, translational termination, and ribosome biogenesis, with associated tRNA modification. These point to a cohesive group of proteins involved in the translation apparatus and its assembly, rather than a broader signaling or metabolic function. A couple of terms (e.g., response to antibiotic) may be ancillary or context-specific, but do not override the primary translation-centric theme.","confidence":"High","size":25,"edges":72,"triangles":140,"max_degree":9,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0070126","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0042254","count":3}]},{"hash":"433733645520079710","title":"ER-Golgi Vesicle Trafficking","description":"The cluster shows a coherent signal for transport and fusion of vesicles between the ER and Golgi, intra-Golgi trafficking, retrograde transport to the Golgi, Golgi ribbon formation, and endocytic recycling, all indicating vesicle trafficking and Golgi organization. While a few terms like xenobiotic response and synaptic potentiation appear, they are less central to the dominant theme of Golgi/ER vesicle flow.","confidence":"High","size":25,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0042144","count":3},{"id":"GO:0006891","count":3},{"id":"GO:0090161","count":3},{"id":"GO:0060291","count":3}]},{"hash":"1355633833416015211","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":79,"triangles":147,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0006369","count":9},{"id":"GO:0000463","count":7},{"id":"GO:0031047","count":7},{"id":"GO:1902626","count":7}]},{"hash":"1681856702951086463","title":"ER stress and protein quality control","description":"This cluster centers on endoplasmic reticulum\u2013related processes (ER to Golgi transport, ER unfolded protein response, ER-associated degradation, and protein import into peroxisomes) and includes apoptotic signaling, all pointing to cellular stress responses and protein quality control. While a few terms like DNA replication and mRNA export appear, the dominant theme is ER stress response and maintenance of proteostasis.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070987","count":5},{"id":"GO:0034198","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0006888","count":4}]},{"hash":"1868713786360433293","title":"Neuronal development, maturation, and migration","description":"The set of GO terms centers on neural development: regulation of neuron maturation, tangential migration from the subventricular zone to the olfactory bulb, and maintenance of cell polarity, plus neuron-associated signaling via GPCR pathways and gene expression regulation (transcription and mRNA decay). While a few terms are general or metabolic, the overall pattern points to proteins involved in neuronal development and signaling.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0034198","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0022028","count":2},{"id":"GO:0030011","count":2}]},{"hash":"1072673694364150153","title":"Chromatin remodeling and transcription regulation in plants","description":"This cluster is dominated by chromatin-related processes: chromatin remodeling (GO:0043044), DNA-templated transcription (GO:0006351), rDNA heterochromatin formation, and histone modification/deubiquitination. It also includes DNA methylation involvement and stress- or signal-related terms, implying a core role in chromatin dynamics and transcriptional control, with plant signaling contexts (cytokinin) and osmotic stress modulation providing contextual nuance. Overall, the strongest signal is chromatin remodeling linked to transcription regulation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043044","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0009736","count":4},{"id":"GO:0043046","count":3},{"id":"GO:0045654","count":3}]},{"hash":"1806722589111674049","title":"Unknown","description":"The top terms cover neural signaling (long-term synaptic potentiation), stress and hormone responses (response to corticosterone, cellular response to hypoxia), immune signaling (Fc-epsilon receptor signaling), and general cell-cycle/kinase regulation (mitotic cell cycle, positive regulation of protein serine/threonine kinase activity, GTPase activity). This mix spans disparate biological themes with no single dominant function, so a cohesive, specific label is not evident. ","confidence":"","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0051412","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0038095","count":3}]},{"hash":"2293074854010167157","title":"RNA/rDNA methylation and chromatin regulation","description":"The top terms emphasize methylation activities on RNA and proteins (rRNA methylation, N-terminal glycine methylation, peptidyl-lysine dimethylation) together with rDNA heterochromatin formation, pointing to an epigenetic/chromatin-regulatory theme centered on RNA processing and methylation. While some metabolic terms (redox, thiamine, lipoylation) appear, they are less central to the core cluster signal, so the label focuses on methylation- and chromatin-related functions.","confidence":"Medium","size":25,"edges":22,"triangles":14,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":6},{"id":"GO:0018013","count":6},{"id":"GO:0031167","count":6},{"id":"GO:0018027","count":6},{"id":"GO:0045454","count":6}]},{"hash":"1095861023265191994","title":"Cell signaling, trafficking, and apoptosis","description":"The Top Terms center on signal transduction and regulation (ubiquitin-dependent SMAD degradation, hippo signaling), membrane trafficking (exocytosis), cytoskeletal organization (actin filament bundle assembly), and cell fate events (apoptosis), with additional development and immune-related terms. This points to proteins involved in signaling pathways that govern trafficking and programmed cell death, with incidental roles in development and immunity, making a label focused on signaling, trafficking, and apoptosis appropriate.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":2},{"id":"GO:0006887","count":2},{"id":"GO:0035331","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0006915","count":2}]},{"hash":"2012658754459096029","title":"Unknown","description":"These terms span diverse processes: proteasomal ubiquitin-dependent protein catabolism, defense against Gram-positive bacteria, metal ion and hypoxia responses, regulation of GTPase and kinase activity, mRNA transport, skeletal morphogenesis, autophosphorylation, and mitotic cell cycle. The cluster lacks a single dominant biological theme or pathway, suggesting heterogeneity rather than a cohesive function. Therefore Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051028","count":3}]},{"hash":"2057114983205216568","title":"Stress Response and Cell Cycle Regulation","description":"This cluster is dominated by GO terms related to stress responses (SOS response, response to cAMP, response to corticosterone) and a cell cycle event (G2/M transition), suggesting a combined theme of responding to stress while controlling cell division. Other terms (translation, brain development, photosystem II assembly, ion transport) indicate broader or species-specific roles and are less cohesive with the core stress/cell-cycle signals, so the primary interpretation centers on stress response and cell-cycle regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0051591","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0051412","count":2}]},{"hash":"647918043481227266","title":"Translation and transcription machinery","description":"The cluster shows strong representation of translation (GO:0006412) and DNA-templated transcription (GO:0006351), with supporting signals from valyl-tRNA aminoacylation (GO:0006438) and regulation of translational fidelity (GO:0006450). Although a few terms like viral process and angiogenesis appear, the dominant theme is proteins involved in protein synthesis and RNA-related processing, justifying a label focused on translation and transcription machinery.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0045190","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1253070818394521889","title":"Bacterial biosynthesis and antibiotic response","description":"This cluster shows a strong emphasis on biosynthetic processes (biotin, menaquinone, methionine) and antibiotic-related functions (antibiotic biosynthetic process, response to antibiotic), along with detoxification pathways, suggesting a metabolic module tied to biosynthesis and antibiotic response. Some terms like photosynthesis and nitrogen utilization are less cohesive but may reflect broader metabolic context or annotation noise.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019740","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0009234","count":2}]},{"hash":"2216109197412724162","title":"Bacterial Growth and Metabolism","description":"These GO terms point to core bacterial processes: ongoing protein synthesis (translation), energy capture and use (photosynthesis and proton transport), and biosynthesis/degradation activities (lipopolysaccharide biosynthesis, CMP-N-acetylneuraminate metabolism, toluene catabolism), plus responses to antibiotics and cell-cycle related processes. The mix suggests a cluster of proteins involved in growth, energy production, and basic metabolism in prokaryotes, with photosynthesis indicating possible specialization in photosynthetic bacteria. The label aims to capture its broad metabolic and growth-related nature without implying a single, narrow pathway.","confidence":"Medium","size":24,"edges":275,"triangles":2002,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0015979","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0007049","count":2}]},{"hash":"945542074994679209","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"Top GO terms indicate transport of phosphate and manganese ions, ATP across mitochondrial membranes, and import of pyrimidine nucleotides into mitochondria, all centered on mitochondrial transport and metabolism. Additional terms point to mitochondrial membrane potential regulation, apoptotic changes in mitochondria, negative regulation of necroptosis, and adaptive thermogenesis, reinforcing a mitochondria-focused functional theme. Together, these terms suggest a cluster of proteins involved in mitochondrial transport and energy-related regulation rather than a single cytosolic pathway.","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":6},{"id":"GO:0006828","count":5},{"id":"GO:1990544","count":4},{"id":"GO:1990519","count":4},{"id":"GO:0008637","count":4}]},{"hash":"1616686321344939837","title":"Golgi sugar transport and glycosylation","description":"The cluster is dominated by GO terms for transmembrane transport of nucleotide sugars into the Golgi lumen (GDP-fucose, UDP-glucose) and related metabolites, plus glycosylation processes such as fucosylation (O-linked and N-glycan). This points to a cohesive function group of Golgi-localized sugar transporters and glycosyltransfer activities. A couple of plant developmental terms (root-related) appear but seem secondary to the main glycosylation/sugar transport theme.","confidence":"High","size":24,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035436","count":2},{"id":"GO:0036085","count":2},{"id":"GO:0036066","count":2},{"id":"GO:0015713","count":2},{"id":"GO:0030206","count":2}]},{"hash":"444172205648454114","title":"SHH-driven embryonic head and sensory development","description":"GO terms center on Smoothened signaling and embryonic development of head and sensory organs (eye, inner ear), with neural tube patterning and left-right axis formation. While a spliceosome-related term is present, the dominant theme is SHH-mediated morphogenesis of cranial/sensory structures, making this label representative of the cluster\u2019s function.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":2},{"id":"GO:0048706","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0043010","count":1},{"id":"GO:0060122","count":1}]},{"hash":"2062031004396760649","title":"Innate immune signaling and TLR pathways","description":"The enriched GO terms point to innate immunity and pattern-recognition receptor signaling, with emphasis on Toll-like receptor pathways (TLR2, MyD88-independent signaling), dendritic cell cytokine regulation, interferon production, and inflammatory responses. Negative regulation of protein kinase activity and GPCR signaling fit within immune signaling networks; a single outlier term (nipple morphogenesis) is likely non-specific noise. Overall, the cluster appears to group proteins involved in innate immune sensing and downstream inflammatory responses.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0002730","count":3},{"id":"GO:0007186","count":3},{"id":"GO:0050729","count":3}]},{"hash":"1998537072999200476","title":"Cardiac development, SA node signaling, and angiogenesis","description":"This cluster centers on heart morphogenesis and specialized cardiac conduction/vascular differentiation, with repeated terms for right atrium morphogenesis, SA node cell communication and action potential regulation, and endothelial differentiation/angiogenesis. Actin filament assembly aligns with cardiomyocyte contractile machinery, reinforcing a cardiac-focused theme. ","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0003213","count":4},{"id":"GO:1903589","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0086070","count":4},{"id":"GO:0007253","count":4}]},{"hash":"1854398721009432677","title":"Nuclear RNA Processing and Transcription Regulation","description":"This cluster is dominated by processes in the nucleus: spliceosomal snRNP assembly, transcription elongation by RNA polymerase II, nuclear mRNA surveillance, and mRNA export, with associated histone methylation/deubiquitination typical of transcription regulation. A few outlier terms like pH response and insulin secretion appear, but the core signal points to RNA processing and transcription control.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0010446","count":1},{"id":"GO:0034729","count":1},{"id":"GO:0051568","count":1},{"id":"GO:0043085","count":1}]},{"hash":"1866368279725581694","title":"Mitochondrial translation and tRNA charging","description":"This cluster is dominated by translation-related GO terms and mitochondrial tRNA aminoacylation (Gly, Ser, Thr, Pro), plus regulation of translational fidelity, indicating mitochondrial protein synthesis machinery.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0097056","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0070159","count":1},{"id":"GO:0006412","count":1}]},{"hash":"540822401017864549","title":"MAPK and NF-kB Immune Signaling","description":"The cluster centers on signaling pathways and immune responses, with multiple GO terms for p38 MAPK cascade, ERK1/ERK2 cascade, NF-kappaB transcription factor activity, innate and B cell\u2013related immune processes, and responses to cytokines and stimuli. Additional terms like viral process and response to phorbol esters support a theme of signaling-driven immune activation, while mRNA processing and microtubule localization appear as ancillary functions. Overall, this points to a cohesive set of proteins involved in MAPK/NF-kB\u2013mediated immune signaling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":3},{"id":"GO:0038066","count":2},{"id":"GO:1904628","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0097011","count":2}]},{"hash":"1201748771110939001","title":"Splicing and Translational Regulation","description":"This cluster is defined by enrichment of GO terms for alternative mRNA splicing via the spliceosome, regulation of mRNA splicing, regulation of translational initiation, translation reinitiation, and ncRNA-mediated gene silencing, indicating a cohesive set of proteins involved in RNA processing and control of translation, with a possible link to development such as eye-antennal disc formation.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0035214","count":2},{"id":"GO:0006446","count":1},{"id":"GO:0075525","count":1}]},{"hash":"177306398146274692","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosome biogenesis (GO:0042254) and ribosomal small subunit biogenesis (GO:0042274), cytoplasmic translation (GO:0002181), and tRNA modification (GO:0006400), all pointing to the core machinery of protein synthesis. The inclusion of cell cycle and cell division terms (GO:0007049, GO:0051301) suggests growth and division processes that are tightly linked to ribosome production. Despite the lack of network edges, the recurring themes center on ribosome assembly and function, plus the translation apparatus.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0002181","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0055114","count":3},{"id":"GO:1903833","count":3}]},{"hash":"2277131133374139643","title":"RNA Processing and Translation","description":"The cluster is dominated by RNA-related functions: translation (GO:0006412), tRNA splicing (GO:0006388, GO:0000379), and RNA processing activities, with additional RNA/DNA maintenance signal from telomeric D-loop disassembly. Some heart development terms appear, suggesting pleiotropic roles or annotation noise, but the strongest pattern across members aligns with RNA maturation and protein synthesis.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0090502","count":1},{"id":"GO:0006388","count":1},{"id":"GO:0000379","count":1}]},{"hash":"286771252135777367","title":"Unknown","description":"The terms cover nuclear processes (DNA replication, chromatin localization), signaling/regulation (Rho signaling, kinase activity), protein folding and proteolysis, redox homeostasis, collagen organization, and apoptosis regulation, with no clear single function tying them together. Because of this dispersion, there is no coherent cluster-level function to name confidently.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034351","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006469","count":2}]},{"hash":"1784776316293025664","title":"Biosynthesis and RNA Modification","description":"This cluster is enriched for several biosynthetic processes (antibiotic biosynthesis; ubiquinone, phosphatidylcholine, and vitamin E biosynthesis), pointing to a core theme of metabolite production. It also includes RNA-related processing terms (tRNA wobble uridine modification; 7-methylguanosine mRNA capping), suggesting involvement in RNA maturation. The presence of aging and stress-response terms indicates broader cellular maintenance roles. Overall, the proteins seem to participate in fundamental biosynthesis and RNA-processing activities rather than a single, unified pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0002098","count":6},{"id":"GO:0006744","count":6},{"id":"GO:0001300","count":5},{"id":"GO:0006370","count":5}]},{"hash":"2246542377249860418","title":"RNA processing and ribosome biogenesis","description":"The cluster is enriched for mRNA splicing, rRNA maturation (5.8S/LSU), mRNA export, and ribosome biogenesis, indicating a coherent theme around RNA maturation and ribosome assembly. Peripheral terms like transcription termination and SOS response are present but do not override the primary RNA-processing/ribosome-related signals.","confidence":"High","size":23,"edges":220,"triangles":1271,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:0000463","count":6},{"id":"GO:0070317","count":5},{"id":"GO:0006369","count":5},{"id":"GO:0000466","count":5}]},{"hash":"536421497190711513","title":"Gene expression regulation and chromatin remodeling","description":"The cluster shows a central theme around transcriptional control and chromatin dynamics (DNA-templated transcription, chromatin remodeling, regulation of mRNA stability in stress), with associated growth and differentiation signals (TGF-beta response, oligodendrocyte differentiation). A couple of outlier terms (lipid catabolism, potassium transport) are present but don\u2019t redefine the main function, which remains gene expression regulation and chromatin remodeling.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0043044","count":2}]},{"hash":"150390041801541753","title":"Unknown","description":"The GO terms are highly heterogeneous: clear glycosylation-related processes (GPI anchor biosynthesis, dolichol-linked oligosaccharide biosynthetic) are present, but many other terms point to reproductive processes (oogenesis, meiosis, pollen tube guidance), signaling (insulin receptor pathway), and epigenetic regulation (DNA methylation, epigenetic programming). There isn\u2019t a single cohesive biological theme linking most of the proteins, so a concise, representative label cannot be confidently assigned.","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0007143","count":1},{"id":"GO:0010923","count":1},{"id":"GO:0048477","count":1},{"id":"GO:0010183","count":1}]},{"hash":"1617409412163887158","title":"Brain and gonadal development cluster","description":"The prominent terms include brain development and seminiferous tubule development, plus broader multicellular organism development and cell proliferation, indicating a developmental program. Additional terms such as positive regulation of GTPase activity suggest signaling pathways driving differentiation, while mRNA splicing and protein homooligomerization reflect core cellular processes supporting growth. Together, these point to coordinated neural and gonadal development, justifying the label.","confidence":"High","size":23,"edges":8,"triangles":5,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0035264","count":9},{"id":"GO:0007568","count":9},{"id":"GO:0007420","count":9},{"id":"GO:0051260","count":9}]},{"hash":"768633594074941334","title":"ER Protein Folding and Unfolded Protein Response","description":"This cluster centers on ER protein quality control, including protein folding, processing, and the unfolded protein response, with additional oxidative stress connections; a few terms appear unrelated and may reflect multifunctional proteins.","confidence":"Medium","size":23,"edges":74,"triangles":15,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0016485","count":2},{"id":"GO:0003407","count":2},{"id":"GO:0030968","count":1},{"id":"GO:0072389","count":1},{"id":"GO:0043335","count":1}]},{"hash":"1941666826790607469","title":"Developmental Growth Signaling and Cell Cycle","description":"This cluster combines GO terms pointing to development and proliferation (positive regulation of cell population proliferation, mitotic cell cycle, cell division, multicellular organism development, skin development) with signaling and regulatory activities (GTPase and kinase regulation, protein autophosphorylation) and supporting processes like mRNA transport and hypoxia response, suggesting a group of proteins coordinating growth, development, and cell cycle progression.","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0008284","count":9},{"id":"GO:0043547","count":8},{"id":"GO:0051028","count":8},{"id":"GO:0031954","count":8},{"id":"GO:0071902","count":8}]},{"hash":"897553106820910612","title":"Ion and metabolite transmembrane transporters","description":"The cluster is mainly enriched for transmembrane transport GO terms across the plasma membrane, including calcium and potassium ion transport, xenobiotic and vitamin transport, which point to transporter-like functions. A few other terms (cell cycle, endothelial-related processes) are present but less central, suggesting the core theme is membrane transport of ions and small molecules.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098703","count":3},{"id":"GO:0006855","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0071805","count":2}]},{"hash":"1557661438494129866","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms for ubiquitination and ubiquitin-dependent proteasomal degradation (including general ubiquitination, SCF-dependent proteasomal degradation, and autoubiquitination), pointing to components of the ubiquitin-proteasome system. Some included terms reference related signaling and physiological processes (TNF signaling, T cell homeostasis, vitamin D response, SA node regulation), but the central theme is protein tagging and degradation via ubiquitin pathways.","confidence":"High","size":23,"edges":2,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0016567","count":7},{"id":"GO:0000083","count":6},{"id":"GO:0033280","count":6},{"id":"GO:0051865","count":6}]},{"hash":"1958556475980742882","title":"Oxidative Stress Response & Protein Quality Control","description":"The cluster is enriched for cellular oxidant detoxification, redox homeostasis, and protein folding/repair processes, pointing to a coordinated proteostasis and oxidative stress response. Some terms touch on nuclear regulation or viral processes, but the dominant theme is redox balance and protein quality control (ER folding and repair).","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0043388","count":2},{"id":"GO:0030091","count":2},{"id":"GO:0046826","count":2}]},{"hash":"727578628154636748","title":"Unknown","description":"The top GO terms are very diverse, including glycolytic and fructose metabolic processes, glycolytic regulation, brain development, cobalamin biosynthesis, cell division and mitotic cell cycle, histone deacetylation, cobalt ion response, and respiratory burst. There\u2019s no single cohesive biological theme linking these functions, and the minimal connectivity (one edge, no triangles) suggests this cluster may reflect a mixture of unrelated processes or a computational artifact rather than a real shared function.","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006096","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1892185675455091443","title":"Developmental regulation and vesicle trafficking","description":"The cluster centers on developmental processes across tissues (substantia nigra, lung, multicellular development) and transcriptional regulation (DNA-templated transcription, negative regulation of transcription by RNA Pol II), with supporting roles in intracellular transport (ER to Golgi) and cytoskeletal remodeling (actin depolymerization). This suggests proteins linked to coordinating development with gene expression and cellular trafficking.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021762","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":3}]},{"hash":"1853067319545120703","title":"Heart development and SA node signaling with angiogenesis","description":"Reasoning: Several top GO terms point to heart morphogenesis (right atrium), SA node signaling, and endothelial differentiation with angiogenesis, plus Notch pathway involvement in heart field development. Actin filament bundle assembly aligns with cardiac muscle structure. While there are a couple outliers (NF-kappaB sequestration and prostate development), the dominant theme is heart and vascular development and cardiac electrical activity.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003213","count":3},{"id":"GO:1903589","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0086070","count":3},{"id":"GO:0007253","count":3}]},{"hash":"2086571981845393577","title":"Translation and tRNA processing","description":"The Top Terms highlight translation (GO:0006412) and tRNA processing (GO:0008033), pointing to a core theme around protein synthesis and RNA maturation. Other terms (lipid/plant biosynthesis, pollen development, xenobiotic response, synaptic regulation) occur but are sparse and likely reflect annotation noise or multifunctionality. With no edges and a mix of unrelated terms, the most representative function is the translation/RNA processing machinery represented by the cluster.","confidence":"Low","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0006695","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0009688","count":2}]},{"hash":"283973497556230770","title":"Ciliary axoneme assembly and motility","description":"The GO terms point to assembly and movement of cilia/axonemes, especially in the sperm flagellum, including associated microtubule post-translational modifications (polyglycylation, polyglutamylation) and regulation of axon extension. This suggests a cohesive cluster focused on cilium/flagellum biogenesis and motility, with possible links to broader developmental signaling via ciliary pathways.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007288","count":2},{"id":"GO:0003351","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0018094","count":2},{"id":"GO:1905419","count":2}]},{"hash":"727249644429026131","title":"GPI-anchored and vacuolar protein sorting","description":"This cluster centers on post-translational modification to attach GPI anchors, along with vacuolar organization/processing and localization to the cell surface, suggesting a shared role in secretory/vacuolar trafficking and membrane anchoring. Some terms (e.g., stomatal patterning, renal system process) are broader or cross-species annotations, but the dominant pattern points to vesicular sorting and membrane attachment pathways.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016255","count":2},{"id":"GO:0010447","count":1},{"id":"GO:1990019","count":1},{"id":"GO:0006624","count":1},{"id":"GO:0034394","count":1}]},{"hash":"1271419571050347566","title":"Unknown","description":"These terms span membrane trafficking, cytoskeletal remodeling, stress response, development, and autophagy with no single prevailing process, so there is no cohesive theme linking the proteins.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903778","count":1},{"id":"GO:0071963","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0098886","count":1},{"id":"GO:0048711","count":1}]},{"hash":"1576066402699712813","title":"Transmembrane Transport of Small Molecules","description":"The set of proteins is enriched for GO terms describing transmembrane transport of various small molecules (arabinose, nitrate, nitrite, phosphate, xenobiotics) and vesicular neurotransmitter loading, as well as related detoxification processes. This shared theme points to membrane transport activity as the unifying function of the cluster, hence the name.","confidence":"High","size":22,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0042891","count":2}]},{"hash":"490502989063719831","title":"Transmembrane Solute Transporters","description":"The top GO terms mainly reflect transmembrane transport of diverse small molecules and nutrients (sialic acid, methotrexate, phosphate, uracil, thiamine, cytosine, amino acids, etc.), suggesting the cluster is composed of membrane transporter proteins that mediate solute movement. A single outlier term (pollen exine formation) is peripheral to the main theme. Overall this name captures the shared function of the cluster.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":2},{"id":"GO:0051958","count":2},{"id":"GO:0035435","count":2},{"id":"GO:1903791","count":1},{"id":"GO:0015888","count":1}]},{"hash":"379021792072017293","title":"Vacuolar amino acid and ion transport","description":"The top GO terms show clear enrichment for transport into the vacuole of various amino acids (histidine, tyrosine, glutamate, proline) and for ion transport and responses (potassium ion starvation, lithium transport), suggesting a cluster centered on vacuolar import and ion homeostasis. A few outlier terms (chiasma assembly, blastocyst formation, ubiquitin-dependent ERAD) may reflect annotation noise or broader, less connected functions. Confidence is moderate because the vacuolar transport signal is strong, but the presence of non-related terms reduces certainty. ","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051026","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001825","count":2},{"id":"GO:0051365","count":1},{"id":"GO:0048829","count":1}]},{"hash":"1107301988224240161","title":"Cell Cycle and Developmental Gene Expression","description":"Based on the top GO terms, the cluster is enriched for core DNA metabolism and cell division (DNA replication, DNA-templated transcription, mitotic cell cycle) together with several developmental processes (forebrain development, neural tube closure, skeletal system development). This points to a cohesive theme of proliferative/gene-expression programs guiding development, with stress-related terms providing contextual regulation rather than a primary function. Therefore, this label best captures the central function of the cluster.","confidence":"Medium","size":22,"edges":25,"triangles":6,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":12},{"id":"GO:0006351","count":9},{"id":"GO:0051301","count":8},{"id":"GO:0071276","count":8},{"id":"GO:0006349","count":8}]},{"hash":"912747289254411877","title":"APC/C-Mediated Cell Cycle Control","description":"The top GO terms cluster around mitotic cell cycle, DNA replication, cell division, and especially APC/C-dependent catabolic processes with K11-linked ubiquitination, indicating regulation of mitosis by ubiquitin-mediated proteolysis. Peripheral terms like innate immune response and cadmium ion response may reflect broader stress signals or annotation noise but do not dominate the cluster.","confidence":"Medium","size":22,"edges":8,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0045087","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0031145","count":3},{"id":"GO:0006260","count":3}]},{"hash":"965367782836953140","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":211,"triangles":1267,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009436","count":10},{"id":"GO:0042853","count":10},{"id":"GO:0007219","count":10},{"id":"GO:0097053","count":10},{"id":"GO:0051591","count":9}]},{"hash":"363085469797798133","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032837","count":1},{"id":"GO:0090307","count":1},{"id":"GO:0060236","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0032066","count":1}]},{"hash":"877717400785115167","title":"Regulation of transcription, splicing, and cell cycle","description":"The cluster features multiple regulatory GO terms, including negative regulation of protein kinase activity and G1/S transition, plus regulation of alternative splicing and transcription elongation. This points to a cohesive theme of controlling gene expression and cellular proliferation, rather than structural roles. Some developmental terms appear but still reflect Regulation of differentiation processes, reinforcing the regulatory nature of the cluster.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0048316","count":1},{"id":"GO:0014904","count":1}]},{"hash":"2229280574788049637","title":"Ribosome biogenesis and RNA modification","description":"The proteins are enriched for rRNA and tRNA pseudouridine synthesis, ribosome biogenesis, and translation, pointing to involvement in forming and modifying ribosomes and supporting protein synthesis; the additional metabolic terms are likely ancillary. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000455","count":2},{"id":"GO:0031119","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":2}]},{"hash":"1083568136318759319","title":"Cardiac muscle development and Wnt signaling","description":"This cluster prominently features GO terms tied to heart and muscle formation and remodeling, including heart development, cardiac muscle hypertrophy in response to stress, and myotube cell development, alongside a Wnt signaling pathway with calcium modulation. These suggest a coherent theme of cardiac and skeletal muscle differentiation and development, possibly coordinated by Wnt/calcium signaling. Other terms like ribosomal export, mitochondrial assembly, and transcription are general cellular processes that may accompany differentiation, while a few terms (seed development, neuroendocrine differentiation) appear less related and likely reflect annotation noise. Overall, the dominant function appears to be cardiac and muscle development with signaling involvement.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0007223","count":2},{"id":"GO:0000055","count":1}]},{"hash":"506444486628264476","title":"Developmental gene expression and cell cycle","description":"The top GO terms cluster around transcription and cell division (DNA-templated transcription, cell division) and protein homooligomerization, with neural development terms like forebrain development and neural tube closure suggesting developmental roles. Additional terms for ER-Golgi transport and microtubule severing point to cytoskeletal dynamics and trafficking, which are important in developing tissues. Overall, the cluster seems to reflect genes involved in developmental gene regulation linked to proliferative and cytoskeletal processes rather than a single pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0071276","count":6},{"id":"GO:0006349","count":6}]},{"hash":"1692208355283262291","title":"Splicing and Transcription Regulation","description":"The top GO terms point to RNA processing (spliceosomal assembly and catalytic spliceosome formation) and transcription-related regulation (DNA-templated transcription and its regulation). Additional terms touch on chromatin modification and deubiquitination, which are linked to gene expression control. Taken together, the cluster appears to be involved in RNA processing and regulation of transcription, with supporting chromatin-level regulatory roles, rather than a single coherent, narrow function. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0000349","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0032502","count":1},{"id":"GO:0030912","count":1}]},{"hash":"1424514743127606983","title":"Neural development and synapse formation","description":"Based on the GO terms, this cluster is enriched for neural development processes such as axonogenesis, corpus callosum development, and positive regulation of synapse assembly, along with neuronal signaling (GPCR signaling) and mechanotransduction; while heart development appears, the strongest collective signal is toward neural connectivity and synaptic formation, making this label representative of the cluster\u2019s function.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0007186","count":3},{"id":"GO:0048681","count":3},{"id":"GO:0051965","count":3}]},{"hash":"776182287049215476","title":"Development and differentiation regulation","description":"This cluster includes GO terms centered on developmental processes (seed, myotube, dendrite, placental morphogenesis) and differentiation control (regulation of muscle differentiation, T cell differentiation) along with transcriptional and epigenetic regulation (DNA-templated transcription elongation, histone H3-K14 acetylation). The dominant theme is development coupled with regulatory control of cell fate, though a toxin-response term is a minor outlier. Confident that the label captures the core function of the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048316","count":2},{"id":"GO:0014904","count":2},{"id":"GO:1904772","count":2},{"id":"GO:0006354","count":2},{"id":"GO:1900006","count":2}]},{"hash":"1131608100065565620","title":"Chloroplast Organization and Protein Import","description":"The cluster\u2019s terms are dominated by chloroplast-related biology: de-etiolation, chloroplast organization, and positive regulation of protein import into the chloroplast stroma, suggesting a cohesive theme around chloroplast biogenesis and function. Additional terms related to transport and stress (xenobiotic transport, phosphate transport, osmotic stress) may reflect chloroplast-associated processes or general stress responses, but the chloroplast-focused terms provide the strongest link. Confidence: Medium.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009704","count":1},{"id":"GO:0009658","count":1},{"id":"GO:1904216","count":1},{"id":"GO:0090197","count":1},{"id":"GO:0005975","count":1}]},{"hash":"431999721161030254","title":"Unknown","description":"The Top Terms are diverse and do not point to a single shared function. They span xylan catabolism, CNS myelin maintenance, mitochondrial inheritance, unsaturated fatty acid biosynthesis, nitric oxide biosynthesis, nitrate assimilation, ergosterol biosynthetic regulation, sebaceous gland differentiation, mannosyl-inositol phosphorylceramide metabolism, and UTP catabolism, among others. With 13 edges and no triangles, there is no clear cohesive pathway or cellular process linking these proteins, so a specific, representative label cannot be confidently assigned.","confidence":"","size":21,"edges":13,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":1},{"id":"GO:0032286","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0006809","count":1}]},{"hash":"1039642348275374871","title":"Stress-Driven Cell Fate and Survival","description":"This cluster centers on stress-responsive processes that influence cell fate decisions and survival, including cell cycle control, mitophagy and apoptosis, and sporulation, along with nutrient signaling and metabolic pathways. The mix suggests coordinated responses to cellular stress that determine whether the cell progresses, halts, or switches to survival programs.","confidence":"Medium","size":21,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0070373","count":2},{"id":"GO:0061734","count":2},{"id":"GO:0006915","count":2}]},{"hash":"615290688847457941","title":"Protein Homeostasis and Ribosome Biogenesis","description":"Based on the GO terms, the strongest signal is ribosome biogenesis and protein synthesis-related processes (ribosomal large subunit biogenesis, maturation of LSU-rRNA, translation) complemented by protein quality control activities (ubiquitination, ERAD, protein targeting). There are additional, less-connected terms like DNA replication and meiosis and mitochondrial inheritance, but they do not outweigh the core theme of ribosome assembly and protein turnover. This suggests a cluster centered on maintaining and producing cellular proteins rather than a single, narrow pathway.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0090394","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006311","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1943814477086521181","title":"Photosynthesis and light-stress response","description":"This cluster's terms cluster around photosynthesis and light-related processes (photosynthesis, light harvesting in PSII, response to red/high light), with oxidative stress signaling and regulatory processes like sumoylation and transcription, suggesting a group of proteins involved in light energy capture and light-induced stress management in plant/chloroplast contexts.","confidence":"Medium","size":21,"edges":23,"triangles":4,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0016925","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0051901","count":2},{"id":"GO:0071222","count":2}]},{"hash":"386777055420737263","title":"Bacterial Translation and Secondary Metabolism","description":"This cluster shows strong translation-related terms (translation, translational termination, tRNA methylation) alongside biosynthetic processes for antibiotics and vitamins (antibiotic biosynthetic process, menaquinone and biotin biosynthesis) and related responses. The combination suggests proteins tied to core protein synthesis together with enzymes for secondary metabolite biosynthesis in bacteria, hence a label focused on both translation and metabolite production.","confidence":"Medium","size":21,"edges":183,"triangles":964,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0009234","count":3}]},{"hash":"1982643044224117444","title":"Ciliary Assembly and Photoreceptor Trafficking","description":"The strongest GO terms are non-motile cilium assembly and protein localization to photoreceptor outer segment, pointing to a core role in ciliogenesis and trafficking to the photoreceptor outer segment. Other terms (innate immune response, defense against virus, metabolism) appear more incidental noise relative to these core ciliary/retinal processes, so the cluster is best labeled around cilia/photoreceptor biology with some annotation noise. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905515","count":3},{"id":"GO:0006478","count":2},{"id":"GO:0051348","count":2},{"id":"GO:0045087","count":2},{"id":"GO:1903071","count":2}]},{"hash":"822148166396461153","title":"Nuclear gene expression and ER protein folding","description":"The cluster\u2019s top terms center on nuclear processes (DNA-templated transcription, DNA replication, regulation of protein export from the nucleus) and ER protein folding, with additional signals for redox homeostasis and cellular stress responses (amino acid starvation, hormone/growth factor stimuli). This suggests a core theme around coordinating gene expression with protein quality control in the endoplasmic reticulum, with some peripheral developmental signaling contexts.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0046826","count":8},{"id":"GO:0045454","count":6},{"id":"GO:0034198","count":5},{"id":"GO:0006260","count":5}]},{"hash":"1472977141134939404","title":"Plant Photosynthesis and Chlorophyll Regulation","description":"The cluster is dominated by photosynthesis-related GO terms, including photosynthesis and negative regulation of chlorophyll biosynthetic processes, pointing to chloroplast/light-energy capture functions in plants. Some terms are obsolete or reflect broader eukaryotic processes (cell cycle, histone modification), suggesting annotation noise, but the primary signal centers on chlorophyll metabolism and photosynthetic activity.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":7},{"id":"GO:0031145","count":4},{"id":"GO:0051348","count":4},{"id":"GO:1903071","count":4},{"id":"GO:0016576","count":4}]},{"hash":"1854772912671141328","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":2},{"id":"GO:0061158","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0051865","count":2},{"id":"GO:2000059","count":2}]},{"hash":"827357422784067762","title":"Actinobacterial Sporulation and Stress-Response","description":"This cluster centers on transcriptional regulation and sporulation, with multiple stress-response processes (starvation, UV, acidic pH, hypoxia signaling) and a hallmark actinobacterial feature, mycothiol biosynthesis, linking development with stress adaptation in Actinobacteria. A neuron projection extension term may be incidental noise. ","confidence":"High","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0010125","count":2},{"id":"GO:1990138","count":1}]},{"hash":"592147042365452925","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0010796","count":2},{"id":"GO:2000300","count":2}]},{"hash":"1036247113430357993","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0021691","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0009245","count":1},{"id":"GO:0046677","count":1}]},{"hash":"1767549782647985189","title":"Ribosome biogenesis and RNA processing","description":"The terms show a strong focus on ribosome assembly (90S preribosome), rRNA and tRNA processing, and translation, indicating proteins in this cluster participate in ribosome biogenesis and RNA maturation rather than unrelated pathways.","confidence":"High","size":21,"edges":93,"triangles":113,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0000188","count":2},{"id":"GO:0034463","count":2},{"id":"GO:0006412","count":2}]},{"hash":"18464302972178165","title":"Ribosome Biogenesis and RNA Methylation","description":"This cluster is dominated by GO terms for ribosomal subunit biogenesis (small and large) and multiple RNA modification processes (tRNA methylation, rRNA methylation, RNA capping, and guanosine methylations), indicating proteins involved in ribosome assembly and RNA processing; observed cell size/endoreduplication terms likely reflect downstream growth effects.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0030488","count":1},{"id":"GO:0032775","count":1},{"id":"GO:0006479","count":1}]},{"hash":"1051813784814295150","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by translation and ribosome biogenesis terms (translation, ribosomal large subunit biogenesis, rRNA maturation), suggesting a core function in ribosome assembly and protein synthesis. Some cell-cycle and trafficking terms appear as secondary signals, but the strongest signal is ribosome-related.","confidence":"High","size":21,"edges":18,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0009556","count":3},{"id":"GO:0007130","count":3}]},{"hash":"724170893877155598","title":"Nuclear import and nuclear pore assembly","description":"This cluster is dominated by GO terms related to nuclear transport and nuclear pore assembly: NLS-bearing protein import into the nucleus, ribosomal protein import into the nucleus, and nuclear pore complex assembly. Additional terms point to regulation of GTPase activity and protein desumoylation, which support regulatory control over transport and protein turnover. A few terms touch on ciliary transport and oocyte localization, but the core theme appears to be nuclear import machinery and its regulation.","confidence":"High","size":21,"edges":25,"triangles":8,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0006607","count":7},{"id":"GO:0035735","count":5},{"id":"GO:0006610","count":5},{"id":"GO:0060188","count":5}]},{"hash":"950006253793133015","title":"Mitotic division and spindle dynamics","description":"This cluster is enriched for cell division and mitosis-related GO terms (cell division, mitotic sister chromatid cohesion, microtubule severing) and spindle-associated processes, suggesting a cohesive role in mitosis and spindle dynamics. Additional terms on vesicle trafficking and mRNA transport may reflect broader cellular logistics that accompany division, but the dominant signal centers on mitotic progression. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":10},{"id":"GO:0043547","count":8},{"id":"GO:0006888","count":8},{"id":"GO:0051260","count":8},{"id":"GO:0051028","count":8}]},{"hash":"1056891075063370197","title":"Nuclear RNA processing and ribosome biogenesis","description":"Predominant themes are nuclear RNA maturation and ribosome biogenesis: mRNA capping, RNA Pol II transcription regulation, RNA and rRNA methylation, ribosome biogenesis, and export of the small ribosomal subunit from the nucleus. These co-occur with cell cycle\u2013related terms, suggesting a proliferation-relevant RNA processing/ribosome production program.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006370","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0000056","count":3},{"id":"GO:0000747","count":3}]},{"hash":"1447171623441706726","title":"Unknown","description":"The top GO terms cover a wide range: stress response to cadmium, transcription, cyclic nucleotide biosynthesis, fungal pseudohyphal and invasive growth, cell proliferation regulation, skeletal muscle and nervous system development, DNA replication, and immune signaling. This scattered mix suggests no single cohesive function or pathway linking the proteins, and there are no edges among them, making a concise, meaningful label infeasible.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009190","count":3},{"id":"GO:0007124","count":3},{"id":"GO:0008285","count":3}]},{"hash":"1510915438455000543","title":"Brain development and dendrite extension","description":"The top GO terms are dominated by brain development and positive regulation of dendrite extension, suggesting the cluster is centered on neuronal development and dendritogenesis. While other terms (e.g., rRNA maturation, mRNA recognition, cadmium response) appear, they are secondary or incidental, so the strongest representative theme is neuronal development and dendrite growth.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0000209","count":2},{"id":"GO:1903861","count":2},{"id":"GO:0000466","count":1},{"id":"GO:0008283","count":1}]},{"hash":"2167280832975417191","title":"Vitamin and cofactor biosynthesis","description":"The GO terms highlight biosynthesis of vitamins and cofactors (menaquinone, cobalamin, biotin) and related metabolic pathways, with some redox detox signals. This points to a cohesive function in cofactor production and metabolism.","confidence":"High","size":21,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0046835","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0009102","count":3}]},{"hash":"511255825556887619","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":6},{"id":"GO:0097171","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009243","count":4},{"id":"GO:0017000","count":4}]},{"hash":"357371215342693154","title":"Nuclear transcription and DNA replication machinery","description":"The cluster centers on transcription-related processes (DNA-templated transcription, RNA Pol II regulation) and core replication components (GINS assembly, DNA replication, mitotic replication initiation, DNA strand elongation), with accompanying RNA processing terms (spliceosome assembly, mRNA/tRNA splicing). This suggests a cohesive nuclear module coordinating transcription, RNA processing, and DNA replication. The viral process term likely reflects incidental annotations rather than a defining function of the cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000244","count":1},{"id":"GO:0045292","count":1}]},{"hash":"1447408241174832241","title":"Neuroimmune Signaling and Innate Immunity","description":"The top GO terms are dominated by innate immune processes (innate immune response, defense against Gram-positive bacteria, TLR2 signaling, dendritic cell cytokine production, regulation of inflammatory response, interferon production) and GPCR-related signaling, with a few terms pointing to neuronal signaling (axonogenesis, cellular response to dopamine). This suggests a cluster enriched for innate immune signaling components that may intersect with neuroimmune or neuromodulatory pathways, hence a label that captures both aspects. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:0007409","count":6},{"id":"GO:0050830","count":6},{"id":"GO:0045087","count":5},{"id":"GO:0002730","count":5}]},{"hash":"556101536154696229","title":"Histone modification and nucleosome assembly","description":"The top GO terms cluster around histone post-translational modifications (H3K4/K27 methylation and acetylation) and nucleosome assembly, coupled with DNA-templated transcription. This indicates an epigenetic/regulatory theme where chromatin state modulates transcription, with repair-related chromatin dynamics as a secondary connection.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:2001040","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0006334","count":2}]},{"hash":"2083533372932930996","title":"Chloroplast transcription and aromatic amino acid biosynthesis","description":"The terms point to plastid-associated processes: prokaryote-like transcription (DNA-templated transcription, transcription antitermination), DNA replication, redox homeostasis, photosynthesis, and the shikimate pathway (chorismate and aromatic amino acid biosynthesis). This combination strongly suggests chloroplast/plastid gene expression linked to metabolic pathways producing aromatic amino acids, with photosynthetic context. ","confidence":"High","size":20,"edges":87,"triangles":142,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0031564","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0070389","count":2}]},{"hash":"1150149537756025997","title":"Spliceosome-Mediated Splicing and Translation Regulation","description":"The top GO terms point to spliceosome-driven mRNA splicing (e.g., GO:0000380, GO:0045292, GO:0000381) and regulation/assembly steps around translation initiation (e.g., GO:0006446, GO:0001731, GO:0002188). Although a few terms are obsolete, the dominant signals suggest a cluster of proteins involved in RNA processing via the spliceosome and in controlling translation initiation/reinitiation. The label reflects both themes without overcommitting to a single function.","confidence":"Medium","size":20,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":3},{"id":"GO:1903586","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006446","count":2}]},{"hash":"11910457277722970","title":"Chloroplast biogenesis and photosynthetic regulation","description":"The terms point to chloroplast/thylakoid functions (granum assembly, thylakoid membrane organization), light-response processes (nonphotochemical quenching, karrikin response), and redox homeostasis, indicating a cluster centered on chloroplast development and regulation of photosynthesis. Some cofactor biosynthesis terms (riboflavin, cobalamin) can be plastid-associated, reinforcing a plastid-related metabolic theme.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045454","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0090391","count":1}]},{"hash":"1118994788755233963","title":"Chloroplast Photosynthesis and Redox Homeostasis","description":"The top GO terms center on photosynthesis, redox balance, oxidative stress response, and detoxification, with supporting translation and redox regulation terms, suggesting a chloroplast-focused cluster involved in light-driven energy production and redox defense. The single neural crest migration term is likely noise. ","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0003147","count":1}]},{"hash":"1379436220417076714","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The top GO terms indicate strong enrichment for ubiquitination and ubiquitin-dependent proteasomal degradation, including SCF-dependent pathways, ERAD-related tagging, polyubiquitination, and autoubiquitination. This points to a cluster focused on tagging proteins for destruction and their clearance by the proteasome, with a few peripheral terms (ribosome biogenesis, apoptotic regulation) likely reflecting broader cellular turnover and stress responses. ","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0000209","count":4},{"id":"GO:0051865","count":4}]},{"hash":"1888344890597027923","title":"Chloroplast Photosynthesis and Redox Defense","description":"The cluster is dominated by photosynthesis-related GO terms (photosynthesis; photosynthetic electron transport in photosystem I) and redox/oxidant detoxification terms, suggesting a chloroplast-focused function with redox balancing. A few translation/spliceosome-related terms appear but are likely incidental, not defining the cluster\u2019s main role. Therefore, the label emphasizes chloroplast photosynthesis with redox defense as the core theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009773","count":1},{"id":"GO:0006438","count":1}]},{"hash":"2237566632510986719","title":"Ribosome biogenesis and cell growth","description":"This cluster is enriched for GO terms related to cell division, ribosome biogenesis, and TORC1 signaling, all central to promoting cell growth and proliferation. The presence of mRNA transport and GTPase activity regulation supports coordinated control of translation and growth, while the cadmium response reflects a general stress context rather than defining the core theme.","confidence":"High","size":20,"edges":22,"triangles":6,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1599200455038068852","title":"Unknown","description":"The GO terms span cellular stress responses (cadmium, hydrogen peroxide), basic metabolism (pyruvate, gluconeogenesis), ion transport, immune/homeostatic processes, and protein modification, with no single cohesive function tying them together. The cluster also has no edges (edges: 0), suggesting a heterogeneous or non-connected set rather than a unified pathway. Therefore, Unknown with None confidence. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0006090","count":1}]},{"hash":"1991819554207249549","title":"Ribosome biogenesis and rRNA processing","description":"The cluster is dominated by GO terms related to ribosome biogenesis and RNA modification/processing (e.g., rRNA and snRNA pseudouridine synthesis, rRNA processing), suggesting a shared role in nuclear ribosome assembly. While a few terms touch on telomere maintenance and DNA replication, these are much less represented, so the primary function inferred is ribosome biosynthesis and RNA maturation.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0031120","count":1},{"id":"GO:0007004","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0031118","count":1}]},{"hash":"514038863746624401","title":"Bacterial cell wall biosynthesis and xenobiotic stress response","description":"These proteins appear to cluster around bacterial-type functions: cell wall organization/biosynthesis, antibiotic biosynthetic potential, and responses to xenobiotics and heavy metals (cadmium, lead). The presence of these terms suggests a theme of cell envelope assembly coupled with environmental stress adaptation. An outlier term (lung development) may be an annotation artifact, but the core signal centers on bacterial metabolism and defense against xenobiotics/metals.","confidence":"Medium","size":20,"edges":12,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0030324","count":3},{"id":"GO:0035690","count":3}]},{"hash":"586826657483283893","title":"Steroid Hormone Signaling and Chromatin Remodeling","description":"Top GO terms point to nuclear receptor\u2013mediated glucocorticoid signaling and regulation of DNA-templated transcription, coupled with chromatin remodeling (nucleosome disassembly, chromatin maintenance) and reproductive development (uterus morphogenesis, estradiol regulation, mammary gland proliferation). Some neural development terms (gliogenesis, dendritic spine development) suggest broader hormone-responsive roles. This combination supports a cohesive theme of steroid hormone\u2013driven transcriptional regulation intertwined with chromatin dynamics and developmental processes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:1990966","count":2},{"id":"GO:0042921","count":1},{"id":"GO:0033601","count":1},{"id":"GO:0006337","count":1}]},{"hash":"475621348656016558","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":7,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009243","count":2},{"id":"GO:0042351","count":2},{"id":"GO:0006012","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0009242","count":2}]},{"hash":"197908150453658186","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0051592","count":1},{"id":"GO:0007512","count":1}]},{"hash":"1464883586550958426","title":"Golgi glycosylation and sugar transport","description":"The top terms point to Golgi-associated processes: import of GDP-fucose and UDP-glucose into the Golgi lumen, and protein O-linked glycosylation via fucose, along with related transmembrane sugar transport terms. While there are a couple of nuclear-related terms (nucleosome assembly and DNA-templated transcription), the strong signal is for Golgi-localized glycosylation and sugar transport functions, suggesting a coherent theme around protein modification in the Golgi. ","confidence":"Medium","size":19,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035436","count":2},{"id":"GO:0036085","count":2},{"id":"GO:0036066","count":2}]},{"hash":"518341244923841600","title":"TLR-Driven Innate Immune Signaling","description":"The top GO terms are centered on toll-like receptor signaling and innate immune functions, including TLR2 signaling, MyD88-independent TLR signaling, innate immune response, cytokine production in dendritic cells, interferon production, and inflammatory regulation. These together point to a cohesive theme of innate immune sensing and downstream cytokine responses. A few terms (dopamine response, nipple morphogenesis) are peripheral and may reflect broader roles but do not override the core immune signaling theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:0045087","count":5},{"id":"GO:0002730","count":5},{"id":"GO:0007186","count":5},{"id":"GO:0050729","count":5}]},{"hash":"1858281028466104093","title":"Plant Development and Transcriptional Regulation","description":"The cluster centers on plant development terms (seed, bract, multicellular organism development) and transcriptional control (DNA-templated transcription and its regulation). Hormone signaling (ABA, auxin) and related processes (wax biosynthesis, defense response, and chitin response) suggest a developmental regulatory module in plants with hormonal and defense context.","confidence":"Medium","size":19,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0048316","count":1},{"id":"GO:0010186","count":1},{"id":"GO:1904276","count":1},{"id":"GO:0060774","count":1},{"id":"GO:0010432","count":1}]},{"hash":"642196308298019714","title":"Proteostasis and vesicle trafficking","description":"The top GO terms cluster around protein quality control and membrane trafficking: ER unfolded protein response, aggresome and inclusion body assembly, and SNARE complex disassembly point to proteostasis and vesicle trafficking dynamics; dephosphorylation may regulate these processes. Some terms (brain development, UV-damage repair) seem less related, likely reflecting noise. Overall, the dominant theme is protein homeostasis with trafficking aspects.","confidence":"Medium","size":19,"edges":12,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016311","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0070914","count":3},{"id":"GO:0030420","count":3},{"id":"GO:0018279","count":3}]},{"hash":"795383080848203387","title":"RNA processing and gene expression regulation","description":"The cluster centers on core gene expression machinery and RNA processing: translation initiation and reinitiation, transcription, mRNA splicing, and RNA methylation, plus ncRNA-mediated gene silencing. Developmental terms like brain development and growth suggest regulation of expression in multicellular contexts. Taken together, these terms point to a cohesive theme of RNA processing and gene expression control.","confidence":"High","size":19,"edges":31,"triangles":0,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0009408","count":2}]},{"hash":"891076067272135021","title":"Multisystem Organogenesis","description":"Most of the GO terms point to morphogenesis and development across multiple organ systems (digestive tract, mammary gland, bile ducts, trachea glands, peripheral nervous system, endocardial cells, embryonic genitalia). The few other terms (tRNA methylation, IgA isotype switching) are minor and not clearly tied to a single function, so the overall cluster suggests a broad developmental program rather than a specific pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048298","count":2},{"id":"GO:0030488","count":1},{"id":"GO:2000726","count":1},{"id":"GO:0048546","count":1},{"id":"GO:0007422","count":1}]},{"hash":"1987030954452214253","title":"Plant Development and Transcription Regulation","description":"This cluster centers on plant developmental processes (seed and bract development, multicellular organism development) and transcriptional control (DNA-templated transcription and its regulation), with supporting hormonal signaling (ABA) and wax biosynthesis terms. A few defense-related terms (response to chitin) appear but do not outweigh the developmental/transcription theme, suggesting a cohort of proteins involved in plant development with transcriptional regulation rather than a single specific pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048316","count":1},{"id":"GO:0010186","count":1},{"id":"GO:1904276","count":1},{"id":"GO:0060774","count":1},{"id":"GO:0010432","count":1}]},{"hash":"543569113688831821","title":"RNA processing and decay","description":"This cluster is enriched for mRNA maturation and decay processes (capping, splicing, and deadenylation-dependent/independent decay) and includes translation, indicating a core RNA metabolism module; a single DNA repair term is present but not central.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0000288","count":2}]},{"hash":"170462335557324950","title":"RNA Splicing and Processing","description":"The strongest signal among the top terms centers on RNA metabolism: RNA splicing, spliceosomal complex assembly, and mRNA processing, with additional tRNA modification; other terms like meristem growth and DNA repair are present but less cohesive, suggesting the core functionrelated cluster is RNA processing-related.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008380","count":1},{"id":"GO:0007629","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0097056","count":1}]},{"hash":"807829822503425349","title":"Light-Responsive Photosynthesis Proteins","description":"This cluster is defined by light-related GO terms (response to blue/red/far-red light, high/low light, UV-A) and photosynthesis terms (photosynthesis, light harvesting in photosystem II, nonphotochemical quenching), suggesting these proteins participate in light perception, photoprotection, and photosynthetic light harvesting.","confidence":"High","size":19,"edges":98,"triangles":214,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0071486","count":2},{"id":"GO:0009769","count":2},{"id":"GO:0010114","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0071492","count":2}]},{"hash":"1631773579748543813","title":"DNA Damage Response and Cell Cycle Regulation","description":"The top GO terms point to DNA repair processes (e.g., homologous recombination, single-strand annealing) and mitotic cell cycle control (G1/S transition, G2 DNA damage checkpoint), suggesting proteins linked to genome integrity maintenance and cell-cycle regulation. A few insulin signaling\u2013related terms appear but do not define the cluster\u2019s main theme, so the core is DNA damage response and cell cycle control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046627","count":1},{"id":"GO:0042733","count":1},{"id":"GO:0038016","count":1},{"id":"GO:0051898","count":1},{"id":"GO:0046325","count":1}]},{"hash":"932796299259534536","title":"Chromatin remodeling and histone modification","description":"The cluster\u2019s top GO terms cluster around chromatin biology: rDNA heterochromatin formation, chromatin remodeling, histone H2A deubiquitination, and multiple methylation processes (N-terminal glycine methylation, lysine dimethylation, rRNA methylation). This points to an epigenetic regulation theme as the core function, with a few terms related to plant secondary metabolism and stress responses suggesting additional, broader regulatory roles. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0018013","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0018027","count":3},{"id":"GO:0043044","count":3}]},{"hash":"314224866289704031","title":"Cytoskeletal remodeling and muscle/neural development","description":"The terms highlight actin filament bundle assembly and intracellular transport, alongside myotube and dendrite development and muscle differentiation regulation, suggesting a common theme of cytoskeletal dynamics guiding muscle and neural development. Some terms are obsolete or broad, indicating possible annotation noise, but the dominant signal points to cytoskeletal organization linked to development.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0032088","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0048316","count":1}]},{"hash":"327264032257795897","title":"Vitamin and metabolite biosynthesis","description":"The top GO terms show a pattern of biosynthetic and metabolic processes (menaquinone, thiamine, biotin, glycogen, and fatty acid biosynthesis, plus amino acid metabolism) indicating a theme of production and processing of various metabolites; a non-metabolic term (box C/D snoRNP assembly) is present but does not dominate, so the cluster reflects diverse metabolic biosynthesis activities.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009234","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0000492","count":2}]},{"hash":"721171557001423379","title":"tRNA modification and RNA processing cluster","description":"The top GO terms are dominated by RNA-related activities, including tRNA wobble uridine modification, tRNA methylation, and mRNA processing, with additional methylation activity on arginine residues. While there are cofactor biosynthesis terms present, the strongest thematic signal is RNA modification/processing, suggesting this cluster centers on RNA metabolism enzymes, with metabolic annotations possibly reflecting overlapping roles or noise.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0009236","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0009102","count":3}]},{"hash":"772709449043782127","title":"Phosphoinositide metabolism and signaling","description":"The top terms show a pattern focused on phosphatidylinositol and inositol phosphate biosynthesis (and related phosphorylation), i.e., phosphoinositide metabolism, with links to ABA-activated signaling and hyperosmotic stress response, suggesting a unit around lipid signaling and plant stress signaling. Some terms (e.g., L-threonine biosynthesis, antibiotic response) are outliers and do not fit the core theme, but the PI-related processes are the strongest signal. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051770","count":2},{"id":"GO:0046854","count":1},{"id":"GO:0046855","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0006661","count":1}]},{"hash":"4772734580794109","title":"DNA repair and chromatid cohesion","description":"This cluster is driven by GO terms for homologous recombination\u2013mediated double-strand break repair and mitotic sister chromatid cohesion, pointing to a role in coordinating DNA repair with chromosome segregation during the cell cycle. A few terms about cell proliferation regulation support a broader growth-related context, while some minor catabolic terms likely reflect incidental annotations. Overall, the dominant theme is DNA repair and chromosome cohesion.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000724","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0008284","count":2},{"id":"GO:2000233","count":1},{"id":"GO:2000781","count":1}]},{"hash":"1161581723785630372","title":"Glycosphingolipid biosynthesis","description":"The top GO terms include globoside biosynthetic process and mannosyl-inositol phosphorylceramide biosynthetic process, both indicating glycosphingolipid biosynthesis. While there are a few miscellaneous modifications (dephosphorylation, methylation, CoA biosynthesis), the clearest signal across the cluster is lipid biosynthesis focused on glycosphingolipids, supporting a cohesive theme around glycosphingolipid metabolism.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0032364","count":1},{"id":"GO:0018401","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0001576","count":1}]},{"hash":"1578186091883135921","title":"Mitotic Chromosome Segregation & Centromere Assembly","description":"These proteins prominently relate to mitosis and chromosome handling: mitotic cell cycle, mitotic sister chromatid segregation, and CENP-A centromeric chromatin assembly are key terms, with supporting roles in centromere function and spindle dynamics (microtubule severing). While vesicle trafficking terms appear, they are less central to the core mitotic theme. Overall, the cluster is best described by chromosome segregation and centromere assembly during cell division.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0051260","count":2}]},{"hash":"676938365939996305","title":"Unknown","description":"The terms span immune response, DNA repair, metabolism, and development with no single coherent function linking the proteins, indicating no clear shared pathway for a concise label.","confidence":"","size":18,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0071222","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1572991350494913352","title":"Chloroplast Photosynthesis and Light-Response Proteins","description":"The top GO terms are dominated by photosynthesis and light-harvesting processes, with multiple entries on responses to blue, red, far-red, and UV-A light, plus high light intensity. A translation term is present but likely secondary, suggesting chloroplast-associated translation. Overall, the cluster appears to group proteins involved in chloroplast photosynthesis and light-sensing/signaling pathways.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0071486","count":2},{"id":"GO:0009769","count":2},{"id":"GO:0010114","count":2}]},{"hash":"598490001368625995","title":"Spliceosome-mediated mRNA processing and translation initiation","description":"The cluster is enriched for spliceosome-mediated mRNA processing and various aspects of translation initiation and reinitiation, including regulation of splicing (including alternative splicing) and assembly of translation preinitiation complexes, indicating a cohesive role in RNA processing coupled to translation control.","confidence":"High","size":18,"edges":142,"triangles":677,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0006446","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0048026","count":3}]},{"hash":"158901638210861244","title":"RNA processing and transcription regulation","description":"The cluster is dominated by RNA-centric processes: transcription regulation by RNA polymerase II, spliceosome-mediated splicing and mRNA maturation, nonsense-mediated decay, regulatory ncRNA\u2013mediated gene silencing, and rRNA maturation, with one or two terms touching on DNA/viral replication. This indicates a coherent theme around RNA metabolism and transcription control, justifying a focused label on RNA processing and transcription regulation.","confidence":"High","size":18,"edges":31,"triangles":14,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0045944","count":9},{"id":"GO:0048026","count":8},{"id":"GO:0000398","count":8},{"id":"GO:0031047","count":8}]},{"hash":"2080052153129519776","title":"Diverse membrane transporters","description":"These proteins are characterized by diverse transmembrane transport activities, including xenobiotic, vitamin, sugar, ion, and neurotransmitter loading into vesicles. The GO terms cluster around broad membrane transport functions across multiple substrates, suggesting a family of transport proteins with wide substrate specificity.","confidence":"High","size":18,"edges":15,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0035435","count":2},{"id":"GO:0015751","count":2}]},{"hash":"714855883972791653","title":"Signal-responsive transcription and chromatin remodeling","description":"The cluster centers on signaling inputs that influence transcription, including positive regulation of RNA Pol II transcription elongation and cellular responses to cAMP and cGMP, along with chromatin remodeling and heterochromatin formation. This suggests a cohesive theme where cyclic nucleotide signaling modulates transcriptional activity and chromatin state. Ion transport and aerotaxis appear secondary or peripheral to this core function. ","confidence":"Medium","size":18,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0009454","count":2},{"id":"GO:0071805","count":2}]},{"hash":"1123053707123682533","title":"Cell wall glycoprotein biosynthesis","description":"The dominant GO terms cluster around glycoprotein processing and cell wall biology (GPI anchor biosynthesis, protein glycosylation in ER, oligosaccharide-lipid intermediate biosynthetic process) with supportive signals from carbohydrate metabolism (glucose and sucrose). While there are outlier DNA repair terms, the strongest theme is glycoprotein maturation linked to cell wall assembly. ","confidence":"Medium","size":18,"edges":11,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0006297","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0042276","count":2},{"id":"GO:0009744","count":2}]},{"hash":"1524602573722372552","title":"Immune Autophagy-Lysosome Dynamics","description":"The cluster features autophagy-lysosome terms (aggrephagy, autophagosome size regulation, lysosome organization, endosome-to-lysosome transport) together with immune functions (leukocyte chemotaxis, NK cell cytotoxicity, defense against bacteria), suggesting a cohesive role in immune cell autophagy and lysosome\u2013mediated processes.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042267","count":1},{"id":"GO:0030220","count":1},{"id":"GO:0035973","count":1},{"id":"GO:0032510","count":1}]},{"hash":"139404785452430367","title":"Endosome-Lysosome Trafficking and Protein Turnover","description":"These proteins show enrichment for ubiquitination and endosomal/lysosomal trafficking terms (protein ubiquitination; protein localization to endosome; endosome to lysosome transport; lysosomal membrane organization), suggesting a core theme of intracellular protein sorting and degradation. Additional terms for ribosome biogenesis and cell cycle imply broader cellular maintenance roles, but the strongest cohesive signal is trafficking and turnover via the endosome-lysosome pathway. Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0036010","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0060753","count":1},{"id":"GO:0090529","count":1}]},{"hash":"238922902286001169","title":"Glycoprotein biosynthesis and sugar metabolism","description":"The top GO terms cluster around glycosylation in the ER (including GPI anchor biosynthesis and protein glycosylation) and carbohydrate handling (glucose, sucrose, mannitol metabolism) plus a fungal alpha-glucan cell wall biosynthesis term. This points to a cohesive theme of glycoprotein assembly and carbohydrate metabolism, with potential overlap into fungal cell wall biosynthesis. Osmotic-stress responses (flooding, water deprivation) may reflect related metabolic adjustments. Overall, the cluster seems best described as glycoprotein biosynthesis and sugar metabolism.","confidence":"Medium","size":18,"edges":13,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009744","count":3},{"id":"GO:0006490","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0005985","count":3},{"id":"GO:0006506","count":3}]},{"hash":"2157528865958675236","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006189","count":4},{"id":"GO:0009088","count":3},{"id":"GO:0046835","count":3},{"id":"GO:0042417","count":3},{"id":"GO:0046038","count":3}]},{"hash":"1720664145992713365","title":"Metabolic-immune signaling and angiogenesis","description":"Proteins in this cluster show enrichment for cellular responses to glucose, angiogenesis regulation, immune defense against Gram-positive bacteria, and signaling control via PI3K, STAT phosphorylation, and eIF2\u03b1-mediated translational regulation. This pattern suggests a cohesive theme of signaling networks that integrate metabolic cues, vascular growth, and stress/immune responses, rather than a single narrow function.","confidence":"Medium","size":18,"edges":50,"triangles":67,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071333","count":12},{"id":"GO:0045766","count":12},{"id":"GO:0050830","count":12},{"id":"GO:0014068","count":12},{"id":"GO:0014850","count":11}]},{"hash":"756773353460385022","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":143,"triangles":682,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001881","count":18},{"id":"GO:0007117","count":18},{"id":"GO:1905869","count":18},{"id":"GO:0051036","count":18},{"id":"GO:1905608","count":18}]},{"hash":"908395780940767898","title":"Mitotic cell cycle regulation","description":"The cluster is enriched for cell division and mitotic cycle terms (GO:0051301, GO:0000278), indicating involvement in mitosis. Additional terms for positive regulation of kinase and GTPase activities, and protein oligomerization, suggest coordinated signaling and complex formation typical of mitotic regulation. While a few stress-response terms (hypoxia, cadmium ion) appear, the dominant theme is control of mitosis and cell proliferation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0051028","count":4}]},{"hash":"851708064233750460","title":"Translation Machinery and Ribosome Biogenesis","description":"The top GO terms are dominated by translation processes (initiation, elongation, termination, cytoplasmic translation) along with ribosome biogenesis and selenocysteine incorporation, indicating core involvement in protein synthesis. A deadenylation-dependent mRNA decay term suggests coupling between translation and mRNA turnover, while a couple of terms like response to antibiotic and glial proliferation may reflect stress-related or context-specific effects. Overall, the cluster appears centered on translation machinery and ribosome assembly.","confidence":"High","size":18,"edges":60,"triangles":123,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0006413","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0045901","count":4},{"id":"GO:0006415","count":3}]},{"hash":"729743269608087150","title":"Unknown","description":"The top GO terms span very disparate biological contexts (leaf development, skeletal muscle development, mammary gland proliferation, angiogenesis, triglyceride metabolism, oxidative stress response, PI3K/AKT signaling, vasodilation, and temperature homeostasis) with no clear, unified function connecting the proteins in this cluster. Therefore there isn\u2019t a cohesive label to accurately represent the cluster.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048366","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0010269","count":1},{"id":"GO:0033599","count":1},{"id":"GO:0060055","count":1}]},{"hash":"2151087871087076517","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms for ribosome biogenesis, rRNA maturation (5.8S and LSU), large subunit export and assembly, and formation of translation preinitiation complexes, plus IRES-dependent translation initiation. Together these point to a cohesive role in ribosome assembly and the initiation phase of protein synthesis, with a few splicing-related terms possibly reflecting multifunctional proteins or annotation noise.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0075522","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000398","count":3}]},{"hash":"8055202548574671","title":"Neuronal development and signaling","description":"The most represented terms are brain development and the reelin-mediated signaling pathway, both pointing to neural differentiation and neural signaling. While other terms appear (membrane repair, fatty acid biosynthesis, transcription), they are less central, so the cluster best fits proteins involved in neuronal development and signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0007420","count":4},{"id":"GO:0046642","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0030579","count":3}]},{"hash":"1666157805197973329","title":"Neuronal endosome trafficking and synaptic regulation","description":"The terms cluster around endosomal trafficking and membrane dynamics (receptor recycling, endosome transport, regulation of endosome size), SNARE complex regulation, and neuronal signaling (glutamatergic transmission, dendrite morphogenesis), suggesting a theme of neuronal membrane trafficking and synaptic regulation. A few terms (cell division, behavioral fear) are less aligned but do not override the core trafficking/synaptic theme. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0001881","count":1},{"id":"GO:0043305","count":1},{"id":"GO:0051036","count":1},{"id":"GO:1900235","count":1}]},{"hash":"1219919136210498233","title":"ER stress response and protein folding quality control","description":"The top GO terms point to chaperone-assisted protein processing, ER stress\u2013related control of translation, and redox/homeostasis balance, suggesting a proteostasis-focused cluster. Terms about chaperone-dependent refolding, translation initiation under ER stress, and redox maintenance support a theme of protein quality control during cellular stress, with some broader terms (e.g., DNA replication, mesoderm formation) likely reflecting multifunctional proteins. Overall, this cluster seems best described as ER stress\u2013related protein folding and quality-control processes.","confidence":"Medium","size":17,"edges":18,"triangles":7,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":8},{"id":"GO:0090084","count":6},{"id":"GO:0070389","count":6},{"id":"GO:0097428","count":6},{"id":"GO:0036494","count":6}]},{"hash":"594841709545568829","title":"Ubiquitin-Driven Proteostasis","description":"This cluster is dominated by ubiquitin- and proteostasis-related processes: autoubiquitination, aggresome assembly, ubiquitin-dependent ERAD, and chaperone-mediated assembly, pointing to protein quality control and degradation pathways as the core theme. Additional terms like transcription and antibiotic responses are present but less central to the main function of the cluster.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0070842","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0030433","count":3}]},{"hash":"758591756856340955","title":"Photosynthesis and Photosystem I electron transport","description":"The cluster is driven by GO terms centered on photosystem I stabilization, photosynthetic electron transport in photosystem I, NADP+ reduction, and overall photosynthesis, suggesting proteins involved in chloroplast photosystem I function. A few lipid biosynthesis terms appear but are much less represented, so the dominant theme is photosynthesis/PSI-related activity.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042550","count":2},{"id":"GO:0009773","count":2},{"id":"GO:0009780","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0036151","count":1}]},{"hash":"509143930451436388","title":"Calcium-regulated exocytosis and vesicle trafficking","description":"The cluster\u2019s top GO terms cluster around calcium-dependent exocytosis, endosome-to-plasma membrane transport, and lysosomal/membrane organization, pointing to a shared role in vesicle trafficking and regulated secretion. Other terms like xenobiotic response and apoptosis may reflect broader stress-related or multifunctional proteins in the set, but the strongest signal is calcium-regulated membrane trafficking. ","confidence":"Medium","size":17,"edges":57,"triangles":47,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0006915","count":2}]},{"hash":"2292335706649471054","title":"Mitochondrial transport and energy regulation","description":"These proteins are linked to mitochondrial ion and nucleotide transport, ATP transmembrane transport, and import into mitochondria, with additional roles in regulating membrane potential and adaptive thermogenesis. The presence of apoptotic mitochondrial changes and mitochondrial genome maintenance signals a mitochondrial-centered function, focusing on energy metabolism and transport. ","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":6},{"id":"GO:0006828","count":5},{"id":"GO:1990544","count":5},{"id":"GO:1990519","count":5},{"id":"GO:0008637","count":5}]},{"hash":"421316880248728064","title":"Spindle assembly and microtubule dynamics","description":"This cluster is dominated by GO terms centered on microtubule organization and spindle function during cell division, including plus-end dynamics, kinetochore attachments, spindle pole separation, cytokinesis-related processes, and establishing microtubule polarity. The presence of meiotic spindle orientation and related microtubule depolymerization terms further supports a cohesive theme of spindle assembly and microtubule dynamics; one term also highlights microtubule-based transport in neurons, which aligns with motor-driven movements along microtubules. Overall, the proteins likely participate in organizing and regulating the mitotic/meiotic spindle and associated microtubule processes.","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":11},{"id":"GO:0070462","count":11},{"id":"GO:0000911","count":11},{"id":"GO:0031535","count":11},{"id":"GO:0099607","count":11}]},{"hash":"862250737645371922","title":"RNA processing and translation with vesicle trafficking","description":"The top GO terms cluster around mRNA export, spliceosome-related splicing regulation, translation initiation and reinitiation, and ncRNA-mediated gene silencing, complemented by ER-to-Golgi vesicle transport and microtubule severing. This points to a cohesive theme of RNA metabolism and protein synthesis linked to intracellular transport and cytoskeletal dynamics. Some terms about DNA replication and viral genome replication are present but appear less central. ","confidence":"Medium","size":17,"edges":29,"triangles":30,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006406","count":6},{"id":"GO:0009432","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0019079","count":5},{"id":"GO:0048026","count":5}]},{"hash":"1867038998658199069","title":"Embryonic neural development and DNA replication","description":"This cluster\u2019s top GO terms center on DNA replication, DNA-templated transcription, and centrosome cycle, indicating a core theme of cell-cycle/DNA replication regulation. At the same time, multiple development-related terms\u2014forebrain development, neural tube closure, and embryonic cranial skeleton morphogenesis\u2014point to roles in embryonic neural development. The presence of broader processes like apoptotic and innate immune responses suggests broader cellular regulation during development, but the strongest signal comes from the coupling of DNA replication/cell-cycle control with neural/embryonic developmental processes.","confidence":"Medium","size":17,"edges":14,"triangles":2,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0006351","count":8},{"id":"GO:0048701","count":6},{"id":"GO:0010571","count":6},{"id":"GO:0007098","count":6}]},{"hash":"1083649838186257922","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000466","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0000463","count":4}]},{"hash":"1826176922339823277","title":"RNA processing and transcription termination","description":"The top GO terms cluster around mRNA maturation steps\u2014polyadenylation, nuclear export, and spliceosome-mediated splicing\u2014as well as termination of RNA polymerase II transcription and CTD dephosphorylation, indicating a cohesive set of RNA processing factors. A minor calcium/NFAT signaling term appears but is not central to the main theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0006406","count":2},{"id":"GO:0043486","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1544505151188699729","title":"Innate Immune Signaling and Transcription Regulation","description":"These proteins cluster around innate immune signaling (MyD88-dependent TLR pathway; type II interferon signaling) and transcriptional control (positive regulation of transcription by RNA polymerase II), with supporting roles in proteasomal degradation and nuclear pore localization. The core theme is coordinating immune signal reception with gene expression and protein turnover, rather than a single enzymatic function; some terms are obsolete, but the main signal is immune response regulation coupled to transcriptional control.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060334","count":1},{"id":"GO:0051572","count":1},{"id":"GO:1901896","count":1},{"id":"GO:0043433","count":1},{"id":"GO:0045944","count":1}]},{"hash":"76355539216812455","title":"Nuclear DNA transcription and chromatin remodeling","description":"This cluster centers on nuclear processes: DNA-templated transcription, DNA replication, cell cycle, chromatin remodeling, and regulation of transcription by RNA polymerase II, as well as chromatin localization. The collection points to genome regulation and maintenance in the nucleus, with oxidative stress response potentially tied to DNA damage response, supporting a label focused on transcriptional and chromatin regulation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007049","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0043388","count":2}]},{"hash":"231218913415812158","title":"Protein quality control and intracellular trafficking","description":"Most of the top GO terms center on fundamental cellular maintenance: ERAD (protein quality control in the ER), retrograde Golgi-ER transport, and regulation of GTPases involved in trafficking. Additional terms touch on RNA processing and ribosome biogenesis, which are general housekeeping processes, while a few items appear as peripheral noise (photosynthesis, reproductive development). Overall, the cluster seems driven by general cellular maintenance and protein handling rather than a single specific pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0015979","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0072520","count":3}]},{"hash":"1530659393992257667","title":"Pol I transcription and ribosome biogenesis","description":"The top terms cluster around RNA polymerase I\u2013driven transcription (regulation and initiation at Pol I promoter), nucleolus organization, and RNA modification activities (rRNA and tRNA pseudouridine synthesis). Together these point to proteins involved in nucleolar ribosome biogenesis and Pol I\u2013mediated transcription, rather than general transcription or cytoplasmic functions. Confidence: High","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045762","count":2},{"id":"GO:0006356","count":1},{"id":"GO:0001180","count":1},{"id":"GO:1902254","count":1},{"id":"GO:0007000","count":1}]},{"hash":"1294944761273702465","title":"Cardiac development and SA node signaling","description":"Enriched terms point to heart formation (cardiac right atrium morphogenesis, Notch signaling in heart field), pacemaker activity (SA node cell signaling), and related vascular development (endothelial differentiation, angiogenesis). Wnt signaling also features in cardiac progenitors, and actin filament assembly relates to cardiomyocyte structure. Overall, the cluster centers on cardiac development and SA node-associated signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0016055","count":5},{"id":"GO:0003213","count":4},{"id":"GO:1903589","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0086070","count":4}]},{"hash":"986997598926131205","title":"Tissue Development and Differentiation","description":"The cluster\u2019s top GO terms cluster around differentiation and development of multiple tissues (trophoblast giant cells, uterus/uterine glands, tarsal glands, hepatocytes), suggesting a common theme of tissue-specific differentiation. Supporting this, there are also general transcriptional regulation terms (DNA-templated transcription, RNA polymerase II transcription regulation) that typically accompany differentiation processes, and a cell-cycle regulation term that can be linked to differentiation timing. The mix points to broad developmental differentiation across tissues rather than a single, cohesive pathway, hence a label of tissue development with transcriptional regulation. ","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0060065","count":2},{"id":"GO:1903709","count":2},{"id":"GO:0097676","count":2},{"id":"GO:1903699","count":2}]},{"hash":"400233052535452960","title":"Nuclear transport and mitotic regulation","description":"The GO terms cluster around nuclear processes: mRNA transport and import of NLS-bearing proteins into the nucleus, plus mitotic nuclear events (nuclear membrane reassembly and sister chromatid separation) and regulation of DNA replication. While some terms (heart development, xenobiotic response) are more divergent, the core set points to nuclear transport and cell-cycle control as the dominant theme of this cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051028","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0035690","count":2}]},{"hash":"2288810262712981960","title":"Unknown","description":"The top GO terms are highly diverse (membrane repair, GTPase regulation, placental morphogenesis, nucleosome assembly, transcription, signaling, granule exocytosis) with no clear shared function, and there are no edges connecting proteins, making it hard to assign a coherent label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001778","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0030579","count":1}]},{"hash":"1758244898352407590","title":"Innate Immune and Development Signaling","description":"The top GO terms show innate immune response and dsRNA-triggered signaling, indicating immune/stress roles, while other terms point to developmental processes (placenta growth, budding, polarity). This suggests a cluster of proteins involved in signaling that links immune/stress responses with development, though the set is heterogeneous.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0007118","count":2},{"id":"GO:2001241","count":2},{"id":"GO:2000114","count":2},{"id":"GO:0001890","count":2}]},{"hash":"1070880875913983787","title":"Unknown","description":"The Top Terms are highly diverse, including nuclear pore assembly, ER organization, plant ABA biosynthesis, mitochondrial ribosome assembly, ethanol metabolism, iron import, vacuolar proteolysis, and other metabolism terms. With no clear common biological function or pathway, and with no edges linking proteins, there isn\u2019t a coherent theme to label a specific cluster name beyond Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042135","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0071786","count":2},{"id":"GO:0009688","count":2},{"id":"GO:0061668","count":1}]},{"hash":"1342846958489735875","title":"Plant Development and Defense Signaling","description":"The terms point to plant-specific development processes (seed/bract development, multicellular development, transcriptional regulation) alongside defense and hormonal signaling (response to chitin, ABA-activated signaling) and wax biosynthesis regulation, suggesting a protein group coordinating growth, cuticle formation, and stress responses in plants.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":2},{"id":"GO:0048316","count":1},{"id":"GO:0010186","count":1},{"id":"GO:1904276","count":1},{"id":"GO:0060774","count":1}]},{"hash":"110781078832787675","title":"Potassium transport and membrane potential regulation","description":"This cluster is dominated by GO terms for potassium ion transport, regulation of resting membrane potential, and membrane repolarization, suggesting proteins involved in cellular excitability and potassium homeostasis. Oxidant detoxification and cold response terms are present but secondary to the core theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0042391","count":2}]},{"hash":"712453927492580785","title":"Unknown","description":"The GO terms are very diverse: translation (cytoplasmic and mitochondrial), aromatic amino acid biosynthesis (shikimate/chorismate), xenobiotic response, nerve growth factor signaling, phosphorylation, and depurination, with no edges connecting the proteins. This lack of a unifying function or pathway suggests there isn\u2019t a single cohesive theme for the cluster, so a specific label is not justifiable.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0032543","count":1},{"id":"GO:1990090","count":1},{"id":"GO:0009073","count":1},{"id":"GO:0046177","count":1}]},{"hash":"1398449814921728129","title":"Chloroplast Photosynthesis and Redox Homeostasis","description":"The top GO terms point to photosynthesis, nonphotochemical quenching, and redox-related processes (oxidant detoxification, redox homeostasis), indicating a cluster of chloroplast-associated proteins that balance light-driven energy capture with protection against oxidative stress. Additional terms related to metal responses and transcription regulation seem secondary or incidental to the core photosynthetic/redox theme.","confidence":"Medium","size":16,"edges":6,"triangles":1,"max_degree":2,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0015979","count":3},{"id":"GO:0071243","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0042619","count":3}]},{"hash":"505542260073124602","title":"Core Cell Cycle and Metabolism","description":"This cluster is enriched for GO terms tied to fundamental cellular operations: mitotic cell cycle, DNA replication, ATP biosynthetic process, and protein localization to kinetochore, plus calcium ion transmembrane transport, indicating core cellular machinery for growth, division, and energy use. Some terms (excitatory postsynaptic potential, visual perception, Schwann cell development) are neural or developmental but appear less tightly connected to the core theme, likely reflecting annotation breadth. Overall, the dominant signal points to core cellular processes rather than tissue-specific functions.","confidence":"Medium","size":16,"edges":32,"triangles":17,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0014044","count":3},{"id":"GO:0000742","count":3},{"id":"GO:0014883","count":3},{"id":"GO:0000278","count":3}]},{"hash":"151180770613807412","title":"Mitochondrial transport and energy regulation","description":"The top GO terms are all centered on mitochondria, including transport of ions and nucleotides across mitochondrial membranes (manganese, phosphate, heme, pyrimidine import), ATP transmembrane transport, and regulation of mitochondrial membrane potential, with additional signals of mitochondrial apoptosis changes and adaptive thermogenesis. This suggests a cohesive theme of mitochondrial transport and energyhomeostasis, with links to mitochondrial-mediated apoptosis and necroptosis regulation.","confidence":"High","size":16,"edges":10,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":7},{"id":"GO:1990544","count":7},{"id":"GO:1990519","count":7},{"id":"GO:0008637","count":7},{"id":"GO:0035435","count":7}]},{"hash":"1234707619900135969","title":"Regulation of transcription and cell differentiation","description":"Consistent with several regulatory GO terms: positive/negative regulation of transcription by RNA Pol II, regulation of protein catabolic and fatty acid biosynthetic processes, and differentiation of neuron and keratinocyte lineages. The mix suggests regulatory proteins that influence gene expression and cell fate across tissues rather than a single cohesive pathway.","confidence":"Medium","size":16,"edges":40,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:2000009","count":2},{"id":"GO:0030579","count":2},{"id":"GO:0019089","count":2},{"id":"GO:0030182","count":2}]},{"hash":"1583867662100893485","title":"Translation initiation and RNA processing regulation","description":"Despite no edges, the top GO terms cluster around translation initiation, reinitiation, IRES-dependent initiation, and preinitiation complex formation, with accompanying mRNA processing/splicing terms. This suggests a cohesive theme of coordinating mRNA maturation with the onset of translation, though some terms appear obsolete or less connected.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2}]},{"hash":"277434433894176294","title":"Methylation-linked transcription regulation","description":"The top GO terms cluster around methylation processes (peptidyl-arginine methylation to asymmetrical-dimethyl arginine, rRNA methylation, histone H4-R3 methylation) and transcriptional control (regulation of DNA-templated transcription, negative regulation of transcription by RNA polymerase II), plus linked themes of cell growth and cellular senescence. Sporulation and stress-related terms may reflect context-specific regulation, but the core pattern is methylation-modification coupled with transcriptional regulation.","confidence":"Medium","size":16,"edges":42,"triangles":47,"max_degree":12,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0090398","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0019919","count":4},{"id":"GO:0016049","count":4},{"id":"GO:0043985","count":4}]},{"hash":"512437013939180856","title":"Unknown","description":"The terms are a disparate mix: fatty acid metabolism, verruculogen and ectoine biosynthesis, thylakoid membrane organization, protein oligomerization/oxidation regulation, and even obsolete NF-kappaB regulation. With no consistent pathway or shared function tying the proteins together and no interactions (Edges 0), there is no coherent theme to name beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097089","count":1},{"id":"GO:1902181","count":1},{"id":"GO:0001561","count":1},{"id":"GO:0019491","count":1},{"id":"GO:0042400","count":1}]},{"hash":"1458167579422103725","title":"Unknown","description":"The top GO terms span polyamine metabolism (putrescine, spermine), amino acid biosynthesis (arginine), various acetylation/propionylation modifications, and broader chromatin/cell-cycle/developmental processes, with no single cohesive function tying all terms together. This makes it hard to assign a specific, representative label to the cluster.","confidence":"","size":16,"edges":39,"triangles":57,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009447","count":11},{"id":"GO:0001525","count":8},{"id":"GO:0030435","count":7},{"id":"GO:0006526","count":7},{"id":"GO:0061606","count":7}]},{"hash":"1975607979755577686","title":"Translation initiation control and RNA processing","description":"The cluster's top GO terms center on regulating translation initiation (including preinitiation complex formation, initiation and reinitiation, and IRES-dependent viral translation) and on RNA processing such as alternative splicing. This combination points to a core role in initiating and controlling protein synthesis and mRNA fate, with ancillary links to transcription regulation and development. Therefore this label captures the main theme without over-extending to unrelated functions.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2}]},{"hash":"2020445405843313828","title":"Transcription and RNA Processing","description":"The top terms center on transcription (DNA-templated transcription, transcription antitermination) and RNA maturation (rRNA processing) with related RNA Pol II CTD dephosphorylation, indicating a cluster tied to gene expression regulation and RNA metabolism; the xenobiotic response adds a stress-related context but does not override the core theme.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":3},{"id":"GO:0070940","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0030433","count":2}]},{"hash":"1040702392949045368","title":"Spliceosome-Driven mRNA Splicing and Translation Regulation","description":"The cluster shows strong enrichment for spliceosome-mediated alternative splicing and mRNA processing (several GO terms about splicing and regulation of splicing), combined with translation initiation/termination regulation and preinitiation complex formation. This suggests a cohesive module focused on post-transcriptional regulation of gene expression at both the splicing and translation levels; the single \"response to cocaine\" term appears as an outlier among mainly RNA-processing and translation-related terms.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":3},{"id":"GO:0048255","count":3},{"id":"GO:0042220","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2}]},{"hash":"859375787238944363","title":"Unknown","description":"The terms do not converge on a single function: they span nervous system development, innate and antibiotic responses, protein homooligomerization, and plant-associated metabolic pathways like carbon fixation and photorespiration, with an obsolete GO term. This dispersion suggests no coherent shared function to label succinctly, so a generic Unknown label is most appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0046677","count":2}]},{"hash":"2234796997485925896","title":"Proteostasis and Ubiquitin/SUMO Modification Network","description":"This cluster centers on proteostasis and protein quality control, with strong enrichment for ubiquitin-cycle processes (deubiquitination, sumoylation) and aggresome formation, plus ER-associated degradation and related stress responses; translation and metabolic regulation terms appear as connected downstream activities.","confidence":"High","size":16,"edges":38,"triangles":31,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":5},{"id":"GO:0016925","count":4},{"id":"GO:1903071","count":3},{"id":"GO:0010636","count":3},{"id":"GO:0070842","count":3}]},{"hash":"1082481647796376118","title":"Vacuolar trafficking and ion homeostasis","description":"The GO terms cluster around vacuolar processes: ER-to-Golgi transport, protein targeting to the vacuole, vacuole organization, and vacuolar acidification, plus proton transmembrane transport and proton-motive force\u2013driven ATP synthesis. This points to coordinated vesicle trafficking to the vacuole and maintenance of ion/proton homeostasis within the vacuolar/organellar system, with copper ion homeostasis also involved. A non-core term like DNA replication appears, but the dominant signal is vacuolar function and ion transport.","confidence":"High","size":16,"edges":37,"triangles":40,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0007035","count":2}]},{"hash":"160602629268872650","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":40,"triangles":44,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":7},{"id":"GO:0048026","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0031047","count":6}]},{"hash":"1190261973391640721","title":"Peripheral nervous system and skin development","description":"The cluster's top GO terms cluster around sensory perception of pain, Schwann cell development (PNS glia), and keratinocyte differentiation (skin), with multicellular organism development also represented. This pattern points to coordinated development and differentiation of nervous tissue (PNS) and epidermal lineages. Other terms (DNA replication, translational regulation) likely reflect general proliferative or stress-related processes in developing tissues or historical annotations, rather than a unifying pathway. Thus, the core theme appears to be nervous system and skin development rather than a single molecular function.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019233","count":10},{"id":"GO:0007275","count":10},{"id":"GO:0006260","count":9},{"id":"GO:1902817","count":8},{"id":"GO:0006977","count":8}]},{"hash":"1454554698793341611","title":"Ciliary assembly and centrosome microtubule anchoring","description":"The top GO terms emphasize ciliogenesis (including non-motile cilium assembly) and regulation of cilium motility, as well as microtubule anchoring at the centrosome, pointing to a shared role in ciliogenesis and centrosomal microtubule organization.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":3},{"id":"GO:0060613","count":2},{"id":"GO:0060296","count":2},{"id":"GO:1902855","count":2},{"id":"GO:0034454","count":2}]},{"hash":"2245004050423195659","title":"Unknown","description":"The top terms span neuronal development, synaptic signaling, cytoskeletal remodeling, and general signaling/ubiquitination processes with no single unifying function, suggesting a mixed set of regulatory proteins rather than a cohesive pathway.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000172","count":1},{"id":"GO:0071169","count":1},{"id":"GO:1902499","count":1},{"id":"GO:0051014","count":1},{"id":"GO:1903215","count":1}]},{"hash":"117776621816988959","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0015979","count":3},{"id":"GO:0010196","count":2},{"id":"GO:0006593","count":1},{"id":"GO:0044205","count":1}]},{"hash":"820211997163323278","title":"Ubiquitin-Proteasome Regulation and NF-kB Signaling","description":"The top GO terms point to ubiquitination and SCF/ERAD-mediated proteasomal degradation, along with activation of NF-kappaB-inducing kinase, indicating a cluster of proteins involved in protein turnover and NF-kB signaling. Additional terms like mRNA transport, protein methylation, and hypoxia response suggest broader regulatory roles tied to signaling and cellular stress; a few outliers (e.g., polysaccharide catabolic process) may reflect annotation noise. Overall, the cluster appears to represent proteostasis and signaling regulation rather than a single enzymatic complex.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":2},{"id":"GO:0007250","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0016567","count":2}]},{"hash":"2108578490097347969","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0019433","count":2},{"id":"GO:1903699","count":2}]},{"hash":"1101006814616029333","title":"Hormone-Regulated Development and Cell Cycle","description":"The cluster includes cell division and cell cycle terms together with developmental processes (heart morphogenesis, prostate gland development, male sex differentiation) and steroid hormone receptor complex assembly, pointing to hormone-driven development and proliferation as the core theme. A subset of terms relates to innate immune and interferon responses, but these appear secondary to the main developmental/cell-cycle pattern.","confidence":"Medium","size":15,"edges":39,"triangles":37,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0035176","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0046661","count":2}]},{"hash":"49092182913224851","title":"Mitochondrial metabolism and autophagy","description":"This cluster centers on energy-related processes: mitochondrial translation and carbohydrate catabolic pathways (maltose, starch, glycophagy) point to mitochondrial- and glycogen-associated metabolism, while positive regulation of macroautophagy and glycophagy suggests a shared autophagic turnover theme. The nuclear glucocorticoid signaling term may reflect a broader metabolic regulatory context, but the core signal ties to mitochondrial energy production and autophagic turnover. Overall, the most coherent theme is metabolism connected to mitochondrial function and autophagy, with a few outliers.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":2},{"id":"GO:0046959","count":1},{"id":"GO:0043609","count":1},{"id":"GO:0016239","count":1},{"id":"GO:0046475","count":1}]},{"hash":"13858165123389242","title":"Unknown","description":"The terms span distinct themes: energy/metabolic processes (gluconeogenesis, glycerol catabolism, redox homeostasis) alongside translation-related activities (tRNA aminoacylation and translation) and separate nuclear telomere maintenance/DNA repair terms. There isn't a single cohesive function linking all terms, so a unique, representative label isn\u2019t clear.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0019563","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0016233","count":1}]},{"hash":"576046026645439382","title":"Mitochondrial metabolism and amino acid biosynthesis","description":"The cluster shows terms tied to mitochondrial complex IV assembly and broader metabolism, including several amino acid biosynthesis processes (tyrosine, homoserine, lysine pathways), magnesium transport, nitrogen utilization, and phosphorylation, with protein folding also present. This points to a cohesive theme of metabolic functions centered on mitochondria and amino acid biosynthesis, though the terms are diverse and not tightly coupled.","confidence":"Medium","size":15,"edges":103,"triangles":430,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0033617","count":1},{"id":"GO:0006457","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0009089","count":1}]},{"hash":"1534384888719919416","title":"Plant transcription and photosynthesis gene cluster","description":"This cluster is enriched for GO terms tied to DNA-templated transcription, transcription regulation, translation, and photosynthesis, including photosystem II oxygen evolving complex assembly. The presence of a plant-specific term (response to cytokinin) supports a plant-context interpretation, suggesting a group of proteins involved in core gene expression tied to photosynthetic machinery, with some stress-response associations as secondary connections.","confidence":"Medium","size":15,"edges":75,"triangles":185,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009735","count":1},{"id":"GO:0010270","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0032784","count":1}]},{"hash":"1901067691123971156","title":"Unknown","description":"The GO terms span xenobiotic and lipid/hormone metabolism (carbazole catabolic, prostaglandin, bile acid, triglyceride), vitamin D response, aldosterone-regulated blood volume, uterus development, and a plant-specific diterpenoid oxidation, with no single cohesive biological theme tying all terms together. ","confidence":"","size":15,"edges":18,"triangles":4,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":5},{"id":"GO:0001516","count":5},{"id":"GO:0032259","count":4},{"id":"GO:0070989","count":4},{"id":"GO:0002017","count":4}]},{"hash":"1043070021295583319","title":"RNA Splicing and Ubiquitination","description":"The top terms are dominated by mRNA processing (spliceosome-mediated splicing and polyadenylation) and protein ubiquitination, suggesting a functional module centered on post-transcriptional regulation and protein turnover, with a few peripheral immune and developmental signals.","confidence":"Medium","size":15,"edges":56,"triangles":69,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0043011","count":1}]},{"hash":"1862806087987332271","title":"DNA Replication and Repair, SOS Response","description":"The cluster is dominated by GO terms for DNA replication and related processes (DNA unwinding, replication, recombination, and double-strand break repair) along with the SOS response, pointing to a cohesive genome-maintenance and damage-response module. Additional terms about hypoxia response and viral genome replication suggest broader stress signaling, while a RNA processing term appears peripheral.","confidence":"High","size":15,"edges":32,"triangles":26,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042766","count":4},{"id":"GO:0006268","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0001666","count":4},{"id":"GO:0006260","count":4}]},{"hash":"286363391641644942","title":"Redox-Linked Nucleotide Metabolism","description":"The cluster centers on redox maintenance (mycothiol biosynthesis, redox homeostasis, hydrogen peroxide response) and nucleotide metabolism (PRPP biosynthesis), with supporting signs of ribosome biogenesis and DNA processing, suggesting a coordinated growth and redox-management program typical of actinobacteria.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006015","count":2},{"id":"GO:0010125","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0042493","count":2}]},{"hash":"716941732144904622","title":"Redox Homeostasis and Aromatic Compound Catabolism","description":"The cluster is dominated by GO terms for oxidation-reduction processes and redox homeostasis, detoxification, and oxidative stress response, with specific xenobiotic catabolic terms for carbazole and camphor. These together point to a program of maintaining cellular redox balance while degrading aromatic compounds; a few outlier terms likely reflect annotation noise from unrelated processes.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0046232","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0080058","count":3}]},{"hash":"469205589318414147","title":"ABA signaling and seed development in plants","description":"This cluster\u2019s top GO terms center on abscisic acid-activated signaling and seed development, pointing to plant-specific developmental and stress-response pathways; additional terms reflect transcriptional regulation and kinase signaling that support growth and development in plants.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1542487852325474993","title":"Developmental signaling and transcriptional regulation","description":"The terms cluster around signaling pathways that influence development (positive regulation of Wnt signaling, hippocampus development, mesoderm formation) alongside transcriptional control (DNA-templated transcription, DNA replication initiation) and regulatory kinase activity, with a note on redox homeostasis. This suggests a theme of signaling-driven transcriptional and replication regulation in developmental contexts, with some broader signaling roles (including T cell receptor signaling) involved.","confidence":"Medium","size":15,"edges":11,"triangles":2,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0033138","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0006351","count":3}]},{"hash":"548648864554499960","title":"Membrane transporters and lipid/carbohydrate metabolism","description":"The top GO terms indicate multiple membrane transport activities (lipoprotein, carbohydrate, glycerophosphodiester, heme, teichoic acid transport) coupled with metabolic processes (very long-chain fatty acid catabolic process, cytochrome complex assembly). This suggests a cluster of proteins involved in membrane transport with linked metabolic pathways, rather than a single narrow function. Some terms (cell division, stem cell proliferation) are peripheral and less cohesive with the core theme. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0042760","count":3},{"id":"GO:0042953","count":3},{"id":"GO:0008643","count":3},{"id":"GO:0010949","count":3}]},{"hash":"938177480119126793","title":"Proteostasis and Translational Regulation","description":"The cluster is dominated by proteostasis-related terms (aggresome assembly, misfolded protein response, ubiquitin-dependent protein catabolic process) and translation control (regulation of translational initiation, translation reinitiation, viral translational termination-reinitiation). A few transcription- or cell-division related terms appear but are less central, suggesting a cohesive theme around protein quality control and regulation of protein synthesis.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:1901407","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0070842","count":2}]},{"hash":"30127055299866657","title":"Nutrient-Responsive Energy Metabolism","description":"This cluster centers on energy production and central metabolism (glycolysis, ATP biosynthesis, pyruvate and serine biosynthesis) and on signaling related to nutrients and hormones (insulin, cAMP, epinephrine) as well as hypoxia, with seed maturation hinting at developmental metabolic remodeling. Overall, it reflects coordinated metabolic regulation in response to nutrients and stress.","confidence":"Medium","size":15,"edges":25,"triangles":41,"max_degree":7,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0032869","count":5},{"id":"GO:0051591","count":4},{"id":"GO:0042866","count":4},{"id":"GO:0006564","count":4},{"id":"GO:0010431","count":3}]},{"hash":"1497274547656074092","title":"Bacterial biosynthesis and metabolism","description":"The terms include antibiotic biosynthetic process, poly-hydroxybutyrate biosynthetic process, and acetoin catabolic process, which together suggest microbial metabolism and production of biopolymers and secondary metabolites. Other terms related to steroid and retinol metabolism are less cohesive within this cluster, but overall the common theme points to bacterial metabolism and biosynthesis of small molecules.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0006541","count":3},{"id":"GO:0006710","count":3}]},{"hash":"1628943658773023503","title":"TLR-Mediated Innate Immune Signaling","description":"Rationale: The cluster\u2019s top GO terms strongly point to innate immunity and Toll-like receptor signaling, including innate immune response, regulation of dendritic cell cytokine production, TLR signaling (including MyD88-independent pathways), positive regulation of inflammatory and interferon production. While a couple terms (cellular response to dopamine, nipple morphogenesis) are less directly related, the dominant theme is TLR-driven innate immune signaling.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0002730","count":2},{"id":"GO:0007186","count":2},{"id":"GO:0050729","count":2},{"id":"GO:0034346","count":2}]},{"hash":"974629828483267393","title":"Unknown","description":"The top GO terms are diverse (brain and uterus development, DNA repair/maintenance, transcription termination, apoptosis, signaling, and stress responses) with no clear shared function linking the proteins, so a coherent, specific label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:1990683","count":1},{"id":"GO:0051152","count":1},{"id":"GO:0006471","count":1},{"id":"GO:0000723","count":1}]},{"hash":"633694243863348004","title":"TLR-driven innate immune signaling cluster","description":"The Top Terms are dominated by innate immune function and Toll-like receptor signaling (innate immune response; TLR2 signaling; MyD88-independent TLR signaling; type III interferon production) with related inflammatory regulation, suggesting a coordinated role in pathogen recognition and inflammatory signaling. Some terms like dopamine response and nipple morphogenesis likely reflect incidental annotations rather than core cluster function, but the TLR/innate immunity theme is clear. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0045087","count":1},{"id":"GO:0002730","count":1},{"id":"GO:0007186","count":1},{"id":"GO:0050729","count":1}]},{"hash":"1642461161850803647","title":"Photosynthesis light responses and photoprotection","description":"This cluster centers on photosynthesis and light-driven responses, with multiple GO terms for photosynthesis, PSII light harvesting, nonphotochemical quenching, and responses to various light qualities (red, blue, far-red, UV-A) and high light. These terms collectively point to chloroplast energy capture and photoprotective regulation under different light conditions; the mitochondrial electron transport term may reflect broader energy metabolism linked to these processes. Overall, the theme is light-regulated photosynthetic activity and photoprotection.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0010196","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0071486","count":1}]},{"hash":"1207843343220053645","title":"Ribosome biogenesis and LSU maturation","description":"This cluster shows strong representation of ribosome-related processes: ribosomal large subunit assembly, translation, and maturation/export steps for LSU and 5.8S rRNA, plus preribosome assembly, indicating a cohesive role in ribosome production and maturation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000466","count":1}]},{"hash":"1930161454187494255","title":"DNA Damage Response and ER-Golgi Transport","description":"The cluster shows clear enrichment for DNA damage response functions (cellular response to ionizing radiation; double-strand break repair via homologous recombination) alongside vesicle trafficking between the ER and Golgi (retrograde and ER-to-Golgi transport). Additional signals (TORC1, mRNA transport, GTPase regulation, dephosphorylation) suggest a regulatory module that coordinates DNA repair with cellular trafficking and signaling under stress, though the mix of themes makes the assignment moderately confident.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071479","count":2},{"id":"GO:0000724","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0043547","count":2}]},{"hash":"872660264777320675","title":"Neural and cardiovascular development regulators","description":"This cluster centers on proteins involved in regulating signaling pathways during development, especially in neural and cardiovascular contexts. The top GO terms emphasize negative regulation of protein kinase activity and phosphorylation, coupled with developmental processes such as heart development, axonogenesis, bone development, and angiogenesis. The combination suggests a cohesive role in modulating signaling to shape neural and cardiovascular development, rather than a single specialized function. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0007409","count":2}]},{"hash":"2247957619021086220","title":"Muscle and heart development with transcription regulation","description":"The proteins are enriched for myotube development and heart development, alongside transcription-related terms (DNA-templated transcription, positive regulation of transcription by RNA polymerase II) and dexamethasone response, suggesting a cluster centered on developmental gene regulation in muscle and cardiac lineages, possibly modulated by glucocorticoid signaling. Additional terms about nucleosome assembly and p53-mediated DNA damage response point to chromatin-level regulation accompanying transcriptional control in this developmental context.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014904","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0071549","count":2},{"id":"GO:0006351","count":2}]},{"hash":"270694403623978336","title":"Diverse small-molecule biosynthesis and detoxification","description":"The top GO terms cluster around biosynthesis of various metabolites (antibiotics, biotin, menaquinone, strigolactone) and detoxification/response to toxic substances, suggesting a broad theme of small-molecule production with detox pathways. Some terms (secondary shoot formation, endocannabinoid signaling) are less coherent with this theme, but the overall signal is biosynthesis of diverse metabolites plus detoxification processes.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":6},{"id":"GO:0009234","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0019260","count":4}]},{"hash":"743460940629803121","title":"Cofactor and amino acid biosynthesis","description":"This cluster's top GO terms cluster around biosynthetic pathways for cofactors (biotin, cobalamin, porphyrin/heme precursor) and amino acids (tyrosine, lysine, alanine), plus related catabolic and redox-related processes. The combination suggests a cohesive theme: synthesis of vitamins/cofactors and amino acids with associated redox balance, despite some broad annotations like transcription or insulin response that may reflect broader regulatory signals. Overall, a concise label capturing cofactors and amino acids fits best.","confidence":"Medium","size":14,"edges":29,"triangles":27,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009102","count":7},{"id":"GO:0006782","count":7},{"id":"GO:0032869","count":6},{"id":"GO:0009236","count":5},{"id":"GO:0006351","count":5}]},{"hash":"1899614569396192907","title":"ER protein folding and stress response","description":"The top terms cluster around ER-focused proteostasis: protein folding in the ER, chaperone-assisted refolding and maturation, and translation initiation in response to ER stress, indicating a proteostasis/UPR-related function. A couple of broader terms (mesoderm formation, DNA replication) seem unrelated, but the dominant theme is ER-associated folding and stress signaling.","confidence":"Medium","size":14,"edges":15,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0051259","count":1}]},{"hash":"2005549969258647713","title":"Cardiac development and conduction system","description":"The top GO terms cluster around heart formation and function: right atrium morphogenesis, SA node cell communication and regulation of SA node action potential, and Notch signaling in heart field cardioblast proliferation, with supporting vascular/endothelial differentiation and actin organization relevant to cardiac tissue. While a few terms are more general (cell cycle, NF-kappaB sequestration), the dominant theme is cardiac morphogenesis and the specialized conduction system, justifying this label.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003213","count":3},{"id":"GO:1903589","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0086070","count":3},{"id":"GO:0007253","count":3}]},{"hash":"2069911793272863402","title":"Chlorophyll Pigment Metabolism and Redox Homeostasis","description":"The top GO terms cluster around chloroplast/pigment processes (chlorophyll metabolic process, xanthophyll cycle, heme biosynthesis) and redox-related metabolism (glutathione metabolism, xenobiotic catabolic process), suggesting a cohesive theme of pigment biosynthesis and oxidative balance in plant cells. Some ribosome-associated degradation terms appear peripheral but do not overshadow the pigment/redox focus. Confidence: Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006783","count":2},{"id":"GO:0010028","count":1},{"id":"GO:0015994","count":1},{"id":"GO:0072344","count":1}]},{"hash":"1488315953569106499","title":"Unknown","description":"These proteins show a broad mix of functions: defense against fungi, autophagy-related processes (piecemeal microautophagy of the nucleus and nucleophagy), various biosynthetic/metabolic steps (thiamine and molybdopterin cofactor biosynthesis, t6A biosynthesis), and regulatory activities (cell cycle and transcription). The set does not converge on a single coherent function or pathway, suggesting a heterogeneous cluster rather than a defined biological module.","confidence":"","size":14,"edges":15,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":3},{"id":"GO:2000146","count":2},{"id":"GO:0034727","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0044805","count":2}]},{"hash":"1340681820920935038","title":"Mammary gland development, lactation, and involution","description":"The top terms strongly cluster around mammary biology: mammary gland development, lactose biosynthesis, and regulation related to involution and lactation, with supporting hints of protein folding in secretory cells. There are a few unrelated developmental terms, but the dominant theme is mammary gland function and remodeling.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0045136","count":1},{"id":"GO:0030879","count":1}]},{"hash":"670156934503959779","title":"Innate antiviral immune signaling","description":"The cluster is dominated by innate immune and antiviral defense terms (innate immune response; defense response to virus), with supporting roles for ubiquitination signaling (K63-linked) and immune regulation (apoptosis and T cell proliferation). Despite some obsolete terms, the core function appears to center on antiviral innate immunity and its regulatory pathways.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0042981","count":1},{"id":"GO:0045087","count":1},{"id":"GO:0070534","count":1},{"id":"GO:0050999","count":1}]},{"hash":"256997363575903849","title":"Developmental transcription and metabolic regulation","description":"The top terms cluster around nuclear processes of gene expression (DNA replication, DNA-templated transcription, transcriptional regulation, and galactose-induced transcription), with additional themes in metabolism (cholesterol biosynthesis, glucose response) and development (embryonic cranial skeleton morphogenesis, angiogenesis) as well as stress/defense responses. This suggests a cohesive theme where transcriptional control coordinates developmental programs and metabolic signaling, with occasional immune-related responses, rather than a single narrowly defined function.","confidence":"Medium","size":14,"edges":8,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0048701","count":5},{"id":"GO:0006695","count":5},{"id":"GO:0071333","count":5},{"id":"GO:0014068","count":5}]},{"hash":"1489497272164573608","title":"Sugar Metabolism and Nucleotide Biosynthesis","description":"Reasoning: The GO terms cluster around diverse sugar catabolic pathways (tagatose-6-phosphate, lactose, sucrose, 6-sulfoquinovose catabolism), a glycolysis-related step (fructose-6-phosphate), and nucleotide biosynthesis/salvage (dATP biosynthesis, adenosine salvage), plus a sugar-nucleotide biosynthesis term. Together these define a theme of carbohydrate processing and related nucleotide metabolism, justifying this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097171","count":4},{"id":"GO:0009744","count":3},{"id":"GO:1902777","count":3},{"id":"GO:2001059","count":3},{"id":"GO:0019303","count":3}]},{"hash":"108972562487433902","title":"ER-Golgi vesicle trafficking and mitosis","description":"The top GO terms cluster strongly around ER-Golgi vesicle transport (retrograde ER-Golgi, ER-to-Golgi transport, COPII budding) and vesicle exocytosis, suggesting core involvement in the secretory pathway. In addition, mitosis-related terms (mitotic spindle assembly, mitotic cell cycle, cell division) indicate a link to cell division. The brain development and multicellular growth terms may reflect broader developmental context, but the dominant shared signal ties to vesicle trafficking with mitotic associations. Confidence in the label reflecting the cluster\u2019s primary theme is High. ","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":8},{"id":"GO:0051301","count":7},{"id":"GO:0090307","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0006890","count":6}]},{"hash":"2060810302552739501","title":"DNA damage response and genome maintenance","description":"This cluster shows enrichment in core genome maintenance and stress-response processes: DNA replication and transcription initiation, SOS response, UV protection, and RNA quality control (nonsense-mediated decay). Development-related terms may reflect broader roles of genome integrity and transcriptional regulation during development. Overall, the common theme ties to DNA damage response and genome maintenance under stress, with some developmental associations.","confidence":"Medium","size":14,"edges":25,"triangles":22,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000184","count":5},{"id":"GO:0006268","count":4},{"id":"GO:0048568","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0001666","count":4}]},{"hash":"784240142442526209","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":71,"triangles":198,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0048026","count":4}]},{"hash":"1584248315924166130","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":2},{"id":"GO:0009793","count":1},{"id":"GO:0090615","count":1},{"id":"GO:1905639","count":1},{"id":"GO:0001682","count":1}]},{"hash":"1509988599610422324","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for translation, cytoplasmic translation, ribosome biogenesis, and tRNA modification, indicating proteins involved in ribosome assembly and the protein synthesis machinery. Some cell cycle/division terms are present but appear secondary to the core ribosomal function.","confidence":"High","size":14,"edges":35,"triangles":32,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":5},{"id":"GO:0002181","count":4},{"id":"GO:1903833","count":3},{"id":"GO:0090529","count":3}]},{"hash":"1599464402484601884","title":"Nucleolar rDNA chromatin regulation","description":"Top GO terms center on DNA-templated transcription and chromatin processes, especially rDNA heterochromatin formation, nucleolar localization to rDNA repeats, and transcriptional regulation relevant to the cell cycle and cohesin loading. These recurring themes suggest a cluster of proteins that modulate chromatin state at rDNA loci and transcription control, with some connection to cellular quality control via aggresome assembly. Therefore, this name highlights the dominant function: nucleolar rDNA chromatin regulation.","confidence":"Medium","size":14,"edges":75,"triangles":214,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0060766","count":3},{"id":"GO:0045668","count":3},{"id":"GO:0000117","count":3},{"id":"GO:0000183","count":2}]},{"hash":"1226563560715235831","title":"Membrane Transport and Transcription Regulation Proteins","description":"The top GO terms point to membrane-associated transport (proton and xenobiotic transmembrane transport) alongside transcriptional regulation (DNA-templated transcription, regulation of transcription) and phosphorelay signaling, suggesting a cluster of proteins involved in membrane transport coupled to regulatory signaling. While there are some metabolic and regulatory terms, the dominant themes are transport across membranes and transcriptional regulation, justifying a combined label rather than separate categories. Confidence reflects moderate support for a cohesive theme given annotation diversity.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015992","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0000160","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2154867174584494678","title":"Diverse biosynthesis pathways","description":"The top GO terms are dominated by various biosynthetic processes (antibiotic, biotin, ubiquinone, phosphatidylcholine, vitamin E), suggesting a theme of metabolite production. A few aging and stress-related terms (cellular senescence, response to toxic substance) appear as well, indicating some linkage to stress responses. Overall, the cluster appears to group proteins involved in diverse biosynthetic pathways, with some aging/stress associations, hence a label of Diverse biosynthesis pathways with moderate confidence.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0006744","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0019380","count":3}]},{"hash":"1349370362794286997","title":"Proteostasis and ubiquitin signaling","description":"The terms converge on protein quality control and turnover: ubiquitin-dependent pathways (ERAD, K63-linked ubiquitination), chaperone-mediated protein assembly, and related redox/chaperone activity, pointing to a proteostasis-focused cluster. A few items (response to chitin, granzyme signaling, plant hormone regulation) suggest broader stress or immune signaling, but they appear ancillary to the main proteostasis theme.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0030579","count":3},{"id":"GO:0034720","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0070534","count":2}]},{"hash":"2137041782514467188","title":"Oxidative Stress Response and Detoxification","description":"The cluster centers on detoxification and redox balance, with multiple terms for cellular oxidant detoxification, redox homeostasis, glutathione metabolism, toxin catabolic and toxic-substance responses. Additional terms for aromatic amino acid metabolism and nucleotide-excision repair point to metabolic adjustment and DNA repair under stress. A calcium-release regulation term is present but likely reflects broader stress signaling rather than a core function of the cluster.","confidence":"Medium","size":14,"edges":63,"triangles":130,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":7},{"id":"GO:0045454","count":6},{"id":"GO:0009407","count":6},{"id":"GO:0042594","count":6},{"id":"GO:0009636","count":6}]},{"hash":"2239754801742816853","title":"Unknown","description":"The top terms are a scattered mix of lignin biosynthesis, catecholamine metabolism, cobalamin biosynthesis, protein methylation, and several obsolete GO terms, with no coherent shared pathway, and there are no edges connecting proteins, so there is no clear functional theme to label the cluster.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009809","count":1},{"id":"GO:0006584","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0042135","count":1}]},{"hash":"2228516910982351617","title":"Mitotic vesicle trafficking and ubiquitin-mediated degradation","description":"The top GO terms point to ER-Golgi vesicle transport (anterograde/retrograde) and ubiquitin-dependent proteolysis, including K11-linked ubiquitination and APC/C-regulated catabolic processes during cell division. Together with mitotic cell cycle terms, this suggests a cluster of proteins coordinating vesicle dynamics with targeted protein degradation in mitosis. Pigmentation appears incidental rather than central to the cluster.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051016","count":2},{"id":"GO:0006890","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0070979","count":2}]},{"hash":"20159148071408866","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042773","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0032955","count":1}]},{"hash":"96428356071782063","title":"Unknown","description":"The GO terms cover a mix of catabolic metabolic processes (tyrosine, valine, galactarate, glyoxylate, shikimate), sporulation, and ion transport (copper and potassium) without a single unifying function. There isn\u2019t a clear cohesive pathway or process that links all proteins, so a specific label isn\u2019t justifiable beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0030435","count":1},{"id":"GO:0006813","count":1},{"id":"GO:0006571","count":1},{"id":"GO:0046392","count":1}]},{"hash":"1979952375011496750","title":"Secretory signaling in neural and immune cells","description":"This cluster combines proteins linked to vesicle-mediated secretion (neurotransmitter release, platelet degranulation) with neuronal processes (axonogenesis, heart rate regulation) and immune signaling (innate immune response, dendritic cell cytokine regulation). Autophagy and regulation of GTPase/kinase activities suggest broader cellular signaling and trafficking roles. The common theme is secretory and signaling pathways that operate in both neural and immune contexts.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0007409","count":2},{"id":"GO:0035751","count":2},{"id":"GO:0002576","count":2},{"id":"GO:0007269","count":2}]},{"hash":"1006620009555353455","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000495","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0090669","count":1},{"id":"GO:0007049","count":1}]},{"hash":"1005346533744629580","title":"Unknown","description":"The GO terms in this cluster are highly diverse (proteolysis, SRP-dependent targeting and protein import, BMP signaling, visual perception, hypoxia response, and muscle development), with no single cohesive function linking them. Because of this heterogeneity, there isn\u2019t a reliable, representative label that captures the cluster\u2019s biology.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0036155","count":2},{"id":"GO:1900037","count":2},{"id":"GO:0048642","count":2},{"id":"GO:0006614","count":1}]},{"hash":"1105629607397631655","title":"Chloroplast metabolism and photosynthesis","description":"Most of the top GO terms center on chloroplast-related functions, especially photosynthesis (GO:0015979) and cytochrome b6f complex assembly (GO:0010190), suggesting a chloroplast-centric role. Additional terms point to metabolic biosynthesis and turnover (nitrogen utilization, biotin biosynthesis, uracil catabolic process) and general translation, which commonly occur in chloroplasts. A couple of terms (secondary shoot formation, regulation of endocannabinoid signaling pathway, xenobiotic degradation) are sporadic and may reflect broader network connections or annotation noise. Overall, the cluster appears to reflect plant chloroplast metabolism and photosynthetic machinery rather than a single narrow process.","confidence":"Medium","size":13,"edges":28,"triangles":19,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0019740","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0010190","count":1}]},{"hash":"1908956858454477424","title":"Protein acetylation cluster","description":"The top GO terms are dominated by various acetylation processes (N-terminal acetylation, N-terminal propionylation, peptidyl-lysine acetylation, spermine acetylation, etc.), suggesting the proteins share a common function related to acetylation modifications. A few terms are less clearly connected (arginine biosynthesis, angiogenesis, heterochromatin formation, sister chromatid cohesion), but the acetylation theme is strong overall. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017196","count":3},{"id":"GO:0006526","count":3},{"id":"GO:0061606","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0018003","count":2}]},{"hash":"138935377157957794","title":"Unknown","description":"The GO terms are diverse and largely singleton, including mitochondrial pyruvate import, insulin secretion regulation, ER-stress\u2013related translation initiation, and assorted unrelated processes. There is no clear shared function or pathway tying these proteins together, so a cohesive label cannot be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902361","count":1},{"id":"GO:0035774","count":1},{"id":"GO:0061732","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0070389","count":1}]},{"hash":"1352312960931307510","title":"Strigolactone Biosynthesis and Shoot Branching","description":"A cluster anchored by strigolactone-related terms (strigolactone biosynthetic process and secondary shoot formation) suggests a module governing strigolactone production and shoot branching in plants. The accompanying mitochondrial and redox-related terms imply metabolic and energy-related support for development, indicating a small, development-focused module with metabolic scaffolding. ","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0070542","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0010223","count":2}]},{"hash":"1789997932569570293","title":"Protein trafficking and quality control","description":"The top GO terms center on processes that regulate protein movement and localization (ER exit, localization to the cell surface, secretion) and on protein quality control (ubiquitin-dependent degradation, refolding). While other terms relate to growth or nutrient responses, the common thread is regulation of protein handling and trafficking within the cell, suggesting this as the cluster\u2019s core function.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000010","count":1},{"id":"GO:0033299","count":1},{"id":"GO:0007124","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0061060","count":1}]},{"hash":"1077373708833492030","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":22,"triangles":6,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":6},{"id":"GO:0000466","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":4}]},{"hash":"1770659045166227055","title":"Unknown","description":"The cluster shows a mix of GO terms across translation, osmotic stress response, sodium ion transport, symbiont entry into host, tRNA aminoacylation, meiotic processes, DNA replication, and RNA splicing. This breadth suggests no single cohesive function tying the proteins together, indicating an Unknown cluster.","confidence":"","size":13,"edges":21,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0030260","count":1},{"id":"GO:0006422","count":1}]},{"hash":"2215294704214368426","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":55,"triangles":110,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0006369","count":5},{"id":"GO:0034476","count":5},{"id":"GO:0071051","count":5}]},{"hash":"2024991964617149460","title":"Metal ion transport and calcium homeostasis","description":"Most terms point to metal ion handling and calcium regulation: intracellular calcium ion homeostasis, copper/zinc/cadmium ion transmembrane transport. Dephosphorylation terms suggest signaling regulation, with a couple of outliers (L-serine biosynthesis, stilbene catabolic process) that may reflect annotation spillover. Overall, the cluster is best characterized by metal ion transport and calcium homeostasis.","confidence":"Medium","size":13,"edges":64,"triangles":181,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":5},{"id":"GO:0006874","count":5},{"id":"GO:0006825","count":5},{"id":"GO:0097755","count":5},{"id":"GO:0033574","count":5}]},{"hash":"1057214235748836682","title":"Ribosome Biogenesis and Ubiquitin Signaling","description":"The cluster shows strong signals for rRNA maturation and ribosome assembly (5.8S and LSU rRNA processing) alongside ubiquitin-related proteostasis (ubiquitin-dependent ERAD pathway and protein autoubiquitination), suggesting a theme of ribosome biogenesis paired with ubiquitin-mediated regulation. Other terms (DNA replication/topology changes, TNF signaling, T cell proliferation) appear ancillary, possibly reflecting broader cell-cycle or immune-related contexts but do not override the ribosome-ubiquitin connection.","confidence":"Medium","size":13,"edges":21,"triangles":12,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0000466","count":2},{"id":"GO:0014070","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1866240307732395095","title":"Muscle differentiation and regeneration signaling","description":"The cluster shows strong ties to muscle biology, including myoblast fusion and satellite cell activation related to skeletal muscle regeneration, along with cytoskeletal regulation and calcium signaling that underpin muscle differentiation and function. While some terms are general stress or unrelated processes, the strongest signal comes from muscle development/regeneration mechanisms, justifying this label.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097264","count":1},{"id":"GO:0070315","count":1},{"id":"GO:0007520","count":1},{"id":"GO:0097050","count":1},{"id":"GO:0051493","count":1}]},{"hash":"91088875295694682","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":20,"triangles":16,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0034476","count":3}]},{"hash":"1451312284172994937","title":"Unknown","description":"The top GO terms do not converge on a single coherent function: they include signaling regulation, neural activity, xenobiotic response, chromatin regulation, and cell-cycle processes. With no edges or tight functional grouping, there isn't a clear common theme tying these proteins together, so a specific biological label can't be confidently assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007052","count":1},{"id":"GO:1901077","count":1}]},{"hash":"1954760663337407066","title":"Cell Cycle and Developmental Signaling","description":"The proteins cluster around core cell-cycle and DNA replication processes (DNA replication, centrosome cycle, nuclear replication regulation) and are linked with key developmental pathways (Wnt, Hippo) as well as differentiation and morphogenesis (keratinocyte differentiation, cranial skeleton morphogenesis) and apoptosis, suggesting a coordinated role in growth control during development.","confidence":"Medium","size":13,"edges":52,"triangles":94,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0046827","count":9},{"id":"GO:0060044","count":8},{"id":"GO:0030216","count":8},{"id":"GO:0035329","count":8}]},{"hash":"1354810851937404437","title":"Ribosome Biogenesis and Translation","description":"The dominant GO terms cluster around protein synthesis: translation (cytoplasmic), ribosome biogenesis (including small subunit), tRNA modification, and mitochondrial translation initiation. This points to a cohesive module of ribosome assembly and protein synthesis machinery.","confidence":"High","size":13,"edges":54,"triangles":109,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0006400","count":3},{"id":"GO:0070124","count":2},{"id":"GO:1903833","count":2}]},{"hash":"1034370846713091070","title":"Developmental transcription and RNA processing","description":"The cluster is enriched for DNA-templated transcription and multicellular organism development (including forebrain development), along with RNA processing activities such as spliceosome-mediated splicing and maturation of rRNA. This suggests proteins involved in regulating gene expression during development and in ribosome biogenesis/RNA processing. A minor cadmium response and cell proliferation signal are present but secondary to the core theme.","confidence":"Medium","size":13,"edges":38,"triangles":39,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000466","count":3}]},{"hash":"1165680242878108782","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":24,"triangles":20,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000447","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000472","count":3}]},{"hash":"62286640500383152","title":"Unknown","description":"The top terms span diverse metabolic and stress-response processes (antibiotic and LPS responses; catabolic pathways for stilbene, uracil, nitrogen, and retinol; and the TCA cycle) with several obsolete annotations, yielding no clear shared function. This makes it inappropriate to assign a focused label.","confidence":"","size":13,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0097755","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0046839","count":2}]},{"hash":"1115192979749362485","title":"Unknown","description":"The proteins show a mix of terms related to synapse localization and dendritic spine morphogenesis, but also include glucose response, immune defense, angiogenesis, keratinocyte differentiation, Wnt signaling, and ion transport. This lack of a single dominant shared function makes it unclear to assign a coherent, representative label.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071333","count":7},{"id":"GO:0014068","count":7},{"id":"GO:0050830","count":7},{"id":"GO:0045766","count":7},{"id":"GO:0030216","count":5}]},{"hash":"583401574884730193","title":"Neuroimmune signaling and axon development","description":"The top GO terms point to neural development processes (synapse assembly, corpus callosum development, axonal fasciculation) alongside innate immune signaling (MyD88-dependent TLR signaling, cytokine signaling, IL-6 production) and modulation of signaling pathways (protein kinase activity). This suggests a cohesive theme of neural circuit development modulated by neuroimmune signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051965","count":5},{"id":"GO:0022038","count":5},{"id":"GO:0006469","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0048681","count":4}]},{"hash":"1165388241568228603","title":"Neurodevelopment and development-related proteins","description":"Based on the Top Terms, several entries point to neural and broader embryonic development (forebrain development, neural tube closure, skeletal system development, DNA-templated transcription). There are other diverse processes included (mitotic cell cycle, ER stress\u2013induced apoptosis, cadmium ion response, defense against Gram-positive bacteria), suggesting the proteins participate in multiple cellular programs rather than a single pathway. The strongest cohesive signal is developmental biology, especially neurodevelopment, making this label representative of the cluster's common theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0001403","count":5},{"id":"GO:0001843","count":5}]},{"hash":"745515115902352550","title":"Heart development and Wnt signaling regulation","description":"This cluster prominently features heart development and broader multicellular development terms, with a specific emphasis on negative regulation of canonical Wnt signaling, plus associated transcriptional regulation and nuclear processes. The combination suggests a cardiac development module coordinated by transcriptional control and Wnt pathway modulation, rather than a single non-cardiac process.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0007275","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0033138","count":3}]},{"hash":"671604305504123450","title":"Bacterial membrane transport and respiration components","description":"This cluster is dominated by transport-related GO terms (lipoprotein transport, carbohydrate transport, teichoic acid transport, glycerophosphodiester transmembrane transport, heme transport) and cytochrome complex assembly, pointing to membrane transport and electron transport/respiration roles. Some terms like DNA-templated transcription and stem cell proliferation are less coherent with the main theme, likely reflecting annotation noise or cross-species data. Overall, the label captures the core functions: membrane transport and respiration-related components, with a possible Gram-positive signal due to teichoic acid transport.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0042760","count":2},{"id":"GO:0042953","count":2},{"id":"GO:0008643","count":2},{"id":"GO:0010949","count":2}]},{"hash":"388425503462432875","title":"Ciliogenesis and developmental cell-cycle processes","description":"The top GO terms cluster around mitotic cell cycle (G1/S transition and general mitotic cycle), ciliogenesis (cilium assembly), and multiple development-related processes (forebrain and skeletal system development, multicellular organism development). This points to a theme where cell division and ciliogenesis coordinate during developmental programs. Some stress/defense terms are present but seem ancillary, so the core label emphasizes ciliogenesis together with developmental cell-cycle control.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0060271","count":2},{"id":"GO:2001274","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1753791321633086392","title":"Cell division and microtubule assembly","description":"The top GO terms are dominated by cell cycle, mitotic spindle midzone assembly, cell septum assembly, and microtubule nucleation, pointing to processes involved in cell division and cytoskeletal organization. Other terms (neuron differentiation, mechanosensory behavior, and translation regulation) are less represented and may reflect secondary roles or annotation variance. Overall, the cluster is best characterized by cell division and microtubule dynamics.","confidence":"High","size":13,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051256","count":2},{"id":"GO:0090529","count":2},{"id":"GO:1905792","count":2},{"id":"GO:2000767","count":2}]},{"hash":"2190603911392947399","title":"Central carbon metabolism and sulfur amino acid biosynthesis","description":"The cluster shows strong representation of energy pathways (glycolysis, pyruvate biosynthesis, TCA cycle) alongside sulfur-containing amino acid biogenesis (transsulfuration, hydrogen sulfide biosynthetic process, cysteine-related pathways). Together these terms point to a group of proteins involved in core metabolism and the biosynthesis of sulfur-containing amino acids, justifying a combined label that reflects both energy production and sulfur amino acid biosynthesis.","confidence":"High","size":13,"edges":43,"triangles":74,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0019346","count":4},{"id":"GO:0070814","count":3},{"id":"GO:0009097","count":3},{"id":"GO:0042866","count":3}]},{"hash":"1863258447748020771","title":"Bacterial biosynthesis and motility","description":"The cluster features GO terms centered on metabolic biosynthesis (cobalamin, ubiquinone, tocopherol), carbohydrate phosphorylation, and a bacterial-type flagellum-dependent motility term, pointing to bacterial metabolism and movement as a unifying theme. Some terms (e.g., Purkinje cell layer morphogenesis) appear unrelated and may be noise, but overall the set supports a bacterial biosynthetic and motility theme.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0007049","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071973","count":2}]},{"hash":"2294451703891021938","title":"Bacterial biosynthesis and catabolic pathways","description":"This cluster includes multiple biosynthetic processes typical of bacteria (lipopolysaccharide, ectoine, L-proline, and antibiotic biosynthesis) as well as catabolic pathways for small molecules (GABA, putrescine) and a note on transcription. The mix suggests a broad bacterial metabolic theme rather than a single precise function, hence a label emphasizing both biosynthesis and catabolism in microbes.","confidence":"Medium","size":13,"edges":7,"triangles":1,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009103","count":2},{"id":"GO:0001561","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0019491","count":2}]},{"hash":"1105242472128432539","title":"Unknown","description":"The terms are scattered across transcription machinery (TFIIIB assembly and Pol III transcription regulation) and unrelated developmental and cellular processes (cardiac development, stomatal opening, Leydig cell differentiation, mammary proliferation, ER stress, and cell cycle re-entry), with no single cohesive theme linking them. ","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070217","count":1},{"id":"GO:0061587","count":1},{"id":"GO:0016480","count":1},{"id":"GO:1903779","count":1},{"id":"GO:0003231","count":1}]},{"hash":"616517600279741582","title":"Glycan biosynthesis and carbohydrate metabolism","description":"The top terms cluster around glycosylation and sugar metabolism, including glycolipid biosynthesis, GPI anchor biosynthesis, and protein glycosylation, along with glucose and sucrose metabolic processes. Some stress-related terms (response to flooding, response to mannitol) may reflect osmotic responses, but the dominant theme is glycan/glycoprotein biosynthesis and carbohydrate metabolism.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009247","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0009744","count":3},{"id":"GO:0006490","count":3},{"id":"GO:0006006","count":3}]},{"hash":"1315778647757981998","title":"Unknown","description":"The cluster shows a highly heterogeneous set of GO terms, including redox-related processes, transcription, tRNA processing, dephosphorylation, development, metabolism, and mitotic phase. There is no clear, cohesive functional theme tying all members together, and the absence of edges further supports the lack of a unified cluster function. Therefore, no interpretable single-label function can be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1236112940612884774","title":"Cell cycle and protein synthesis","description":"The top terms cluster around cell cycle, cell division, and translation/ribosome biogenesis, suggesting proteins involved in cell growth and proliferation through protein synthesis. A few reproductive development terms appear but are less representative of the main theme. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0006463","count":2}]},{"hash":"1335470431193433950","title":"Unknown","description":"The top GO terms span metabolism (CoA and pantothenate pathways, tetrahydromethanopterin biosynthesis), protein regulation and oxidation, sporulation, metal ion homeostasis, plant ethylene signaling, and immune-related processes, with no clear unifying function across the cluster. This heterogeneity suggests there isn\u2019t a single coherent biological theme to name; Unknown fits best.","confidence":"","size":12,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032461","count":1},{"id":"GO:1904808","count":1},{"id":"GO:0015941","count":1},{"id":"GO:1901285","count":1},{"id":"GO:0015937","count":1}]},{"hash":"2050317363879937992","title":"Mitochondrial Transporters and Metabolic Regulation","description":"The cluster centers on mitochondrial transport and metabolism, with multiple transport terms (ADP, alpha-ketoglutarate, ornithine, manganese, pyridoxal phosphate) and links to membrane potential and stress signaling (fatty acid response, insulin secretion, necroptosis regulation), suggesting a cohesive mitochondrial transport/metabolic regulation theme.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":4},{"id":"GO:0051881","count":3},{"id":"GO:0060546","count":3},{"id":"GO:0015742","count":3},{"id":"GO:0031921","count":3}]},{"hash":"567522491204708130","title":"Unknown","description":"The Top Terms are spread across developmental processes (brain and root development) and diverse metabolic and cellular processes (translation, nucleotide salvage, thiamine metabolism, phosphorylation). There is no single pathway or function linking most terms, so a cohesive label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0030389","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006238","count":1}]},{"hash":"1195474972998873768","title":"Redox Homeostasis and Transcription Regulation","description":"The terms show a clear emphasis on oxidative stress response and redox balance (cellular oxidant detoxification, cell redox homeostasis, cellular response to oxidative stress) alongside transcription-related processes (DNA-templated transcription, negative regulation of RNA polymerase II regulatory region binding). This mix suggests a cluster of proteins that link redox regulation with transcriptional control, possibly including stress-responsive transcriptional regulation and nucleotide maintenance in response to redox changes; the neural crest migration term is likely incidental noise. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0003147","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1288987690499667362","title":"Spliceosome assembly and genome maintenance","description":"The strongest terms are spliceosome assembly (snRNP/spliceosomal complex assembly) and DNA-related maintenance (DNA recombination and related processes). A few oxidative stress and mitotic terms appear but are secondary. This suggests a nuclear cluster focused on RNA processing and genome maintenance.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0030091","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0070301","count":1},{"id":"GO:1990355","count":1}]},{"hash":"2089313877507891597","title":"Mitochondrial Energy Metabolism","description":"The top GO terms strongly point to mitochondrial functions related to energy production, including mitochondrial ribosome assembly, aerobic respiration, and mitochondrial electron transport with proton translocation. Additional terms implicate protein homeostasis (ubiquitin recycling, protein oligomerization) aspects that support mitochondrial function. Some terms about host\u2013microbe interactions appear as outliers, but the dominant theme is mitochondrial energy metabolism.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061668","count":2},{"id":"GO:0006067","count":2},{"id":"GO:0032461","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0016032","count":2}]},{"hash":"1226790613220119483","title":"Methyltransferases in Hematopoietic Differentiation","description":"The top GO terms are dominated by methylation activities: rRNA methylation, various methylations of peptidyl-lysine and N-terminal residues, and rDNA heterochromatin formation, which point to methyltransferases and chromatin-modifying enzymes. A subset of terms also references regulation of erythrocyte and megakaryocyte differentiation, suggesting these methylation/epigenetic factors may influence hematopoietic differentiation. Overall, the cluster appears to center on methylation and chromatin regulation with a hematopoietic differentiation context.","confidence":"High","size":12,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":4},{"id":"GO:0018027","count":4},{"id":"GO:0045648","count":3},{"id":"GO:0045654","count":3},{"id":"GO:0010725","count":3}]},{"hash":"1259019010384295928","title":"Endosomal Transport and Ubiquitin-Dependent Degradation","description":"The top GO terms cluster around endosome-to-lysosome, endosome-to-Golgi, and endosome-to-late endosome transport, plus Cvt/autophagy-related transport and ubiquitin-dependent proteolysis (including protein autoubiquitination). This points to a coherent function involving intracellular vesicle trafficking and targeted protein turnover via ubiquitination, with a few additional terms likely representing secondary associations. ","confidence":"High","size":12,"edges":26,"triangles":28,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0034498","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0048714","count":2}]},{"hash":"93367535586784760","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":25,"triangles":23,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0006378","count":4},{"id":"GO:0010610","count":4}]},{"hash":"2209026430561571031","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":28,"triangles":29,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0000902","count":8},{"id":"GO:0007100","count":8},{"id":"GO:0042220","count":8},{"id":"GO:0032212","count":8}]},{"hash":"249539006361199631","title":"Developmental differentiation and signaling","description":"The cluster\u2019s GO terms point mainly to developmental and differentiation processes: embryonic cranial skeleton morphogenesis, keratinocyte differentiation, and positive regulation of Wnt signaling, with related neuronal aspects like protein localization to synapse and dendritic spine morphogenesis. DNA replication and apoptotic processes appear as broad cellular contexts that accompany development. Overall, the common theme is development and cell fate regulation via signaling pathways, spanning skin, craniofacial development, and neural synapse organization.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0007100","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0030216","count":5}]},{"hash":"1557350323077774575","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms point to maturation of SSU/LSU/5.8S rRNA and ribosomal large subunit biogenesis, indicating a core function in ribosome assembly and rRNA maturation. While there are additional terms related to splicing, ubiquitination, and other processes, the dominant signal is ribosome-related, justifying this label. These secondary terms may reflect broader multifunctionality or annotation noise.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000466","count":3},{"id":"GO:0048568","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000462","count":3}]},{"hash":"1522834890238856534","title":"Translation initiation and spliceosome-mediated splicing regulation","description":"The top GO terms cluster around regulation of translational initiation, formation of the translation preinitiation complex, translation reinitiation, and regulation of alternative mRNA splicing via the spliceosome, suggesting a coordinated role in controlling gene expression at both translation initiation and mRNA processing.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0002188","count":2}]},{"hash":"1330666326328429353","title":"Mitotic Regulation and Growth Signaling","description":"This cluster centers on mitosis-related processes (centrosome separation, kinetochore localization, CDK activity regulation) and major growth/regulatory signaling pathways (Wnt and Hippo), with additional notes on differentiation and tissue-specific proliferation. The combination suggests proteins that coordinate cell division with signaling controls for development and growth, rather than a single pathway. Potassium transport appears as a peripheral note but does not dominate the theme. ","confidence":"High","size":12,"edges":16,"triangles":5,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007100","count":6},{"id":"GO:0030216","count":6},{"id":"GO:0043552","count":6},{"id":"GO:0090263","count":6},{"id":"GO:0046827","count":6}]},{"hash":"691756931124565459","title":"Cardiac and vascular development","description":"The top GO terms center on heart formation and vascular processes (cardiac right atrium morphogenesis, Notch signaling in heart field proliferation, venous endothelial differentiation, and sprouting angiogenesis), with additional signals for SA node cell communication, supporting a cardiovascular development theme. While there are general cellular processes like actin assembly and cell cycle present, the strongest signal is heart and blood vessel development.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0003213","count":2},{"id":"GO:1903589","count":2},{"id":"GO:0051017","count":2}]},{"hash":"694134023606107310","title":"Neural development and signaling","description":"The top terms center on nervous system development and function, including neuron differentiation, Schwann cell development, excitatory postsynaptic potential, and locomotion tied to neural activity. Although there are also terms related to other developmental processes (lung development, lymphangiogenesis), the neural-related terms are the strongest signal, justifying this label.","confidence":"Medium","size":12,"edges":24,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":3},{"id":"GO:0043278","count":3},{"id":"GO:0050728","count":3},{"id":"GO:0035562","count":2},{"id":"GO:0031987","count":2}]},{"hash":"1302227514663766199","title":"Ubiquitination-driven proteasomal degradation","description":"The cluster centers on ubiquitination processes and proteasome-mediated protein degradation, with multiple ubiquitin linkage types (K48, K63, K6) and autoubiquitination, plus SCF-dependent degradation. These terms together point to protein tagging for degradation and regulation of signaling pathways, including NF-kappaB and apoptosis, making ubiquitin-mediated control the core theme. A vitamin D response term is present but appears secondary to the primary ubiquitination/degradation theme.","confidence":"High","size":12,"edges":6,"triangles":0,"max_degree":6,"top_function":"autophagy","top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0051865","count":6},{"id":"GO:0033280","count":5},{"id":"GO:0070534","count":5}]},{"hash":"1669305625711711997","title":"Ribosome biogenesis and translation machinery","description":"The top GO terms point strongly to ribosome assembly and protein synthesis (cytoplasmic translation, ribosomal subunit biogenesis, tRNA modification, translation), suggesting these proteins function together in ribosome biogenesis and translation. Additional terms related to cell cycle/division and septum assembly may reflect growth-division coordination or stress responses, but the dominant theme is ribosome-related processes.","confidence":"High","size":12,"edges":31,"triangles":45,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0046677","count":3},{"id":"GO:1903833","count":2},{"id":"GO:0090529","count":2}]},{"hash":"2039339298349945800","title":"Translation and ribosome biogenesis","description":"Dominant signals are translation-related: translation, translational initiation, ribosome biogenesis, and tRNA modification, pointing to protein synthesis machinery. Secondary terms for cell cycle/division and mitochondrial organization hint at broader cellular housekeeping; the sensory perception of sound term is likely unrelated. The cluster is best captured by ribosome biogenesis and translation.","confidence":"High","size":12,"edges":51,"triangles":113,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0007049","count":4},{"id":"GO:0006400","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0051301","count":3}]},{"hash":"2002369533792481769","title":"Vitamin and Amino Acid Biosynthesis; Metal Ion Import","description":"The cluster's top GO terms show multiple biosynthetic pathways (cobalamin, pantothenate, L-tyrosine) and metal ion import (copper, iron), suggesting a grouping of proteins involved in diverse metabolic biosynthesis and metal ion transport rather than a single specific function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0015677","count":1},{"id":"GO:0015940","count":1},{"id":"GO:1903206","count":1}]},{"hash":"1553616344692405104","title":"Amino acid biosynthesis and redox stress response","description":"Most top GO terms cluster around biosynthesis of amino acids (isoleucine, arginine, tryptophan, transsulfuration, short-chain fatty acids) and redox-related processes (cell redox homeostasis, oxidation-reduction). A few terms hint at xenobiotic response and signaling (cAMP), implying metabolic regulation and stress responsiveness. There is an outlier term for cerebral cortex development, which is likely annotation noise in this context; overall theme centers on amino acid biosynthesis and redox/stress response.","confidence":"Medium","size":12,"edges":21,"triangles":13,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":2},{"id":"GO:0006526","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0055114","count":2}]},{"hash":"272414423323564683","title":"Translation initiation complex formation and regulation","description":"Terms point to translation initiation: formation of translation preinitiation and cytoplasmic translation initiation complexes, as well as the general translation process and its negative regulation. A few neural development-related terms are present but seem peripheral. Overall, the cluster appears centered on components and regulators of translation initiation machinery.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0014002","count":1},{"id":"GO:0001732","count":1}]},{"hash":"472272760735621458","title":"Unknown","description":"The GO terms span apoptosis, ER protein folding, ubiquitin-proteasome quality control, heat stress response, DNA replication, and other nuclear/mitochondrial processes with no single cohesive theme; thus there is no clear function tying all proteins together.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006924","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0000002","count":1},{"id":"GO:1905259","count":1},{"id":"GO:0006260","count":1}]},{"hash":"1660967748025472571","title":"Unknown","description":"The top GO terms span redox homeostasis, detoxification, signaling, transcriptional regulation, protein repair, and even viral processes, with no single dominant function tying the proteins together; such heterogeneity prevents a confident, specific label beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1},{"id":"GO:0043388","count":1}]},{"hash":"461273549900204301","title":"Plant PI and inositol lipid biosynthesis under osmotic stress","description":"The cluster is dominated by GO terms for phosphatidylinositol/inositol biosynthesis and related lipid signaling (e.g., phosphatidylinositol biosynthetic process, phosphatidylinositol phosphate biosynthetic process, inositol biosynthetic process), which are often linked to osmotic stress signaling in plants, including abscisic acid-activated pathways. A few terms (gluconeogenesis, sulfate assimilation, neural precursor proliferation, ethanol response) seem ancillary or annotation-related, but the core pattern suggests lipid-mediated osmotic stress signaling in plants.","confidence":"Medium","size":12,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046854","count":2},{"id":"GO:0046855","count":2},{"id":"GO:0006661","count":2},{"id":"GO:0042538","count":2},{"id":"GO:0006021","count":2}]},{"hash":"1710059437712839982","title":"Plasma Membrane Solute Transport","description":"The cluster centers on diverse transport activities across the plasma membrane, including xenobiotic, urate, organic anion, glucose, selenite, and ascorbate transport, along with cellular responses to osmotic and nutrient stress. The GO terms point to multiple substrate transport processes (e.g., xenobiotic transport, urate transport, D-glucose transmembrane transport, organic anion transport, plasma membrane selenite transport, L-ascorbic acid metabolic process) and stress responses, suggesting a family of proteins functioning in general solute transport rather than a single substrate pathway.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":1},{"id":"GO:0042908","count":1},{"id":"GO:0015747","count":1},{"id":"GO:0060731","count":1},{"id":"GO:0042149","count":1}]},{"hash":"1618109176910910994","title":"Redox homeostasis and xenobiotic response","description":"The cluster centers on oxidative stress management and detoxification, as shown by enrichment for redox homeostasis, cellular oxidant detoxification, response to xenobiotic stimulus, and response to toxic substances. While there are also biosynthetic and DNA-related terms present, the core theme appears to be maintaining redox balance and handling xenobiotic challenges.","confidence":"Medium","size":12,"edges":11,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0009636","count":2}]},{"hash":"909715783758278305","title":"Unknown","description":"The top terms are a mix of core cell-cycle processes (mitotic cell cycle, cell division), nucleotide and sugar metabolism (pentose-phosphate shunt, ribose and uridine biosynthesis), and several unrelated processes (myelination in PNS, cuticle development, intra-Golgi transport, GTPase regulation), with no clear, single shared function linking all proteins. This suggests a heterogeneous set rather than a cohesive pathway or process.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006098","count":1}]},{"hash":"1298066065532645054","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001682","count":2},{"id":"GO:0000294","count":2},{"id":"GO:1905267","count":2},{"id":"GO:0034965","count":2},{"id":"GO:0055114","count":1}]},{"hash":"2213450451917505233","title":"Neuronal Synaptic Vesicle Cycling","description":"This cluster is enriched for GO terms tied to vesicle trafficking and synaptic function, including regulation of synaptic vesicle exocytosis and endocytosis, excitatory postsynaptic potentials, and related neuronal development (e.g., substantia nigra development). These points together suggest a core theme of synaptic vesicle cycling in neurons, with other terms (bone ossification, mitotic cycle) likely reflecting broader or indirect associations.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043931","count":4},{"id":"GO:0006893","count":3},{"id":"GO:0021762","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0035690","count":3}]},{"hash":"1156064063760669105","title":"Glutathione-driven redox homeostasis and detoxification","description":"The cluster centers on redox balance and detoxification, highlighted by GO terms for cell redox homeostasis, glutathione metabolic process, and protein glutathionylation, plus cellular oxidant detoxification and arsenic response. Mitochondrial membrane potential regulation and DNA repair signals (nucleotide-excision repair) suggest a broader context where redox state influences genome maintenance. While a few terms point to other metabolisms, the dominant theme is redox control and detoxification via glutathione pathways.","confidence":"Medium","size":11,"edges":19,"triangles":14,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0051881","count":3},{"id":"GO:0006749","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0006289","count":3}]},{"hash":"33382663089073739","title":"Unknown","description":"The top GO terms are a mix of regulatory and stress-related processes, with many obsolete terms and no single cohesive function. They point to diverse roles such as kinase activity regulation, mitochondrial calcium import, ER stress\u2013related translation, and development, rather than a unified pathway. Therefore a concise, representative label cannot be assigned.","confidence":"","size":11,"edges":16,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0036444","count":3},{"id":"GO:0090084","count":2},{"id":"GO:0070389","count":2}]},{"hash":"1165295586467245604","title":"Neuronal synaptic vesicle cycling","description":"This cluster is driven by neural synaptic processes: regulation of vesicle exocytosis and endocytosis, excitatory postsynaptic potentials, and development of the substantia nigra, pointing to a module of neuronal synaptic vesicle trafficking and signaling. Some terms (xenobiotic response, microautophagy, GTPase regulation) are broader regulatory processes that may intersect with neuronal function.","confidence":"Medium","size":11,"edges":9,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0060079","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0016237","count":3},{"id":"GO:0021762","count":3}]},{"hash":"1544355921054644780","title":"Lipid mobilization under glucose starvation","description":"The terms are dominated by triglyceride catabolic and mobilization processes and a cellular response to glucose starvation, pointing to energy release through lipid breakdown during nutrient stress. Phospholipid catabolic processes (phosphatidylethanolamine and phosphatidylcholine) suggest membrane lipid remodeling accompanying this metabolic shift. A couple of unrelated terms (centrosome localization, meiosis pairing) may reflect broader cellular changes or annotation noise, but do not override the main lipid-energy theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042149","count":2},{"id":"GO:0006642","count":1},{"id":"GO:2000480","count":1},{"id":"GO:0046338","count":1},{"id":"GO:0019433","count":1}]},{"hash":"1064880892787067449","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000466","count":4},{"id":"GO:0048568","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000462","count":4}]},{"hash":"1171678791139468613","title":"RNA splicing and chromatin remodeling","description":"The cluster features GO terms centered on RNA processing\u2014mRNA splicing via the spliceosome, its regulation, snoRNA release from pre-rRNA, and rRNA maturation\u2014together with chromatin remodeling, suggesting a nucleus-focused program coordinating RNA processing with chromatin dynamics. Some terms related to development or learning are less directly connected and may reflect broader regulatory roles or annotation noise.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":9},{"id":"GO:0031047","count":9},{"id":"GO:0000398","count":6},{"id":"GO:0071894","count":5},{"id":"GO:0000466","count":5}]},{"hash":"1626650449324431015","title":"Translation machinery and ribosome biogenesis","description":"The dominant signals are translation-related GO terms: translation, ribosome biogenesis, translation initiation/elongation/termination, and even selenocysteine incorporation, all pointing to protein synthesis and ribosome function. There is also a connected mRNA decay process and positive regulation of cytoplasmic translation, reinforcing a theme of active translation and ribosome assembly. A couple of outliers (glial proliferation and antibiotic response) are present but do not disrupt the central translation-focused pattern. ","confidence":"High","size":11,"edges":27,"triangles":36,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0001514","count":3},{"id":"GO:0000288","count":3},{"id":"GO:0006413","count":3}]},{"hash":"1527804701984319781","title":"Protein targeting and membrane translocation","description":"The cluster is dominated by GO terms for guiding and moving proteins to membranes and across compartments, including SRP-dependent cotranslational targeting, Sec complex\u2013mediated transport, post-translational targeting, and ER-to-cytosol retrograde transport. Development-related terms appear only modestly, suggesting the core function is protein trafficking rather than cell-cycle control.","confidence":"High","size":11,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0070843","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0039019","count":1}]},{"hash":"813605409897889187","title":"Intracellular transport and development","description":"The cluster is dominated by terms for intracellular transport processes (intraciliary transport, ER-to-Golgi vesicle transport) and coupled regulatory processes (GTPase activity, ubiquitin-proteasome degradation, spindle orientation) with a developmental signal (brain development). Some terms are obsolete, suggesting noise, but the core theme centers on trafficking/regulation within cells tied to development.","confidence":"Medium","size":11,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043984","count":2},{"id":"GO:0043981","count":2},{"id":"GO:0043982","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0035735","count":2}]},{"hash":"1184538754734514083","title":"Mitochondrial Translation and RNA Processing","description":"The strongest, most coherent signal in the top GO terms is mitochondrial translation and overall translation (GO:0006412, GO:0070124), suggesting these proteins participate in mitochondrial protein synthesis. Supporting terms point to RNA-related processing/modification, such as 7-methylguanosine mRNA capping and various methylation events, which fit with a broader role in RNA maturation linked to translation. A few outlier terms (lignin biosynthesis, hyperosmotic response, cellular senescence) may reflect annotation noise or multifunctional roles in stress-related pathways, but they do not override the central theme of mitochondrial protein synthesis and RNA processing.","confidence":"Medium","size":11,"edges":13,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0051301","count":2},{"id":"GO:0070124","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0001300","count":1}]},{"hash":"1576083163601100173","title":"Ribosome Biogenesis and Cytoplasmic Translation","description":"The dominant GO terms describe ribosomal subunit biogenesis, translation, translational initiation, and cytoplasmic translation, pointing to proteins involved in ribosome assembly and protein synthesis. A minor outlier relates to base-excision repair, but the core cluster centers on ribosome biogenesis and translation.","confidence":"High","size":11,"edges":41,"triangles":79,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006413","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2}]},{"hash":"233967309653125536","title":"Plant endomembrane trafficking and tropic signaling","description":"This cluster centers on endosome organization/transport and Golgi Ca2+ transport, plus chloroplast protein import and plastid-related organization, alongside plant-specific tropic responses like phototropism and gravitropism (amyloplast organization). The common thread is plant endomembrane/organellar coordination involved in plastid targeting and gravity/light-directed growth, yielding a cohesive, plant-focused label.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":1},{"id":"GO:0040039","count":1},{"id":"GO:1902954","count":1},{"id":"GO:0007032","count":1},{"id":"GO:2000641","count":1}]},{"hash":"904462722690992709","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The cluster is dominated by GO terms tied to ubiquitination and proteasome-driven protein catabolism (e.g., ubiquitin-dependent ERAD, SCF-dependent proteasomal degradation, K63-linked ubiquitination, autoubiquitination), pointing to a core theme of regulated protein turnover. Some additional terms (defense, development) appear peripheral but do not obscure the main proteostasis signal.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0030579","count":3},{"id":"GO:0060528","count":3},{"id":"GO:0070534","count":3}]},{"hash":"1879646146157056583","title":"DNA Replication and Proteostasis During Cell Division","description":"The cluster shows strong representation of core cell cycle and DNA replication terms (cell division, DNA replication), together with protein quality control and stress responses (protein unfolding, ER unfolded protein response, ribosomal assembly, oxidative stress). This combination suggests a group of proteins coordinating DNA replication and cell cycle progression with proteostasis and stress management mechanisms. Medium","confidence":"","size":11,"edges":22,"triangles":23,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006260","count":4},{"id":"GO:0030968","count":3},{"id":"GO:0072389","count":3},{"id":"GO:0043335","count":3}]},{"hash":"938970260985928894","title":"Bacterial cell wall polysaccharide biosynthesis","description":"These terms center on glycosylation and synthesis of cell-wall polysaccharides (teichoic acids, hyaluronan, cellulose) and their sugar donors (UDP-glucose, arabinopyranosyl units). This points to a cohesive role in bacterial cell wall glycan assembly and modification, beyond isolated eukaryotic processes like immunoglobulin production.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018242","count":2},{"id":"GO:0018243","count":2},{"id":"GO:0019350","count":2},{"id":"GO:0006011","count":2},{"id":"GO:0036108","count":2}]},{"hash":"2237667266087992194","title":"S1P signaling in brain development and angiogenesis","description":"These terms cluster around sphingosine-1-phosphate signaling, including S1P receptor signaling and sphingosine biosynthesis, and extend to NF-kB\u2013 and TNF-related inflammatory signaling, calcium signaling, and processes linked to brain development, angiogenesis, and synaptic plasticity. The convergence on neurodevelopmental and vascular growth processes, together with NF-kB signaling, supports a coherent module centered on S1P-mediated signaling in brain and angiogenic contexts.","confidence":"High","size":11,"edges":12,"triangles":2,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045766","count":4},{"id":"GO:0019722","count":2},{"id":"GO:0042346","count":2},{"id":"GO:0003376","count":2},{"id":"GO:0010803","count":2}]},{"hash":"1942521237023963075","title":"Glycan and polysaccharide biosynthesis","description":"This cluster features GO terms centered on UDP-sugar metabolism and cell wall\u2013related polysaccharide production (callose deposition, glucan biosynthesis), indicating a shared role in glycan formation and cell wall assembly. Some terms (e.g., palmitoylation, sebaceous gland development) appear peripheral, but the carbohydrate biosynthesis signals dominate.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018230","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0033356","count":1},{"id":"GO:0052543","count":1}]},{"hash":"1157235932650442053","title":"Mitochondrial tRNA charging and telomere maintenance","description":"The terms emphasize mitochondrial tRNA aminoacylation and translation, plus telomere-related processes (capping, maintenance, localization) and DNA repair/recombination, suggesting a cluster rooted in nucleic acid metabolism and genome maintenance that spans both RNA processing/translation and telomere stability.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0070156","count":1},{"id":"GO:0016233","count":1},{"id":"GO:0006422","count":1},{"id":"GO:0070146","count":1}]},{"hash":"1887519926086416891","title":"Retinoid metabolism and RA signaling","description":"The cluster is dominated by retinol and retinal metabolic processes and by regulation of retinoic acid receptor signaling, implying a cohesive retinoid metabolism/signal group. Several other terms (bile acid biosynthesis, methylglyoxal response) are present but appear peripheral to this core theme.","confidence":"High","size":11,"edges":49,"triangles":126,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":7},{"id":"GO:0046370","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0042574","count":5},{"id":"GO:0048385","count":4}]},{"hash":"1949642394776849590","title":"Ubiquitin-Proteasome\u2013Mediated Innate Immunity","description":"This cluster centers on ubiquitin-dependent protein degradation (including SCF pathways and autoubiquitination) paired with innate immune and antiviral defense signals, indicating coordinated roles in proteasome-mediated regulation of immune responses and TNF signaling.","confidence":"High","size":11,"edges":8,"triangles":0,"max_degree":8,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0045087","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0033280","count":4},{"id":"GO:0051865","count":4}]},{"hash":"2097400829897606016","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning bacterial vitamin/cofactor biosynthesis (menaquinone, biotin), nitrogen metabolism and regulation, and several unrelated eukaryotic signaling processes. There is no clear, single function tying the cluster together, so a precise label is not evident.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0009405","count":2},{"id":"GO:0006542","count":2},{"id":"GO:0090295","count":2}]},{"hash":"1808067639334019469","title":"Unknown","description":"The top GO terms span plastid-related processes (plastid transcription, thylakoid organization, menaquinone biosynthesis) but also include nuclear histone methylation and some development terms (muscle and stem cell differentiation). The lack of a single cohesive function and the absence of protein\u2013protein edges suggest these annotations reflect diverse, non-overlapping roles rather than a unified pathway, so a specific functional label could not be assigned.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0032088","count":1},{"id":"GO:0010027","count":1},{"id":"GO:0018023","count":1}]},{"hash":"1343811387128218188","title":"Unknown","description":"The top GO terms are highly heterogeneous: two terms point to ER-Golgi vesicle transport, but other terms relate to retina development, pigmentation, rRNA maturation, cell proliferation, actin dynamics, mitotic checkpoints, and tissue development. This lack of a unifying function across the cluster makes a coherent, specific label inappropriate.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0000466","count":1}]},{"hash":"1316637422433215623","title":"Unknown","description":"The top GO terms are highly diverse, spanning lipid biosynthesis/remodeling, ER protein retention, redox homeostasis, proline hydroxylation, cutin biosynthesis, and various developmental processes, with no single cohesive function tying the proteins together. This lack of a common theme makes a specific, representative label unlikely. ","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001238","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0036151","count":1}]},{"hash":"19178847314532159","title":"Mitotic progression and ER-Golgi trafficking","description":"The top GO terms point to mitosis (mitotic cell cycle, cell division, kinetochore localization) and ER-to-Golgi vesicle transport (ER-Golgi vesicle-mediated transport) with related GTPase regulation, suggesting a cluster of proteins involved in both cell cycle progression and intracellular trafficking. While other terms indicate broader proliferation signals, the shared themes center on mitotic control and vesicular transport. Confidence: Medium","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1758508082519203954","title":"Unknown","description":"The GO terms are highly diverse, spanning lung differentiation, prostaglandin biosynthesis, amino acid metabolism, calcium-regulated muscle contraction, smell, vitamin C response, amino acid response, glucocorticoid signaling, plant auxin signaling, and nitrogen utilization, with no single cohesive function linking them. Confidence: None","confidence":"","size":10,"edges":12,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0060510","count":3},{"id":"GO:0001516","count":3},{"id":"GO:0009072","count":2},{"id":"GO:0014810","count":2},{"id":"GO:0007608","count":2}]},{"hash":"147778623769874630","title":"Light-harvesting and photosystem II components","description":"The cluster\u2019s GO terms are dominated by photosynthesis and light-response categories, especially light harvesting in photosystem II and photosynthesis, plus responses to blue, red, far-red, and UV-A light, suggesting chloroplast-associated light capture proteins and photosynthetic machinery. A single mitochondrial-import term appears as noise rather than core function. ","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0071486","count":1},{"id":"GO:0009769","count":1},{"id":"GO:0010114","count":1}]},{"hash":"295867500899429466","title":"RNA methylation and capping","description":"The cluster is dominated by RNA modification terms (tRNA/rRNA methylation, mRNA capping, and related guanosine methylation metabolism) plus some protein methylation, pointing to a shared function in RNA modification processing. A few developmental or growth terms are secondary. ","confidence":"Medium","size":10,"edges":11,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0032775","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0009452","count":1}]},{"hash":"1748719076978009966","title":"ER Stress Response and Protein Folding","description":"These proteins cluster around endoplasmic reticulum (ER) quality control and stress response, with terms like protein folding in the ER, response to ER stress, and regulation of translation initiation in response to ER stress, plus chaperone/refolding-related terms. While a couple of terms (DNA replication, mesoderm formation) appear peripheral, the ER folding and UPR-related terms provide a coherent core theme for the cluster.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070542","count":4},{"id":"GO:0090084","count":4},{"id":"GO:0070389","count":4},{"id":"GO:0097428","count":4},{"id":"GO:0036494","count":4}]},{"hash":"94146693611504494","title":"Translation and mitochondrial stress responses","description":"The dominant term is translation, with several entries for responses to translation inhibitors (cycloheximide, antibiotic), indicating a cluster centered on protein synthesis and its stress responses. The presence of mitochondrial electron transport and apoptotic processes suggests a link between translation-related stress and mitochondrial/ apoptotic pathways. Some older or unrelated terms appear, but the core theme is translation-associated stress with mitochondrial involvement.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046898","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006120","count":1},{"id":"GO:0061458","count":1}]},{"hash":"126209429995189185","title":"Mitochondrial Translation and Sulfur Metabolism","description":"The cluster shows enrichment for mitochondrial processes: translation and maturation of SSU-rRNA, and proton motive force-driven ATP synthesis, alongside sulfur metabolism such as transsulfuration, homocysteine catabolism, and hydrogen sulfide biosynthesis. The angiogenesis term may reflect H2S signaling linked to mitochondrial sulfur metabolism, suggesting a cohesive theme around mitochondrial protein synthesis coupled with sulfur-based metabolic signaling.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0019346","count":2},{"id":"GO:0042776","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0031564","count":1}]},{"hash":"2214235306943559890","title":"Gene Expression and Cell Fate Regulation","description":"The cluster\u2019s top GO terms center on regulating transcription (negative regulation of transcription by RNA polymerase II), protein turnover (polyubiquitination), immune signaling (regulation of TLR signaling), and cell fate decisions (necroptosis, apoptosis, cell cycle), plus stress responses (SOS response) and DNA processing. Together these suggest a regulatory module that modulates gene expression and cell fate in stress or host-interaction contexts, rather than a single straightforward pathway.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060544","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0071157","count":1}]},{"hash":"1602878891164364554","title":"RNA Modification and Transcription Regulation","description":"Most prominent terms center on nucleic acid modification and RNA processing: tRNA wobble uridine modification, methylation (including peptidyl-glutamine methylation) and 7-methylguanosine mRNA capping, plus a link to transcription control via RNA Pol II. Although antibiotic biosynthesis and cobalamin biosynthesis appear in the set, these likely reflect organism-specific metabolism rather than the cluster\u2019s core function. Overall, the cluster seems enriched for RNA modification and transcription-related processes.","confidence":"Medium","size":10,"edges":30,"triangles":53,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0002098","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0055114","count":3}]},{"hash":"534977534555577071","title":"Nuclear transport and mitosis","description":"The terms cluster around transport across the nuclear envelope (snRNA export, mRNA export under heat stress, nuclear pore organization, NLS-bearing protein import) and core mitotic processes (chromosome condensation, sister chromatid separation). This points to a shared role in coordinating nuclear-cytoplasmic trafficking with chromosome segregation during cell division. A vesicular trafficking term (Golgi to lysosome transport) is less central but does not contradict the dominant theme.","confidence":"Medium","size":10,"edges":15,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006408","count":1},{"id":"GO:0031990","count":1},{"id":"GO:0006999","count":1},{"id":"GO:0072417","count":1},{"id":"GO:0060188","count":1}]},{"hash":"1282432173954369313","title":"Developmental transcription regulation","description":"These proteins show terms tied to organ development (lung saccule development, heart morphogenesis, bone marrow development) and to transcriptional control (DNA-templated transcription and its regulation), with additional references to retinoic acid signaling. The common thread appears to be roles in developmental gene regulation rather than a single pathway, supporting a Developmental transcription regulation label.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060430","count":1},{"id":"GO:0048386","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0035522","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1633257836929374321","title":"Neural and epithelial development with Wnt signaling","description":"These proteins cluster around developmental processes, especially neural lineage and epithelial differentiation, as evidenced by axonogenesis, Schwann cell development, keratinocyte differentiation, and multicellular organism development, with signaling involvement (Wnt). While there are proliferation terms (DNA replication, mitotic cell cycle), they likely reflect growth during development rather than a single pathway, so the overall theme is developmental signaling driving neural and epidermal differentiation.","confidence":"Medium","size":10,"edges":18,"triangles":11,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0007118","count":4},{"id":"GO:0014044","count":4}]},{"hash":"1163425238148485","title":"MAPK and Wnt Signaling Regulators with Cell Cycle Control","description":"Top GO terms indicate regulation of MAPK pathways (JNK and ERK) and canonical Wnt signaling, along with cell-cycle processes like DNA replication and mitotic re-entry. Some terms point to development and adhesion, but the strongest, common theme is regulators of key signaling cascades that coordinate cell cycle progression. ","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0009190","count":4},{"id":"GO:0046330","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0000320","count":4}]},{"hash":"1243694603630974866","title":"Transmembrane transporters (ions and nutrients)","description":"This cluster centers on transmembrane transport across membranes, with GO terms covering xenobiotic, ion (sodium, nitrate, nitrite, phosphate), vitamin, arabinose, and other substrate transport, plus neurotransmitter loading into vesicles. The unifying theme is membrane transporter proteins handling diverse substrates, suggesting a coherent transporter function group.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0042891","count":1},{"id":"GO:0015706","count":1},{"id":"GO:0015707","count":1}]},{"hash":"1879105437697415784","title":"DNA replication and cell division","description":"The cluster is dominated by GO terms related to DNA replication (DNA replication, primer synthesis, and related unwinding) and cell division, plus growth regulation, indicating a core theme of DNA synthesis and cell cycle progression. A few other terms (defense response, viral genome replication, ER-Golgi transport) appear but are less central to the primary signal. Overall, the proteins appear to cluster around replication and proliferation processes.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006268","count":4},{"id":"GO:0006269","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0050830","count":3}]},{"hash":"2068051889427957289","title":"Unknown","description":"The set of GO terms is highly heterogeneous, including viral process, mRNA transport, TORC1 signaling, transcription regulation, and cellular responses to cadmium, with no clear shared pathway or cellular function across the proteins. There are no edges connecting proteins, so there is no cohesive functional theme to label beyond Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0001938","count":2},{"id":"GO:0038202","count":2}]},{"hash":"1639502746346545533","title":"Developmental transcriptional regulation","description":"The cluster includes diverse development-related terms across tissues (pituitary, pancreas, bronchiole, cortical interneurons) along with core transcriptional processes (DNA-templated transcription, RNA polymerase II transcription, regulation of transcription). This suggests proteins involved in regulating gene expression during development rather than a single tissue-specific function.","confidence":"High","size":10,"edges":23,"triangles":21,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":3},{"id":"GO:0090009","count":2},{"id":"GO:0006351","count":2},{"id":"GO:2001016","count":2},{"id":"GO:0006355","count":2}]},{"hash":"34827133106505219","title":"Quinone biosynthesis and broad metabolic pathways","description":"The top GO terms cluster around biosynthesis of quinones (menaquinone, phylloquinone) and related metabolic activities, with supporting signals for antibiotic biosynthesis, fatty acid beta-oxidation, and amino acid catabolism. This suggests a cohesive bacterial metabolic module centered on quinone production and energy metabolism, with links to broader biosynthetic and degradative pathways.","confidence":"Medium","size":10,"edges":41,"triangles":94,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0009234","count":4},{"id":"GO:0010124","count":4},{"id":"GO:0042372","count":4},{"id":"GO:0006635","count":4}]},{"hash":"1719384723666953667","title":"Unknown","description":"The top GO terms are a heterogeneous mix: rRNA maturation, neuron and inner cell mass development, yeast spindle pole body duplication and cell cycle re-entry, plus multiple post-translational modification processes (phosphorylation, ubiquitin-related pathways, deglycosylation, deubiquitination). The lack of a cohesive shared function or pathway across the cluster, along with zero edges or triangles, suggests no clear common theme to unite these proteins; thus an Unknown label with no confidence is appropriate.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0030182","count":2},{"id":"GO:0000321","count":1},{"id":"GO:0006468","count":1},{"id":"GO:0001827","count":1}]},{"hash":"1230398548663193450","title":"Redox Homeostasis and ER Protein Folding","description":"The GO terms show a clear emphasis on redox balance and detoxification (redox homeostasis, cellular oxidant detoxification, oxidation-reduction processes) with supportive signals for cytochrome complex assembly and protein folding in the endoplasmic reticulum, suggesting a theme of managing oxidative stress and maintaining proper protein folding. Some terms (outer membrane assembly, viral process, epithelial differentiation) are less directly connected, but the redox-related terms are dominant, supporting a cohesive label. The lack of edges indicates limited observed connectivity in this dataset, but the suggested theme remains the best representation of the cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0043165","count":2},{"id":"GO:0030855","count":2},{"id":"GO:0043388","count":1}]},{"hash":"703982162066434703","title":"Nuclear RNA Splicing and Processing","description":"The top GO terms cluster around spliceosome assembly, mRNA splicing, and transcription-coupled RNA processing/repair, indicating proteins involved in nuclear RNA maturation. Additional terms for tRNA processing and P-body assembly reflect broader RNA metabolism, while some terms like neuron differentiation seem less central.","confidence":"High","size":10,"edges":12,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":2},{"id":"GO:0033962","count":2},{"id":"GO:0006369","count":2},{"id":"GO:0000245","count":2},{"id":"GO:0030182","count":2}]},{"hash":"1364891799125267503","title":"Diverse Metabolic Pathways","description":"Top terms indicate a broad mix of biosynthetic and catabolic processes (antibiotic biosynthesis, PHB biosynthesis, androgen/glucocorticoid/retinol metabolism, acetoin and sphinganine metabolism) plus sporulation and transcription regulation. There is no single cohesive function tying all terms together, suggesting these proteins participate in varied metabolic roles. Therefore the label reflects a broad metabolic theme rather than a specific pathway.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0030435","count":1},{"id":"GO:0006710","count":1}]},{"hash":"1690072275934735909","title":"Unknown","description":"The top GO terms span developmental processes (forebrain development, neural tube closure, skeletal development), transcription and cell cycle (DNA-templated transcription, mitotic cell cycle), plus broad stress and defense responses (cadmium ion response, ER stress\u2013induced apoptosis, defense against Gram-positive bacteria), with no single cohesive function linking them. This diversity suggests no unified cluster function can be confidently assigned.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0001843","count":4}]},{"hash":"2210812576747632906","title":"Developmental Regulation and Stress Responses","description":"The top GO terms point to broader roles in developmental processes (forebrain and skeletal development, multicellular development) and transcriptional regulation, while also highlighting various stress/immune-related responses (cadmium exposure, LPS, defense against Gram-positive bacteria). This suggests a cluster of genes involved in coordinating development with general stress and immune signaling, though the mix indicates functional heterogeneity. ","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0043536","count":3},{"id":"GO:0006349","count":3}]},{"hash":"1128289564476726872","title":"Unknown","description":"The proteins shown have a highly diverse set of GO terms (rRNA processing, cell proliferation, multiple tissue development processes, cadmium response, splicing, GTPase regulation, fertilization, Golgi-ER transport, skin development, and stress signaling) with no clear single function or pathway linking them, and there are no edges connecting the proteins, so there is no cohesive theme to name beyond Unknown.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0072520","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000348","count":2}]},{"hash":"1960958527356103304","title":"Nucleotide salvage and growth-related metabolism","description":"This cluster contains explicit nucleotide salvage terms (CMP salvage, CTP salvage, UMP salvage) alongside growth- and adipose-related terms (multicellular organism growth, adipose tissue development, corticosterone secretion). While other terms are more general (phosphorylation, protein-containing complex assembly) or less directly connected (cobalamin biosynthesis, selenium response), the dominant theme appears to be metabolic processes linked to growth regulation, supporting the chosen name.","confidence":"Medium","size":10,"edges":8,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":1},{"id":"GO:0010269","count":1},{"id":"GO:0035934","count":1},{"id":"GO:0060612","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1168147304349809900","title":"Ubiquitination and ERAD Pathways","description":"The cluster is dominated by ubiquitin-related processes: protein ubiquitination, polyubiquitination, autoubiquitination, sumoylation, and an ubiquitin-dependent ERAD pathway, all pointing to protein quality control and degradation. Additional terms like innate immune response and peroxisomal import suggest related regulatory layers in proteostasis and trafficking. This cohesive theme supports a label focused on ubiquitin-mediated regulation and ERAD-associated pathways.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0016925","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0033280","count":3}]},{"hash":"2264067645677907993","title":"Central carbon metabolism","description":"The top GO terms point to glycolysis, the TCA cycle, and related anaplerotic steps (malate and oxaloacetate metabolism), plus menaquinone biosynthesis, all core components of cellular energy production. This suggests the cluster reflects central carbon metabolism rather than a narrow, single pathway. A few stimulus-response terms appear ancillary, likely noise. ","confidence":"High","size":10,"edges":13,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006108","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0009234","count":3}]},{"hash":"2048913026583134579","title":"Mitotic Cell Cycle and Endosomal Sorting","description":"The cluster shows strong representation of mitotic/cell cycle terms (cell cycle, exit from mitosis, mitotic cell cycle, cell division, cell population proliferation) together with endosomal trafficking terms (multivesicular body assembly, multivesicular body sorting pathway), plus related cytoskeletal remodeling (stress fiber assembly) and autophagy regulation. This pattern suggests a theme where cell-cycle progression is coordinated with vesicle trafficking and cytoskeleton dynamics, hence a label that combines mitosis with endosomal sorting.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:1902902","count":2},{"id":"GO:0036258","count":2},{"id":"GO:0045773","count":2},{"id":"GO:0010458","count":2}]},{"hash":"110470668765165903","title":"Bacterial lipid and metabolite biosynthesis","description":"The top GO terms point to bacterial biosynthetic and catabolic processes, including lipopolysaccharide and lipid core region biosynthesis, polyhydroxybutyrate biosynthesis, acetoin catabolism, and antibiotic biosynthesis. This suggests a cluster driven by diverse bacterial metabolic pathways centered on cell envelope components and small-molecule metabolite production, rather than a single unified eukaryotic pathway. Some annotations (e.g., steroid biosynthesis) may be noise or broad annotations, but the strongest signal is bacterial metabolism. Confidence: Medium","confidence":"","size":10,"edges":13,"triangles":2,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042619","count":4},{"id":"GO:0097171","count":3},{"id":"GO:0009244","count":3},{"id":"GO:0009103","count":3}]},{"hash":"2240331880680991038","title":"Innate antiviral defense and ciliary motility","description":"The cluster's top GO terms cluster around innate immune response and defense against virus, plus regulation of cilium beat frequency, suggesting a shared theme of antiviral defense linked to ciliary motility; a few outliers (morphine response, gluconeogenesis regulation) are less central.","confidence":"Medium","size":10,"edges":37,"triangles":70,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043278","count":8},{"id":"GO:0045070","count":5},{"id":"GO:0060296","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0051348","count":5}]},{"hash":"1028836529048398804","title":"Central carbon metabolism and sporulation","description":"This cluster centers on core metabolic pathways: glycolysis, the TCA cycle, glucose and alanine catabolism, nitrate assimilation, and PRPP biosynthesis, with a couple terms pointing to sporulation and its regulation. The dominant theme is central carbon metabolism; sporulation terms may reflect organism-specific regulation or incidental annotation. ","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1584141129276512791","title":"Antibiotic response and microbial biosynthesis","description":"The top GO terms cluster around biosynthetic and metabolic processes, especially antibiotic biosynthetic/response activities, along with other biosynthesis pathways (lipopolysaccharide, polyhydroxybutyrate) and related metabolism. While there\u2019s some cross-species annotation (e.g., androgen/glucocorticoid biosynthesis), the common theme appears to be biosynthesis and metabolic regulation, with an emphasis on antibiotic-related pathways. This suggests a functionally cohesive, though broad, biosynthetic/metabolic module rather than a single precise function.","confidence":"Medium","size":10,"edges":9,"triangles":1,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0042619","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009103","count":4}]},{"hash":"572100975476072137","title":"Innate immune signaling with ubiquitination","description":"Several top terms point to innate immune activity (innate immune response, defense response to virus, and vitamin D-related signaling). The concurrent enrichment for multiple ubiquitination terms (protein ubiquitination, polyubiquitination, and K63-linked ubiquitination) suggests that ubiquitin-dependent signaling is a core feature of this cluster, aligning with antiviral immune pathways. While other terms touch on mechanical stimuli, axonogenesis, and cold response, they appear less central to the cluster\u2019s main function.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0000209","count":2}]},{"hash":"1780383521765093571","title":"TLR-Mediated Antiviral Innate Immunity","description":"This cluster is dominated by innate immune and antiviral signaling terms (innate immune response, defense response to virus, TLR signaling, interferon production, dendritic cell cytokine regulation), with a few outliers, reflecting the core function as antiviral innate immune signaling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0045842","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0002730","count":2},{"id":"GO:0007186","count":2}]},{"hash":"1442786431710088637","title":"Organelle-Specific Autophagy","description":"The top GO terms cluster around selective autophagy processes across organelles: nucleophagy (piecemeal microautophagy of the nucleus, nucleophagy), mitophagy, reticulophagy, glycophagy, and related autophagy pathways (Cvt). This suggests the proteins function together in organelle-specific autophagic turnover rather than a single universal process, with some vesicle trafficking involvement (Golgi-ER transport) supporting autophagic flux. Confidence reflects a coherent, high-level theme across several distinct autophagy subtypes.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0034727","count":1},{"id":"GO:0035096","count":1},{"id":"GO:0034497","count":1},{"id":"GO:0044805","count":1},{"id":"GO:0000422","count":1}]},{"hash":"1055720850893003940","title":"Organelle Energy Metabolism and Redox","description":"The terms point to energy-related and redox processes across organelles: photosynthesis indicates chloroplast energy capture, hydrogen peroxide response and oxidation-reduction processes reflect redox regulation, proton transmembrane transport ties to proton motive forces in mitochondria/chloroplasts, and mitochondrial protein import/insertion specifies mitochondrial function. Nitrate assimilation and carbazole catabolic processes suggest broader metabolic activities linked to redox status. Overall, the cluster seems to reflect energy metabolism and redox homeostasis across organelles, rather than a single tight pathway, hence this label. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0000001","count":2},{"id":"GO:1902600","count":2}]},{"hash":"418047029134781690","title":"Transsulfuration and H2S biosynthesis","description":"The top GO terms repeatedly point to sulfur-containing amino acid metabolism, notably homocysteine/cysteine catabolism, transsulfuration, and hydrogen sulfide biosynthesis, with supporting signals from serine/cysteine metabolism and related pathways. This suggests a cohesive cluster centered on sulfur amino acid turnover and H2S production.","confidence":"High","size":9,"edges":32,"triangles":62,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0043418","count":4},{"id":"GO:0006535","count":4},{"id":"GO:0009310","count":4},{"id":"GO:0070814","count":4},{"id":"GO:0009097","count":4}]},{"hash":"2245467117047990335","title":"Protein homeostasis and cell growth","description":"The terms cluster around protein assembly and modification (homooligomerization, polyubiquitination, cellular fusion conjugation), together with growth-related processes (cell division, multicellular development) and ribosome biogenesis, suggesting a theme of protein synthesis, assembly, and turnover during growth. Some transporter-related GO terms are present but less cohesive with the central theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007275","count":2}]},{"hash":"2074355263460078521","title":"Ribosome biogenesis and translation regulation","description":"Based on the prominent GO terms, most proteins are linked to translation and ribosomal RNA maturation (SSU- and LSU-rRNA processing) and to regulation of translation. The presence of rRNA maturation terms alongside translation-related terms points to a cluster around ribosome assembly and protein synthesis. Additional terms on transcription antitermination and antibiotic response suggest auxiliary RNA metabolism and stress-response roles, but the core theme remains ribosome biogenesis and translation control.","confidence":"Medium","size":9,"edges":33,"triangles":64,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000462","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000470","count":1}]},{"hash":"1276889282443405767","title":"Unknown","description":"The top terms include immune (T cell proliferation), metabolic (insulin secretion, response to glucose), developmental (male sex differentiation) and protein aggregation (amyloid fibril formation); there is no coherent shared pathway or function tying these proteins together, suggesting no clear cluster theme.","confidence":"","size":9,"edges":11,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0022417","count":2},{"id":"GO:0032515","count":1},{"id":"GO:0042098","count":1},{"id":"GO:0030073","count":1},{"id":"GO:0009749","count":1}]},{"hash":"116343754522405895","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":16,"triangles":14,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006268","count":4},{"id":"GO:0048701","count":4},{"id":"GO:0000466","count":3},{"id":"GO:0048026","count":3}]},{"hash":"565431830947706895","title":"Nuclear RNA processing and DNA replication stress response","description":"The top GO terms cluster around nuclear RNA metabolism (splicing regulation, ncRNA-mediated silencing, rRNA maturation, mRNA decay, RNA-protein cross-linking) together with DNA-related processes (DNA replication, SOS response, viral genome replication). This suggests a nuclear program coordinating RNA processing with DNA replication/repair responses. The embryonic skeletal morphogenesis term appears as an outlier, likely annotation noise rather than a core function of this cluster.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0042766","count":3}]},{"hash":"2286094754898582508","title":"Ubiquitin-Mediated Innate Antiviral Immunity","description":"The top terms cluster around ubiquitination pathways (general ubiquitination, ubiquitin-dependent degradation, and K63-linked ubiquitination) together with innate immune and antiviral responses (innate immunity, defense against virus, negative regulation of viral transcription). Additional terms like vitamin D response and NOS regulation suggest immune signaling context. This combination points to a cohesive theme of ubiquitin-driven modulation of innate antiviral defense.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0033280","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0042787","count":4}]},{"hash":"1431157086698452524","title":"ER protein folding and stress-induced translation regulation","description":"The top GO terms cluster around endoplasmic reticulum proteostasis: protein folding in the ER, chaperone-assisted refolding, and regulation of translation initiation in response to ER stress, pointing to unfolded protein response and quality control. Additional terms touch on redox homeostasis and protein complex assembly, which can relate to ER-related folding and maturation processes. Some terms (mesoderm formation, DNA replication) seem less connected and may reflect broader annotations or incidental associations in this set. Overall, the cluster seems centered on ER proteostasis and stress response rather than a single, completely uniform function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0051259","count":1}]},{"hash":"2272493039715994163","title":"Neural differentiation and cell cycle regulation","description":"The top GO terms show neural development (neuron differentiation, excitatory postsynaptic potential, Schwann cell development) together with cell-cycle processes (DNA replication, regulation of cell cycle, DNA damage checkpoint signaling) and EMT. This pattern points to a cluster of proteins involved in neural development with collateral ties to cell-cycle control and developmental transitions.","confidence":"Medium","size":9,"edges":9,"triangles":0,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0051726","count":2},{"id":"GO:0035562","count":2},{"id":"GO:0031987","count":2},{"id":"GO:0060079","count":2}]},{"hash":"1931626036826312445","title":"Unknown","description":"The top GO terms cover a wide and seemingly unrelated set of functions: metal ion transport (zinc, cadmium, copper) and calcium homeostasis, diverse metabolic and biosynthetic processes (lipopolysaccharide biosynthesis, L-serine biosynthesis, stilbene catabolic process, epoxygenase P450 pathway), and phospholipid dephosphorylation. There is no single cohesive biological theme that clearly ties all of these terms together for this protein set, suggesting the cluster is functionally heterogeneous rather than a distinct, well-defined pathway.","confidence":"","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:0006874","count":3},{"id":"GO:0019373","count":3},{"id":"GO:0071577","count":3},{"id":"GO:0070574","count":3}]},{"hash":"1195216848035524621","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":17,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006458","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0090084","count":1},{"id":"GO:0009809","count":1}]},{"hash":"1462498617082447158","title":"Protein N-terminal and polyamine acetylation","description":"The top GO terms cluster around acetylation-related modifications, including N-terminal acetylation and spermidine/spermine acetylation, with several related post-translational modification terms. Although a few terms touch on other processes, the acetylation theme dominates, supporting a cohesive label around these protein and polyamine modifications.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":4},{"id":"GO:0006526","count":3},{"id":"GO:0061606","count":3},{"id":"GO:0045150","count":3},{"id":"GO:0018003","count":3}]},{"hash":"1079262817917240383","title":"Antigen presentation and innate immune activation","description":"Based on the top GO terms, the proteins cluster around immune-related processes: regulation of MHC class II biosynthesis, myeloid dendritic cell differentiation, natural killer cell\u2013mediated cytotoxicity, and inflammatory signals such as chemotaxis to arachidonate and vascular wound healing, along with TGF-beta2 production. A few terms appear unrelated (segmental identity) and several entries are obsolete, but the dominant theme is immune surveillance and antigen presentation with innate immune activation.","confidence":"High","size":9,"edges":15,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045348","count":4},{"id":"GO:0043011","count":3},{"id":"GO:0042267","count":3},{"id":"GO:0007381","count":3},{"id":"GO:0032915","count":3}]},{"hash":"1979208175179237319","title":"Unknown","description":"This cluster shows a diverse set of GO terms spanning cell cycle regulation, cell migration, telomere maintenance, RNA processing, proteasome assembly, muscle stretch response, adipocyte differentiation, cholesterol biosynthesis, and insulin-related glucose import. The lack of a unifying biological theme or pathway suggests no cohesive function for a single label.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":2},{"id":"GO:0016477","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0006397","count":2}]},{"hash":"1899831246934153702","title":"Chromatin Remodeling and Histone Modification","description":"The top GO terms cluster around chromatin dynamics and epigenetic marks (rDNA heterochromatin formation, chromatin remodeling, histone deubiquitination, and regulation of histone acetylation), pointing to a core role in chromatin structure regulation. Some terms reflect plant stress or metabolism contexts, but they do not override the chromatin-focused signal.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":2},{"id":"GO:0043044","count":2},{"id":"GO:1900386","count":2},{"id":"GO:0006970","count":2},{"id":"GO:0035522","count":2}]},{"hash":"1291524291864810702","title":"Protein synthesis and ribosome biogenesis","description":"Based on the top GO terms, the dominant signal in this cluster is translation-related (GO:0006412) and ribosome biogenesis (GO:0042254), with several translation-associated terms appearing (e.g., cytoplasmic translation). While there are a couple of transcription-related terms and a few unrelated annotations (retina development, mitotic checkpoint signaling), the core theme centers on protein synthesis machinery. Confidence: Medium","confidence":"","size":9,"edges":31,"triangles":56,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0046677","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006353","count":2}]},{"hash":"684653726354735016","title":"Membrane transport of diverse nutrients","description":"The top GO terms cluster around various membrane transport processes for multiple substrates\u2014lipids, carbohydrates, metals (heme), amino acids (methionine), glycerophosphodiesters, teichoic acids, etc.\u2014suggesting a shared role in moving diverse nutrients across membranes. While a few terms diverge (e.g., cytochrome complex assembly), the dominant signal is transport, so this label is representative. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042760","count":3},{"id":"GO:0042953","count":3},{"id":"GO:0008643","count":3},{"id":"GO:0010949","count":3},{"id":"GO:0017004","count":3}]},{"hash":"1694744609481824783","title":"TLR2-driven innate immunity and autophagy","description":"This cluster centers on innate immune signaling with autophagy regulation, as shown by terms like positive regulation of macroautophagy, innate immune response, toll-like receptor 2 signaling, MyD88-independent TLR signaling, and regulation of interferon and inflammatory responses. The combination suggests proteins functioning in TLR2-mediated immune sensing and downstream autophagy-linked regulation of cytokine production, with some potential dopaminergic signaling cross-talk; overall, the dominant theme is innate immunity and autophagy.","confidence":"High","size":9,"edges":9,"triangles":1,"max_degree":8,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0016239","count":6},{"id":"GO:0045087","count":5},{"id":"GO:0002730","count":5},{"id":"GO:0007186","count":5},{"id":"GO:0050729","count":5}]},{"hash":"533189000693845515","title":"SCF-Mediated Ubiquitination and Mitotic Control","description":"This cluster centers on ubiquitin-dependent proteolysis and SCF-mediated ubiquitination, implying proteasome-driven degradation, and includes mitotic cell cycle and G1 DNA damage checkpoint signaling terms, pointing to cell-cycle regulation and genome integrity control. The connection to cadmium response suggests stress-linked regulation of these pathways, supporting a role in ubiquitin-proteasome\u2013driven mitotic control and DNA damage response.","confidence":"High","size":9,"edges":9,"triangles":1,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:0042787","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0000209","count":3}]},{"hash":"807964518183425219","title":"Unknown","description":"The terms are very diverse, including proteasomal degradation, transcription regulation, collagen catabolism, immune response to LPS, biotin biosynthesis, and oxidant detoxification. With zero edges and no clear unifying function across the proteins, there isn\u2019t a coherent shared role to label; thus Unknown with None. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":2},{"id":"GO:0030574","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0031146","count":2}]},{"hash":"574605934366765715","title":"ER Stress and Protein Quality Control","description":"This cluster is enriched for endoplasmic reticulum\u2013related processes: unfolded protein response, protein folding/unfolding, ER-to-Golgi transport, and degradation of misfolded proteins, all central to ER proteostasis. Oxidative stress response also aligns with ER stress conditions. A couple of terms (centriole elongation, ribosomal subunit assembly) are less clearly connected, so the label focuses on the ER quality-control theme.","confidence":"Medium","size":9,"edges":14,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0034599","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0030968","count":2},{"id":"GO:0072389","count":2},{"id":"GO:0043335","count":2}]},{"hash":"108914187216514939","title":"Translation machinery and ribosome biogenesis","description":"The cluster is dominated by GO terms tied to translation and ribosome assembly, including translation, translational termination, ribosomal small subunit biogenesis, and positive regulation of translational elongation, pointing to proteins involved in protein synthesis and ribosome construction. A few other terms (cell cycle, glial cell proliferation, septum assembly) appear less central and may reflect broader cellular roles or annotation noise, but the core signal centers on the translation apparatus.","confidence":"High","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0090529","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0014009","count":2}]},{"hash":"1247190325538824830","title":"Chromatin regulation and transcriptional control","description":"This cluster is dominated by GO terms tied to chromatin state and transcription control (histone H3-K4 methylation regulation, rDNA heterochromatin formation, and negative regulation of transcription by RNA polymerase II), suggesting a core theme of epigenetic regulation of gene expression. Some other terms (developmental or stress-related) may reflect broader functional contexts or annotation noise, but the chromatin/transcription link is the strongest.","confidence":"Medium","size":9,"edges":21,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0000183","count":2},{"id":"GO:0007296","count":2},{"id":"GO:0000122","count":2}]},{"hash":"451437959684706019","title":"RNA and Protein Methylation Enzymes","description":"The top GO terms are all methylation-related: rRNA methylation, tRNA wobble uridine modification, N-terminal peptidyl-glycine methylation, and peptidyl-lysine dimethylation. This points to enzymes that add methyl groups to RNA and proteins, i.e., methyltransferases or methylation-associated factors. Some other terms (immune or metabolic processes) may be incidental, but the strongest signal is methylation machinery.","confidence":"High","size":9,"edges":18,"triangles":15,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0018027","count":3},{"id":"GO:0032515","count":2}]},{"hash":"291102016645343569","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":2},{"id":"GO:0042790","count":2},{"id":"GO:0031440","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0006363","count":2}]},{"hash":"60500062699624509","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":9,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0008615","count":1},{"id":"GO:1903507","count":1},{"id":"GO:0002047","count":1},{"id":"GO:0040008","count":1}]},{"hash":"890521592078731613","title":"Unknown","description":"The most frequent terms pull in opposite directions: transcription/DNA-templated transcription and its regulation on one hand, and several scattered developmental or obsolete terms on the other, with minimal connectivity (edges=2, triangles=0). This lack of a single coherent biological theme makes a meaningful cluster label difficult.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0021592","count":3},{"id":"GO:0042265","count":3}]},{"hash":"2072692259019759680","title":"Unknown","description":"The terms mix nuclear DNA maintenance (DNA replication, DNA repair, SOS response, transcription regulation) with photosynthesis and membrane/secretory processes (photosystem I assembly, photosynthesis, GPI anchor biosynthesis) and some archaic/obsolete terms, yielding no single coherent function. The lack of interactions (edges) and the heterogeneous GO terms suggest the cluster does not reflect one clear biological role, so an Unknown label is appropriate.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0048564","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0006465","count":1},{"id":"GO:0006281","count":1}]},{"hash":"2078346075058732357","title":"Neuronal development and protein trafficking","description":"These terms cluster around nervous system development, including neural tube patterning and dendrite/spine development, with supporting hints from Hedgehog signaling (Smoothened). There are also signals of intracellular protein trafficking/localization (Golgi localization, lysosomal membrane organization), suggesting the proteins function in neuronal differentiation and the targeted transport essential for neuron morphology and function. Overall, the cluster appears to represent neurons-involved development with a trafficking/localization angle rather than a single pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902307","count":1},{"id":"GO:2000171","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0046909","count":1},{"id":"GO:0097212","count":1}]},{"hash":"560800113219225336","title":"Hepatic Energy Metabolism","description":"Top GO terms center on central carbon metabolism (TCA cycle, glycolysis, gluconeogenesis) and lipid synthesis (malonyl-CoA, long-chain fatty acids), plus amino acid catabolism and liver development. The combination indicates a liver-specific metabolic cluster focused on energy production and lipid metabolism.","confidence":"High","size":8,"edges":25,"triangles":41,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0001889","count":2},{"id":"GO:0006552","count":2},{"id":"GO:0042759","count":2}]},{"hash":"199427730583574042","title":"Diverse substrate transmembrane transporters","description":"This cluster contains GO terms for transmembrane transport of a wide range of substrates (nitrate, phosphate, arabinose, sialic acid, galactose, 4-hydroxyphenylacetate, potassium, xenobiotic), plus a vesicular neurotransmitter loading term, indicating a group of membrane transport proteins with broad substrate specificity rather than a single, narrow function.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":4},{"id":"GO:0035435","count":3},{"id":"GO:0015751","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0015739","count":3}]},{"hash":"2027127519081787074","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA processing and ribosome assembly\u2014mRNA splicing via spliceosome, spliceosome dynamics, mRNA decay, and ribosome biogenesis\u2014indicating a core theme of gene expression and ribosome production. A few sugar metabolism terms and habituation-related terms appear but are less central to the primary signal. ","confidence":"Medium","size":8,"edges":20,"triangles":23,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046959","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000388","count":1}]},{"hash":"1767348030320366955","title":"Organ Development and Differentiation","description":"The top GO terms indicate involvement in morphogenesis and differentiation across a variety of organs (heart, digestive tract, mammary gland, bile duct, trachea, genitalia, nervous system) plus a chromatin-related process and general transcriptional elongation. There isn\u2019t a single unified function, but the common thread is broad developmental and tissue differentiation activity, rather than a specific pathway or tissue. This supports labeling as an organ-development/differentiation cluster.","confidence":"Medium","size":8,"edges":14,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1990141","count":2},{"id":"GO:2000726","count":1},{"id":"GO:0048546","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0007422","count":1}]},{"hash":"2148781083601499057","title":"Mitochondrial transport and membrane potential regulation","description":"The cluster centers on mitochondrial function, with multiple transport-related GO terms (manganese, phosphate, nucleotide import into mitochondrion, ATP transmembrane transport, heme transport) and terms touching mitochondrial energetic regulation (regulation of mitochondrial membrane potential) and apoptosis/necroptosis. The combination suggests proteins involved in mitochondrial transport and regulation of mitochondrial energy and death pathways.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":4},{"id":"GO:0006828","count":2},{"id":"GO:1990544","count":2},{"id":"GO:1990519","count":2},{"id":"GO:0008637","count":2}]},{"hash":"253938813718822243","title":"Polysaccharide Metabolism","description":"This cluster's proteins link to multiple carbohydrate-transforming processes, including starch, trehalose, maltose, sucrose, and glycogen metabolism, in both catabolic and biosynthetic directions, suggesting a shared role in polysaccharide processing and storage.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0005983","count":1},{"id":"GO:0030980","count":1},{"id":"GO:0019252","count":1},{"id":"GO:0005985","count":1},{"id":"GO:0005992","count":1}]},{"hash":"761245849803922034","title":"Regulation of differentiation and signaling","description":"This cluster centers on broad regulatory roles rather than a single pathway: terms for GTPase and kinase activity regulation, cytokinesis, and transcription regulation point to signaling control; additional terms for lung epithelial differentiation, G1\u2013G0 transition in differentiation, chromatin binding, and calcium channel regulation suggest involvement in cell-state changes and differentiation processes, with some link to neural signaling via excitatory postsynaptic potential. The proteins appear functionally diverse but collectively emphasize regulatory control over cellular differentiation and signaling rather than a specific metabolic function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0032465","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0060487","count":2}]},{"hash":"1293155300351970338","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0034476","count":3},{"id":"GO:0071051","count":3},{"id":"GO:0034475","count":3}]},{"hash":"2006086801552608275","title":"Mitotic signaling and cell cycle control","description":"Top GO terms emphasize regulation of GTPase activity, various phosphorylation events (serine/threonine and tyrosine), and processes linked to mitosis such as the mitotic cell cycle and spindle pole body duplication. This points to a cohesive theme of signaling pathways that control cell division and proliferation. Some terms like mRNA transport or skin development are present but appear less central to the core mitotic signaling focus.","confidence":"Medium","size":8,"edges":8,"triangles":3,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0031954","count":6},{"id":"GO:0071456","count":6},{"id":"GO:0000278","count":6}]},{"hash":"92560542789840313","title":"Chromatin assembly and cell division","description":"The cluster\u2019s top terms are dominated by chromatin-related processes (CENP-A chromatin assembly, DNA-templated transcription) and mitotic machinery (cell division, microtubule severing), with ties to development, suggesting a core theme of genome maintenance and chromosome segregation during cell proliferation. Some outlier terms (aggresome assembly, ER-Golgi transport, skin development) point to broader cellular organization and stress responses but do not override the central chromatin/cell cycle signal. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3}]},{"hash":"639114127812011986","title":"Ubiquitin-dependent regulation of apoptosis and signaling","description":"This cluster centers on ubiquitination activities (K48- and K6-linked, autoubiquitination) and their role in controlling protein turnover, with additional connections to apoptosis regulation and signaling pathways (JNK, Wnt receptor turnover). The presence of chromatin-related terms (histone catabolic/methylation) suggests downstream effects of ubiquitination on chromatin dynamics as well. Overall, it reflects a theme of ubiquitin-mediated control of signaling and cell fate.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042981","count":2},{"id":"GO:0036205","count":2},{"id":"GO:1900095","count":2},{"id":"GO:0070936","count":2},{"id":"GO:0038018","count":2}]},{"hash":"1078179011544176604","title":"Protein acetylation and chromatin regulation","description":"The cluster\u2019s top GO terms are dominated by various acetylation events (N-terminal acetylation, peptidyl-lysine acetylation, spermidine/spermine acetylation) and chromatin-associated processes (mitotic sister chromatid cohesion at centromeres, subtelomeric heterochromatin formation). This suggests a unifying theme around acetylation-mediated regulation in chromatin context, with supporting links to metabolism via arginine and polyamine pathways, making \u201cProtein acetylation and chromatin regulation\u201d a concise, representative label.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":4},{"id":"GO:0061606","count":4},{"id":"GO:0045150","count":4},{"id":"GO:0018003","count":4},{"id":"GO:0071962","count":4}]},{"hash":"725508960463051392","title":"Synaptic signaling and protein localization","description":"The cluster is enriched for terms tied to synaptic function and protein trafficking, including protein localization to the synapse, receptor clustering, and Rho-mediated signaling, with potassium ion transport supporting neuronal excitability. Additional terms on glucose response and eIF2\u03b1-regulated translation suggest metabolic and translational control in a neuronal context. A single immune-related term is present but does not dominate the theme.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":6},{"id":"GO:0035418","count":6},{"id":"GO:0071333","count":6},{"id":"GO:0006813","count":6},{"id":"GO:0043113","count":6}]},{"hash":"634520875368716421","title":"Unknown","description":"The GO terms are scattered across amino acid biosynthesis (lysine, leucine, biotin), gluconeogenesis, various metabolic and processing steps, plus a few unrelated terms (plant development, endocannabinoid signaling regulation, xenobiotic and lipid catabolism), offering no single cohesive function for the cluster.","confidence":"","size":8,"edges":21,"triangles":23,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0009102","count":2},{"id":"GO:0009098","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0006515","count":1}]},{"hash":"463528166754054164","title":"RNA and protein methylation enzymes","description":"Dominant methylation signals (tRNA/rRNA/protein methylation) suggest the cluster is enriched for methyltransferase activities, despite a few diverse metabolic terms that may reflect incidental annotations in a small set.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0006571","count":1}]},{"hash":"453774750035796944","title":"Sulfur-containing amino acid metabolism","description":"The cluster is enriched for GO terms related to metabolism and breakdown of sulfur-containing amino acids, notably L-cysteine, L-serine, and L-homocysteine, plus related sulfur compounds such as hydrogen sulfide. There is also a minor representation of antibiotic biosynthetic process and other amino acid catabolic pathways, but the dominant theme is sulfur amino acid metabolism and associated transformations.","confidence":"Medium","size":8,"edges":23,"triangles":31,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0043418","count":1},{"id":"GO:0006535","count":1},{"id":"GO:0009310","count":1}]},{"hash":"733727974606048233","title":"Membrane transport and vesicle trafficking","description":"The top GO terms point to ER-to-Golgi vesicle transport and various transmembrane transport processes (glucose, biotin, inositol, pantothenate, sodium ions), suggesting proteins involved in membrane trafficking and transport across membranes. Some signaling-related terms are present but appear secondary to the transport theme.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0015878","count":1},{"id":"GO:1904659","count":1},{"id":"GO:0008292","count":1}]},{"hash":"997841577107779093","title":"Auxin signaling and plant metabolic stress responses","description":"The top GO terms include auxin-activated signaling (a plant hormone pathway) and several metabolic/regulatory processes (nitrogen utilization, mitochondrial membrane potential, glutathione biosynthesis, and responses to starvation) plus growth/development terms. This pattern suggests a cluster centered on plant growth modulation linked to metabolic stress and detoxification, rather than a single specific pathway, hence a label emphasizing auxin signaling plus metabolic stress responses in plants.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":2},{"id":"GO:0006808","count":2},{"id":"GO:0051881","count":2},{"id":"GO:1902000","count":2},{"id":"GO:0009407","count":2}]},{"hash":"2056506590500492583","title":"ER Proteostasis and UPR Activation","description":"This cluster centers on endoplasmic reticulum quality control, including ubiquitin-dependent degradation of misfolded proteins, ER-assisted folding, and translation upregulation in response to ER stress, pointing to a coordinated proteostasis/UPR program. Redox homeostasis and oligomerization data further support a network maintaining protein quality in the ER, with a minor nod to development signals.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0090084","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0097428","count":3},{"id":"GO:0036494","count":3}]},{"hash":"2047879510084816726","title":"Geranylgeranylation and GTPase Activation","description":"The top GO terms point to post-translational lipid modification (protein geranylgeranylation) and the activation of GTPase activity, suggesting the cluster centers on prenylation-dependent regulation of small GTPases and related trafficking/signaling. While there are outliers related to RNA splicing and development, the strongest shared function appears to be geranylgeranylation-linked GTPase regulation. ","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006376","count":1},{"id":"GO:0045843","count":1},{"id":"GO:2000541","count":1},{"id":"GO:0050771","count":1},{"id":"GO:0018344","count":1}]},{"hash":"205532399924363948","title":"Unknown","description":"This cluster's GO terms span diverse processes\u2014from immune functions (antigen processing with MHC I, dendritic cell chemotaxis, phagocytosis) and ER stress to development and cell cycle regulation\u2014without a single unifying function. Because there isn't a coherent common theme that ties all terms together, a specific label can't be confidently assigned.","confidence":"","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007339","count":1},{"id":"GO:0033144","count":1},{"id":"GO:0030968","count":1},{"id":"GO:0002502","count":1},{"id":"GO:2000510","count":1}]},{"hash":"692953651134254570","title":"Mitochondrial Transport and Membrane Potential","description":"Proteins in this cluster predominantly relate to mitochondrial transport and regulation, including ATP/ion transport, nucleotide import into mitochondria, and control of the mitochondrial membrane potential, with also apoptotic/necroptotic regulatory aspects and thermogenesis. This cohesive mitochondrial theme supports labeling as a mitochondria-centered transport and energy-regulation cluster.","confidence":"High","size":7,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":1},{"id":"GO:1990544","count":1},{"id":"GO:1990519","count":1},{"id":"GO:0008637","count":1},{"id":"GO:0035435","count":1}]},{"hash":"730107580359237248","title":"Diverse Substrate Membrane Transporters","description":"The top GO terms are all about transmembrane transport of a variety of substrates\u2014xenobiotics, sugars, ions, vitamins, and even neurotransmitter loading into vesicles\u2014indicating a cluster of membrane transporter proteins with broad substrate scope.","confidence":"High","size":7,"edges":8,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0015707","count":2}]},{"hash":"1388426402659182280","title":"Unknown","description":"The GO terms span ribosome biogenesis and rRNA processing, chloroplast-associated photosynthesis, and membrane trafficking with endocytosis and actin regulation, representing disparate processes. There is no single cohesive function that ties these terms together for this cluster, so Unknown is most appropriate with None confidence.","confidence":"","size":7,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0018298","count":1},{"id":"GO:0019684","count":1},{"id":"GO:0015979","count":1}]},{"hash":"2078681008456258818","title":"Viral translation initiation and reinitiation","description":"The most frequent GO terms center on regulation and initiation of translation, including translation reinitiation, formation of the preinitiation complex, and IRES-dependent viral initiation, pointing to a cluster focused on viral takeover and control of host translation. While a few terms touch on DNA replication and differentiation, these do not override the dominant translation-initiation signal, supporting a label around viral translation control.","confidence":"Medium","size":7,"edges":12,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1708438077398823564","title":"Unknown","description":"This cluster lists GO terms spanning immune response to interferon, male sex differentiation, prostate gland development, steroid hormone receptor complex assembly, and photosynthesis, with little overlap and only a single edge linking proteins. The terms point to disparate biological contexts, giving no cohesive shared function to name. Therefore, label is Unknown with no confidence.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071357","count":4},{"id":"GO:0046661","count":3},{"id":"GO:0030850","count":3},{"id":"GO:0006463","count":3},{"id":"GO:0015979","count":3}]},{"hash":"807582701121812634","title":"Endolysosomal Trafficking and Membrane Transport","description":"The GO terms converge on membrane transport, especially endosomal and lysosomal pathways (endosome to plasma membrane transport, late endosome to lysosome transport, lysosomal membrane organization) and ion export across membranes (amino acids, calcium, sodium). This suggests a core function in vesicle trafficking and endolysosomal routing; a few outlier terms (mammary gland proliferation, dendritic spine development, myeloid apoptosis) may reflect secondary roles or noise. Overall, the label aligns with the dominant function.","confidence":"Medium","size":7,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":1},{"id":"GO:1990034","count":1},{"id":"GO:1902307","count":1},{"id":"GO:0033601","count":1},{"id":"GO:0097212","count":1}]},{"hash":"707502197491161697","title":"Unknown","description":"The terms span glucose transport, glucose response, dopamine signaling, immune defense, nematode development, cell-cycle regulation, and chromatin-related processes, with no clear shared function or connectivity, so a single representative label cannot be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":2},{"id":"GO:0061186","count":1},{"id":"GO:0071333","count":1},{"id":"GO:1903351","count":1},{"id":"GO:0035206","count":1}]},{"hash":"2202963310127949064","title":"Bacterial amino acid biosynthesis and cell envelope biogenesis","description":"The cluster is enriched for amino acid biosynthetic processes (lysine via aminoadipic acid, tyrosine, histidine) along with lipid A biosynthesis, fatty acid homeostasis, and cell wall organization, all hallmark activities of bacterial metabolism and envelope assembly. The mix of biosynthetic and cell envelope\u2013related terms supports a coherent theme around producing essential metabolites and building the cell envelope, with some older/obsolete terms present but not altering the core signal.","confidence":"Medium","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":3},{"id":"GO:0006515","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0071555","count":2}]},{"hash":"1016881799900772254","title":"Endocytosis and endosome-lysosome trafficking","description":"This cluster centers on vesicular transport processes: endocytosis, endosome-to-lysosome transport, and lysosomal membrane organization, with supporting signals for actin remodeling (formin-nucleated actin) and GTPase regulation that drive vesicle budding and trafficking. While a few terms appear more peripheral (e.g., transcription by RNA polymerase III, mast cell chemotaxis), the strongest shared functions point to endocytic pathways and lysosomal routing. Confidence: Medium.","confidence":"","size":7,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006897","count":3},{"id":"GO:0034260","count":3},{"id":"GO:1900242","count":3},{"id":"GO:0060753","count":2},{"id":"GO:0090529","count":2}]},{"hash":"1858619498833483459","title":"Capsule and cell wall polysaccharide biosynthesis","description":"The top GO terms point to synthesis and assembly of surface polysaccharides like capsule and teichoic acids, plus related cell wall organization and transport processes. This suggests the cluster groups proteins involved in producing and exporting bacterial polysaccharides used for the cell surface, supported by the UDP-glucose\u2013related biosynthesis term as a donor sugar source.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018242","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0018243","count":1},{"id":"GO:0019350","count":1},{"id":"GO:0006011","count":1}]},{"hash":"1306922376664443943","title":"RNAi and miRNA Processing","description":"The top GO terms strongly point to RNA silencing pathways, with regulatory ncRNA-mediated post-transcriptional gene silencing, ds siRNA to siRNA in RNA interference, and primary miRNA processing suggesting a shared role in RNA interference and miRNA biogenesis. Other terms appear more diverse (neuronal stem cell maintenance, patterning, telomerase assembly, mismatch repair, etc.), which could reflect multifunctional proteins or annotation noise. Overall, the strongest signal centers on RNA silencing and miRNA maturation, justifying this label.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097150","count":1},{"id":"GO:2000011","count":1},{"id":"GO:0050829","count":1},{"id":"GO:0016246","count":1},{"id":"GO:0045071","count":1}]},{"hash":"727022808616355591","title":"Cytoskeleton-Driven Vesicle Trafficking","description":"Proteins in this cluster are linked by cytoskeletal remodeling (tubulin complex assembly and actin cable assembly) and vesicle trafficking processes (endosome-to-lysosome transport, lysosomal membrane organization, and regulation of synaptic vesicle exocytosis). The presence of brain development as well supports neuronal contexts where cytoskeleton dynamics coordinate vesicle transport and signaling. A few terms (mating projection growth, mast cell chemotaxis) hint at broader motility roles but do not override the central theme of cytoskeletal control of vesicle trafficking.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0031384","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0010796","count":2}]},{"hash":"1043807905605972510","title":"RNA processing and chromatin regulation","description":"The top GO terms are dominated by RNA-related processes (mRNA capping, tRNA wobble modification, protein methylation) and a key chromatin process (rDNA heterochromatin formation), suggesting a shared nuclear RNA processing/chromatin regulation theme, with several outlier terms. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0018364","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0090398","count":1}]},{"hash":"187247394533937178","title":"Ubiquitin-Proteostasis Regulation","description":"The dominant GO terms point to ubiquitin-related pathways, including ubiquitin-dependent ERAD, sumoylation, and regulation of deubiquitinase activity, all of which connect to protein degradation and turnover. A few peripheral or obsolete terms appear, but the core theme is proteostasis control via ubiquitin/SUMO pathways.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0016925","count":2},{"id":"GO:2000157","count":2},{"id":"GO:1903094","count":2},{"id":"GO:0042921","count":1}]},{"hash":"1655782192538113180","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0045292","count":2}]},{"hash":"18801550493072746","title":"ER Stress\u2013Driven Apoptosis and Development Signals","description":"The top GO terms show a strong link to intrinsic apoptotic signaling in response to ER stress, with concurrent development-related terms (brain and placenta) and immune-related functions (cytokine production, NK cell cytotoxicity). This hints at a module where ER stress triggers apoptosis while also influencing developmental and immune-regulatory processes.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0042267","count":1},{"id":"GO:0007381","count":1},{"id":"GO:0035470","count":1}]},{"hash":"718631192868390263","title":"Hepatic ER-Golgi transport and stress response","description":"Proteins here point to ER-to-Golgi transport (COPII regulation), stress signaling leading to hepatocyte apoptosis (JNK cascade, hepatocyte apoptotic process), and liver-associated processes like ribosome biogenesis and cholesterol homeostasis, suggesting a liver secretory/stress-response cluster rather than a single, tightly connected module.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0003400","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1737939443236490616","title":"Cytoskeletal remodeling in development and stress response","description":"The top GO terms point to actin and microtubule regulation (cortical actin cytoskeleton, negative regulation of protein localization to microtubule) along with developmental signals (Schwann cell development, keratinocyte differentiation, regulation of developmental growth) and stress response pathways (p53-mediated DNA damage response, eIF2\u03b1 phosphorylation). This suggests a cohesive theme of cytoskeletal dynamics linked to developmental differentiation and cellular stress signaling.","confidence":"Medium","size":7,"edges":19,"triangles":25,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1902817","count":6},{"id":"GO:0006977","count":6},{"id":"GO:0010998","count":6},{"id":"GO:0001324","count":6},{"id":"GO:0042517","count":6}]},{"hash":"1083593546484846886","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":9,"triangles":7,"max_degree":4,"top_function":"autophagy","top_go_terms":[{"id":"GO:0031146","count":4},{"id":"GO:0051759","count":4},{"id":"GO:1902104","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0042981","count":3}]},{"hash":"1736539539979323168","title":"Carbohydrate metabolism and nucleotide-sugar biosynthesis","description":"The GO terms are dominated by sugar-related processes, including catabolism of ribose, tagatose-6-phosphate, lactose, sucrose, and sulfoquinovose, alongside nucleotide-sugar biosynthesis and salvage (ADP-L-glycero-beta-D-manno-heptose, dATP, adenosine salvage). This suggests a cohesive theme around carbohydrate metabolism and nucleotide-sugar pathways, even though the specific enzymes span diverse steps. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006655","count":2},{"id":"GO:0009744","count":1},{"id":"GO:1902777","count":1},{"id":"GO:2001059","count":1},{"id":"GO:0019303","count":1}]},{"hash":"1835123960441042667","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902131","count":2},{"id":"GO:1902128","count":2},{"id":"GO:1902123","count":2},{"id":"GO:1902138","count":2},{"id":"GO:1901006","count":2}]},{"hash":"2197740468761446049","title":"Unknown","description":"The terms cover energy metabolism (ATP synthesis, ferredoxin), ion transport, and various regulatory processes in vascular development and lactation, spanning very different biological contexts. This mix suggests there isn\u2019t a single cohesive function tying these proteins together, so a generic Unknown label is appropriate.","confidence":"","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042773","count":2},{"id":"GO:0045602","count":2},{"id":"GO:0006814","count":2},{"id":"GO:1900747","count":2},{"id":"GO:0010124","count":2}]},{"hash":"1108026592998653050","title":"Membrane Transporters and Mitochondrial Protein Import","description":"Top GO terms indicate diverse membrane-transport activities, including D-glucose, organic anions, phosphate, urate, and xenobiotic transport, plus general protein transport and mitochondrial inner membrane protein insertion/import. Although one term relates to intestinal epithelial structure maintenance, the overarching pattern is proteins involved in moving solutes across membranes and importing proteins into mitochondria. ","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032979","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0042908","count":1}]},{"hash":"656358972002335800","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0045292","count":3},{"id":"GO:1904246","count":2}]},{"hash":"1659274811883678494","title":"RNA Splicing and Processing","description":"The top GO terms cluster around mRNA and RNA maturation steps: mRNA splicing via the spliceosome, spliceosomal snRNP assembly, maturation of rRNA, tRNA processing, and mRNA decapping/decay via P-body-related processes, plus import into the nucleus for RNA-processing activities. These together point to a core function in RNA processing and metabolism, with nuclear import supporting the spliceosome machinery and P-body involvement reflecting mRNA turnover. A few terms touch on chromatin-related roles, but the strongest signal is RNA processing.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":1},{"id":"GO:0051170","count":1},{"id":"GO:1990141","count":1},{"id":"GO:0030490","count":1},{"id":"GO:0070317","count":1}]},{"hash":"1420702383489213051","title":"ER stress response and protein quality control","description":"The dominant terms center on proteostasis and stress signaling in the secretory pathway: endoplasmic reticulum unfolded protein response, protein unfolding, stress granule disassembly, and ubiquitin-dependent ER-associated degradation. A link to oxidative stress and RNA\u2013protein interactions reinforces the theme of cellular quality control under stress. Some terms (root development, centriole elongation, flavin catabolism) are less clearly connected, suggesting a mixed cluster where proteostasis signals predominate.","confidence":"Medium","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0048364","count":2},{"id":"GO:0030968","count":1},{"id":"GO:0018144","count":1}]},{"hash":"779379709102235802","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":2},{"id":"GO:0032933","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1903764","count":1},{"id":"GO:0072578","count":1}]},{"hash":"1254511837971952720","title":"Gene expression and stress-responsive signaling","description":"The top GO terms point to core gene expression machinery (translation, ribosome biogenesis, DNA-templated transcription) alongside phosphorylation events and JNK cascade regulation, indicating signaling involvement. The antibiotic response supports a stress-related angle, while tocopherol cyclase and ubiquinone biosynthesis terms appear more peripheral. Together, the cluster seems centered on expression processes with stress-signaling roles.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0046330","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006351","count":2}]},{"hash":"973015858480029303","title":"Cell Division and Organelle Fission","description":"The GO terms cluster around cell division processes (cell cycle, division, septum assembly, spindle/microtubule dynamics) and organelle fission (chloroplast fission), suggesting a unified theme of cytokinesis and organelle division across organisms.","confidence":"Medium","size":6,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051256","count":1},{"id":"GO:0010020","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0000917","count":1},{"id":"GO:2000767","count":1}]},{"hash":"1414039130393056195","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:1901407","count":2},{"id":"GO:0000466","count":1},{"id":"GO:0018144","count":1}]},{"hash":"1478468580856509803","title":"Unknown","description":"There is no GO enrichment or common functional annotation available for this cluster (Top Terms are empty), and with only one edge among six proteins, a coherent shared function cannot be inferred. The note about ReCIPE does not provide biological context for labeling.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"824329298834365847","title":"Steroid and Retinoid Hormone Metabolism","description":"The cluster shows strong representation of retinoid metabolism (retinol/retinal) and regulation of retinoic acid receptor signaling, alongside androgen- and testosterone-related biosynthetic processes. This points to a shared theme of hormone-related metabolism and signaling, particularly involving steroid and retinoid pathways, with some peripheral metabolic terms included. ","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042574","count":4},{"id":"GO:0008209","count":4},{"id":"GO:0061370","count":4}]},{"hash":"1536411263658346447","title":"Proteostasis via Ubiquitin-ERAD and Autophagy","description":"The cluster's top GO terms center on ubiquitin-dependent protein degradation (deubiquitination, ERAD) and degradative processes like aggresome assembly and nucleus-specific autophagy, indicating a cohesive proteostasis/theme; other terms like translation or spindle pole duplication appear less central, possibly reflecting broader cellular processes in the same protein set.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0030433","count":3},{"id":"GO:1903071","count":2},{"id":"GO:0010636","count":2},{"id":"GO:0070842","count":2}]},{"hash":"659938164743991831","title":"Diverse biosynthesis pathways","description":"Most of the GO terms point to biosynthetic processes across amino acids, fatty acids, and chlorophyll/heme intermediates, indicating a cluster centered on varied metabolic biosynthesis rather than a single pathway. A few terms touch on catabolism or stress responses, but the dominant theme is diverse biosynthetic activity.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0019483","count":2},{"id":"GO:0051790","count":1},{"id":"GO:0019367","count":1}]},{"hash":"1532582745488778421","title":"Ciliogenesis and Centrosome-Microtubule Organization","description":"These proteins cluster around ciliary and centrosomal processes: multiple GO terms refer to cilium assembly and cilium beat regulation, and microtubule anchoring at the centrosome, pointing to roles in ciliogenesis and centrosome\u2013microtubule organization. Some terms (fat pad development, root hair tip growth) are less specific to cilia and may reflect shared cytoskeletal themes, but the dominant signal is ciliary/centrosomal.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060613","count":1},{"id":"GO:0060296","count":1},{"id":"GO:1902855","count":1},{"id":"GO:0034454","count":1},{"id":"GO:0090526","count":1}]},{"hash":"1716649103132307689","title":"Sterol transport and vacuolar protein processing","description":"This cluster is annotated with intracellular sterol transport and vacuolar protein processing, which together suggest involvement in endomembrane lipid trafficking and vacuolar maturation. Although the terms are represented by a single protein each and there are no edges, the pair points to a common theme of intracellular lipid handling within vesicular/vacuolar pathways.","confidence":"Low","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032366","count":1},{"id":"GO:0006624","count":1}]},{"hash":"2243555187130710889","title":"Mitochondrial respiration and translation","description":"The top GO terms reveal a coherent mitochondria-centered program: respiratory electron transport chain and proton transmembrane transport point to energy production, while mitochondrial-specific tRNA aminoacylation and translation terms (and regulation of translational fidelity) indicate mitochondrial protein synthesis. The presence of a single photosynthesis term is an outlier, but the prevailing signals define a mitochondrial respiration and translation cluster.","confidence":"High","size":5,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0022904","count":3},{"id":"GO:0006122","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0097056","count":1}]},{"hash":"2239301502490835451","title":"Multiorgan development","description":"The GO terms are all related to development and morphogenesis across a variety of organs and tissues (e.g., heart, digestive tract, nervous system, mammary gland, bile ducts, trachea, genitalia, endocardium). This points to a broad theme of organ/tissue development rather than a single specific pathway or function, hence a label of multiorgan development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000726","count":1},{"id":"GO:0048546","count":1},{"id":"GO:0007422","count":1},{"id":"GO:0030879","count":1},{"id":"GO:0035622","count":1}]},{"hash":"1540913468112434033","title":"Proteostasis and stress-response","description":"The top terms point to ubiquitin-dependent ER-associated degradation (ERAD), aggresome assembly, and cellular responses to toxic substances, all central to protein quality control under stress. Although other terms touch on translation, deglycosylation, and mitochondrial fusion regulation, the dominant theme is proteostasis\u2014maintaining protein homeostasis through degradation and stress response pathways.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:1903071","count":5},{"id":"GO:0010636","count":5},{"id":"GO:0070842","count":5},{"id":"GO:0097237","count":5}]},{"hash":"722863960591779261","title":"Unknown","description":"The terms are diverse and only weakly related, including defense responses, plant development (seed germination), wound healing, extracellular matrix organization, and even sensory perception, with no shared pathway or function tying the proteins together. With zero edges and a mix of unrelated processes, there is no clear functional theme to name the cluster. Confidence: None","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042742","count":1},{"id":"GO:0036085","count":1},{"id":"GO:0042060","count":1},{"id":"GO:1902074","count":1}]},{"hash":"450727172760750460","title":"Heart development and endothelial angiogenesis","description":"This cluster centers on cardiac morphogenesis and heart-field development, with terms like cardiac right atrium morphogenesis, Notch signaling in heart field cardioblast proliferation, SA node cell communication, and venous endothelial differentiation, along with an angiogenesis-related term (endothelial cell proliferation in sprouting). Additional terms such as calcium ion import and actin filament bundle assembly reflect muscle function and cytoskeletal organization relevant to developing cardiac tissue. Together, these signals point to a cohesive theme of heart formation paired with vascular differentiation, justifying the label.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098703","count":2},{"id":"GO:0007000","count":1},{"id":"GO:0003213","count":1},{"id":"GO:1903589","count":1},{"id":"GO:0051017","count":1}]},{"hash":"1717664821135941155","title":"RNA splicing and translation regulation","description":"The cluster is characterized by strong representation of spliceosome-mediated mRNA splicing terms (GO:0000398, GO:0006378, GO:0048026, GO:0031047, GO:0045292) and regulatory terms related to mRNA stability and translation initiation (GO:0010610, GO:0006446), with additional hints of RNA silencing and stress-responsive regulation. Together, these indicate a functional module focused on post-transcriptional RNA processing and control of translation, rather than a single enzyme or pathway.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0045292","count":3}]},{"hash":"973946128586222414","title":"Wnt Signaling and Cell Growth","description":"This cluster is dominated by GO terms for the Wnt signaling pathway and cell growth, suggesting a core functional theme around growth regulation via Wnt signaling. The other terms (translation, mRNA catabolic process, telomere maintenance) appear less coherent with the main theme and may reflect broader or incidental annotations.","confidence":"Medium","size":5,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0016055","count":2},{"id":"GO:1990683","count":1},{"id":"GO:0006402","count":1},{"id":"GO:0043577","count":1}]},{"hash":"1903514194895697617","title":"Transmembrane Transport of Small Metabolites","description":"Top GO terms show transmembrane transport for a variety of substrates (glucose, arabinose, urate, xenobiotics, organic anions, phosphate, selenite) and related osmotic stress responses. This convergence supports a theme of membrane transport of small metabolites across the cell surface.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006970","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0042908","count":1},{"id":"GO:0015747","count":1},{"id":"GO:0060731","count":1}]},{"hash":"1180547285139999651","title":"Unknown","description":"Top terms are spread across DNA repair, proteostasis (ER stress response, aggresome/inclusion body assembly), vesicle trafficking (SNARE disassembly), metabolism (FAD catabolic process), and mitochondrial DNA replication regulation, with no single dominant function linking the proteins. This dispersion makes a cohesive, specific label unsupported.","confidence":"","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070914","count":1},{"id":"GO:0030420","count":1},{"id":"GO:0018279","count":1},{"id":"GO:0070842","count":1},{"id":"GO:0030968","count":1}]},{"hash":"2101067091709048443","title":"Nuclear RNA Processing and mRNA Turnover","description":"The top GO terms cluster around RNA processing events in the nucleus (mRNA splicing via spliceosome; spliceosomal snRNP assembly; tRNA processing; maturation of SSU-rRNA; import into nucleus) and mRNA turnover/processing bodies (deadenylation-dependent decapping; P-body assembly). This pattern suggests a cohesive role in RNA maturation and RNA metabolism, spanning both nuclear processing and cytoplasmic mRNA decay/storage.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":4},{"id":"GO:0008033","count":4},{"id":"GO:0051170","count":3},{"id":"GO:1990141","count":3},{"id":"GO:0030490","count":3}]},{"hash":"703473154570611233","title":"Protein acetylation and polyamine metabolism","description":"The cluster is enriched for acetylation-related GO terms (peptidyl-lysine N6-acetylation, N-terminal acetylation, spermine and spermidine acetylation) and related metabolic activities such as arginine biosynthesis and acetoin catabolism. This suggests a unifying theme around acetylation events and polyamine-related metabolism, with some chromatin-related terms likely reflecting acetylation regulation.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":2},{"id":"GO:0061606","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0018003","count":2},{"id":"GO:0071962","count":2}]},{"hash":"651342950628942466","title":"Mitotic spindle assembly and microtubule dynamics","description":"All terms describe microtubule dynamics and spindle organization during cell division\u2014plus-end depolymerization, kinetochore interactions, spindle orientation, pole separation, and cytoskeletal polarity. A single term on dendritic transport is less connected. This supports a label focusing on mitotic spindle assembly and microtubule dynamics.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":1},{"id":"GO:0070462","count":1},{"id":"GO:0000911","count":1},{"id":"GO:0031535","count":1},{"id":"GO:0099607","count":1}]},{"hash":"374402234744056760","title":"Unknown","description":"The cluster contains diverse GO terms spanning RNA pseudouridine synthesis (snRNA/mRNA/tRNA) to vesicle transport (ER to Golgi), mitochondrial membrane potential regulation, oxidative-stress\u2013related apoptotic signaling, and regulation of glutamate transport. There isn\u2019t a single coherent biological theme connecting these terms, making it unclear how these proteins function together as a unit.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002037","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0031120","count":1}]},{"hash":"192804244264277886","title":"Peroxisomal fatty acid metabolism","description":"The cluster\u2019s top GO terms predominantly center on fatty acid metabolism: beta-oxidation, ketone body biosynthesis/catabolism, short-chain fatty acid biosynthesis, and glyoxysome organization, which points to peroxisomal involvement in lipid processing. While sporulation and apoptotic signaling regulation appear among the terms, they are less representative of the core theme. Overall, the proteins seem linked to peroxisomal lipid metabolism across contexts, justifying the label.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":2},{"id":"GO:0019619","count":2},{"id":"GO:1901029","count":2},{"id":"GO:0051790","count":2},{"id":"GO:0006635","count":2}]},{"hash":"703103679720411466","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000466","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0018144","count":3},{"id":"GO:0034476","count":3},{"id":"GO:0006268","count":3}]},{"hash":"2161089040424378667","title":"Unknown","description":"The GO terms are highly diverse (ribosome rRNA maturation, plasmid maintenance, homooligomerization, actin capping, spindle checkpoint, tissue development, metal ion response, mRNA splicing, and GTPase regulation) with only one connection observed. There is no clear, shared biological theme to tie these proteins into a specific functional cluster, so a meaningful label cannot be assigned.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0006276","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0051016","count":2}]},{"hash":"1497991580248479757","title":"Unknown","description":"The terms are highly diverse (methylation/demethylation, bile acid and triglyceride metabolism, xenobiotic processes, vitamin D response, and developmental/hormonal functions) with no single shared function, and the cluster has no interactions. This makes a coherent label unreliable.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":2},{"id":"GO:0070989","count":1},{"id":"GO:0002017","count":1},{"id":"GO:0060065","count":1},{"id":"GO:0046232","count":1}]},{"hash":"1746305575543530449","title":"Protein and RNA Methylation","description":"The top GO terms are centered on methylation of both proteins (N-terminal and peptidyl methylation, overall protein methylation) and RNA (7-methylguanosine mRNA capping), indicating a shared function in methyltransferase activities affecting proteins and RNA. While other terms like aging, senescence, and lipid biosynthesis appear, they are less cohesive with this core theme, so the label highlights the strongest common thread.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":1},{"id":"GO:0001300","count":1},{"id":"GO:0018364","count":1},{"id":"GO:0006972","count":1},{"id":"GO:0006370","count":1}]},{"hash":"626771031669973618","title":"Unknown","description":"The GO terms are spread across detoxification, muscle relaxation regulation, halogen metabolism, calcium channel regulation, chromatin binding regulation, neural development, synaptic activity, neural precursor proliferation, and Schwann cell development with only one annotation each. This scattered set lacks a cohesive function or pathway to define a specific cluster name, so I mark it Unknown with no confidence.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":1},{"id":"GO:1901077","count":1},{"id":"GO:0070276","count":1},{"id":"GO:1901339","count":1},{"id":"GO:0035562","count":1}]},{"hash":"1733794283329168483","title":"Neural development and tissue morphogenesis","description":"These proteins cluster around neural development signals (neuron differentiation, Schwann cell development, excitatory postsynaptic potential, locomotion behavior) and tissue morphogenesis (lymphangiogenesis, branching of blood vessels) with EMT as a related cell-state transition. The combined emphasis on neural lineage differentiation and general morphogenetic processes suggests a label focusing on neural development coupled with broader tissue morphogenesis. Negative regulation of chromatin binding and DNA damage checkpoint signaling are more general regulatory themes but do not override the dominant developmental/morphogenetic signal. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035562","count":5},{"id":"GO:0031987","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0030182","count":5},{"id":"GO:0001946","count":5}]},{"hash":"835425297591434814","title":"Histone deacetylation and heterochromatin formation","description":"The GO terms cluster around chromatin state and silencing: rDNA heterochromatin formation, heterochromatin maintenance, nucleosome-related regulation, and notably peptidyl-lysine deacetylation, pointing to histone-modifying enzymes driving chromatin silencing and transcription control. While some terms are obsolete or broad, the strongest signals relate to chromatin organization and transcription regulation via deacetylation and heterochromatin formation.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":3},{"id":"GO:0045820","count":3},{"id":"GO:0006344","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0060303","count":3}]},{"hash":"1345364104013784884","title":"Translation initiation and mRNA cap methylation","description":"This cluster is dominated by GO terms tied to initiating and regulating translation (translation reinitiation, preinitiation complex formation, regulation of translational initiation) and RNA cap biology (7-methylguanosine mRNA capping, guanine-N7 methylation), plus several methyltransferase-related protein modifications (N-terminal peptidyl-glycine and peptidyl-glutamine methylation). The combination points to a group of proteins involved in initiating translation and modifying the RNA cap/related methylation processes; a few ancillary terms (aging, hyperosmotic response) appear more peripheral. Overall, the label captures the core theme of translational initiation with cap methylation activity.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0018013","count":1},{"id":"GO:0001300","count":1}]},{"hash":"2279365201050787084","title":"Potassium Transport and Proton-Motive Energy Production","description":"The cluster is dominated by GO terms for potassium ion transport across membranes (import/export) and intracellular potassium homeostasis, with multiple terms pointing to maintaining ion gradients and membrane potential. Additional signals for proton-motive force\u2013driven ATP synthesis (mitochondrial and plasma membrane) reinforce a theme of energy production coupled to proton gradients. A few transcription-related terms appear minor and likely do not define the core function of this cluster.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0030007","count":2},{"id":"GO:1990573","count":2},{"id":"GO:0042776","count":1}]},{"hash":"1258196585188704498","title":"Peroxisome Biogenesis and Protein Import","description":"The Top Terms point to peroxisome-focused processes, including membrane biogenesis and import of proteins into both the peroxisome membrane and matrix, as well as ER-dependent peroxisome organization. While a few terms are obsolete or unrelated, the core themes consistently indicate peroxisomal assembly and protein import pathways as the shared function of this cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990022","count":1},{"id":"GO:0021552","count":1},{"id":"GO:0044376","count":1},{"id":"GO:0002244","count":1},{"id":"GO:0045046","count":1}]},{"hash":"407175143481117583","title":"Ribosome biogenesis and translation regulation","description":"Dominant GO terms point to ribosomal large subunit biogenesis and assembly, along with translation and associated protein targeting/stabilization, suggesting a cluster centered on ribosome production and control of protein synthesis; ubiquitin/neddylation-related terms hint at linked protein quality control, while the cilium motility term appears incidental.","confidence":"High","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000435","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0042273","count":1}]},{"hash":"185712717057097289","title":"ER Stress and Protein Quality Control","description":"This cluster is dominated by GO terms related to the endoplasmic reticulum unfolded protein response, protein unfolding, and ER-to-Golgi transport, pointing to roles in ER quality control and protein folding/degradation (ERAD). Additional terms on ubiquitin-specific protease activity and oxidative stress support a broader stress-response and protein turnover context. Some terms appear less related or obsolete, but the core signal is ER stress\u2013related protein quality control.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030968","count":3},{"id":"GO:0072389","count":3},{"id":"GO:0043335","count":3},{"id":"GO:1903724","count":3},{"id":"GO:0034599","count":3}]},{"hash":"195551460433905582","title":"DNA double-strand break repair and recombination","description":"This cluster is dominated by terms involved in repairing DNA damage, especially double-strand break repair via homologous recombination, sister chromatid exchange, interstrand cross-link repair, and meiotic joint molecule formation. The presence of protein phosphorylation regulation hints at signaling controls coordinating these repair processes. While translation/transcription terms appear too, the core theme is DNA repair and recombination.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990414","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010569","count":2},{"id":"GO:0006468","count":1},{"id":"GO:0001932","count":1}]},{"hash":"1634538867739132294","title":"Unknown","description":"The GO terms show a mix of amino acid catabolism/biosynthesis, central carbon metabolism, fatty acid homeostasis, and signaling pathways (Notch and salicylic acid\u2013mediated defense) with no single cohesive function linking the proteins. This makes a concise, specific label unsupported.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":4},{"id":"GO:0007219","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0006571","count":3},{"id":"GO:0019550","count":3}]},{"hash":"1008306457345950147","title":"Unknown","description":"The GO terms span a highly diverse set of processes (xenobiotic response, neural precursor proliferation, alternative splicing, embryonic development, dopamine catabolism, cAMP signaling, quinolinate and glutamate biosynthesis, erythrocyte differentiation, and chromatin binding regulation) with no clear shared function or pathway, and there are no edges connecting the proteins in this cluster. This makes it impossible to assign a concise, representative label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:2000179","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0042420","count":2}]},{"hash":"1880493463329864689","title":"Proteasome- and APC-Driven Cell Cycle Regulation","description":"The cluster centers on proteasome function and APC-dependent degradation, including proteasome core assembly, ubiquitin\u2011independent protein catabolism, and negative regulation of G2/M. This points to a coherent theme of regulated protein degradation controlling cell cycle progression, with other terms like viral process or stress responses likely supporting annotations rather than core themes.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0009651","count":1},{"id":"GO:0002223","count":1}]},{"hash":"286836541990282404","title":"Mitochondrial respiration and lipid biosynthesis","description":"The top GO terms point to mitochondrial energy metabolism (mitochondrial electron transport, aerobic respiration, respirasome assembly, proton transmembrane transport) and lipid biosynthesis/regulation (unsaturated fatty acid biosynthesis, sphingosine biosynthesis, ergosterol biosynthetic processes). Although a couple terms are unrelated or obsolete, the dominant pattern connects mitochondrial function with lipid metabolism and sterol pathways, suggesting this cluster centers on energy production alongside membrane lipid synthesis. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006123","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0097250","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0006636","count":1}]},{"hash":"1309291238468795624","title":"Nuclear import and chromatin dynamics","description":"The highest GO terms point to nuclear localization and chromatin-related processes (NLS-bearing import into nucleus, localization to nuclear inner membrane, chromatin silencing/puffing), suggesting a cluster of proteins involved in nuclear transport and chromatin dynamics. Some related terms on ubiquitin-dependent degradation and signaling regulation appear, but the dominant theme remains nuclear transport plus chromatin/chromosome regulation.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035392","count":2},{"id":"GO:0036228","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0035080","count":2},{"id":"GO:0046604","count":1}]},{"hash":"1408826596674810517","title":"Carnitine Transport and Metabolism","description":"Based on the GO terms, the cluster is tied to carnitine handling: 4-(trimethylammonio)butanoate transport and (R)-carnitine transmembrane transport, plus carnitine metabolic process. This consistent focus on transport and metabolism of carnitine suggests a cohesive functional unit.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900751","count":2},{"id":"GO:1902270","count":2},{"id":"GO:0009437","count":2}]},{"hash":"1743568775018204865","title":"Diverse organ development","description":"The GO terms are all development-related across multiple organs (digestive tract, peripheral nervous system, mammary gland, bile ducts, trachea glands, embryonic genitalia morphogenesis, epithalamus, endocardial differentiation). No single process dominates; the shared theme is organ morphogenesis and differentiation across tissues.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000726","count":1},{"id":"GO:0048546","count":1},{"id":"GO:0007422","count":1},{"id":"GO:0030879","count":1},{"id":"GO:0035622","count":1}]},{"hash":"1710686490338149926","title":"Nucleic Acid Metabolism and Chromatin Regulation","description":"The top GO terms point to nuclear processes involving nucleic acids and chromatin (DNA metabolic process, rDNA heterochromatin formation, histone modification) and, alongside translation, suggest a broad theme of gene expression regulation rather than a single pathway. The presence of obsolete terms also indicates historical annotations but does not alter the core nuclear focus.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006259","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0090305","count":1},{"id":"GO:0000183","count":1},{"id":"GO:0031393","count":1}]},{"hash":"798382568274332580","title":"MAPK, Wnt, and PI3K signaling activators","description":"It is labeled as MAPK, Wnt, and PI3K signaling activators because the top GO terms emphasize positive regulation of JNK and ERK (MAPK) cascades, canonical Wnt signaling, and PI3K activity, along with ephrin receptor signaling and focal adhesion regulation. This pattern points to proteins that enhance multiple signaling pathways rather than a single pathway, though some development-related terms may reflect broader roles in tissue signaling contexts.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046330","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0051893","count":3}]},{"hash":"1825694983134151364","title":"Golgi UDP-sugar transporters","description":"The top GO terms point to transmembrane transport of UDP-sugars into the Golgi lumen (UDP-N-acetylglucosamine and UDP-galactose), suggesting a common function as Golgi nucleotide-sugar transport proteins. Other transport terms (sialic acid, taurin e) appear but are less directly connected; the beam of evidence centers on nucleotide-sugar transport needed for glycosylation and polysaccharide biosynthesis in plants, which relates to cell wall and pollen exine formation processes. Thus, the cluster is best described as Golgi UDP-sugar transporters, with a moderate level of confidence given some annotation noise. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010584","count":1},{"id":"GO:1902183","count":1},{"id":"GO:1990569","count":1},{"id":"GO:1903857","count":1},{"id":"GO:0015739","count":1}]},{"hash":"211076192928033608","title":"RNA Splicing and Translational Regulation","description":"The proteins cluster around regulation of translational initiation and reinitiation, preinitiation complex formation, and spliceosome-mediated mRNA splicing/alternative splicing, suggesting a shared role in coordinating RNA processing with translation control.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0000381","count":1},{"id":"GO:0002188","count":1}]},{"hash":"1922561150399416823","title":"Ribosome and Translation Machinery","description":"The cluster is dominated by translation-related GO terms, especially translation and ribosomal large subunit assembly, indicating involvement in protein synthesis machinery. The single interleukin-4 response term appears incidental; overall the functions align with ribosome/translation components.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0071353","count":1},{"id":"GO:0000027","count":1}]},{"hash":"965684207684064843","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0008615","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0009089","count":3},{"id":"GO:0051402","count":3}]},{"hash":"1477967487375890356","title":"Stress-related mRNA processing and translation regulation","description":"The cluster\u2019s GO terms center on post-transcriptional control: stress-related mRNA stability regulation, regulation of translational initiation and reinitiation, formation of the translation preinitiation complex, and spliceosome-mediated regulation of mRNA splicing. This points to a cohesive role in coordinating mRNA fate and translation under stress.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0006446","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0000381","count":2}]},{"hash":"1092057007174169639","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0031120","count":1},{"id":"GO:0007338","count":1},{"id":"GO:0000470","count":1}]},{"hash":"2162098947491944260","title":"RNA splicing and translation initiation regulation","description":"This cluster centers on RNA-level regulation, with GO terms for mRNA splicing via the spliceosome (including alternative splicing) and multiple aspects of translation initiation/reinitiation, plus ncRNA-mediated gene silencing. Together, they point to a unit involved in post-transcriptional gene expression control at both splicing and translation steps.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006446","count":1},{"id":"GO:0075525","count":1},{"id":"GO:0000381","count":1}]},{"hash":"1025779943957888104","title":"Proteasome-Mediated Proteolysis and Cell Cycle Regulation","description":"The top GO terms cluster around proteolysis and mitotic control: proteasome core complex assembly, proteasomal ubiquitin-independent protein catabolic process, APC-dependent catabolic process, and negative regulation of G2/M transition, which together point to protein turnover governing cell-cycle progression. Other terms (salt stress, C-type lectin receptor signaling, Fc-epsilon signaling, viral process) suggest broader stress and signaling roles but do not undermine the central theme of proteostasis linked to cell-cycle regulation. Overall, these proteins seem to participate in proteolysis-related control of mitosis, with some accompanying signaling context.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009651","count":3},{"id":"GO:0002223","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0051437","count":3}]},{"hash":"337910385868858614","title":"Developmental differentiation and stress-activated cytoskeletal remodeling","description":"This cluster blends terms tied to stress responses (eIF2\u03b1-regulated translation initiation, p53-mediated DNA damage response) with cytoskeletal organization (actin/microtubule-related processes) and differentiation programs (Schwann cell development, keratinocyte differentiation, developmental growth). The common thread appears to be differentiation processes that are modulated by cellular stress and involve cytoskeletal remodeling, rather than a single strictly defined pathway.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1902817","count":3},{"id":"GO:0006977","count":3},{"id":"GO:0010998","count":3},{"id":"GO:0001324","count":3},{"id":"GO:0042517","count":3}]},{"hash":"2118148400212761144","title":"Redox Balance and Oxidative Stress Response","description":"This cluster shows multiple redox-related GO terms (oxidation-reduction, cellular oxidant detoxification, cell redox homeostasis, deglutathionylation) plus connections to oxidative protein folding (ER) and cytochrome complex assembly, all pointing to maintaining cellular redox state and antioxidant defenses. Some terms are less central (viral process, DNA-binding regulation) but do not override the core redox theme. Confidence: Medium.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0043388","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0017004","count":1},{"id":"GO:0080058","count":1}]},{"hash":"2040211715578452704","title":"Ribosome Biogenesis and Translation","description":"These proteins cluster around the core functions of making and using ribosomes: translation (translation, cytoplasmic translation) and ribosomal large subunit biogenesis/export, plus rRNA maturation signals. Additional RNA processing terms (intron splicing, RNA folding) align with broader RNA maturation steps that support ribosome assembly. The combination strongly suggests a shared role in ribosome biogenesis and protein synthesis, with antibiotic response potentially reflecting translation-targeting effects. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0033120","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0034337","count":1}]},{"hash":"2056075582849718431","title":"Ribosome biogenesis and translation","description":"The top GO terms cluster around rRNA maturation and processing, rRNA and tRNA methylation, ribosome assembly (cytosolic and preribosome/large subunit), ribosome biogenesis, and overall translation, including mitochondrial translation. This pattern points to proteins involved in forming and functioning the ribosome and protein synthesis machinery, justifying a label that centers on ribosome biogenesis and translation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":1},{"id":"GO:0070475","count":1},{"id":"GO:0042256","count":1},{"id":"GO:0002127","count":1},{"id":"GO:1902626","count":1}]},{"hash":"570876661872395643","title":"Unknown","description":"The GO terms cover a wide range of processes (sporulation, arginine biosynthesis, various acetylation events, heterochromatin formation, chromatid cohesion, angiogenesis) without a single cohesive biological theme connecting all four proteins. While acetylation-related terms appear, the diversity of contexts suggests no consistent function across the cluster. Thus a specific, representative label cannot be confidently assigned.","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":4},{"id":"GO:0006526","count":4},{"id":"GO:0061606","count":4},{"id":"GO:0045150","count":4},{"id":"GO:0018003","count":4}]},{"hash":"748747174174044423","title":"Retinoid metabolism and signaling","description":"The cluster is dominated by retinol and retinal metabolic processes and the regulation of retinoic acid receptor signaling, which together indicate a core function in retinoid metabolism and signaling. Additional terms like bile acid and norepinephrine metabolism suggest broader metabolic involvement, but retinoid-related terms are the strongest signal, supporting a focused label around vitamin A metabolism and signaling.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":4},{"id":"GO:0042574","count":4},{"id":"GO:0048385","count":2},{"id":"GO:0060135","count":2},{"id":"GO:0042415","count":2}]},{"hash":"182817754565947323","title":"BMP/TGF-\u03b2 signaling regulators","description":"This cluster is dominated by GO terms about negative regulation of BMP signaling and TGF-\u03b2 receptor signaling, SMAD complex assembly, and cellular responses to TGF-\u03b2, as well as dephosphorylation of threonine residues, pointing to modulation of BMP/TGF-\u03b2 pathways. Some terms are from broader regulatory contexts, but the core theme is signaling regulation in the BMP/TGF-\u03b2 axis.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":3},{"id":"GO:0010991","count":3},{"id":"GO:0010074","count":3},{"id":"GO:0042006","count":3},{"id":"GO:0061191","count":3}]},{"hash":"1609543275003732196","title":"Plant meiosis and gametogenesis","description":"The GO terms point to meiosis-associated processes (double-strand break repair, reciprocal meiotic recombination) and gametophyte development (embryo sac and pollen development), indicating a cluster of plant proteins involved in meiotic recombination and gametogenesis.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009553","count":1},{"id":"GO:0007131","count":1},{"id":"GO:0006302","count":1},{"id":"GO:0009555","count":1}]},{"hash":"996456634178839690","title":"Ubiquitin-Mediated ERAD and Protein Turnover","description":"The GO terms cluster around ubiquitination/deubiquitination and ER-associated degradation (ERAD), plus glycoprotein deglycosylation and catabolic processes, indicating a cohesive role in protein quality control and turnover, especially for glycoproteins in the ER. Obsolete ERAD terms and a few unrelated terms appear, but the dominant pattern supports ubiquitin-dependent protein processing.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006468","count":1},{"id":"GO:0001827","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0030474","count":1}]},{"hash":"1323394874231331420","title":" Cellular energy metabolism","description":"The top GO terms center on ATP synthesis coupled electron transport and ferredoxin metabolism, indicating energy production and redox processes as the core function. The other terms (sodium ion transport, lactation, regulation of vascular development, nitrogen fixation, and various catabolic processes) are more diverse, suggesting possible annotation noise or multi-functionality in a small cluster. Given three proteins and a limited interaction set, labeling the cluster by a unifying energy metabolism theme is most representative.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042773","count":2},{"id":"GO:0045602","count":2},{"id":"GO:0006814","count":2},{"id":"GO:1900747","count":2},{"id":"GO:0010124","count":2}]},{"hash":"408212186106755222","title":"Autophagy-linked carbohydrate and lipid catabolism","description":"These terms cluster around autophagy (positive regulation of macroautophagy, glycophagy) and the catabolic metabolism of carbohydrates and glycerophospholipids, suggesting a theme of autophagy-driven breakdown of energy stores (glycogen) and lipid/carbohydrate catabolism. The presence of glycophagy and macroautophagy terms supports a cohesive functional group focused on autophagy-related degradation and energy mobilization.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046959","count":1},{"id":"GO:0043609","count":1},{"id":"GO:0016239","count":1},{"id":"GO:0046475","count":1},{"id":"GO:0000025","count":1}]},{"hash":"485652620750086778","title":"Ribosome Biogenesis and Translation Regulation","description":"The top GO terms cluster around ribosome assembly (large subunit and preribosome) and translation, including both positive regulation of ribosome biogenesis and negative regulation of translation preinitiation, indicating proteins involved in ribosome biogenesis and initiation control rather than general metabolic roles.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0090070","count":1},{"id":"GO:1901194","count":1}]},{"hash":"1525213005619109877","title":"Metabolic signaling and amino acid responses","description":"This cluster shows a mix of metabolic and nutrient/hormone-response terms (iron import, heme catabolism, arginine biosynthesis, responses to insulin, growth hormone, oleic acid, and amino acids) along with a developmental term (midgut development). The lack of a single cohesive pathway suggests a broad role in metabolic regulation and nutrient sensing rather than a specific process, hence the label Metabolic signaling and amino acid responses. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0033212","count":1},{"id":"GO:0042167","count":1},{"id":"GO:0042984","count":1},{"id":"GO:0071400","count":1}]},{"hash":"599562855921848927","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"GO terms point to mitochondrial membrane transport (manganese, phosphate, nucleotide import, heme), ATP transmembrane transport, and regulation of membrane potential, along with apoptotic mitochondrial changes and thermogenesis. This suggests a cohesive module focused on mitochondrial transport, energy homeostasis, and apoptosis regulation.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":3},{"id":"GO:1990544","count":3},{"id":"GO:1990519","count":3},{"id":"GO:0008637","count":3},{"id":"GO:0035435","count":3}]},{"hash":"990799969462556138","title":"Oxidative stress response and detoxification","description":"The GO terms here cluster around redox biology and detox pathways (mercury detoxification, methylglyoxal response) along with regulation of proteins and metabolic processes tied to oxidative stress (NAD(P)H oxidase activity, oxidative phosphorylation regulation, and protein modification). While some terms are niche, the overall theme is cellular defense against oxidative and metabolic stress, with detoxification features. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050787","count":1},{"id":"GO:0033864","count":1},{"id":"GO:0006517","count":1},{"id":"GO:1903384","count":1},{"id":"GO:2000825","count":1}]},{"hash":"308077770786713336","title":"Nucleotide biosynthesis and salvage","description":"The top GO terms converge on nucleotide metabolism, including ADP biosynthesis, AMP salvage, purine ribonucleotide interconversion, and pathways like ITP and GTP metabolism, indicating a coherent theme of nucleotide biosynthesis and salvage. The brain and liver development terms are likely incidental annotations rather than defining the cluster\u2019s function. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0046940","count":3},{"id":"GO:0015951","count":3},{"id":"GO:0006172","count":3},{"id":"GO:0044209","count":3}]},{"hash":"1191247439689258546","title":"Unknown","description":"No GO terms are provided to identify a shared function among the three proteins, and with just three nodes and a sparse edge pattern there is no clear theme to name the cluster. Therefore the safe label is Unknown.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"460575948684746377","title":"Mitochondrial transport and membrane potential regulation","description":"The GO terms cluster around mitochondrial transport (ions and metabolites), membrane potential regulation, and related apoptosis/necroptosis processes, plus adaptive thermogenesis, suggesting a coherent theme of mitochondrial transport and energy regulation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":1},{"id":"GO:1990544","count":1},{"id":"GO:1990519","count":1},{"id":"GO:0008637","count":1},{"id":"GO:0035435","count":1}]},{"hash":"2042004414277835206","title":"Golgi nucleotide-sugar transporters","description":"The top GO terms cluster around transmembrane import of nucleotide sugars (GDP-fucose, UDP-glucose) into the Golgi lumen and related glycosylation processes (protein O-linked glycosylation via fucose). This points to a cohesive role as Golgi sugar transporters driving glycosylation in plant cells; a few other transport terms are present but do not override the central theme. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035436","count":1},{"id":"GO:0032973","count":1},{"id":"GO:0036085","count":1},{"id":"GO:0036066","count":1},{"id":"GO:0015713","count":1}]},{"hash":"1550997052333406071","title":"Central carbon metabolism","description":"The terms cluster around core energy and carbon-flow pathways: glycolysis, pyruvate decarboxylation to acetyl-CoA, the TCA cycle, acetyl-CoA\u2013related processes, and downstream metabolic activities like amino acid catabolism and fatty acid biosynthesis. Translation-related term may reflect a ribosomal component association rather than defining the cluster. Overall, it suggests enzymes involved in fundamental metabolism rather than a single specialized function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002181","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006552","count":1},{"id":"GO:0033512","count":1},{"id":"GO:0006086","count":1}]},{"hash":"1093341395799886629","title":"Heat shock response and chaperone activity","description":"The three proteins cluster around heat-related and protein folding processes, with GO terms like response to heat and chaperone/cofactor-dependent refolding, plus ER-stress-related translation regulation. Despite some obsolete terms, the strongest recurring theme is heat-induced protein quality control and chaperone activity, indicating involvement in managing misfolded proteins during heat stress. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0090084","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0036494","count":1}]},{"hash":"1728401953410999480","title":"Regulation of apoptosis and innate immune signaling","description":"Top terms indicate regulation of necroptosis, apoptosis, TLR signaling, transcription, and cell cycle, suggesting a cluster of regulatory proteins that modulate cell fate and immune responses, often via ubiquitination.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060544","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0071157","count":1}]},{"hash":"117460667756170515","title":"Unknown","description":"No GO terms are available to define a shared function for these proteins, and the small, sparse network (3 edges, 1 triangle, max degree 2) provides no clear functional theme. Therefore, the label Unknown is appropriate.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"1393243788657418852","title":"Glycation detoxification and oxidative stress response","description":"The GO terms cluster around detoxification of glycation products (methylglyoxal removal, deglycosylation/deglycation), proteolysis, and oxidative stress signaling (neuron apoptosis, NADPH oxidase regulation), suggesting a shared function in processing glycated/damaged proteins and mitigating oxidative stress.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0050787","count":1},{"id":"GO:0033864","count":1},{"id":"GO:0006517","count":1},{"id":"GO:1903384","count":1}]},{"hash":"1083520544197866689","title":"Mitotic spindle assembly and microtubule dynamics","description":"These proteins appear tied to mitotic spindle assembly and microtubule regulation: plus-end dynamics, microtubule depolymerization, kinetochore attachments, spindle pole separation, and cytokinesis-related events. The recurrent GO terms point to a common function in organizing the microtubule cytoskeleton during cell division, with one outlier term about neuronal transport.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":3},{"id":"GO:0070462","count":3},{"id":"GO:0000911","count":3},{"id":"GO:0031535","count":3},{"id":"GO:0099607","count":3}]},{"hash":"286327166310333757","title":"DNA replication and telomere maintenance","description":"This cluster\u2019s top GO terms center on DNA replication, DNA binding regulation, DNA cross-link repair, and telomere dynamics (telomeric loop disassembly and telomere regulation), suggesting a shared role in genome maintenance during replication and telomere maintenance. The absence of network edges temper confidence, but the convergent themes point to a genome integrity function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0008283","count":1},{"id":"GO:0043388","count":1},{"id":"GO:0036297","count":1},{"id":"GO:0007284","count":1}]},{"hash":"729966760803612431","title":"Mitotic spindle assembly and microtubule dynamics","description":"These proteins map to mitotic spindle assembly and microtubule remodeling\u2014plus-end depolymerization, kinetochore attachment, spindle orientation, and cytokinesis\u2014consistent with chromosome segregation roles.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":3},{"id":"GO:0070462","count":3},{"id":"GO:0000911","count":3},{"id":"GO:0031535","count":3},{"id":"GO:0099607","count":3}]},{"hash":"1781188706836865776","title":"P53-mediated DNA damage response and RNA processing","description":"The proteins are linked by GO terms tying DNA damage signaling (p53 pathway, gamma radiation response) to transcription and RNA metabolism (rRNA processing, mRNA capping, transcription elongation/termination, RNA biosynthesis, translation). This suggests a functional cluster centered on how cells respond to DNA damage by coordinating transcriptional control and RNA processing.  ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006977","count":1},{"id":"GO:2000232","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0071480","count":1}]},{"hash":"1988701042175732090","title":"Unknown","description":"These GO terms are highly heterogeneous (rRNA maturation, xenobiotic response, symbiont entry, raffinose biosynthesis, endothelial migration, learning, and more), showing no clear shared function among the proteins. This likely reflects annotation noise or incidental associations rather than a coherent biological module, so the label is Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0042493","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0010325","count":1},{"id":"GO:0043542","count":1}]},{"hash":"135277886283690489","title":"Unknown","description":"The top terms are diverse and largely incongruent (e.g., ER stress response/folding, photosystem II assembly, mesoderm formation, DNA replication, redox homeostasis), with no clear unifying function across the three proteins. Obsolete terms further suggest weak, inconsistent annotation. Therefore a cohesive label cannot be determined.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0051259","count":1}]},{"hash":"377491611325908343","title":"Plant chlorophyll metabolism and gibberellin signaling","description":"This cluster's GO terms center on chlorophyll catabolic process and regulation of chlorophyll biosynthesis, with a notable link to gibberellin signaling (growth hormone pathway). Despite some obsolete terms, the common theme is chlorophyll turnover combined with growth regulation in plants, suggesting a plant-specific metabolism/hormone regulation cluster rather than a single enzymatic activity.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015996","count":1},{"id":"GO:0016042","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0051348","count":1},{"id":"GO:0016576","count":1}]},{"hash":"610115310891888977","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051533","count":1},{"id":"GO:0045694","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000395","count":1},{"id":"GO:0006196","count":1}]},{"hash":"116309828855031104","title":"Chloroplast Photosynthesis and Translation","description":"This cluster centers on photosynthesis-related terms (photosystem I assembly, photosynthesis, ATP synthesis coupled electron transport) and translation, suggesting plastid-encoded or chloroplast-associated proteins involved in energy production and protein synthesis. A few outlier terms related to lactation and vascular regulation appear, likely noise. Overall, the core theme points to chloroplast photosynthetic machinery and translation, supporting this label with moderate confidence.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048564","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042773","count":1},{"id":"GO:0045602","count":1}]},{"hash":"1963212690797108782","title":"Nucleotide Salvage Pathways","description":"Most of the top GO terms relate to salvage or catabolic steps of nucleotides (AMP salvage, GMP catabolic, guanine salvage, uracil salvage), suggesting the proteins in this cluster participate in nucleotide recycling and metabolism. A few other terms (dopamine metabolism, striatum development, lactation, transcription regulation) appear sparsely and may reflect broader annotation noise or multifunctionality, but the dominant theme is nucleotide salvage.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":2},{"id":"GO:0042417","count":1},{"id":"GO:0046038","count":1},{"id":"GO:0006178","count":1},{"id":"GO:0006223","count":1}]},{"hash":"1695053377462969042","title":"Ribosome Biogenesis and Translation","description":"Dominated by GO terms about ribosome biogenesis, small subunit export from the nucleus, and translation, indicating a core cluster of proteins involved in ribosome assembly and protein synthesis; some non-specific terms appear as minor noise.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006407","count":3},{"id":"GO:1905053","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0042274","count":2}]},{"hash":"1040596026177298622","title":"Cellular stress response and metabolism","description":"The GO terms cluster mainly around cellular responses to stressors (cadmium, methylglyoxal) and a set of metabolic/biosynthetic processes (ascorbic acid, bile acids, norepinephrine) plus tissue homeostasis and development signals. This suggests proteins involved in managing stress while supporting metabolism and organ maintenance, though the terms are diverse, making the connection moderate. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0048385","count":2},{"id":"GO:0060135","count":2},{"id":"GO:0042415","count":2},{"id":"GO:0097238","count":2}]},{"hash":"75826006334297141","title":"BMP/TGF-beta signaling regulation","description":"The top GO terms are dominated by negative regulation of BMP signaling and related TGF-\u03b2 pathway components (e.g., negative regulation of TGF-\u03b2 receptor signaling, cellular response to TGF-\u03b2 stimulus, SMAD-related regulation, and dephosphorylation). While some terms hint at plant-specific processes (meristem identity), the cohesive theme across most terms is modulation of BMP/TGF-\u03b2 signaling and SMAD activity, suggesting these proteins act as pathway regulators. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":3},{"id":"GO:0010991","count":3},{"id":"GO:0010074","count":3},{"id":"GO:0042006","count":3},{"id":"GO:0061191","count":3}]},{"hash":"2178464679323853584","title":"Keratinocyte Growth and Differentiation Regulation","description":"The top terms center on epidermal keratinocytes, including negative regulation of keratinocyte proliferation, regulation of epidermal cell division, and keratinocyte differentiation, plus associated growth and CDK activity regulation and glucocorticoid signaling. Taken together, they point to coordinated control of skin epidermal cell cycle and maturation, with hormonal signaling modulating these processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010839","count":2},{"id":"GO:0042921","count":1},{"id":"GO:0006977","count":1},{"id":"GO:0010482","count":1},{"id":"GO:0000079","count":1}]},{"hash":"127846707183429166","title":"Centrosome/centriole biogenesis and nuclear transport","description":"This cluster is dominated by GO terms linking centrosome/centriole processes (protein localization to centrosome, positive regulation of centriole replication) and nuclear transport (regulation of protein import into nucleus), with accompanying meiosis-related terms (spermatogenesis, oocyte karyosome formation) that suggest a germ-cell division context. The common thread appears to be coordinated control of centrosome function and nuclear trafficking during cell division.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900034","count":2},{"id":"GO:0007283","count":2},{"id":"GO:0042306","count":2},{"id":"GO:0045742","count":2},{"id":"GO:0043123","count":2}]},{"hash":"1726342502586159872","title":"Folate and One-Carbon Metabolism","description":"The cluster shows a clear enrichment for folate-related processes (THF interconversion, folic acid biosynthesis/catabolism, formate metabolism) and one-carbon transfer needs (histidine biosynthesis), suggesting a cohesive theme around folate-driven one-carbon metabolism. Some additional terms like DNA binding regulation and redox maintenance may reflect broader roles of the included proteins, but the core signal points to folate/one-carbon pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000105","count":1},{"id":"GO:0015942","count":1},{"id":"GO:0035999","count":1},{"id":"GO:0046657","count":1},{"id":"GO:0009396","count":1}]},{"hash":"692914792810714047","title":"Protein acetylation and chromatin regulation","description":"The top GO terms cluster around various protein acetylation processes (N-terminal acetylation, peptidyl-lysine N6-acetylation, spermidine/spermine acetylation) and chromatin-associated functions (centromeric cohesion, subtelomeric heterochromatin formation), with a possible link to angiogenesis in a proliferative context. Some metabolic terms appear, but the dominant pattern points to acetylation-based regulation affecting chromatin dynamics.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":3},{"id":"GO:0061606","count":3},{"id":"GO:0045150","count":3},{"id":"GO:0018003","count":3},{"id":"GO:0071962","count":3}]}]