[{"hash":"2262720023929571850","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006238","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0044211","count":3},{"id":"GO:0006206","count":3}]},{"hash":"2283283839459220689","title":"Chromatin modification and vesicle trafficking","description":"This cluster includes histone modification terms (H3 K4/K79 methylation, H2A deubiquitination), ubiquitin-dependent protein turnover, and DNA-templated transcription, alongside vesicle transport between the ER and Golgi and cell division. The common thread appears to be regulation by post-translational modifications and links to transcriptional control and intracellular trafficking, suggesting a theme of chromatin-related regulation intertwined with membrane trafficking processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0035522","count":2},{"id":"GO:0006351","count":2}]},{"hash":"668792971024411834","title":"Viral Entry and DNA Integration","description":"The top GO terms cluster around viral/symbiont entry and DNA integration, including viral penetration into the host nucleus, symbiont entry into host cells, proviral latency establishment, and DNA integration, with some transcription regulation and immune-related processes. This suggests the proteins participate in host-virus/symbiont interactions and genome-integrating activities, rather than a single developmental or metabolic pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0075732","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0039651","count":3}]},{"hash":"1926752316473537054","title":"Insect salivary gland development and epithelial differentiation","description":"This cluster centers on transcription by RNA polymerase II and explicit signals of epithelial morphogenesis in insects (epithelial cell maturation in salivary gland development; leading edge cell differentiation), with supporting hints from stress/ER pathways (UPR/ER stress, calcium signaling) and insect-specific traits (cuticle pigmentation). The combination suggests a developmental program governing salivary gland epithelial differentiation in an insect context, rather than a single canonical pathway.","confidence":"Medium","size":28,"edges":366,"triangles":3003,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":5},{"id":"GO:0009737","count":5},{"id":"GO:0006990","count":5},{"id":"GO:1990440","count":5},{"id":"GO:0035026","count":4}]},{"hash":"1225601818883980116","title":"Cell Cycle and RNA Pseudouridine Synthesis","description":"The cluster centers on cell cycle and division terms (cell cycle, cell division, proliferation), indicating a proliferative state. A subset of terms refers to RNA pseudouridine synthesis across mRNA, snRNA, and tRNA, suggesting concurrent RNA modification activity. Other terms (adhesion, chemokine production, vitamin K response) are less representative, so the dominant theme remains cell cycle/proliferation with some RNA modification involvement.","confidence":"Medium","size":28,"edges":106,"triangles":63,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008283","count":1},{"id":"GO:0007155","count":1}]},{"hash":"1783317216469175697","title":"Membrane Transport & ER Stress Response","description":"The top GO terms cluster around transmembrane transport of various substrates (heme, taurine, monoatomic anions) and cellular stress/quality-control processes (ER unfolded protein response) with related organelle dynamics (vacuole fusion). A few terms (antibiotic biosynthesis, liver regeneration, insulin secretion) appear more peripheral, suggesting some annotation breadth. Overall, the cluster best aligns with membrane transport and ER stress-related processes, hence this label.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":3},{"id":"GO:0032024","count":2},{"id":"GO:0006995","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1798918724859143984","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0015074","count":2},{"id":"GO:0031120","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0071353","count":2}]},{"hash":"1419189766259178021","title":"RNA processing and ribosome biogenesis","description":"This cluster centers on RNA metabolism (mRNA splicing, transcription regulation, antitermination) and ribosome biogenesis/export, with supporting signals for translation regulation, suggesting a coordinated role in RNA processing and ribosome assembly for gene expression.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:1903026","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0032298","count":2}]},{"hash":"2249581144100809804","title":"Central carbon metabolism","description":"The dominant GO terms are glycolytic process, tricarboxylic acid cycle, gluconeogenesis, and 2-oxoglutarate metabolism, pointing to core energy and carbon-flux pathways. Thiamine biosynthesis relates to cofactors for these pathways, supporting the overall metabolic theme. A few peripheral terms (ER stress translation regulation, histone methylation, sex differentiation) appear unrelated to the core metabolism but do not override the main signal.","confidence":"High","size":28,"edges":306,"triangles":1937,"max_degree":26,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006099","count":9},{"id":"GO:0006096","count":8},{"id":"GO:0019878","count":5},{"id":"GO:0006094","count":5},{"id":"GO:0006103","count":4}]},{"hash":"1046499089482673167","title":"Unknown","description":"The Top Terms include both transcription-related processes (DNA-templated transcription, regulation of transcription by RNA polymerase II), chromatin remodeling (rDNA heterochromatin formation), and a variety of metabolic/catabolic processes (lipid A biosynthetic process, fatty acid biosynthetic process, tyrosine catabolic process), plus xenobiotic/antibiotic response and an obsolete oxidation\u2013reduction term. The spread across transcription, chromatin, metabolism, and xenobiotic response shows no single cohesive function tying the cluster together, so a specific label is not supported. ","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006351","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0009245","count":1},{"id":"GO:0006633","count":1}]},{"hash":"977689769225912772","title":"Essential metabolite biosynthesis and stress responses","description":"Most top GO terms point to biosynthetic processes for essential molecules (capsule and cell wall polysaccharides, protoporphyrinogen IX, and thiamine) with a few terms indicating stress responses (response to antibiotic, cellular response to oxidative stress) and SRP-dependent protein targeting to membranes. Photosynthesis appears but is not the dominant theme. This suggests a cohesive theme around metabolite/macromolecule biosynthesis with some linked stress-related processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0045227","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0006614","count":2}]},{"hash":"638723318322716640","title":"Nuclear RNA Decay","description":"The cluster is enriched for nuclear RNA catabolic processes, notably nuclear polyadenylation-dependent rRNA and snRNA catabolic processes, along with histone mRNA catabolic process. These points suggest a shared theme of nuclear RNA turnover/decay among the proteins. Some other terms (ER inheritance, leucine response, stem cell maintenance) are less central to this core function, likely reflecting broader annotations of the included proteins. Therefore, Nuclear RNA Decay is a concise and representative label, with Medium confidence. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071035","count":2},{"id":"GO:0071044","count":2},{"id":"GO:0019827","count":1},{"id":"GO:0051151","count":1},{"id":"GO:0016320","count":1}]},{"hash":"1296132636351091674","title":"Embryonic Development and Tissue Differentiation","description":"The top GO terms point to embryonic and placental development (trophoblast differentiation, placenta-related processes), endocrine system development, and tissue morphogenesis (cartilage), plus developmental patterning (left/right) and EMT in heart development, all indicating broad developmental and differentiation programs. Some terms about transcriptional regulation and host interactions are more peripheral, but the core theme is embryogenesis and organogenesis. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0035270","count":2},{"id":"GO:0003198","count":2},{"id":"GO:0060806","count":2}]},{"hash":"324155748331964984","title":"Viral DNA integration and proviral latency","description":"GO terms in this cluster center on viral entry into host cells, DNA transposition and integration, and establishment of proviral latency, with related references to retrotransposition and cell cycle changes. This suggests a coherent theme of genome mobility driven by viral integration and provirus maintenance, rather than a single, narrow molecular function. Some terms touch broader host-symbiont interactions, but the dominant signal aligns with viral genome integration and latency mechanisms.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075732","count":2},{"id":"GO:0032197","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0075713","count":2}]},{"hash":"370133380208921254","title":"Unknown","description":"The proteins span a broad set of GO terms including neural processes (synaptic vesicle budding, Purkinje cell maturation, locomotory behavior), metabolism (fatty acid beta-oxidation, insulin signaling), RNA processing (spliceosomal assembly), protein folding and chaperone activity, immune signaling, and even photosynthesis. This wide diversity shows no single coherent function or pathway tying the cluster together, so a generic label of Unknown with no confidence is appropriate.","confidence":"","size":27,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032000","count":2},{"id":"GO:0016185","count":2},{"id":"GO:0008344","count":2},{"id":"GO:0008286","count":2},{"id":"GO:0021691","count":2}]},{"hash":"809109386674027697","title":"Vesicle trafficking and neural development","description":"Dominant GO terms point to intracellular membrane trafficking (ER\u2013Golgi, retrograde Golgi\u2013ER, Golgi-to-plasma membrane transport) as the core function, with neural development terms (brain and nervous system development) as prominent secondary themes. The presence of cell cycle and apoptotic terms suggests additional, indirect processes rather than a single cohesive function, so the label emphasizes the primary trafficking role with neural development context.","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":8},{"id":"GO:0007420","count":7},{"id":"GO:0007049","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0051301","count":6}]},{"hash":"2015026273024244943","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster\u2019s top terms center on translation initiation (formation of preinitiation complex, reinitiation) and ribosome biogenesis, plus related protein interactions like homooligomerization and links to cell division. Although several terms are marked obsolete, the prevalent functions point to the protein set\u2019s role in assembling and regulating the translation machinery and associated cell-cycle processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051567","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0000747","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0001731","count":6}]},{"hash":"1467209910014064068","title":"Chromatin Remodeling and Transcription Regulation","description":"This cluster is enriched for chromatin-related processes (chromatin remodeling, DNA-templated transcription, histone modification regulation) and transcription control (negative regulation of RNA Pol II), suggesting a shared role in controlling chromatin state and gene expression. Some outlier terms (biosynthetic processes, transposition) likely reflect annotation noise or multifunctional genes, but the dominant theme remains chromatin dynamics and transcription regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043044","count":5},{"id":"GO:0006351","count":5},{"id":"GO:2000616","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0017000","count":4}]},{"hash":"1253877192720110363","title":"Cyanobacterial Photosynthesis and Chlorophyll Biosynthesis","description":"The top GO terms center on photosynthesis and chlorophyll biosynthesis (including the light-independent pathway), which points to a cluster of proteins involved in the photosynthetic apparatus and chlorophyll production common in cyanobacteria. Additional terms like RNA methylation and translation reflect supporting gene expression processes, while some other terms (e.g., nodulation, cobalamin biosynthesis) may reflect broader bacterial capabilities but do not override the primary photosynthetic theme.","confidence":"Medium","size":27,"edges":320,"triangles":2250,"max_degree":26,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0006596","count":2},{"id":"GO:0016049","count":2}]},{"hash":"676058770481503873","title":"Ribosome biogenesis and rRNA maturation","description":"Most of the top GO terms center on ribosome assembly and rRNA processing, including maturation of SSU and LSU rRNA and overall ribosome biogenesis. There are also cell division terms, suggesting nucleolar activity linked to the cell cycle. A few terms on splicing and histone methylation are less central, but the dominant signal is ribosome production and rRNA maturation.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":9},{"id":"GO:0000462","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0000466","count":9},{"id":"GO:0000398","count":9}]},{"hash":"619061527258629703","title":"Genome Maintenance and Telomere Regulation","description":"This cluster is strongly enriched for DNA replication, repair, and recombination terms, as well as telomere capping and telomere lengthening, pointing to a module focused on genome integrity and telomere maintenance; the mitotic checkpoint signals further support a cell cycle\u2013coupled DNA maintenance role. Some mitochondrial tRNA aminoacylation terms and related lysine modification terms appear ancillary, likely reflecting dual-localization enzymes rather than core functions of this cluster.","confidence":"High","size":27,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0071915","count":5},{"id":"GO:0016233","count":5},{"id":"GO:0070154","count":5},{"id":"GO:0007093","count":5}]},{"hash":"1117290149413507625","title":"Glycan and Proteoglycan Biosynthesis","description":"This cluster centers on carbohydrate-related processes: protein glycosylation, biosynthesis of glycans such as glycogen, sucrose, and starch, and especially proteoglycan biosynthesis (e.g., chondroitin sulfate). The presence of cell wall organization reinforces a glycan/ECM theme, while additional terms touch on extracellular matrix interactions and reproductive or wound-healing contexts (sperm binding to zona pellucida, epithelial proliferation in wound healing, mammary gland involution). Overall, the shared function appears to be glycan and proteoglycan biosynthesis within ECM/cell-wall\u2013related processes, with some cross-species context contributing to the heterogeneity. Confidence: Medium.","confidence":"","size":27,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0005978","count":3},{"id":"GO:0050650","count":3},{"id":"GO:0005985","count":2}]},{"hash":"1996913866646590293","title":"Unknown","description":"The Top Terms are highly heterogeneous, including developmental morphogenesis terms (wing disc, swim bladder, prostatic bud), TOR signaling, transcription regulation, signal transduction, and even DNA transposition, with many terms having only a single annotation. There is no strong, coherent biological theme tying the proteins together, so a concise, representative label cannot be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031929","count":1},{"id":"GO:0045943","count":1},{"id":"GO:0035308","count":1},{"id":"GO:0007472","count":1},{"id":"GO:1903361","count":1}]},{"hash":"1726808449335202313","title":"mRNA maturation and translation regulation","description":"This cluster centers on RNA processing and control of gene expression, with terms covering mRNA polyadenylation, nuclear export, spliceosome-mediated splicing, stability under stress, and formation/regulation of the translation preinitiation complex, plus small-subunit processome assembly and mRNA stabilization. Together, these indicate coordinated maturation of mRNA and regulation of translation initiation. ","confidence":"High","size":26,"edges":91,"triangles":175,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0006406","count":5},{"id":"GO:0045292","count":5},{"id":"GO:0001825","count":4},{"id":"GO:0048025","count":4}]},{"hash":"706276157594759353","title":"Epigenetic methylation and chromatin remodeling","description":"The cluster is dominated by GO terms for various methylation types (protein, tRNA, rRNA) and chromatin remodeling, alongside transcription-related processes (DNA-templated transcription, negative regulation of RNA Pol II). This points to a cohesive group of proteins involved in epigenetic regulation and RNA processing that modulates transcription, with some metabolic/dna-integrating terms as ancillary connections.","confidence":"High","size":26,"edges":153,"triangles":324,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006479","count":6},{"id":"GO:0009236","count":6},{"id":"GO:0030488","count":5},{"id":"GO:0070476","count":5},{"id":"GO:0000122","count":5}]},{"hash":"1932345984835494382","title":"Neurodevelopment and DNA maintenance","description":"The cluster is enriched for neural-development terms (neural tube closure, forebrain development, nervous system development, dendrite morphogenesis) alongside core DNA processes (DNA replication, DNA-templated transcription, DNA repair, mitotic cell cycle). This suggests proteins coordinating cell division with neural differentiation in proliferating neural progenitors.","confidence":"High","size":26,"edges":50,"triangles":41,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":23},{"id":"GO:0006351","count":21},{"id":"GO:0006281","count":21},{"id":"GO:0000278","count":21},{"id":"GO:0001843","count":19}]},{"hash":"1541489973374924097","title":"Diverse metabolite biosynthesis and degradation","description":"This cluster shows a mix of biosynthetic and catabolic processes across amino acids (lysine, alanine), vitamins (biotin), porphyrin/heme (protoporphyrinogen IX), lipids (sphinganine), and central metabolism (oxaloacetate), suggesting a broad metabolic module. Annotations like Notch signaling appear to be outliers or noise rather than defining the group.","confidence":"Medium","size":26,"edges":317,"triangles":2422,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":12},{"id":"GO:0097053","count":11},{"id":"GO:0006782","count":11},{"id":"GO:0007219","count":11},{"id":"GO:0009102","count":11}]},{"hash":"2039446811019448172","title":"Organelle lipid biosynthesis and protein import","description":"Enriched lipid biosynthesis terms (very long-chain fatty acid biosynthesis, fatty acid elongation, sphingolipid biosynthesis, poly-hydroxybutyrate biosynthesis) alongside organelle protein import terms (mitochondrial matrix/inner membrane, chloroplast stroma) point to proteins tied to organelle lipid metabolism and associated import/ targeting functions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":3},{"id":"GO:0045039","count":3},{"id":"GO:0042761","count":2},{"id":"GO:0030148","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1894521497427799753","title":"Translation Initiation and Cell Cycle Regulators","description":"Top GO terms strongly emphasize translation initiation (formation of translation preinitiation complex; translation reinitiation) and key cell cycle processes (mitotic cell cycle; APC-dependent catabolic process; cell division), suggesting proteins that coordinate protein synthesis with cell cycle progression. Supporting terms for RNA methylation and histone methylation indicate broader regulation of gene expression during these processes, while hypoxia response adds a stress-related aspect. Overall, the cluster appears to represent a group of factors linking translation initiation to cell cycle control.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":14},{"id":"GO:0002188","count":14},{"id":"GO:2001162","count":10},{"id":"GO:0036265","count":10},{"id":"GO:0030433","count":10}]},{"hash":"929072270467282818","title":"Transposon activity and chromatin remodeling","description":"The top GO terms include DNA integration, DNA transposition, and chromatin remodeling, plus transcriptional regulation, suggesting a shared theme of genome mobility and chromatin-state control among these proteins. While a few terms are obsolete, the strongest signals point to transposon-related functions and chromatin regulation as the cohesive theme.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":6},{"id":"GO:0006313","count":6},{"id":"GO:0043044","count":5},{"id":"GO:0046718","count":4},{"id":"GO:0043046","count":4}]},{"hash":"267524097584442284","title":"Viral integration and proviral latency","description":"This cluster is dominated by GO terms describing DNA integration, DNA transposition, retrotransposition, and DNA-templated transcription, along with viral processes and establishment of integrated proviral latency. The presence of symbiont entry into host cells and symbiont-mediated activation of host apoptosis further supports a theme of intracellular viral or transposable-element activity and latent provirus states, with translation/transcription terms reflecting core cellular machinery tied to these processes. Overall, the shared function appears to center on integration of viral or transposable elements and their latent maintenance.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0006313","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0006351","count":2}]},{"hash":"853980384992914158","title":"Multi-tissue developmental signaling","description":"The cluster includes GO terms spanning nervous system, muscle, and hippocampus development, melanocyte migration, and immune signaling (B cell receptor signaling and GM-CSF response), all linked by central signaling pathways such as the ERK cascade and cytoskeletal/microtubule localization. This pattern suggests a broad theme of signaling-driven development and cell behavior across multiple tissues rather than a single tissue-specific function.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0035372","count":2}]},{"hash":"1497641612938237321","title":"Ribosome biogenesis and rRNA processing","description":"The top GO terms are dominated by ribosome biogenesis and rRNA maturation (e.g., 5.8S rRNA processing, large subunit biogenesis), indicating the proteins mostly participate in ribosome assembly and rRNA maturation. Other terms like vesicle transport and transcription appear less central, possibly reflecting broader cellular roles or annotation noise. Overall, the cluster likely comprises ribosome biogenesis factors and rRNA-processing proteins.","confidence":"High","size":25,"edges":16,"triangles":0,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0000724","count":2}]},{"hash":"448424516842109536","title":"Growth signaling and developmental morphogenesis","description":"The top GO terms cluster around growth-related signaling (positive regulation of angiogenesis; PI3K signaling) and development (embryonic cranial skeleton morphogenesis; dendritic spine morphogenesis), along with cell-cycle processes (DNA replication; centrosome cycle) and receptor organization (receptor clustering). This suggests a coherent theme of growth signaling coordinating proliferation and morphogenesis during development, with some immune-related terms that may reflect broad signaling overlaps. Overall, these terms indicate a cluster centered on growth signaling coupled to developmental processes.","confidence":"Medium","size":25,"edges":16,"triangles":0,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045766","count":13},{"id":"GO:0014068","count":13},{"id":"GO:0071333","count":13},{"id":"GO:0006260","count":13},{"id":"GO:0050830","count":13}]},{"hash":"2110140814643671006","title":"Ribosome biogenesis and proteostasis","description":"The cluster appears enriched for ribosome-related processes (translation and ribosomal subunit assembly) and protein quality control/ folding pathways (unfolded protein response, chaperone-assisted refolding, ER-associated degradation), plus snoRNP assembly. This points to a functional theme of ribosome biogenesis coupled to proteostasis. Minor terms related to chromatin modification or signaling are present but do not define the cluster's primary function.","confidence":"High","size":25,"edges":13,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0032781","count":2}]},{"hash":"1493811598465348739","title":"Cofactor biosynthesis and protein modification","description":"This cluster centers on biosynthetic pathways for cofactors and related protein modifications: biotin, lipoate, and heme precursor biosynthesis, plus lipoylation and ubiquitination/NF-kappaB signaling, suggesting a cohesive theme of metabolic cofactor production with post-translational modifications.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0016567","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0000162","count":1}]},{"hash":"903490714829710629","title":"Ubiquitin-Dependent Proteolysis","description":"The cluster\u2019s top GO terms are dominated by ubiquitination and ubiquitin-mediated protein degradation, including ubiquitin-dependent proteolysis, autoubiquitination, various ubiquitin linkages (K48, K63, K6), SCF-dependent proteasomal degradation, and ER-associated degradation (ERAD). This points to a cohesive function in tagging substrates for degradation and turnover, including histone catabolism, rather than a specific interaction module. Confidence: High","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0051865","count":7},{"id":"GO:0070936","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0030433","count":5}]},{"hash":"1924651628919389309","title":"Ubiquitin-Mediated Proteolysis and Mitosis","description":"The cluster's top GO terms cluster around ubiquitin-dependent degradation (ERAD, protein catabolic process) and key mitotic processes (sister chromatid cohesion and segregation) with related cell-cycle proliferation regulation. This suggests proteins involved in regulated proteolysis that drives cell division, despite a couple outlier terms. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0090344","count":2},{"id":"GO:0032466","count":2},{"id":"GO:0008284","count":2},{"id":"GO:2000060","count":2}]},{"hash":"70733856924204878","title":"Bacterial LPS and sugar nucleotide biosynthesis","description":"Top terms strongly point to lipopolysaccharide biosynthesis (LPS, O-antigen) and sugar-nucleotide precursor pathways (dTDP-rhamnose, ADP-L-glycero-beta-D-manno-heptose), along with related galactose metabolism and bacterial storage polymer biosynthesis, suggesting a cluster focused on bacterial cell-surface polysaccharide assembly and sugar-derivative biosynthesis.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0009103","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0006012","count":5},{"id":"GO:0042619","count":5}]},{"hash":"1248400814790380083","title":"Meiotic DSB Repair and Recombination","description":"The top GO terms cluster around meiotic double-strand break formation and processing, repair pathways involved in meiotic recombination, and related genome maintenance (e.g., synthesis-dependent strand annealing, mitochondrial DSB repair, repetitive DNA stability) plus ascospore formation, indicating a cohesive theme of meiosis-linked DNA repair and sporulation. An outlier term for neuron differentiation appears but does not override the dominant meiotic/recombination signal.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0031573","count":3},{"id":"GO:0030437","count":3},{"id":"GO:1990918","count":3},{"id":"GO:0010791","count":3}]},{"hash":"1965869080295172291","title":"Carbohydrate and lipid metabolism during development","description":"This cluster is enriched for glycogen biosynthesis, fatty-acyl-CoA biosynthesis, and beta-oxidation terms, along with carnitine metabolism and amino acid catabolism, indicating a set of proteins involved in energy storage and lipid/energy metabolism. The presence of post-embryonic development and starvation response GO terms suggests these metabolic activities are linked to growth and developmental transitions, with cell wall organization aligning with growth-related remodeling. Overall, the cluster appears to reflect energy provisioning and utilization during development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":6},{"id":"GO:0042594","count":5},{"id":"GO:0071555","count":4},{"id":"GO:0019254","count":4},{"id":"GO:0046949","count":4}]},{"hash":"1796927021906510820","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000132","count":2}]},{"hash":"875832726264950996","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0032973","count":1},{"id":"GO:0046963","count":1},{"id":"GO:0034221","count":1},{"id":"GO:0015786","count":1}]},{"hash":"2005849731974770448","title":"P450-driven xenobiotic metabolism and lipid processing","description":"The top GO terms emphasize omega-hydroxylase P450 pathways and xenobiotic/organic compound catabolism (carbazole, camphor), along with triglyceride metabolism and liver-related processes, pointing to detoxification and lipid handling as a unifying theme. A few ancillary terms (e.g., immune signaling) are present but do not override the core metabolic pattern.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046232","count":13},{"id":"GO:0070365","count":12},{"id":"GO:0097267","count":12},{"id":"GO:0033068","count":12},{"id":"GO:0006697","count":12}]},{"hash":"1568700443746894745","title":"Diverse transmembrane transport of ions and metabolites","description":"This cluster is best described by the prominence of GO terms related to transmembrane transport across membranes for a variety of substrates (taurine, monoatomic anions, vitamins, cysteine, glycerophosphodiesters, molybdate) along with oligopeptide export from mitochondrion and involvement in fatty acid metabolism. The common theme appears to be membrane transport processes moving diverse molecules, with a couple of outliers (antibiotic response, O-linked glycosylation) that may reflect secondary annotations. Thus, the label captures the primary function suggested by the GO terms. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0035269","count":2},{"id":"GO:0015734","count":2},{"id":"GO:0099133","count":2},{"id":"GO:0035461","count":2}]},{"hash":"1111384301621651155","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0034244","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0000480","count":2}]},{"hash":"1959964640174462838","title":"Developmental signaling and stress-induced apoptosis","description":"The top GO terms cluster around development (brain and multicellular organism development) and stress/apoptosis pathways (glial and cardiac apoptotic processes, ER-stress\u2013induced intrinsic apoptosis), with supporting signals from TGF-beta, DNA damage response, and nutrient signaling, suggesting a cohesive theme of developmental signaling guiding cell fate through stress-related apoptotic responses.","confidence":"Medium","size":24,"edges":5,"triangles":2,"max_degree":3,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0007568","count":13},{"id":"GO:0007275","count":11},{"id":"GO:0072432","count":10},{"id":"GO:0007584","count":10},{"id":"GO:0071560","count":10}]},{"hash":"784784543141075882","title":"Unknown","description":"The top GO terms span diverse functions (deglycosylation, neuronal development, proteolysis, DNA replication, unfolded protein response, histone modification, metal ion response, glucocorticoid signaling, and morphine response) with no clear cohesive theme, so a single representative label cannot be confidently assigned.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006517","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0006508","count":3},{"id":"GO:0035753","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1134204420998347610","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0060041","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0008584","count":3},{"id":"GO:0042273","count":3}]},{"hash":"1038966820652334914","title":"Mitochondrial Transporters and Redox Regulation","description":"GO terms indicate mitochondrial membrane potential regulation, oxidative stress response, and transport of substrates (NAD, deoxynucleotides, Mn, thiosulfate, fatty acids), suggesting a cluster of mitochondrial carrier proteins involved in energy metabolism and thermogenesis.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000303","count":3},{"id":"GO:0051881","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0035352","count":2},{"id":"GO:0030302","count":2}]},{"hash":"1008685074667085343","title":"DNA Replication and Cell Cycle Regulation","description":"This cluster shows strong enrichment for DNA replication (GO:0006260) and mitotic DNA replication checkpoint signaling, suggesting a primary theme in replication and cell-cycle control. Additional terms point to supporting processes such as transcription elongation regulation, energy metabolism, and protein folding/trafficking, which are components of general cellular maintenance during replication. Overall, the dominant signal is DNA replication and cell cycle regulation, with auxiliary housekeeping roles.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006888","count":6},{"id":"GO:0018279","count":6},{"id":"GO:0016558","count":5},{"id":"GO:0033314","count":5}]},{"hash":"1378264524213187060","title":"Ribosome biogenesis and translation","description":"Dominant terms are centered on translation and ribosome assembly (cytoplasmic translation, ribosome biogenesis, small subunit biogenesis, translation initiation/termination, rRNA maturation), indicating proteins involved in ribosome function and production, with only peripheral links to antibiotic response.","confidence":"High","size":23,"edges":8,"triangles":0,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0000463","count":2}]},{"hash":"662280232220110456","title":"Adhesion-Driven MAPK Signaling and Survival","description":"This cluster centers on integrin-mediated signaling, receptor clustering, and substrate adhesion-dependent spreading, together with the ERK1/ERK2 cascade and anti-anoikis/survival and ER-stress\u2013related apoptotic signaling, pointing to adhesion-mediated MAPK signaling that promotes cell survival, with some inclusion of cell cycle terms.","confidence":"Medium","size":23,"edges":35,"triangles":27,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070371","count":15},{"id":"GO:0034446","count":15},{"id":"GO:0043113","count":15},{"id":"GO:0043277","count":15},{"id":"GO:2000811","count":15}]},{"hash":"2282986102069566377","title":"Ribosome Biogenesis and Translation Machinery","description":"The cluster is dominated by GO terms for ribosome biogenesis (large and small subunits), ribosomal subunit export from the nucleus, cytoplasmic translation, and tRNA modification, pointing to a cohesive group centered on ribosome assembly and protein synthesis. Additional terms for cell cycle and cell division reflect growth-related contexts where translation is critical. Overall, the theme is ribosome production and function.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":9},{"id":"GO:0051301","count":8},{"id":"GO:0000747","count":7},{"id":"GO:0000055","count":6},{"id":"GO:0007049","count":6}]},{"hash":"356464107485924713","title":"Cardiovascular, neural, and muscle development signaling","description":"The cluster shows enrichment for developmental processes across heart, vasculature, muscle, and nervous system (e.g., heart development, angiogenesis, myoblast fusion, Schwann cell development, neural activity). It also includes cell-cycle and signaling regulation terms (mitotic cycle, G2/M transition, phosphorylation) that support proliferative and differentiative contexts. The abscisic acid-activated signaling term may reflect cross-species annotation noise rather than a shared plant-specific function; overall the proteins cluster around tissue development and differentiation across multiple lineages.","confidence":"Medium","size":23,"edges":227,"triangles":1326,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009738","count":21},{"id":"GO:0007520","count":21},{"id":"GO:0007507","count":21},{"id":"GO:0000278","count":21},{"id":"GO:0000086","count":21}]},{"hash":"2106071570891835573","title":"Plastid quinone and chlorophyll biosynthesis","description":"The top GO terms cluster around plastid pigment and quinone biosynthesis: plastoquinone, phylloquinone (vitamin K), menaquinone, and chlorophyll biosynthesis, with related heme O biosynthesis. This points to plastid metabolism and pigment biosynthesis in plants, with an outlier developmental term (cotyledon vascular tissue pattern formation) and no reported interactions, suggesting a broad set of biosynthetic enzymes rather than a single pathway network.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010236","count":1},{"id":"GO:0032194","count":1},{"id":"GO:0042372","count":1},{"id":"GO:0042371","count":1},{"id":"GO:0009234","count":1}]},{"hash":"1543519702214409016","title":"Mobile genetic elements and host interactions","description":"Enriched for DNA mobility and integration (DNA integration, transposition, retrotransposition, proviral latency), i.e., mobile genetic elements. The additional GO terms hint at bacterial symbiont interactions with host cells and envelope processes, suggesting MGEs in symbionts/viruses that interface with host biology.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0015074","count":4},{"id":"GO:0006313","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0008360","count":2},{"id":"GO:0009252","count":2}]},{"hash":"1550009078685629208","title":"DNA Transposition and piRNA Silencing","description":"The cluster is dominated by GO terms for DNA integration, DNA transposition, and retrotransposition, with supportive terms like proviral latency and viral entry, along with piRNA processing. This points to a set of proteins involved in mobile genetic elements (transposons/retroelements) and the host piRNA pathway that defends against them, making the label representative of transposable element activity and its silencing. Some terms appear as noise (e.g., ribosomal export, certain virus-like interactions), but the core theme remains transposition and piRNA-mediated defense.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":6},{"id":"GO:0006313","count":5},{"id":"GO:0046718","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0032197","count":2}]},{"hash":"1701482717299656004","title":"Root hair development and cytoskeleton remodeling","description":"Root hair development, Rac-mediated signaling, and cytoskeleton organization cluster together, suggesting a module focused on plant root hair growth driven by actin remodeling and cell movement. The presence of root hair development, Rac signaling, and cytoskeleton terms supports this, with transport-related terms likely reflecting membrane dynamics during tip growth. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032973","count":2},{"id":"GO:1990034","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0016539","count":2},{"id":"GO:0006911","count":1}]},{"hash":"1652484417321014574","title":"Chloroplast thylakoid biogenesis and photosystem II assembly","description":"The terms cluster around chloroplast/plastid functions, especially thylakoid membrane import and organization, photosystem II assembly, and chlorophyll catabolic processes, with supporting plastid-localized metabolism (tryptophan biosynthesis, PRPP metabolism). This points to a plastid-biogenesis/photosynthesis-focused module rather than general cytosolic processes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0000162","count":1},{"id":"GO:0046391","count":1},{"id":"GO:2000070","count":1}]},{"hash":"1315205777057608554","title":"Amino acid catabolism and vitamin/cofactor biosynthesis","description":"This cluster is dominated by amino acid catabolic processes (valine, alanine, kynurenine) and multiple vitamin/cofactor biosynthetic steps (phylloquinone, menaquinone), along with central carbon metabolism activities (pyruvate biosynthesis, fatty acid beta-oxidation). These terms point to a cohesive metabolic module focused on energy-yielding pathways and cofactor production, rather than signaling or regulatory functions. The Notch signaling term appears less represented and may be a peripheral or outlier signal. Overall, the cluster best represents metabolism centered on amino acid breakdown and vitamin/cofactor biosynthesis.","confidence":"Medium","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0006574","count":7},{"id":"GO:0042372","count":7},{"id":"GO:0006635","count":7},{"id":"GO:0010124","count":7}]},{"hash":"852171284048128025","title":"Ribosome Biogenesis and Translation","description":"Cluster shows strong enrichment for translation and ribosome biogenesis processes (translation, cytoplasmic translation, ribosome biogenesis, small subunit biogenesis, translational initiation/termination), indicating a cohesive protein-synthesis machinery module; other terms like antibiotic response and iron transport are peripheral.","confidence":"High","size":22,"edges":230,"triangles":1520,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:0042254","count":11},{"id":"GO:0006407","count":7},{"id":"GO:0042274","count":6},{"id":"GO:0046677","count":5}]},{"hash":"6930032345691074","title":"Symbiont Photosynthesis and Terpenoid Biosynthesis","description":"The cluster shows strong terms for photosynthesis and terpenoid/isoprenoid biosynthesis via the MEP pathway, plus ubiquinone biosynthesis, which together point to a photosynthetic metabolic program. The presence of \u201csymbiont entry into host cell\u201d and \u201cresponse to host iron concentration\u201d suggests a host-associated (symbiotic) context, reinforcing a theme of energy/metabolic processes linked to symbiotic lifestyle. Some terms may be less related (e.g., angiensin maturation), likely annotation noise, but the dominant theme is coherent. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0019288","count":1},{"id":"GO:0075139","count":1},{"id":"GO:0016114","count":1}]},{"hash":"611375768019233082","title":"Mitochondrial energy metabolism and redox homeostasis","description":"This cluster is dominated by mitochondrial-related processes: dihydrolipoamide and lipoate metabolism, NADH dehydrogenase/electron transport, and regulation of membrane potential, all central to mitochondrial energy production and redox balance. Some terms (aging, gastrulation, sperm capacitation) are likely broader-context annotations and less representative of the core function.","confidence":"High","size":22,"edges":78,"triangles":114,"max_degree":21,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0051068","count":14},{"id":"GO:0042391","count":14},{"id":"GO:0045454","count":14},{"id":"GO:0006120","count":14},{"id":"GO:0009106","count":14}]},{"hash":"1833226429888805610","title":"Ubiquitin-Proteasome Mediated Protein Degradation","description":"This cluster is dominated by ubiquitination-related terms (K48, K11, K6 linkages), SCF-dependent ubiquitination, ERAD, autoubiquitination, and ubiquitin-dependent proteasomal degradation, pointing to a cohesive theme of tagging proteins for proteasomal degradation and quality control.","confidence":"High","size":22,"edges":71,"triangles":16,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902564","count":15},{"id":"GO:0051301","count":7},{"id":"GO:0016558","count":5},{"id":"GO:0070936","count":5},{"id":"GO:0070979","count":5}]},{"hash":"1242638795877780929","title":"Developmental and stress-response genes","description":"The cluster\u2019s top GO terms cluster around developmental processes (skeletal system development, multicellular organism development, neural tube closure, forebrain development) while also highlighting stress/immune-related responses (ER-stress\u2013induced apoptotic signaling, cadmium response, defense against Gram-positive bacteria) and cell cycle activity, suggesting a set of proteins involved in development that also participate in cellular stress and immune pathways.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":9},{"id":"GO:0000278","count":8},{"id":"GO:0050830","count":8},{"id":"GO:0070059","count":8},{"id":"GO:0006349","count":8}]},{"hash":"1224226063491084265","title":"Mitotic cell cycle and chromatid cohesion","description":"The top GO terms point to mitosis and chromosome segregation: mitotic cell cycle, APC-dependent proteolysis, centromeric sister chromatid cohesion, and chromatin regulation. Additional terms on GTPase activity, serine dephosphorylation, mRNA transport, and TORC1 signaling align with processes coordinating cell growth and division. Taken together, these proteins appear to function in mitotic progression and chromosome cohesion mechanisms.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0038202","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0051301","count":4}]},{"hash":"799117625480448979","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":146,"triangles":538,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0006289","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0046677","count":5}]},{"hash":"243112471619686560","title":"Developmental proliferation and signaling regulators","description":"The top GO terms cluster around multicellular development, skin development, pigmentation, and regulation of cell proliferation, with signals involving serine/threonine kinase activity and protein autophosphorylation, suggesting a theme of developmental signaling controlling growth. Some terms may reflect annotation noise (e.g., obsolete oxidation-reduction or cellulose catabolic process), but the dominant pattern points to development and proliferation regulation in multicellular organisms.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008284","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0043473","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0000278","count":2}]},{"hash":"26750458334662129","title":"RNA Pol II transcription elongation and mRNA processing","description":"The top GO terms cluster around RNA polymerase II transcription elongation and various mRNA processing steps (capping, deadenylation/decay, and translation regulation), suggesting a coherent module of transcriptional and post-transcriptional gene expression control. Some developmental terms appear, but the core theme remains RNA synthesis and mRNA lifecycle regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0000749","count":1},{"id":"GO:0000289","count":1}]},{"hash":"1943426841994213799","title":"Chromatin modification and neural development","description":"This cluster centers on neural development terms (brain development and neuron projection development) and epigenetic regulation (histone methylation, RNA methylation, and transcription factor localization), suggesting a shared role in chromatin-mediated control of neural differentiation. Some outlier terms (e.g., fungal-type cell wall biogenesis) reduce cohesion, so the label is plausible but not unequivocal.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0051567","count":3},{"id":"GO:2001162","count":3},{"id":"GO:0032995","count":3},{"id":"GO:2001125","count":3}]},{"hash":"1468103058381443268","title":"Oxidative detoxification and glutathione metabolism","description":"Proteins in this cluster are enriched for cellular oxidant detoxification and redox homeostasis, with strong representation of glutathione metabolism and toxin catabolic processes, pointing to antioxidant defense and detox pathways as the core theme. Some additional GO terms (calcium signaling, osteoblast differentiation, chloride transport, nucleotide-excision repair) may reflect pleiotropic roles of individual proteins rather than defining the cluster\u2019s main function.","confidence":"High","size":21,"edges":205,"triangles":1238,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":13},{"id":"GO:0045454","count":10},{"id":"GO:0009072","count":8},{"id":"GO:0009407","count":8},{"id":"GO:0006749","count":8}]},{"hash":"1762593908672743658","title":"RNA Transcription and Ribosome Biogenesis Module","description":"GO terms point to core transcription processes across RNA polymerases I\u2013III (initiation/elongation/termination) and RNA-templated transcription, with a secondary signal for ribosome biogenesis and DNA repair. This suggests a module of RNA synthesis/processing machinery, with ribosome biogenesis represented as a minor association.","confidence":"Medium","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0070893","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0006366","count":1}]},{"hash":"1563461641867888085","title":"Regulatory Signaling and Proteostasis","description":"This cluster\u2019s GO terms cluster around regulation of signaling pathways (lipopolysaccharide signaling, NF-kappaB activity), negative regulation of inflammatory responses, and protein quality control (deubiquitination, aggresome assembly). While there are no edges or interactions shown, the common theme is modulation of cellular signaling and proteostasis, suggesting a regulatory, stress-response role.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031664","count":1},{"id":"GO:0051092","count":1},{"id":"GO:0048572","count":1},{"id":"GO:0090086","count":1},{"id":"GO:0070842","count":1}]},{"hash":"1810230875553273382","title":"Iron-Sulfur Cluster Biogenesis and Oxidative Stress Response","description":"The top terms point to iron-sulfur ([2Fe-2S]) cluster assembly and maturation, alongside cellular oxidant detoxification, indicating a core theme of Fe-S biogenesis and redox homeostasis. Some transcription-related and obsolete iron-response terms appear, but the dominant signal is Fe-S cluster handling and oxidative stress management.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903026","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0044571","count":1},{"id":"GO:0051220","count":1}]},{"hash":"802786171478818099","title":"Ribosome Biogenesis and Cell Division","description":"The cluster is enriched for translation and ribosome biogenesis terms, along with mitotic and cell cycle components (mitotic spindle assembly, cell division, multicellular growth, and cell population proliferation). This points to a coordinated program of protein synthesis with cell-cycle progression and proliferation. The included vesicle trafficking terms (COPII budding, Golgi-to-ER transport) likely support membrane needs during growth and division, reinforcing a growth-and-division theme. ","confidence":"High","size":20,"edges":13,"triangles":0,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0008283","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0035264","count":2},{"id":"GO:0000278","count":2}]},{"hash":"2008161253000869619","title":"Eukaryotic growth, development, and stress response","description":"The top GO terms cluster around core growth processes (ribosome biogenesis, mitotic cycle, cell division) together with stress-related pathways (ERAD, ER-stress\u2013induced apoptosis, cadmium response) and development. This suggests a broad cellular-growth framework with integrated stress signaling and developmental processes, rather than a single specialized function.","confidence":"Medium","size":20,"edges":87,"triangles":202,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0071276","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0000278","count":4}]},{"hash":"149003748174133350","title":"Translational Machinery and Regulation","description":"The top GO terms are overwhelmingly about translation and its regulation (translation, translational initiation/termination, positive regulation of elongation, cytoplasmic translation, and selenocysteine incorporation). While cell cycle and glial proliferation terms appear, they likely reflect increased protein synthesis during proliferation rather than a separate pathway. Overall, the cluster centers on the ribosome/translation machinery and its control.","confidence":"High","size":20,"edges":89,"triangles":178,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0046677","count":7},{"id":"GO:0001514","count":4},{"id":"GO:0045901","count":4},{"id":"GO:0007049","count":4}]},{"hash":"428784713374773412","title":"Metabolic Biosynthesis and Transcriptional Regulation","description":"These proteins show enrichment for biosynthetic processes (L-threonine and phosphatidylcholine biosynthesis) and regulatory aspects (phosphorylation, negative regulation of transcription by RNA polymerase II, ribosomal subunit export). Some stress-response terms (response to antibiotic/cocaine) may be noise or broader signals. Overall, the cluster appears to reflect metabolism coupled with gene-expression regulation rather than a single cohesive pathway, so this label captures the dominant themes with Medium confidence. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":7},{"id":"GO:0019284","count":5},{"id":"GO:0009088","count":5},{"id":"GO:0016310","count":5},{"id":"GO:0019509","count":5}]},{"hash":"64792987846477372","title":"Viral Integration and Retrotransposon Activity","description":"The cluster is dominated by terms for DNA integration, transposition, retrotransposition, and proviral latency, with supporting terms about viral entry into host nucleus and host\u2013pathogen interactions, pointing to mobile genetic elements and integrated viral elements as the shared function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015074","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0070940","count":4},{"id":"GO:0075732","count":3},{"id":"GO:0032197","count":3}]},{"hash":"2266986878120754320","title":"Meiotic Recombination and Telomere Maintenance","description":"This cluster centers on meiotic chromosome dynamics, including reciprocal recombination, meiosis I, chiasma assembly, and telomere maintenance/capping, with DNA replication involved in chromosomal processes; a few translation-related terms appear but do not define the core theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007131","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0051026","count":1},{"id":"GO:0016233","count":1},{"id":"GO:0007093","count":1}]},{"hash":"2285440170512689537","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010390","count":1},{"id":"GO:0090262","count":1},{"id":"GO:0070911","count":1},{"id":"GO:2001173","count":1},{"id":"GO:0033523","count":1}]},{"hash":"256200643722871369","title":"Unknown","description":"The GO terms are scattered across very different biological themes (peptidyl-prolyl isomerization; male sex differentiation and prostate development; steroid receptor assembly; cell division; photosynthesis and UV-A response; NOD2 signaling regulation; cardiac electrical conduction; T cell proliferation), suggesting no single cohesive function or pathway ties these proteins together. This points to either a mixed-function cluster or annotation noise rather than a defined biological module.","confidence":"","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0000413","count":3},{"id":"GO:0046661","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1510390853896738770","title":"Chromatin remodeling and heterochromatin formation","description":"The cluster is dominated by GO terms related to heterochromatin formation (silent mating-type cassette and rDNA), chromatin assembly during DNA replication, and transcription initiation-coupled chromatin remodeling, plus transcription repression by RNA Pol II. This points to a cohesive theme of chromatin structure regulation and gene expression control, with some developmental roles (spermatogenesis, male gonad development) suggesting chromatin regulation in germline development. ","confidence":"High","size":19,"edges":58,"triangles":95,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030466","count":7},{"id":"GO:0051290","count":6},{"id":"GO:0045815","count":6},{"id":"GO:0006335","count":6},{"id":"GO:0000183","count":6}]},{"hash":"631142935969974036","title":"DNA replication and telomere maintenance","description":"The terms emphasize DNA metabolism: DNA duplex unwinding, recombination, replication fork reversal, and telomerase/telomere regulation, plus mitochondrial genome maintenance and DNA repair. Together they define a coherent set of proteins involved in DNA replication, genome maintenance, and telomere regulation, hence the chosen label.","confidence":"High","size":19,"edges":52,"triangles":75,"max_degree":14,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0032508","count":13},{"id":"GO:0006310","count":12},{"id":"GO:0032211","count":11},{"id":"GO:0090305","count":11},{"id":"GO:0043504","count":10}]},{"hash":"1149260249422442809","title":"Endomembrane trafficking and organelle dynamics","description":"The top GO terms cluster around endosome-Golgi transport, Rab signaling, endosomal vesicle fusion, and endocytic recycling, with supporting hints from filopodium assembly and mitochondrial membrane organization/inheritance, pointing to a shared theme of vesicle trafficking and organelle dynamics; a few terms like ribosome biogenesis and substantia nigra development are less directly connected but may reflect broader cellular contexts.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0045792","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0034498","count":3},{"id":"GO:0032482","count":3},{"id":"GO:0046847","count":3}]},{"hash":"1412396965124446270","title":"Developmental morphogenesis and organogenesis","description":"The top GO terms cluster around embryonic development, morphogenesis, and organ formation (gastrulation, axis elongation, organogenesis, pancreas and prostate development, primitive hematopoiesis), with additional regulatory processes (transcription, growth control, deglycosylation). This pattern suggests the proteins are involved in broad developmental pathways rather than a single specific function, supporting this label.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042074","count":1},{"id":"GO:0014812","count":1},{"id":"GO:0060215","count":1},{"id":"GO:0060770","count":1},{"id":"GO:0060028","count":1}]},{"hash":"1202570099539201058","title":"Mitotic Cell Cycle and DNA Repair","description":"The top GO terms cluster around mitosis (cell division, mitotic cell cycle, APC/C-dependent catabolic process) and DNA repair (nucleotide-excision repair), with ubiquitin-dependent ERAD indicating proteostasis during growth. Some obsolete or plant-specific terms appear, but the dominant signal points to a cell-cycle/maintenance program.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0009877","count":3},{"id":"GO:0006289","count":3}]},{"hash":"1228183549105845515","title":"Ubiquitin-Proteasome Regulation and Stress Signaling","description":"The cluster centers on ubiquitin-proteasome system activity, with deubiquitination and SCF-dependent proteasomal degradation as core functions, suggesting coordinated protein turnover. It also groups signaling pathway regulation (Wnt, TNF) and environmental stress responses (salt, cadmium), plus viral process associations that often interact with ubiquitin pathways, indicating a proteostasis-linked signaling module. ","confidence":"High","size":19,"edges":80,"triangles":165,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":6},{"id":"GO:0016032","count":5},{"id":"GO:0010950","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0031146","count":4}]},{"hash":"152312515182414069","title":"Cofactor biosynthesis and nucleotide transport","description":"This cluster is enriched for thiamine biosynthetic processes (GO:0009228, GO:0009229) and transport-related terms such as NAD transmembrane transport (GO:0035352) and deoxynucleotide transport (GO:0030302), pointing to a cohesive theme of cofactor biosynthesis and nucleotide/nicotinamide transport. Some terms (e.g., obsolete or unrelated ones like DNA integration, transcription regulation, or adaptive thermogenesis) appear as noise or outliers, but the core terms suggest a shared metabolic/transport role centered on cofactors and nucleotides.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0015074","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0009229","count":2},{"id":"GO:0000122","count":2}]},{"hash":"488002081762620774","title":"Nuclear/chromatin regulation and neuronal development","description":"The top GO terms cover core nuclear processes (ribosome biogenesis, mitotic cohesion, nuclear pore localization, histone methylation) alongside neuronal development terms (brain development, neuron projection development), suggesting a cluster tied to nuclear/chromatin regulation with roles in neuronal development.  ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0007064","count":4},{"id":"GO:0031081","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0051567","count":3}]},{"hash":"2299942772627477925","title":"Embryogenesis and Organogenesis","description":"The dominant GO terms point to embryonic development and the formation of organs and tissues (gastrulation, in utero embryonic development, brain/retina/skeletal system development). Growth and morphogenesis terms (cell population proliferation) support this theme, though a couple entries are obsolete or peripheral. Overall, the cluster seems to group proteins involved in developmental programs rather than a single pathway. ","confidence":"High","size":19,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0016575","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0007369","count":3},{"id":"GO:0001701","count":3}]},{"hash":"1568654181302891049","title":"Developmental Regulation and Stress Response","description":"This cluster centers on transcriptional control and developmental processes (DNA-templated transcription; forebrain and neural tube development; multicellular development) while also showing signals for DNA repair and cellular stress responses (ER-stress\u2013induced apoptosis, mitotic cell cycle). The mix suggests proteins involved in regulating gene expression during development and coordinating cellular stress responses, rather than a single cohesive pathway; the immune-defense term appears as a broader stress/defense context rather than a core developmental function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0001843","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0050830","count":2}]},{"hash":"930865433202006115","title":"Cofactor Biosynthesis and RNA Modification","description":"The top GO terms are dominated by biosynthetic processes for cofactors and related metabolites (biotin, menaquinone, molybdopterin cofactor, polyamines) and by tRNA methylation. This points to a functional theme of small-molecule cofactor production together with RNA modification, with a few regulatory terms suggesting broader cellular control. Overall, the cluster seems best described as a group of proteins involved in biosynthesis of cofactors and RNA processing/modification.","confidence":"Medium","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0007049","count":2}]},{"hash":"323369631734936080","title":"Central Carbon Metabolism and Energy Homeostasis","description":"This cluster is strongly enriched for glycolytic process, TCA cycle, gluconeogenesis, and fatty acid homeostasis, pointing to central carbon metabolism and energy balance as the core shared function. Circadian rhythm and interleukin-4 response terms suggest regulatory or context-specific connections to metabolism, but the dominant theme is energy metabolism.","confidence":"High","size":19,"edges":21,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":5},{"id":"GO:0055089","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0071353","count":3},{"id":"GO:0007623","count":3}]},{"hash":"686383031001970913","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":1},{"id":"GO:0001308","count":1},{"id":"GO:0007475","count":1},{"id":"GO:0034063","count":1},{"id":"GO:1902039","count":1}]},{"hash":"1170982151602128912","title":"ER-Golgi and Endosomal Vesicle Trafficking","description":"The common theme across the terms is intracellular vesicle transport, including ER-to-Golgi and endosome-to-Golgi trafficking, plus regulation of GTPase activity that governs trafficking, with autophagy as a related vesicle-related process. Although some development terms are present, the core signal points to vesicle transport and its regulation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016358","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0045212","count":1}]},{"hash":"781454351889187445","title":"Ubiquitin-Dependent Proteolysis","description":"The top GO terms show clear enrichment for ubiquitin-mediated degradation, including the ubiquitin-dependent ERAD pathway and general ubiquitin-dependent protein catabolic processes. While other terms touch on transcription regulation, histone turnover, and peroxisomal import, the strongest signal is proteostasis via ubiquitin tagging and proteasomal degradation, suggesting a cluster of proteins involved in protein turnover. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0016558","count":2}]},{"hash":"1903356768788282467","title":"Neural development and synaptic vesicle signaling","description":"The top GO terms emphasize brain development, regulation of synaptic vesicle exocytosis, and Wnt signaling, all pointing to neural development and neuronal communication through vesicle trafficking. Additional terms on ER-Golgi transport and cytoskeletal processes support cellular infrastructure for neurons, while some terms appear more general or organism-specific (immune response, mating projection growth), but the dominant theme remains neural development linked to vesicle signaling. Confidence in this label is Medium.","confidence":"","size":18,"edges":26,"triangles":6,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0007420","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0042088","count":4}]},{"hash":"889836501029591004","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"The cluster is dominated by GO terms centered on ubiquitin-dependent protein catabolic processes and ubiquitination, including SCF-dependent proteasomal degradation and ERAD. These point to core proteostasis via the ubiquitin-proteasome system, with cell cycle-related terms likely reflecting degradation during mitosis; a few immune signaling terms (RIG-I, neutrophil activation) illustrate regulatory roles of ubiquitination. Overall, the common theme is ubiquitin-driven protein turnover.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:1902564","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000209","count":2}]},{"hash":"2116234335857743111","title":"DNA replication and prophage integration cluster","description":"This cluster shows strong representation of DNA replication, DNA-templated transcription, DNA recombination, and DNA integration, plus signals of proviral latency establishment. These terms strongly indicate involvement in genome maintenance and mobile element life cycles, i.e., DNA metabolism with prophage integration dynamics. While ribosome biogenesis and mycothiol biosynthesis are present, they seem secondary to the dominant DNA-related terms. Hence the label reflects the dominant theme of DNA replication/repair and prophage integration.","confidence":"Medium","size":18,"edges":58,"triangles":78,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0009405","count":3}]},{"hash":"110057515256201297","title":"Membrane Ion Transporters and Homeostasis","description":"The top GO terms indicate transport and homeostasis for multiple ions (K+, Na+, Ca2+, Mn2+) across the plasma membrane and associated changes in membrane potential (hyperpolarization). This pattern is characteristic of ion channels and transporters that maintain intracellular ion balance and membrane excitability; phospholipid translocation aligns with membrane-associated activity, and the touch-detection term may reflect mechanosensitive channel involvement. Overall, the cluster likely represents membrane ion transporters coordinating ionic homeostasis.","confidence":"High","size":18,"edges":60,"triangles":75,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":4},{"id":"GO:1990573","count":4},{"id":"GO:0097623","count":3},{"id":"GO:0060081","count":3},{"id":"GO:0098703","count":3}]},{"hash":"298676985643808969","title":"DNA Repair and Oxidative Stress Response","description":"The cluster shows enrichment for DNA repair processes (DNA recombination; base-excision repair) and oxidative stress handling (cellular response to hydrogen peroxide; redox homeostasis), with xenobiotic stimulus response reinforcing stress detoxification. Peripheral obsolete terms exist but do not override the main pattern linking genome maintenance to redox/detox pathways.","confidence":"High","size":18,"edges":89,"triangles":198,"max_degree":16,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":6},{"id":"GO:0042493","count":5},{"id":"GO:0006284","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0090502","count":3}]},{"hash":"2022526333576503728","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms center on ribosome biogenesis and maturation/processing of rRNA (SSU/ITS1-related cleavage and rRNA maturation), indicating a module of proteins involved in ribosome assembly. Other terms like phosphorylation, threonine biosynthesis, and antibiotic response are less central and may reflect incidental associations. Overall, the cluster is best described as a ribosome biogenesis/rRNA processing module.","confidence":"Medium","size":18,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019284","count":4},{"id":"GO:0009088","count":4},{"id":"GO:0016310","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0019509","count":4}]},{"hash":"2057877357431514501","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0000447","count":4},{"id":"GO:0000466","count":4},{"id":"GO:0000398","count":4}]},{"hash":"1210880285724679945","title":"Mitochondrial Translation and Oxidative Stress Response","description":"The top GO terms point to mitochondrial-associated processes: translation and import into the mitochondrial matrix, along with oxidative stress related activities (response to hydrogen peroxide, redox-related oxidation). While some terms are obsolete or peripheral, the core signals suggest a cluster of mitochondrial protein synthesis/import linked to redox/oxidative stress responses.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0030150","count":1},{"id":"GO:0042158","count":1},{"id":"GO:0019471","count":1}]},{"hash":"1017400319663811391","title":"Chloroplast\u2013mitochondrial gene expression and signaling","description":"The terms cluster around organelle-specific gene expression and inter-organelle communication: chloroplast processes like phytochromobilin biosynthesis and chloroplast-nucleus signaling, plus mitochondrial import and translation components (protein insertion into mitochondrial inner membrane, mitochondrial tRNA aminoacylation, translation, and tRNA processing). This suggests a cohesive theme of gene expression and protein targeting across chloroplasts and mitochondria, with nucleus-to-organelle signaling involved. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0007584","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010024","count":1},{"id":"GO:0010019","count":1}]},{"hash":"516994244041833068","title":"DNA Transposition and Chromatin Regulation","description":"Enrichment for DNA integration and transposition, along with nucleosome assembly and subtelomeric heterochromatin formation, suggests a genome-dynamics and chromatin-remodeling theme.","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0015074","count":5},{"id":"GO:0006313","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0051572","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1209328560052303311","title":"Steroid and lipid metabolism","description":"The cluster\u2019s top GO terms are dominated by steroid hormone biosynthesis/metabolism (androgen metabolic process, testosterone biosynthetic process, hormone catabolic process) and a sphingolipid metabolism term (mannosyl-inositol phosphorylceramide metabolic process), with supporting skin and CNS lipid-associated functions (sebaceous gland differentiation, CNS myelin maintenance). This points to a cohesive theme around lipid- and steroid-related metabolism and membrane-associated processes, even though a few broader terms (viral process, proton transport) appear in the set. Confidence reflects this as a plausible shared theme rather than a perfectly tight grouping.","confidence":"Medium","size":18,"edges":19,"triangles":16,"max_degree":7,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0008209","count":4},{"id":"GO:0061370","count":4},{"id":"GO:0032286","count":4},{"id":"GO:0006675","count":4},{"id":"GO:0001949","count":4}]},{"hash":"1348594328811207071","title":"TORC1-regulated ribosome biogenesis and translation","description":"The top terms center on ribosome biogenesis, formation of the translation preinitiation complex, and translation reinitiation, with TORC1 signaling linking nutrient status to protein synthesis. While there are some RNA processing and trafficking terms (splicing, ER\u2013Golgi transport) present, the dominant theme is coordinated ribosome production and translation initiation under TORC1 control.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1848585320685245293","title":"Oxidative stress response and ER protein quality control","description":"The cluster combines redox-related processes (cell redox homeostasis, cellular response to oxidative stress) with ER-focused protein folding/repair (protein folding in endoplasmic reticulum, protein repair, deglutathionylation), suggesting proteins that coordinate defense against oxidative damage and maintain protein quality, possibly linking transcriptional regulation under stress as a secondary aspect.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0034599","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0033158","count":1}]},{"hash":"1768066531752615851","title":"Neural and retina development","description":"The top GO terms include neural tube closure and retina development, pointing to vertebrate neural/eye development as a shared theme. Additional terms like transcriptional control, GTPase signaling, and proliferation support a developmental signaling network. Some terms are obsolete or off-target (oxidation-reduction, histone methylation), indicating noise, but the core signals align with neural/retinal development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0007584","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0060041","count":3}]},{"hash":"2066211835656678670","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"The cluster is dominated by terms related to actin cytoskeleton dynamics, stress fiber regulation, and cell migration, indicating proteins involved in remodeling the cytoskeleton to promote motility, with supporting signals from related exocytosis and transcription-related terms.","confidence":"High","size":17,"edges":45,"triangles":32,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0006915","count":3},{"id":"GO:2000251","count":3},{"id":"GO:0045956","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1579595054184886303","title":"Developmental morphogenesis and signaling","description":"Top terms indicate involvement in brain and gland development (Bergmann glial differentiation, cerebellar cortex formation, salivary gland morphogenesis/cavitation) and in broad signaling pathways (insulin receptor, T cell receptor signaling) as well as axon regeneration regulation. Together these suggest a cluster of proteins participating in developmental signaling and tissue morphogenesis rather than a single, cohesive pathway. ","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060020","count":3},{"id":"GO:0048679","count":2},{"id":"GO:0021697","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0008286","count":2}]},{"hash":"1504543971277480594","title":"Mitotic Chromosome Assembly and Protein Quality Control","description":"This cluster centers on mitotic and chromatin-related processes (cell division, CENP-A chromatin assembly, mitotic DNA replication checkpoint signaling), with additional signals pointing to protein trafficking and quality-control pathways (ER-Golgi transport, peroxisomal import, stress granule disassembly, aggresome assembly). The core theme appears to be chromosome maintenance during cell division, with supporting roles in protein handling and transport. Confidence: Medium","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006888","count":2},{"id":"GO:0048219","count":2},{"id":"GO:0016558","count":2},{"id":"GO:1903007","count":2}]},{"hash":"1035867124192875743","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0090394","count":17},{"id":"GO:1990416","count":17},{"id":"GO:0000716","count":17},{"id":"GO:0006269","count":17},{"id":"GO:0000464","count":17}]},{"hash":"1121887635023097989","title":"RNA processing and protein complex assembly","description":"The cluster shows strong signals for RNA processing (mRNA splicing via spliceosome; rRNA maturation) and for assembling multimeric protein complexes (protein heterotrimerization and homooligomerization), suggesting roles in RNA maturation and complex formation, with additional links to development and cell division.","confidence":"High","size":17,"edges":115,"triangles":438,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070208","count":5},{"id":"GO:0048568","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0032508","count":3}]},{"hash":"764156608529401139","title":"Bacterial LPS and related biosynthesis","description":"The Top Terms show a strong emphasis on lipopolysaccharide (LPS) biosynthesis, including lipopolysaccharide biosynthetic process, LPS core region biosynthetic process, and ADP-L-glycero-beta-D-manno-heptose biosynthetic process, suggesting a core focus on LPS assembly in bacteria. Additional terms point to other bacterial biosynthetic pathways (histidine and purine nucleotide biosynthesis, antibiotic biosynthesis, poly-hydroxybutyrate biosynthesis), indicating a broader theme of bacterial metabolite production. The neutrophil homeostasis term appears less central and may reflect annotation noise or context rather than a core function of these proteins. Overall, the cluster seems to group proteins involved in bacterial biosynthesis with a primary link to LPS pathways.","confidence":"Medium","size":17,"edges":83,"triangles":221,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0009103","count":4},{"id":"GO:0000105","count":3},{"id":"GO:1902987","count":3},{"id":"GO:0017000","count":3}]},{"hash":"262674412970845952","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by translation (GO:0006412), ribosome biogenesis and subunit assembly, indicating proteins involved in ribosome production and protein synthesis. Additional terms such as mitochondrial translational termination and RNA-templated transcription support this ribosome/translation-centered theme, while a few terms like response to antibiotic can reflect ribosome-related stress responses. Overall, the cluster centers on ribosome assembly and translation.","confidence":"High","size":17,"edges":133,"triangles":638,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":16},{"id":"GO:0000027","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0070126","count":3}]},{"hash":"1451403729515972000","title":"Mitochondrial fission, distribution, and transport","description":"The proteins are strongly linked to mitochondrial biology: membrane fission, intracellular distribution of mitochondria, and transport across mitochondrial membranes, with supporting terms for genome maintenance and adaptive thermogenesis. The occasional non-mitochondrial term (sensory perception of sound) appears incidental rather than representative of the core function.","confidence":"High","size":17,"edges":29,"triangles":5,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":6},{"id":"GO:0090149","count":4},{"id":"GO:0007605","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0048312","count":3}]},{"hash":"2047445259924144786","title":"Cell growth and division with RNA modification","description":"This cluster centers on fundamental cellular proliferation processes, highlighted by mitotic cell cycle, APC-dependent catabolic control of division, and general cell division signals. It also includes RNA processing/modification activities (RNA guanine-N7 methylation, rRNA modification) and supportive housekeeping pathways (ER-to-Golgi transport and sterol biosynthesis) that commonly accompany growing, dividing cells. The GO terms collectively point to a core proliferative and maintenance program rather than a specialized pathway, justifying a label focused on growth/division with RNA modification.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0001300","count":2},{"id":"GO:0016126","count":2},{"id":"GO:0036265","count":2}]},{"hash":"2262684125656615728","title":"Ribosome biogenesis and RNA processing","description":"The cluster is heavily enriched for ribosome-related processes: large subunit biogenesis, rRNA maturation (5.8S and LSU/SSU transcripts), and preribosome assembly, along with translation and RNA-splicing related regulation and stress-granule localization. This points to a core function in ribosome assembly and broader RNA metabolism, with secondary links to mRNA processing and stress responses.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000184","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000466","count":2}]},{"hash":"3943028013112959","title":"Carbohydrate metabolism and LPS biosynthesis","description":"The top GO terms cluster around sugar metabolism and polysaccharide biosynthesis, including galactose catabolism, glucose-1-phosphate metabolism, glycogen biosynthesis, and nucleotide-sugar biosynthesis (UDP-GlcNAc, GDP-mannose) as well as lipopolysaccharide O-antigen biosynthesis. This points to functions involved in carbohydrate processing and construction of cell-surface polysaccharides. A quirky term like detection of gravity is present but does not alter the overall carbohydrate/cell-envelope theme. ","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019388","count":3},{"id":"GO:0009298","count":3},{"id":"GO:0019255","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0006148","count":3}]},{"hash":"1037267270063028462","title":"RNA Modification and Transcription Regulation","description":"The Top Terms show multiple RNA modification processes (tRNA/dihydrouridine and rRNA pseudouridine synthesis) and a GO term for DNA-templated transcription, with occasional related terms like DNA integration/transposition and circadian regulation of gene expression. The strongest common theme is RNA maturation/modification and transcription control, though the presence of DNA mobility terms slightly weakens the link. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0002943","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0015074","count":1}]},{"hash":"70743128894134557","title":"Chromatin organization and transcription regulation","description":"The cluster shows dominant themes in chromatin remodeling and organization (chromatin organization; rDNA heterochromatin formation; mitotic chromosome condensation) and transcription control by RNA polymerase II (regulation of transcription by RNA polymerase II; transcription elongation by RNA polymerase II), along with related DNA topology changes. Additional terms point to broader nuclear regulatory processes such as circadian regulation of gene expression and cellular division events. Overall, the proteins likely function together in chromatin-based gene expression regulation and chromosome dynamics.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006265","count":1},{"id":"GO:0032922","count":1},{"id":"GO:0006357","count":1},{"id":"GO:0000019","count":1},{"id":"GO:0000183","count":1}]},{"hash":"1163476928949914049","title":"Developmental cell cycle and morphogenesis","description":"This cluster is enriched for DNA replication and mitotic cell cycle terms, plus development-related processes like skeletal system development and neural tube closure, along with Wnt signaling regulation, suggesting proteins that coordinate cell division with developmental morphogenesis rather than a single pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0006311","count":4},{"id":"GO:0007100","count":3}]},{"hash":"1849200593158221759","title":"Membrane Ion Transport and Homeostasis","description":"This cluster is dominated by ion homeostasis and transmembrane transport terms for Na+, K+, Ca2+, Zn2+, and Cd2+, indicating a cohesive role in maintaining cellular ionic balance across membranes; a secondary signal is serine biosynthesis, but the primary theme is ion transport.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006883","count":9},{"id":"GO:0097755","count":9},{"id":"GO:0030007","count":9},{"id":"GO:0006564","count":9},{"id":"GO:0071577","count":9}]},{"hash":"1867338437680451392","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0001666","count":6},{"id":"GO:0007568","count":6},{"id":"GO:0006310","count":5},{"id":"GO:0006269","count":5}]},{"hash":"1598762665342000842","title":"RNA Polymerase Transcription Initiation","description":"The top GO terms cluster around transcription initiation and promoter dynamics for RNA polymerase II and III, including start-site selection, promoter binding and open complex formation, and initiation at Pol II/III promoters. This points to a cohesive role in transcription initiation machinery, with an outlier term for thrombocyte differentiation likely unrelated to the core function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001174","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0045945","count":1},{"id":"GO:0042795","count":1},{"id":"GO:0006367","count":1}]},{"hash":"1883989779250417459","title":"Skin Development and Wound Healing Signaling","description":"The cluster includes GO terms tied to epidermal biology: keratinocyte differentiation, Wnt signaling in its canonical pathway, angiogenesis, and defensive responses at the skin barrier. Additional terms like DNA repair, apoptotic process, glucose response, and ion transport reflect the metabolic and stress-adaptive state of skin cells under injury or stress. Together, these functions point to a cohesive theme of skin development, barrier maintenance, and wound repair signaling.","confidence":"High","size":16,"edges":75,"triangles":184,"max_degree":14,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046827","count":11},{"id":"GO:0090263","count":10},{"id":"GO:0006915","count":10},{"id":"GO:0045766","count":10},{"id":"GO:0014068","count":10}]},{"hash":"1676192803615584876","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms related to protein synthesis and ribosome assembly, including translation (GO:0006412), regulation of translation (GO:0006417), ribosomal small subunit assembly (GO:0000028), and maturation of SSU-rRNA (GO:0000462), pointing to involvement in ribosome biogenesis and translation machinery. Some stress-related terms (response to cycloheximide/antibiotic) also appear, suggesting contextual regulation under translational stress, but the core signal centers on ribosome function.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006417","count":1},{"id":"GO:0009615","count":1},{"id":"GO:0045787","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1730668906437438281","title":"Plant metabolite and bacterial cell-wall biosynthesis","description":"The Top Terms show diverse biosynthetic processes, including plant-specific phenylpropanoid, anthocyanin, and sporopollenin biosynthesis, alongside bacterial cell-wall component biosynthesis (colanic acid, lipopolysaccharide core, and sugar biosynthesis like rhamnose and ADP-heptose). This suggests a cross-kingdom theme of biosynthesis rather than a single, cohesive pathway, so the label reflects both plant metabolite production and bacterial envelope biosynthesis.","confidence":"Medium","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009699","count":3},{"id":"GO:0009718","count":3},{"id":"GO:0009242","count":3},{"id":"GO:0006012","count":3}]},{"hash":"2239891835698745739","title":"Unknown","description":"The GO terms are highly diverse (signal transduction, ethylene signaling, chromosome segregation, DNA replication, placenta development, chemotaxis, telomerase assembly, IL-4 response) with several obsolete terms, and there are no edges linking proteins into a cohesive functional group. This lack of a unifying theme or pathway makes a specific, reliable label inappropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000160","count":3},{"id":"GO:0010105","count":2},{"id":"GO:0007059","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0006261","count":2}]},{"hash":"1971303083071680406","title":"Biosynthesis and RNA Modification","description":"The cluster shows strong enrichment for diverse biosynthetic processes (antibiotic, menaquinone, biotin, polyamine, phosphatidylcholine biosynthesis) together with RNA modification activities (guanine-N7 methylation and rRNA modification). While there are outliers such as regulation of endocannabinoid signaling and an obsolete redox term, the dominant theme is enzymes involved in biosynthesis and nucleic acid modification, suggesting a metabolism/processing-focused group. Confidence: Medium.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009234","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0019433","count":4},{"id":"GO:2000124","count":4}]},{"hash":"2142383540498498808","title":"Muscle development and transcription regulation","description":"This cluster features multiple GO terms tied to muscle biology, including somatic muscle development, ventricular cardiac muscle cell action potential, and response to muscle stretch, plus terms about regulation of DNA-templated transcription. While some items (ethanol response, tRNA methylation, ERAD) are more general or stress-related, the recurring muscle development and transcription control themes suggest a shared function in muscle biology and gene expression regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071361","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0090035","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2114861876715816051","title":"TORC1 Signaling and Gene Regulation","description":"Top GO terms point to a regulatory module involving TORC1 signaling, regulation of GTPase activity, serine dephosphorylation, and mRNA transport, with hints of histone methylation control and ubiquitin ligase regulation. This combination suggests a cluster of proteins coordinating nutrient sensing and downstream control of transcription/translation, though a few terms (fungal cell wall biogenesis, neuron development) appear peripheral.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0051567","count":2}]},{"hash":"1472947753719410931","title":"Unknown","description":"The top GO terms cover a very broad mix of processes\u2014from basic cellular activities (proton transmembrane transport, cytokinesis) to diverse organ- or tissue-specific development (root development, oviduct development, cranial ganglion development, fungiform papilla formation) and other functions (DNA damage response, heart rate regulation). There isn\u2019t a single cohesive biological theme tying these proteins together, so a concise, representative label cannot be assigned beyond Unknown.","confidence":"","size":15,"edges":100,"triangles":396,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":10},{"id":"GO:0048364","count":9},{"id":"GO:0007050","count":9},{"id":"GO:0003340","count":8},{"id":"GO:0060066","count":8}]},{"hash":"2001586576179667814","title":"Protein quality control and morphogenesis","description":"The cluster centers on protein handling and modification (sumoylation, unfolded protein response, chaperone-dependent refolding, and membrane targeting) along with processes tied to cellular form changes (cell morphogenesis and dendritic spine development). Additional terms like iron-sulfur cluster assembly and occasional beta-glucan biosynthesis hints suggest broader metabolic roles but do not override the main theme of protein quality control coupled with morphological remodeling.","confidence":"Medium","size":15,"edges":63,"triangles":145,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016925","count":6},{"id":"GO:0060996","count":5},{"id":"GO:0031204","count":4},{"id":"GO:0006880","count":4},{"id":"GO:0000902","count":4}]},{"hash":"194504213077088138","title":"RNA splicing regulation and translation initiation control","description":"The top terms center on post-transcriptional regulation: positive/negative regulation of mRNA splicing via the spliceosome, ncRNA-mediated gene silencing, regulation of mRNA stability, formation of the translation preinitiation complex, and regulation of translational initiation, along with small-subunit processome assembly and mRNA stabilization. This points to a cohesive cluster of RNA processing and translation control functions, with one outlier term (blastocyst formation) likely reflecting broader developmental associations. Confidence that this label captures the cluster\u2019s core theme is High.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":10},{"id":"GO:0031047","count":10},{"id":"GO:0010610","count":7},{"id":"GO:0006378","count":7},{"id":"GO:0001825","count":6}]},{"hash":"1563956541924451395","title":"Metal Ion Transport and Membrane Processes","description":"The cluster shows multiple metal ion transport terms (copper, zinc, cadmium) and calcium ion homeostasis, indicating membrane-associated transport activity. Lipid-related processes (phospholipid dephosphorylation, lipopolysaccharide biosynthesis) further support a membrane/membrane-environment theme, with a few metabolic terms (carbohydrate, L-serine biosynthesis) present but less central. Overall, the strongest common thread is ion transport across membranes and related membrane biology, justifying a membrane-associated transport label.","confidence":"Medium","size":15,"edges":59,"triangles":85,"max_degree":11,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":3},{"id":"GO:0097755","count":2},{"id":"GO:0006825","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0046839","count":2}]},{"hash":"1171165332220500864","title":"Chloroplast pigment and quinone biosynthesis","description":"The top GO terms cluster around biosynthesis of pigments and cofactors essential for photosynthesis, including chlorophyll, plastoquinone, phylloquinone (vitamin K), menaquinone, and heme O, consistent with chloroplast/plastid-related pigment and cofactor production. A few terms like protein stabilization or obsolete processes are less central, but the dominant theme ties to pigment and quinone biosynthesis in photosynthetic organisms.","confidence":"High","size":15,"edges":15,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0015979","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0010236","count":1},{"id":"GO:0032194","count":1}]},{"hash":"566670654497109095","title":"Ubiquitin-Dependent Proteolysis","description":"The Top Terms are dominated by ubiquitin-related catabolic processes and polyubiquitination, including SCF-dependent proteasomal degradation, which collectively point to the ubiquitin-proteasome system governing protein turnover. Additional terms touch on transcription regulation and immune signaling (NF-kappaB, T cell proliferation, TLR pathways), which are commonly influenced by ubiquitination. Taken together, the cluster appears to represent proteins involved in ubiquitin-mediated protein degradation, with secondary roles in signaling and transcriptional control.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0000209","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0033280","count":3}]},{"hash":"1753437216654259626","title":"Unknown","description":"The Top Terms span diverse cellular processes: transcriptional regulation, organelle biogenesis (vacuole fusion, cristae formation), developmental remodeling (blood vessel branching), cell division (mitotic spindle elongation), and ribosome quality control (rescue of stalled ribosome, ubiquitin-dependent degradation). The lack of a clear, shared function among these terms, along with zero edges in the cluster, suggests the proteins do not converge on a single cohesive theme. Therefore, no confident, specific label can be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0001569","count":2},{"id":"GO:0042407","count":2},{"id":"GO:0061087","count":2}]},{"hash":"453017709958891747","title":"Ubiquitin-Proteasome Regulation and TLR Signaling","description":"This cluster is enriched for ubiquitination and proteasomal degradation processes (polyubiquitination, ubiquitin-dependent proteolysis, SCF-dependent degradation, ERAD) alongside regulators of Toll-like receptor signaling, transcription, apoptosis/necroptosis, and cell cycle. The combination suggests a cohesive module of ubiquitin-mediated proteolysis that modulates immune signaling and cell fate decisions across development.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":4},{"id":"GO:0034121","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0043066","count":3}]},{"hash":"2166746927863950160","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060628","count":1},{"id":"GO:0060576","count":1},{"id":"GO:0046963","count":1},{"id":"GO:0034221","count":1},{"id":"GO:0015786","count":1}]},{"hash":"1222790954234027367","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061038","count":2},{"id":"GO:0006730","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0033320","count":1}]},{"hash":"141437809614269604","title":"Unknown","description":"This cluster shows a mix of GO terms from nuclear DNA replication and chromatin-related processes, ribosomal assembly, pre-replicative complex formation, and also from photosynthesis, bacteriochlorophyll biosynthesis, gas vesicle organization, cilium movement, and neuronal vesicle transport. The spread across diverse biological contexts suggests there is no single coherent function tying these proteins together in this cluster. ","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0030466","count":6},{"id":"GO:0030163","count":6},{"id":"GO:0006267","count":6},{"id":"GO:0030494","count":6}]},{"hash":"84220999883262124","title":"Ribosome Biogenesis and RNA Processing","description":"Top GO terms indicate coordinated RNA metabolism: mRNA splicing via spliceosome, maturation of 5.8S and LSU/SSU rRNA, and ribosomal large subunit biogenesis, along with translation initiation and reinitiation. This suggests a functional module for RNA processing and ribosome assembly, with ancillary links to regulatory ncRNA pathways and protein import. High","confidence":"","size":14,"edges":19,"triangles":7,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0000466","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0042273","count":4}]},{"hash":"123438464925724787","title":"Retinoid and Steroid Hormone Metabolism","description":"The GO terms show enrichment for retinol and retinal metabolic processes, regulation of retinoic acid receptor signaling, and androgen/C21-steroid hormone biosynthesis, pointing to a core theme of retinoid and steroid metabolism and signaling. Some ancillary terms (calcium signaling, JAK-STAT regulation) may reflect broader signaling roles but do not override the dominant metabolic theme.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":11},{"id":"GO:0042574","count":10},{"id":"GO:0046370","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0006700","count":7}]},{"hash":"461742078217570250","title":"Ribosome biogenesis and translational fidelity","description":"The cluster is dominated by GO terms related to translation (GO:0006412) and ribosome biogenesis (GO:0042254), with additional signals for tyrosyl-tRNA aminoacylation and rRNA pseudouridine synthesis, all pointing to components of protein synthesis and ribosome assembly. Terms on transcription and antibiotic response appear secondary to the core translation theme, suggesting RNA metabolism and stress-linked regulation but not defining the cluster. The dense network of translation- and ribosome-related processes supports labeling this group as centered on ribosome biogenesis and translational fidelity.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0042254","count":4},{"id":"GO:0045903","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0031564","count":2}]},{"hash":"470868739273163096","title":"DNA transposition and integration proteins","description":"The cluster is driven by strong enrichment for DNA integration and DNA transposition terms (each with 7 proteins), pointing to a set of proteins associated with mobilizing genetic elements. While other terms (protein folding, transcription, metabolism, chemotaxis, cocaine response) appear at lower frequencies, they do not define the group, so the main theme is DNA mobility and integration.","confidence":"High","size":14,"edges":21,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":7},{"id":"GO:0006313","count":7},{"id":"GO:1901407","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0006351","count":2}]},{"hash":"35152341918326068","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0008286","count":6},{"id":"GO:0051492","count":5},{"id":"GO:0072709","count":5},{"id":"GO:0046329","count":5}]},{"hash":"1987980843653147378","title":"Bacterial redox detoxification and metabolism","description":"The top GO terms center on cellular oxidant detoxification and redox homeostasis, with additional metabolism-related terms (biotin biosynthesis, antibiotic biosynthetic process, cytochrome complex assembly) that together suggest a cluster of bacterial proteins involved in redox balance and metabolic pathways. Some terms (e.g., symbiont entry, gonad development) may reflect annotation noise or cross-species signals, so the core theme is redox-related metabolism. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0017000","count":3}]},{"hash":"528214908327745883","title":"Steroid, retinoid, and lipid metabolism","description":"This cluster shows strong enrichment for metabolic processes involving retinol and retinoic acid, sphingolipid and very long-chain fatty acid biosynthesis, and steroid-related biosynthesis (testosterone, C21-steroid hormones). Together, these GO terms point to a cohesive module centered on lipid-derived and steroid/retinoid metabolic pathways, with a possible pigment-related reflection via melanin biosynthesis. Overall, the dominant theme is lipid, retinoid, and steroid biosynthesis/metabolism.","confidence":"High","size":14,"edges":51,"triangles":92,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042572","count":11},{"id":"GO:0042438","count":11},{"id":"GO:0006666","count":11},{"id":"GO:0042761","count":11},{"id":"GO:0002138","count":11}]},{"hash":"1293709128514390247","title":"Actin-Driven vesicle trafficking and immune migration","description":"The cluster shows a convergence of actin-based cytoskeletal remodeling (actin filament branching) with vesicle trafficking components (regulation of synaptic vesicle exocytosis; maintenance of presynaptic active zone), alongside immune-related processes (dendritic cell migration; Th1 immune response; defense against protozoan). This suggests proteins that coordinate cytoskeletal dynamics and vesicle trafficking in immune and neuronal contexts, rather than a single specialized pathway. ","confidence":"Medium","size":13,"edges":20,"triangles":0,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031384","count":5},{"id":"GO:0010796","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0032467","count":4},{"id":"GO:0090135","count":4}]},{"hash":"601072935188177460","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000961","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0031426","count":1}]},{"hash":"872978879133261920","title":"NF-kappaB Signaling and Ubiquitin-Proteasome Immunity","description":"The cluster\u2019s top GO terms center on immune system functions: defense response to virus and negative regulation of neutrophil activation, plus development terms for lymph nodes and spleen. The presence of ubiquitin-dependent proteasomal protein catabolic processes and SCF-dependent degradation points to regulation of signaling pathways (notably NF-kappaB) via proteasomal turnover. This combination suggests a group of proteins involved in NF-kappaB\u2013mediated immune responses modulated by ubiquitin-proteasome processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1902564","count":8},{"id":"GO:0042787","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0090073","count":4},{"id":"GO:0051607","count":4}]},{"hash":"723946001789987901","title":"Chromatin assembly & DNA replication control","description":"The top GO terms are dominated by nuclear processes: CENP-A\u2013containing chromatin assembly, mitotic DNA replication checkpoint signaling, and DNA-templated transcription, pointing to chromatin organization and replication control as a central theme. There are also stress-related terms (stress granule disassembly, aggresome assembly) that reflect proteostasis during cellular stress, which can intersect with transcription and chromatin regulation, but vesicle trafficking terms (ER-to-Golgi, inter-Golgi transport) and peroxisomal import are less central to the core theme. Overall, the cluster most coherently aligns with chromatin assembly and DNA replication control. ","confidence":"Medium","size":13,"edges":55,"triangles":98,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006888","count":4},{"id":"GO:0048219","count":4},{"id":"GO:0016558","count":4},{"id":"GO:1903007","count":4}]},{"hash":"316795644444380440","title":"Spliceosome-Mediated mRNA Splicing","description":"The terms are dominated by mRNA splicing via the spliceosome and regulation of splicing (GO:0000398, GO:0048026, GO:0000390), with an additional emphasis on RNA processing via regulatory ncRNAs (GO:0031047). This suggests the cluster groups proteins involved in the spliceosome machinery and mRNA processing, with possible ancillary roles in RNA silencing. While a few terms touch on neuronal signaling or DNA repair, the core signal is strongly aligned with RNA splicing and processing.","confidence":"High","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":10},{"id":"GO:0031047","count":10},{"id":"GO:0000398","count":9},{"id":"GO:0000390","count":8},{"id":"GO:0014070","count":8}]},{"hash":"1170568112332026367","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":60,"triangles":135,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":13},{"id":"GO:0006351","count":11},{"id":"GO:0000278","count":11},{"id":"GO:0048701","count":10},{"id":"GO:0006281","count":10}]},{"hash":"1391356566690195134","title":"Neural Development and Morphogenesis","description":"The cluster is enriched for neural-development-related processes: cell morphogenesis, neural tube closure, and regulation of axon extension, suggesting a primary theme around neural development and morphogenesis. In addition, transcription-related terms (DNA-templated transcription, translation initiation complex formation) imply coordinated gene expression during development. A few immune-defense terms appear as potential annotation noise rather than core functions of this group.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000902","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0001731","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0009244","count":3}]},{"hash":"1218441032453102040","title":"Ribosome Biogenesis and Translation Initiation","description":"Dominant GO terms point to ribosome assembly and translation initiation steps, including ribosome biogenesis, large subunit biogenesis, and formation of translation preinitiation complex. Additional RNA-processing terms like guanine-N7 methylation support a broader RNA maturation context linked to ribosome function. Other terms are less central (e.g., histone methylation, viral mRNA export) and likely incidental.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:1904668","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0042254","count":3}]},{"hash":"1801833393938222783","title":"Embryonic Tissue Differentiation","description":"The top GO terms point to embryonic tissue differentiation across diverse lineages (placenta/trophoblast, pancreas, endocrine system, heart cushions, cartilage, liver). This suggests a cluster of proteins involved in developmental differentiation rather than a single pathway, with EMT and bilateral patterning as common themes.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":2},{"id":"GO:0003323","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0003198","count":1},{"id":"GO:0060806","count":1}]},{"hash":"193654137317239617","title":"Unknown","description":"The GO terms are highly diverse and each appears only once, with multiple obsolete terms and no coherent common theme linking the functions (ranging from hypoxia response and proteolysis to mitotic checkpoint signaling, hormone maturation, feeding behavior, and antibacterial peptide regulation). Because there is no single unifying biological process or pathway represented by the cluster, a concise functional label cannot be confidently assigned. ","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900039","count":1},{"id":"GO:0035103","count":1},{"id":"GO:0060049","count":1},{"id":"GO:0032516","count":1},{"id":"GO:0032515","count":1}]},{"hash":"545513706393217684","title":"Cyanobacterial nitrogen fixation and heterocyst development","description":"The top GO terms cluster around nitrogen utilization regulation, heterocyst development, and sporulation regulation, plus signaling pathways (phosphorelay and cytokinin-like signaling) and transcriptional regulation. This combination points to cyanobacterial differentiation programs for nitrogen fixation via heterocysts, with supportive motility/chemotaxis responses, rather than a general metabolic or plant-specific signaling theme.","confidence":"Medium","size":12,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006808","count":2},{"id":"GO:0080117","count":2},{"id":"GO:0071973","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0006355","count":2}]},{"hash":"2211786782900736823","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":29,"triangles":38,"max_degree":11,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0044205","count":3},{"id":"GO:0071548","count":3},{"id":"GO:0070365","count":3}]},{"hash":"1387607144120282779","title":"Intracellular protein assembly and trafficking","description":"The term set centers on protein assembly (homooligomerization, ribosome biogenesis) and organelle trafficking (ER\u2013Golgi, Golgi cisterna, peroxisome import), plus protein quality-control dynamics (stress granule disassembly, aggresome assembly), suggesting a cohesive theme of intracellular protein biogenesis coupled with sorting and handling of misfolded proteins.","confidence":"Medium","size":12,"edges":60,"triangles":168,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":8},{"id":"GO:0006888","count":7},{"id":"GO:0048219","count":7},{"id":"GO:0016558","count":7},{"id":"GO:1903007","count":7}]},{"hash":"271691176597768197","title":"Mitochondrial translation and respiration","description":"The cluster is dominated by mitochondrial-specific translation processes, including multiple mitochondrial tRNA aminoacylation activities (histidine, threonine, alanine, serine) and a strong signal for the mitochondrial respiratory chain, suggesting a cohesive role in mitochondrial protein synthesis linked to energy production. A few terms like sodium ion transport or embryonic development appear less central and may reflect broader associations in the data.","confidence":"High","size":12,"edges":19,"triangles":11,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":2},{"id":"GO:0006427","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0022904","count":2},{"id":"GO:0070159","count":2}]},{"hash":"1050682044221451010","title":"Bacterial central metabolism and envelope biosynthesis","description":"The top GO terms point to core metabolic activities (TCA cycle, oxaloacetate, glutamine/glutamate metabolism) and biosynthetic pathways (lipopolysaccharide and cobalamin biosynthesis), with additional signals for transcription and protein quality control. This suggests a broad bacterial metabolism/biosynthesis cluster rather than a single, narrow function, hence a general but descriptive label.","confidence":"Medium","size":12,"edges":49,"triangles":99,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0009103","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0009236","count":2}]},{"hash":"1536406436721398354","title":"Translational Initiation Regulation and Proteasome Assembly","description":"The cluster is enriched for translation-related terms (formation of translation preinitiation complex; regulation of translational initiation) and proteostasis-related terms (proteasome assembly; ubiquitin-dependent protein catabolic process), suggesting a functional module where initiation of protein synthesis is coordinated with proteasome-mediated protein turnover. Secondary terms like phosphorylation and antibiotic response appear less central. ","confidence":"High","size":12,"edges":29,"triangles":25,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0019284","count":2},{"id":"GO:0009088","count":2}]},{"hash":"521425057186472399","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is dominated by GO terms tied to RNA maturation and ribosome assembly: rRNA processing, tRNA processing, and 90S preribosome assembly, with supporting signals from RNA exonuclease activity and mRNA polyadenylation. While a few terms relate to stress or antibiotic response, the strongest and most frequent terms point to ribosome biogenesis and RNA processing as the shared function of these proteins.","confidence":"High","size":12,"edges":20,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":5},{"id":"GO:0006364","count":4},{"id":"GO:0008033","count":4},{"id":"GO:0098789","count":4},{"id":"GO:0034463","count":3}]},{"hash":"2304095794142002141","title":"Photosynthesis Light Harvesting and Light Response","description":"The top GO terms cluster around photosynthesis and light-regulated processes\u2014light harvesting in photosystems I and II, nonphotochemical quenching, and responses to red/far-red and high light\u2014suggesting a cohesive set of light-energy capture and photoprotective functions. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0010196","count":1},{"id":"GO:0009769","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0010114","count":1}]},{"hash":"1358558914919684074","title":"Ubiquitin-Proteasome\u2013Mediated Cell Cycle Regulation","description":"The set of GO terms centers on ubiquitin-dependent protein catabolic processes, proteasome assembly, and APC-dependent proteolysis, all tied to mitotic cell cycle and cell division, indicating the proteins cluster around regulated protein turnover during mitosis. Additional terms related to translation initiation/reinitiation suggest broader roles in gene expression, but the strongest signal remains proteolysis coupled to cell cycle control.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1036007036400615204","title":"Mitochondrial transport and fission dynamics","description":"The cluster shows a clear emphasis on mitochondrial processes: multiple transport terms across mitochondrial membranes (NAD, deoxynucleotide, manganese, thiosulfate) along with explicit mitochondrial membrane fission terms and adaptive thermogenesis, which ties energy metabolism to mitochondrial function. While a couple of terms are more general (e.g., response to IGF stimulus), the convergence on transport and fission within mitochondria supports a mitochondria-centric theme.","confidence":"High","size":12,"edges":25,"triangles":11,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035352","count":8},{"id":"GO:0030302","count":8},{"id":"GO:0070542","count":8},{"id":"GO:1990845","count":8},{"id":"GO:0090152","count":8}]},{"hash":"216603114789773978","title":"Neuronal Synaptic Signaling and Plasticity","description":"The terms center on neuronal communication and plasticity (glutamatergic synaptic transmission, long-term potentiation, and regulation of synaptic plasticity), with related processes like glial/apoptotic regulation and sphingolipid biosynthesis that support synaptic signaling and membrane signaling. A plant hormone pathway term appears incidental; overall the cluster points to neuronal synaptic function and plasticity with survival signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0031914","count":2},{"id":"GO:0060963","count":2},{"id":"GO:0090153","count":2}]},{"hash":"1410053386747620394","title":"Transsulfuration and H2S biosynthesis","description":"This cluster shows a clear enrichment for sulfur amino acid metabolism: transsulfuration, homocysteine catabolism, and hydrogen sulfide biosynthesis, suggesting a shared role in sulfur metabolism and H2S signaling; other terms like mitotic cell cycle or retina development may reflect broader or incidental annotations but do not dominate the theme.","confidence":"Medium","size":12,"edges":63,"triangles":191,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0019343","count":5},{"id":"GO:0051289","count":5},{"id":"GO:0045722","count":5},{"id":"GO:1902593","count":5}]},{"hash":"2224059770057885586","title":"Ribosome biogenesis and translation regulation","description":"Top GO terms are dominated by translation and ribosome assembly, with a notable instance of negative regulation of translation, suggesting a core role in protein synthesis and ribosome biogenesis. The presence of transcription-related terms hints at broader gene expression regulation or dual-function proteins, but the strongest signal is ribosome biology and translation control.","confidence":"Medium","size":12,"edges":50,"triangles":117,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0002181","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0017148","count":1},{"id":"GO:0042255","count":1}]},{"hash":"815901002018591090","title":"Multi-tissue Signaling and Development","description":"The proteins map to diverse GO terms including immune signaling (interleukin-1, T cell receptor), neural activity (glutamatergic transmission, long-term potentiation, synaptic plasticity), muscle development (myoblast fusion), vascular development in the labyrinthine layer, and core processes like DNA replication and aging-related responses. This points to a broad set of signaling and developmental roles across tissues rather than a single cohesive pathway, so the label should reflect general multi-tissue signaling and development.","confidence":"Medium","size":12,"edges":12,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0060716","count":2},{"id":"GO:0001324","count":2},{"id":"GO:0070498","count":2},{"id":"GO:0001402","count":2},{"id":"GO:0050852","count":2}]},{"hash":"2194912354222016349","title":"Ubiquitin\u2013Proteasome System with Antigen Presentation","description":"The cluster is enriched for protein deubiquitination, SCF-dependent proteasomal ubiquitin-dependent catabolic processes, proteasome core complex assembly, and antigen processing/presentation via MHC I, indicating a core theme of proteostasis and immune antigen processing. Additional terms for stress responses and signaling (cadmium, salt, TNF, Wnt) suggest cross-talk between proteostasis and immune/stress signaling, with viral processes potentially reflecting antigen presentation activity.","confidence":"High","size":12,"edges":62,"triangles":184,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":8},{"id":"GO:0031146","count":6},{"id":"GO:0046686","count":6},{"id":"GO:0090263","count":6},{"id":"GO:0033209","count":6}]},{"hash":"187280849017621192","title":"DNA replication and chromatin assembly during cell cycle","description":"The dominant terms point to nuclear genome maintenance and gene expression regulation (DNA replication, CENP-A chromatin assembly, RNA processing, and cell division), with fewer terms related to ER trafficking, suggesting the core function is chromatin dynamics during the cell cycle and associated transcription/splicing steps.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0006888","count":2}]},{"hash":"145924769450259785","title":"Translation Regulation and mRNA Decay","description":"The cluster shows GO terms centered on translation (translation, initiation, elongation, termination, cytoplasmic translation) and related regulation (positive regulation of translational elongation, fidelity) plus mRNA turnover (deadenylation-dependent decay) and selenocysteine incorporation, pointing to proteins involved in translation machinery and its control. A glial cell proliferation term is likely contextual rather than core, and an antibiotic response term appears ancillary; overall, this cluster clusters around translation regulation and fidelity.","confidence":"High","size":11,"edges":39,"triangles":78,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:2000767","count":7},{"id":"GO:0014009","count":7},{"id":"GO:0006412","count":7},{"id":"GO:0000288","count":7},{"id":"GO:0006415","count":7}]},{"hash":"940468034890208566","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":19,"triangles":5,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0006351","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0048701","count":4},{"id":"GO:0009432","count":4}]},{"hash":"379192935070515632","title":"Meiosis and Nuclear Transport Machinery","description":"This cluster's top GO terms center on meiotic nuclear division and chromosome segregation (female meiotic nuclear division, meiotic sister chromatid cohesion centromeric, mitotic sister chromatid separation), paired with nuclear transport processes (NLS-bearing protein import into nucleus, mRNA transport, nuclear pore complex assembly) and related regulatory activities (peptidyl-serine dephosphorylation, regulation of protein desumoylation). The combination suggests a cohesive role in coordinating nuclear transport and chromosome dynamics during meiosis.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007143","count":2},{"id":"GO:0051754","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0051292","count":2}]},{"hash":"948482917259236065","title":"Nuclear RNA Processing and Chromatin Regulation","description":"This cluster centers on nuclear RNA maturation and splicing activities (RNA Pol II termination, spliceosome assembly, mRNA splicing, tRNA processing) together with chromatin-related processes (histone mRNA metabolism, pericentric heterochromatin formation) and nuclear import, suggesting a cohesive module linking RNA processing with chromatin organization and cell cycle regulation. Some terms like ABA response and hair cycle are less tightly connected but may reflect broader regulatory roles.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":7},{"id":"GO:0008033","count":7},{"id":"GO:0000245","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0051170","count":6}]},{"hash":"1439651597001055958","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":18,"triangles":17,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0042255","count":2},{"id":"GO:0006351","count":2}]},{"hash":"438892552954102480","title":"Vertebrate development and transcription regulation","description":"The top GO terms cluster around embryonic and neural development (forebrain development, neural tube closure, skeletal system development, multicellular organism development) and DNA-templated transcription, indicating a focus on developmental processes and gene expression control in vertebrates. Some stress-related terms (ER stress\u2013induced apoptosis, cadmium response, immune defense) appear as auxiliary responses but do not define the core theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0001501","count":3}]},{"hash":"1785770693086724571","title":"Golgi- and SNARE-mediated synaptic vesicle trafficking","description":"This cluster centers on vesicle transport between the ER, Golgi, and post-Golgi compartments, Golgi ribbon organization, and SNARE complex assembly, plus functional terms for exocytic insertion of postsynaptic receptors and modulation of synaptic strength. The convergence of Golgi trafficking with synaptic vesicle priming and potentiation points to a cohesive role in delivering and preparing vesicles for neurotransmission at synapses.","confidence":"High","size":11,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0048280","count":6},{"id":"GO:0006891","count":6},{"id":"GO:0090161","count":6},{"id":"GO:0098967","count":5}]},{"hash":"2297822872250554192","title":"Chloroplast Photosynthesis and Light-Response Proteins","description":"These proteins cluster around photosynthesis and light-driven processes, including chloroplast/chromophore linkage and light-intensity responses, indicating a cohesive set of chloroplast-associated photosynthetic components. Some terms (e.g., ascorbate response, cadmium response, ureteric bud development) appear as noise or broader stress-related annotations, but the dominant theme is photosynthesis-related function.","confidence":"High","size":11,"edges":31,"triangles":39,"max_degree":9,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0018298","count":7},{"id":"GO:0015979","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0033591","count":2},{"id":"GO:0009642","count":2}]},{"hash":"1830072339696044053","title":"Proteasome- and ubiquitin-mediated protein degradation","description":"The top terms cluster around the ubiquitin-proteasome system (SCF-dependent ubiquitin tagging, proteasome core complex assembly) and related protein catabolic processes, suggesting a common theme of protein turnover; other terms on stress responses or signaling (Wnt/TNF) can tie into degradation-regulated signaling, but the proteasome/ubiquitin theme is the strongest signal.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050774","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0031146","count":1},{"id":"GO:0046686","count":1},{"id":"GO:0090263","count":1}]},{"hash":"2041536448927763282","title":"Mitochondrial lipid biosynthesis and remodeling","description":"The top GO terms are dominated by lipid biosynthesis and remodeling (ether lipids, cardiolipin remodeling, phosphatidylcholine remodeling, CDP-diacylglycerol biosynthesis, triglyceride biosynthesis) and include mitochondrial ATP synthesis coupled to electron transport, pointing to a theme of lipid metabolism tied to mitochondrial function. Some development terms are present, but the strongest signal is lipid metabolism with mitochondrial involvement.","confidence":"Medium","size":11,"edges":21,"triangles":18,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0008611","count":5},{"id":"GO:0035965","count":5},{"id":"GO:0002071","count":5},{"id":"GO:0042775","count":5},{"id":"GO:2001246","count":5}]},{"hash":"1880928045318656754","title":"DNA transposition and proviral integration","description":"This cluster is dominated by GO terms tied to DNA mobility and integration\u2014DNA recombination, replication, integration, retrotransposition, and transposition\u2014along with RNA-templated DNA synthesis and proviral latency, and even viral/symbiont entry into host cells. Together these terms point to processes involving mobile genetic elements, DNA rearrangements, and provirus establishment rather than standard metabolic pathways.","confidence":"Medium","size":11,"edges":7,"triangles":0,"max_degree":7,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0075732","count":4},{"id":"GO:0046718","count":4},{"id":"GO:0039651","count":4}]},{"hash":"308058338355730871","title":"DNA-Templated Transcription Regulators","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, pointing to a core function as transcription regulators. A few other terms (calcium signaling, development, metabolism) appear sparsely and may reflect multifunctionality or annotation noise rather than a shared core function. Overall, the strongest and most consistent signal is transcriptional regulation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071277","count":1},{"id":"GO:0051343","count":1},{"id":"GO:0008218","count":1}]},{"hash":"1962528116229684978","title":"Ubiquitin-mediated protein turnover and DNA damage signaling","description":"The cluster\u2019s top terms center on ubiquitin-dependent protein degradation and deubiquitination, implying regulation of protein stability. Additional terms point to regulation of transcription and the DNA damage response (p53 pathway), suggesting a broader role in gene expression and DDR alongside some chromatin modification signals. However, several terms are diverse (hypoxia response, muscle development, histone methylation), so the link is strongest around ubiquitin-associated regulation and DDR rather than a single, narrow function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033138","count":1},{"id":"GO:1900037","count":1},{"id":"GO:0045184","count":1},{"id":"GO:0010452","count":1},{"id":"GO:0006511","count":1}]},{"hash":"908635251121533416","title":"Neuronal development and vesicle trafficking","description":"This cluster centers on neural development and function, with terms pointing to nervous system formation (vestibulocochlear nerve formation), neuromuscular control (involuntary skeletal muscle contraction, neuromuscular process controlling posture), sensory perception (smell), and cytoskeletal organization of neurons, complemented by intracellular trafficking processes (Golgi vesicle budding, retrograde transport from Golgi to ER). The mix suggests proteins involved in neural development/function alongside secretory/transport pathways.","confidence":"Medium","size":10,"edges":41,"triangles":90,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":2},{"id":"GO:0003333","count":1},{"id":"GO:0003011","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0021650","count":1}]},{"hash":"1314767242802018744","title":"Unknown","description":"The terms are diverse, including cell division, vesicle transport between ER and Golgi, inter-Golgi transport, peroxisome import, photosystem II repair, and mitotic checkpoint signaling, plus obsolete terms. There is no single cohesive function linking the proteins, and there are no edges to reinforce a specific theme, so a precise label cannot be confidently assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0048219","count":1}]},{"hash":"1901353493860753602","title":"Redox metabolism and extracellular signaling regulation","description":"The cluster shows a mix of metabolic processes tied to redox chemistry (oxidation-reduction, NADH oxidation, ethanol oxidation), carbon metabolism (retinol and fructose biosynthesis, PPP-related steps), and a notable GO term for extracellular negative regulation of signal transduction, plus a general drug response term. This suggests proteins linked to cellular energy/redox balance that also influence signaling outside the cell, justifying a label centered on redox metabolism with an aspect of extracellular signaling regulation.","confidence":"Medium","size":10,"edges":13,"triangles":5,"max_degree":5,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042572","count":4},{"id":"GO:1900116","count":4},{"id":"GO:1901159","count":4},{"id":"GO:0046370","count":4}]},{"hash":"1628879846806065492","title":"DNA transposition and proviral latency","description":"The cluster's top GO terms cluster around DNA movement and genome insertion: DNA transposition, DNA integration, retrotransposition, and establishment of integrated proviral latency, indicating involvement in mobile genetic elements and proviral genome incorporation. A few terms refer to symbiont entry and host apoptosis, and vesicle trafficking, but these are less central to the main theme of genome integration. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0075732","count":1},{"id":"GO:0032197","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0039651","count":1}]},{"hash":"1747629025651537038","title":"Mitotic cell cycle regulation via ubiquitin-proteasome","description":"The term set is dominated by cell-cycle control signals: G1/S and G2/M transitions, mitotic cell cycle, and negative regulation of mitotic DNA replication initiation, along with SCF-dependent ubiquitin-proteasomal protein degradation. These point to a coherent theme of mitotic regulation through targeted proteolysis. Other terms like translation and DNA repair appear ancillary or context-specific but don\u2019t override the primary pattern. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000086","count":1},{"id":"GO:1903467","count":1},{"id":"GO:0031146","count":1},{"id":"GO:2000819","count":1}]},{"hash":"644803232239168099","title":"Mitochondrial transport and fission","description":"The enriched GO terms point to transport across mitochondrial and cellular membranes (NAD, dNTP, manganese, thiosulfate transport) and to mitochondrial dynamics (mitochondrial membrane fission), with related metabolic and stress-response contexts (adaptive thermogenesis, fatty acid response, oxidative stress). This pairing suggests a cohesive theme around mitochondrial transport, morphology, and energy metabolism.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035352","count":3},{"id":"GO:0030302","count":3},{"id":"GO:0070542","count":3},{"id":"GO:1990845","count":3},{"id":"GO:0090152","count":3}]},{"hash":"357370490591063243","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":39,"triangles":79,"max_degree":9,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0051492","count":10},{"id":"GO:0072709","count":10},{"id":"GO:0046329","count":10},{"id":"GO:0070935","count":10},{"id":"GO:0034501","count":10}]},{"hash":"1575854503775933245","title":"Unknown","description":"The top GO terms span very diverse processes\u2014from cell size regulation and DNA replication to chemotaxis, metabolism, placenta development, cytoskeletal remodeling, osmotic stress response, and JNK signaling regulation\u2014offering no single cohesive theme to unify the cluster. A concise, representative label is not well-supported.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045793","count":7},{"id":"GO:0033160","count":7},{"id":"GO:0006935","count":7},{"id":"GO:0042220","count":7},{"id":"GO:0006260","count":7}]},{"hash":"1078494073571082098","title":"Central carbon metabolism and fatty acid biosynthesis","description":"The top GO terms are dominated by glycolysis, the TCA cycle, gluconeogenesis, and the pyruvate-to-acetyl-CoA step, plus malonyl-CoA and long-chain fatty acid biosynthesis, pointing to core carbon metabolism feeding lipid synthesis. Additional terms like protein quality control and xenobiotic response appear secondary to this central theme. Thus, a label capturing central energy metabolism with lipid biosynthesis is appropriate.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0006094","count":3},{"id":"GO:0006515","count":2},{"id":"GO:0042493","count":2}]},{"hash":"317806234092797135","title":"Unknown","description":"Top Terms are empty and there are no edges or GO annotations, leaving no basis for a common function. With only a single protein and no shared signals, a meaningful label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"385004494752583359","title":"RNA processing and translation regulation","description":"The cluster centers on RNA metabolism and protein synthesis: regulation of mRNA splicing via spliceosome, mRNA stabilization, regulation of translational initiation, formation of translation preinitiation complex, and small-subunit processome assembly, plus mitochondrial ribosome assembly. A couple of terms (ethanol metabolic process, blastocyst formation) seem less connected, possibly noise. Overall, these proteins appear linked to RNA processing and initiation of translation.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006067","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0010610","count":1}]},{"hash":"217172350494115877","title":"Lipid biosynthesis and Ca2+/metal transport","description":"This cluster shows enrichment for lipid biosynthetic processes (lipopolysaccharide and glycolipid biosynthesis) alongside several calcium and metal ion transport/regulation terms (Ca2+ transport, ER calcium handling, calcium-dependent exocytosis, zinc and cadmium transport). The common thread appears to be membrane-associated metabolism with ion transport roles, rather than a single specific pathway, hence a combined label focused on lipid biosynthesis with ion transport is appropriate. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0009247","count":3},{"id":"GO:0097755","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0032470","count":2}]},{"hash":"1830534755381343641","title":"Developmental differentiation across tissues","description":"The cluster shows enrichment for differentiation-related terms across several tissues (erythrocyte/megakaryocyte differentiation, lung, Purkinje cell maturation, nephron differentiation, uterus development) and IL-4 production, suggesting a broad role in tissue development and lineage specification rather than a single specific pathway. Some terms are obsolete, but the overall theme is developmentally oriented differentiation across multiple contexts.","confidence":"Medium","size":9,"edges":28,"triangles":38,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0010725","count":4},{"id":"GO:0045648","count":4},{"id":"GO:1900477","count":3}]},{"hash":"1391428125193716766","title":"RNA processing and viral lifecycle signals","description":"The top GO terms include several RNA processing/regulation terms (splicing, ncRNA-mediated silencing, RNA-templated DNA biosynthesis) along with virion assembly and viral life cycle terms, suggesting a link between RNA processing functions and viral-related processes. However, several outlier terms (leukocyte migration, sepal formation) reduce the overall coherence, lowering confidence.","confidence":"Low","size":9,"edges":8,"triangles":1,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":6},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0019058","count":4},{"id":"GO:0050900","count":4}]},{"hash":"1190665462428812151","title":"Unknown","description":"The nine proteins show a mix of GO terms including glycolytic process, glyoxysome organization, lipid transport, and apoptosis-related regulation, with several obsolete annotations. This combination does not reveal a single cohesive function or pathway, so a confident, representative label cannot be assigned.","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0009097","count":3},{"id":"GO:0014070","count":2}]},{"hash":"172091828759464416","title":"Unknown","description":"The highest-frequency terms include mycothiol and ectoine biosynthesis, acetylation-related processes (spermine acetylation, N-terminal acetylation, N-acetylglucosamine metabolism), and unrelated eukaryotic processes (angiogenesis, melatonin biosynthesis, subtelomeric heterochromatin formation). This mix spans bacteria and eukaryotes with divergent themes, and there is no single cohesive function that ties all terms together. Therefore no intuitive, specific label can capture the cluster.","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":9},{"id":"GO:0032919","count":9},{"id":"GO:0060358","count":9},{"id":"GO:0017196","count":9},{"id":"GO:0019491","count":9}]},{"hash":"746273231501900670","title":"Cell wall biosynthesis and morphogenesis","description":"The enriched terms cluster around the construction and organization of the cell wall, including peptidoglycan, lipid A, fungal-type walls, and mannoprotein biosynthesis, along with regulation of cell shape and morphogenesis. This suggests a cohesive role in wall assembly and associated structural remodeling, rather than unrelated metabolic pathways.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":5},{"id":"GO:0000902","count":4},{"id":"GO:0009298","count":4},{"id":"GO:0009245","count":4},{"id":"GO:0009272","count":4}]},{"hash":"1194497126663082734","title":"RNA Processing and Translation Regulation","description":"This cluster centers on RNA metabolism and the control of gene expression at the RNA level, with terms for mRNA splicing regulation, mRNA stability in response to stress, mRNA export, ribosome/translation initiation, and processome assembly. The convergence of spliceosome regulation, mRNA stabilization/export, and translation initiation/termination terms indicates a cohesive theme of RNA processing linked to translation control, despite one developmental term (blastocyst formation) present. ","confidence":"High","size":9,"edges":19,"triangles":17,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001825","count":3},{"id":"GO:0048025","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3}]},{"hash":"1670578613528180421","title":"Unknown","description":"The top GO terms are highly disparate (angiogenesis, several biosynthetic and metabolic processes across bacteria, protein acetylation, telomere-related chromatin formation). There isn\u2019t a clear, unifying molecular function or pathway connecting these proteins, so a cohesive, intuitive label cannot be assigned.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":6},{"id":"GO:0010125","count":5},{"id":"GO:0032919","count":5},{"id":"GO:0060358","count":5},{"id":"GO:0017196","count":5}]},{"hash":"377863087141840422","title":"Sulfur and Cysteine Biosynthesis Cluster","description":"This cluster is enriched for sulfur and cysteine metabolism: mycothiol biosynthesis, L-cysteine biosynthesis, hydrogen sulfide biosynthesis, and sulfate assimilation. Cysteinyl-tRNA aminoacylation links to protein synthesis, while phosphorylation/dephosphorylation terms may reflect regulation of these pathways. Overall, the dominant theme is sulfur/cysteine biosynthesis and related metabolism, with some peripheral signals.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":3},{"id":"GO:0006423","count":3},{"id":"GO:0016310","count":2},{"id":"GO:0019344","count":1},{"id":"GO:0070814","count":1}]},{"hash":"2212475693069007225","title":"Nitrogen metabolism and regulation","description":"The cluster shows a strong set of GO terms around ammonia assimilation, nitrogen fixation, and nitrogen-responsive transcriptional regulation (e.g., ammonia assimilation cycle, nitrogen fixation, nitrogen catabolite repression of transcription), indicating a cohesive theme of nitrogen metabolism and its regulation. Some terms appear unrelated (e.g., insulin secretion, epithelial proliferation), likely due to pleiotropy or annotation noise, but the dominant signal supports labeling as nitrogen metabolism-related.","confidence":"Medium","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019676","count":3},{"id":"GO:0010756","count":3},{"id":"GO:0032024","count":3},{"id":"GO:1904797","count":3},{"id":"GO:0009405","count":3}]},{"hash":"1615134789185671223","title":"Nutrient-sensing and stress-responsive growth signaling","description":"The cluster shows enrichment for responses to nutrients and stress (insulin stimulus, starvation, amino acids) along with growth regulation and lipid metabolism, plus adhesion-related signaling, indicating a cohesive theme of integrating metabolic cues with growth control.","confidence":"Medium","size":9,"edges":16,"triangles":12,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0040008","count":5},{"id":"GO:0045471","count":5},{"id":"GO:0033591","count":4},{"id":"GO:0043651","count":4},{"id":"GO:0071285","count":4}]},{"hash":"1678287976124701949","title":"Renal development and epithelial water transport","description":"The top GO terms cluster around kidney-related processes (metanephric collecting duct development; metanephric glomerulus vasculature development) and epithelial water handling (transepithelial water transport; intracellular water homeostasis; cerebrospinal fluid secretion), suggesting proteins involved in nephron formation and renal water balance. Some metabolic terms appear incidental, but the dominant theme is kidney development plus epithelial water movement.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0035377","count":2},{"id":"GO:0042476","count":2}]},{"hash":"1460141997305125494","title":"Cell Division and Stress Response Regulation","description":"The cluster is enriched for mitotic cell cycle and cell division terms, suggesting a core involvement in proliferation. Additional terms point to proteostasis and immune signaling, including unfolded protein response, type I interferon response, and ubiquitination. Together, these terms hint at a network coordinating cell division with protein quality control and immune-related regulation.","confidence":"Medium","size":9,"edges":26,"triangles":30,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":6},{"id":"GO:0051301","count":5},{"id":"GO:1902564","count":4},{"id":"GO:0071357","count":3},{"id":"GO:0070206","count":3}]},{"hash":"1062092719878830494","title":"Ribosome biogenesis and cell cycle signaling","description":"The cluster is dominated by GO terms for maturation of LSU and 5.8S rRNA, pointing to ribosome biogenesis. Additional terms like TORC1 signaling, mitotic cytokinesis, and cell division suggest a link between growth signaling and the cell cycle, with some supporting roles in GTPase regulation and mRNA transport. The SOS response term may reflect annotation noise or cross-talk with stress pathways. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0038202","count":2},{"id":"GO:0000281","count":2}]},{"hash":"962914787822661142","title":"Oxidative stress response and RNA processing","description":"The top GO terms show redox homeostasis and cellular oxidant detoxification, indicating an oxidative stress angle, while multiple terms relate to RNA metabolism and translation initiation/processing, suggesting co-regulation of RNA processing under stress.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0001825","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0010610","count":1}]},{"hash":"783597698212594262","title":"Unknown","description":"The GO terms span diverse functions\u2014from transcription to various biosynthetic and regulatory processes\u2014without a clear shared theme or interaction pattern, so there isn\u2019t a cohesive label that accurately describes the cluster.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0051567","count":1}]},{"hash":"661477973764965738","title":"Cardiac Conduction and Calcium Signaling","description":"This cluster centers on heart-related processes: ventricular cardiac muscle tissue morphogenesis, electrical coupling in cardiac conduction, and regulation of calcium-release channels, plus calcium-mediated signaling. Despite a couple of unrelated terms, the dominant theme is cardiac development and excitation-contraction signaling, supporting this label.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046661","count":1},{"id":"GO:0086064","count":1},{"id":"GO:0042098","count":1},{"id":"GO:0007183","count":1},{"id":"GO:0000412","count":1}]},{"hash":"2000232708358947690","title":"Plant Developmental Signaling Inhibitors","description":"The terms cluster around negative regulation of signaling pathways (BMP and TGF-beta receptor signaling, non-canonical NF-kappaB), plus peptidyl-threonine dephosphorylation, suggesting proteins that dampen signaling activity. Some plant-specific terms (maintenance of meristem identity) point to developmental regulation, while other annotations (photosystem and vacuole-related processes) indicate broader cellular roles. Overall, the set most coherently centers on inhibitors/modulators of signaling during development, especially in plants.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0000173","count":2},{"id":"GO:0080005","count":2},{"id":"GO:0042347","count":2}]},{"hash":"333405290061548865","title":"Mitochondrial respiration and redox regulation","description":"The cluster\u2019s top GO terms center on mitochondrial electron transport (cytochrome c to oxygen; ubiquinol to cytochrome c), cytochrome c\u2013heme linkage, and hydrogen peroxide metabolic processes, pointing to functions in oxidative phosphorylation and redox signaling/maintenance. Some terms like photosynthesis and an obsolete apoptotic activation term appear, but the core signal is mitochondrial respiration and redox balance, making this a cohesive functional theme for the cluster.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006123","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0008635","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006122","count":3}]},{"hash":"2054988352124209676","title":"Proteostasis and vesicle trafficking","description":"The cluster\u2019s GO terms cluster around protein handling and transport, including ER to Golgi vesicle transport, inter-Golgi cisterna transport, and peroxisomal matrix import, along with proteostasis-related processes like aggresome assembly and stress granule disassembly. While there are a couple of nuclear terms (CENP-A chromatin assembly, mitotic checkpoint signaling), the dominant signal is cytosolic protein trafficking and quality control. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0048219","count":2},{"id":"GO:0016558","count":2},{"id":"GO:1903007","count":2}]},{"hash":"434971935517448259","title":"DNA Repair and Ubiquitin-Proteasome Quality Control","description":"The cluster features strong signals for DNA damage response pathways (global genome nucleotide-excision repair and error-prone translesion synthesis) alongside ubiquitin-mediated proteostasis (cytoplasmic protein quality control and free ubiquitin chain polymerization), suggesting a coordinated response to genomic stress and damaged proteins. While some terms touch broader processes like peroxisomal import, interferon signaling, and development, the dominant theme links DNA repair/tolerance with ubiquitin-dependent protein maintenance.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070911","count":8},{"id":"GO:0016558","count":8},{"id":"GO:0042276","count":8},{"id":"GO:0060340","count":8},{"id":"GO:0070076","count":8}]},{"hash":"2242021433606866737","title":"Cofactor Metabolism and Growth Signaling","description":"The top GO terms are dominated by metabolic processes involving vitamins and cofactors (riboflavin, folic acid, one-carbon metabolism) and growth-related processes (cell growth, developmental growth, axon regeneration), with a few stress/immune-related terms. This suggests a cohesive theme around maintaining metabolic support for growth and regenerative signaling, rather than a single specific pathway.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009231","count":2},{"id":"GO:0006730","count":1},{"id":"GO:0051000","count":1},{"id":"GO:0034097","count":1}]},{"hash":"761684951347756088","title":"Oxidative Stress Response and DNA Repair","description":"This cluster prominently features redox homeostasis and responses to hydrogen peroxide, together with base-excision repair, suggesting a role in protecting cells from oxidative damage and maintaining genome integrity, despite several obsolete or peripheral terms in the set.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":1},{"id":"GO:2000327","count":1},{"id":"GO:0046856","count":1},{"id":"GO:0014912","count":1},{"id":"GO:0070301","count":1}]},{"hash":"1034347459011586428","title":"Drosophila eye and wing development","description":"The cluster features terms tied to eye development (compound eye cone cell fate commitment, visual perception) and wing development (wing cell fate specification), suggesting a shared role in insect organ patterning. Additional terms about EGFR ligand maturation and proteolysis/unfolded protein response imply associated protein processing during development, supporting a cohesive developmental theme. Confidence: Medium","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904211","count":1},{"id":"GO:0038005","count":1},{"id":"GO:0042676","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0034620","count":1}]},{"hash":"1900253024904013602","title":"Cell cycle and protein processing regulators","description":"The cluster includes GO terms for regulation of the cell cycle and positive regulation of cell growth, along with protein folding and establishment/export of Golgi localization, suggesting a theme around coordinating cell proliferation with protein maturation/trafficking. The skin/keratinocyte and substantia nigra development terms appear broader/less coherent with a single tissue program, likely reflecting annotation breadth rather than a unified tissue-specific function. Overall, the functions point to regulators involved in cell-cycle control and protein processing pathways.","confidence":"Medium","size":7,"edges":11,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0006457","count":2},{"id":"GO:0043154","count":1},{"id":"GO:0030307","count":1},{"id":"GO:0043588","count":1}]},{"hash":"1050576993107168619","title":"Chromosome segregation and nuclear transport","description":"The cluster centers on meiotic and mitotic chromosome dynamics (meiotic nuclear division, sister chromatid cohesion/separation) and nuclear transport/process assembly (nuclear pore complex assembly, NLS-mediated import, proteasome/ protein complex assembly), pointing to coordinated chromosomal segregation and nuclear-cytoplasmic trafficking. Some terms are broader cellular processes, but the dominant pattern supports this label.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007143","count":2},{"id":"GO:0051754","count":2},{"id":"GO:2001241","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0051292","count":2}]},{"hash":"1898727799356213347","title":"Methyltransferases (histone, RNA, N-terminal)","description":"The top GO terms are dominated by various methylation processes: histone methylation, arginine methylation, rRNA methylation, and N-terminal methylation, plus related methyltransferase activity in cobalamin and polyamine biosynthesis. This strongly suggests a cluster of methyltransferase enzymes acting on proteins and RNAs, potentially linking epigenetic regulation, ribosome modification, and metabolic methyl transfers to broader cellular outcomes like transcription control, growth, and senescence. An outlier term like nodulation is less directly connected, but does not outweigh the shared methylation theme.","confidence":"High","size":7,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":6},{"id":"GO:0043985","count":6},{"id":"GO:0019919","count":6},{"id":"GO:0009236","count":6},{"id":"GO:0090398","count":6}]},{"hash":"906446383505811825","title":"RNA/tRNA methylation enzymes","description":"The cluster is enriched for methylation-related terms, especially protein methylation, rRNA methylation, tRNA methylation, and tRNA wobble uridine modification, which together point to RNA modification enzymes as the core function. Other terms such as dopamine catabolic process and mercury detox may reflect ancillary metabolic roles in the same dataset, but the dominant pattern centers on RNA modification/methylation activity.","confidence":"High","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006479","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0070476","count":3},{"id":"GO:0042135","count":3},{"id":"GO:0042420","count":3}]},{"hash":"1914747794445776535","title":"Protein folding and quality control","description":"The top GO terms emphasize detection of misfolded proteins, protein stabilization, and chaperone-related folding, which together suggest a cluster centered on protein quality control and folding under stress. Some terms (virion/pore complex assembly, sperm binding) appear less connected and may reflect annotation noise or broader structural roles, but the core signal aligns with chaperone-mediated protein maintenance.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007339","count":7},{"id":"GO:1901998","count":7},{"id":"GO:0046686","count":7},{"id":"GO:0046931","count":7},{"id":"GO:0002236","count":7}]},{"hash":"1358785976082236900","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006407","count":3},{"id":"GO:0045903","count":2},{"id":"GO:0046677","count":2},{"id":"GO:1990145","count":2}]},{"hash":"1570433071840231171","title":"DNA Replication and Damage Response","description":"The cluster is dominated by GO terms for DNA replication (DNA replication; synthesis of primer) and DNA damage processing (SOS response; transcription-coupled nucleotide-excision repair), indicating a core theme of DNA metabolism and damage response. A smaller group of terms relates to RNA processing and silencing, which may reflect coordinated gene expression regulation under stress; overall, the DNA replication/repair theme is strongest.","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0006269","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0006268","count":5}]},{"hash":"1843317868243792968","title":"RNA Modification and Translation Machinery","description":"The cluster is dominated by translation-related GO terms (cytoplasmic translation and general translation) and RNA modification processes (tRNA pseudouridine synthesis, rRNA pseudouridine synthesis), indicating involvement in ribosome function and translation quality control. The presence of responses to translation-targeting antibiotics (cycloheximide, actinomycin D) further supports a theme of translation regulation. Extra terms (protein-DNA complex disassembly, ubiquitin pathway regulation) may reflect ancillary regulatory roles but do not override the core signal. ","confidence":"High","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1}]},{"hash":"1539330077942744939","title":"Mitochondrial electron transport and complex III assembly","description":"The top GO terms cluster around mitochondrial respiration and the electron transport chain, including aerobic respiration, proton transmembrane transport, and mitochondrial ETC steps from ubiquinol to cytochrome c, as well as complex III/cytochrome complex assembly and related heme transport. While lipid and retinol metabolism terms appear, the dominant pattern points to mitochondrial energy production and respiratory complex assembly, supporting this label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0034551","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0017004","count":1}]},{"hash":"428926873970822191","title":"Spliceosome Components","description":"The top GO terms are dominated by mRNA splicing via spliceosome and spliceosomal complex disassembly, indicating the proteins are mainly spliceosome components involved in RNA processing. While other terms (e.g., protein import, DNA damage response, various signaling/behavioral responses) appear, they are less represented and likely reflect secondary annotations rather than the core function of the cluster. Overall, the strongest signal is RNA splicing machinery.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000390","count":1},{"id":"GO:0090394","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0017038","count":1}]},{"hash":"816376975252317951","title":"Microtubule-Driven Cell Division and Neuronal Migration","description":"This cluster centers on cytoskeletal machinery involved in the cell cycle, spindle assembly, and microtubule organization, with peripheral terms pointing to neuronal migration and mechanosensory functions that also rely on microtubule dynamics.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":6},{"id":"GO:0043093","count":5},{"id":"GO:0001764","count":5},{"id":"GO:0007020","count":5},{"id":"GO:0031122","count":5}]},{"hash":"2283122265380022144","title":"DNA replication and chromosome maintenance","description":"The cluster centers on core genome maintenance processes: DNA replication and templated replication, replication fork progression, telomere maintenance, DNA recombination, and chromosome segregation/condensation. These together point to a cohesive role in maintaining genome integrity during replication and cell division.","confidence":"High","size":7,"edges":16,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006265","count":1},{"id":"GO:0043007","count":1},{"id":"GO:0097046","count":1},{"id":"GO:0007004","count":1},{"id":"GO:0006310","count":1}]},{"hash":"1875473293440382423","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051492","count":2},{"id":"GO:0072709","count":2},{"id":"GO:0046329","count":2},{"id":"GO:0070935","count":2},{"id":"GO:0034501","count":2}]},{"hash":"1157846145541618218","title":"Wnt Pathway Regulators","description":"The most frequent GO terms are about regulation of canonical Wnt signaling (both positive and negative), suggesting these proteins mainly function as modulators of the Wnt pathway. Other terms like T cell receptor signaling and DNA replication/repair appear, but they don\u2019t override the central Wnt regulation signal. This makes the label plausible but with some multifunctionality, hence Medium confidence.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0090263","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0051304","count":3},{"id":"GO:0051436","count":3}]},{"hash":"362787737660011438","title":"Fatty Acid Transport and Metabolism","description":"The top GO terms are dominated by fatty acid transport and related metabolic processes (long-chain/medium-chain fatty acids, fatty-acyl-CoA metabolism). This pattern points to a cluster function centered on uptake and processing of fatty acids, with additional metabolic terms as peripheral annotations.","confidence":"Medium","size":7,"edges":11,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008218","count":3},{"id":"GO:0044539","count":3},{"id":"GO:0090410","count":3},{"id":"GO:0001579","count":3},{"id":"GO:0043041","count":3}]},{"hash":"1777864049879500573","title":"DNA Transposition and Integration Proteins","description":"The dominant GO terms are DNA integration and DNA transposition (both with multiple hits), with a supporting signal for DNA-templated transcription, suggesting a core function related to genome mobility and related transcriptional processes. The other terms (lipid biosynthesis and obsolete annotations) appear incidental and do not define the main theme. Therefore, the label reflects the primary function of the cluster.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0015074","count":4},{"id":"GO:0006313","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0097502","count":2},{"id":"GO:0009247","count":2}]},{"hash":"118848717052845356","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":8,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0033314","count":1},{"id":"GO:0000727","count":1},{"id":"GO:0072429","count":1},{"id":"GO:0010520","count":1},{"id":"GO:0009650","count":1}]},{"hash":"1120267875886050125","title":"DNA Repair and Ubiquitin-Proteasome Proteostasis","description":"The cluster is defined by DNA damage response terms (global genome nucleotide-excision repair and error-prone translesion synthesis) and ubiquitin-proteasome\u2013dependent protein quality control (cytoplasm protein quality control and free ubiquitin chain polymerization). Additional terms point to broader roles in cell cycle, development, viral processes, and peroxisomal import, but the strongest common theme is genome maintenance tied to proteostasis via ubiquitin signaling.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070911","count":7},{"id":"GO:0016558","count":7},{"id":"GO:0042276","count":7},{"id":"GO:0060340","count":7},{"id":"GO:0070076","count":7}]},{"hash":"1338821381588602418","title":"Neural tube and forebrain development","description":"Among the top terms, neural tube closure and forebrain development dominate, indicating a neural developmental theme. The cluster also includes broader developmental terms (multicellular organism development, skeletal system development) but the neural-related terms provide a coherent central theme. Some terms (immune response, cadmium response) seem ancillary or noisy with respect to development.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1216663587871018415","title":"Lignan and Phenylpropanoid Biosynthesis","description":"The top GO terms are dominated by secoisolariciresinol and lariciresinol biosynthetic processes, along with phenylpropanoid biosynthesis and sporopollenin biosynthesis. These collectively point to lignan/phenylpropanoid secondary metabolism and pollen-wall-related biosynthesis in plants, with a few outliers among carbohydrate/sugar-nucleotide biosynthesis terms. Thus the cluster likely represents proteins involved in lignan and phenylpropanoid biosynthesis and related plant secondary metabolism.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1902138","count":1},{"id":"GO:0080110","count":1},{"id":"GO:0009699","count":1},{"id":"GO:1902131","count":1}]},{"hash":"1103586030268099266","title":"Zinc and Cadmium Ion Homeostasis and Transport","description":"Based on the top GO terms, the proteins are enriched for zinc ion homeostasis and zinc transmembrane transport, cadmium ion transport and cellular detoxification of cadmium, and a response to zinc ion, with some related but obsolete iron-homeostasis signals. This pattern indicates a cohesive module devoted to maintaining zinc/cadmium ion levels, mediating their transport, and detoxification/sequestration of cadmium stress.","confidence":"High","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006882","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0006876","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0055072","count":2}]},{"hash":"971773598991903719","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000390","count":1},{"id":"GO:1902570","count":1},{"id":"GO:0045347","count":1},{"id":"GO:0000494","count":1},{"id":"GO:0007175","count":1}]},{"hash":"192205320895941925","title":"Unknown","description":"The GO terms span DNA replication, regulation of kinase activity, detoxification and deglycation, oxidative phosphorylation regulation, cellular response to glyoxal, inflammatory response, and fertilization. This broad mix lacks a unifying function or pathway; the cluster also shows low connectivity (low degree, no triangles). Because there is no coherent theme linking the terms, I cannot assign a meaningful specific label.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0050787","count":1},{"id":"GO:0036526","count":1},{"id":"GO:2000277","count":1}]},{"hash":"954149020154648644","title":"RNA processing and translation initiation regulation","description":"The top terms cluster around post-transcriptional RNA metabolism and the initiation of protein synthesis\u2014splicing regulation, mRNA stability control, preinitiation complex formation, and initiation-related processes\u2014suggesting a cohesive theme of RNA processing and translation initiation. A few terms like cobalamin biosynthesis appear incidental and do not define the core function of the cluster.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0001825","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0010610","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1775639205086561585","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070893","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0001172","count":1}]},{"hash":"1353378978833874983","title":"Nuclear DNA Replication and Transcription","description":"The top terms are dominated by DNA replication, viral genome replication, DNA-templated transcription, and DNA recombination, which together point to core nuclear functions related to genome maintenance and transcription. A smaller subset includes vesicle transport and peroxisomal import terms, which are less central to these processes and may reflect broader multifunctionality or annotation overlap. Overall, the cluster appears best characterized by DNA replication and transcription-related activities.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0019079","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0006888","count":3}]},{"hash":"872772952641708637","title":"Amino acid metabolism and sulfur biosynthesis","description":"The top GO terms cluster around amino acid metabolism, including serine/threonine/tryptophan biosynthesis, amine catabolic processes, transsulfuration, and hydrogen sulfide production, along with related carbon skeleton pathways (pyruvate, 2-oxobutyrate) and coenzyme M biosynthesis. This points to a cohesive function centered on amino acid turnover and sulfur-containing metabolite production.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006565","count":4},{"id":"GO:0009310","count":2},{"id":"GO:0019295","count":2},{"id":"GO:0019346","count":2},{"id":"GO:0046360","count":2}]},{"hash":"631970563245349073","title":"Cytoplasmic Translation and Ribosome Biogenesis","description":"The top GO terms cluster around protein synthesis: translation, cytoplasmic translation, ribosomal small subunit biogenesis, translational termination, translational fidelity, and positive regulation of cytoplasmic translation, indicating involvement with the translation machinery and ribosome assembly. A few outlier terms (cell septum assembly, conjugation) appear but do not define the main function. Overall, the cluster appears to represent the core protein synthesis machinery.","confidence":"High","size":6,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0002181","count":2},{"id":"GO:0001172","count":1},{"id":"GO:0090529","count":1},{"id":"GO:1903833","count":1}]},{"hash":"1531660259863278137","title":"Ribosome Biogenesis and Translation","description":"Top GO terms indicate a strong focus on translation, translation initiation, and ribosome assembly/export (e.g., translation, maturation of SSU-rRNA, ribosomal large subunit biogenesis and export). This suggests the cluster largely consists of factors involved in ribosome biogenesis and the protein synthesis machinery, with a couple of outliers that may reflect broader annotations. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000462","count":2},{"id":"GO:0000055","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0031365","count":1}]},{"hash":"812953919940380739","title":"ER protein folding and trafficking","description":"These proteins cluster around endoplasmic reticulum\u2013related processing: targeting and translocation to ER membranes, ER protein folding with chaperones, and ER stress\u2013associated regulation of translation, along with redox considerations tied to folding. One term about parathyroid hormone signaling appears peripheral, but the dominant theme is ER-based protein handling and quality control.","confidence":"Medium","size":6,"edges":13,"triangles":13,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0031204","count":6},{"id":"GO:0036494","count":6},{"id":"GO:0070389","count":6},{"id":"GO:0034975","count":6},{"id":"GO:0090084","count":6}]},{"hash":"1588014691691059679","title":"Ribosome biogenesis and translation machinery","description":"The top GO terms concentrate on ribosome and translation processes: cytoplasmic translation, translation initiation regulation, ribosomal large subunit and ribosome assembly, and rRNA processing (ITS2 cleavage). The inclusion of mitochondrial translational termination further supports a translation-centric role, potentially across organelles. The antibiotic response term aligns with ribosome-targeting mechanisms, reinforcing the link to the translation machinery. Collectively, these proteins appear to participate in ribosome assembly and functional translation, justifying the label.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:1901194","count":2},{"id":"GO:0002181","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0046677","count":1}]},{"hash":"1691977771178171246","title":"Unknown","description":"The top GO terms span diverse biosynthetic and acetylation processes (mycothiol, ectoine, melatonin, N-acetylglucosamine; N-terminal and spermine acetylation) but also include unrelated eukaryotic terms (angiogenesis, subtelomeric heterochromatin formation). There isn\u2019t a single coherent functional theme linking these proteins, so the cluster cannot be confidently labeled with a specific biology. ","confidence":"","size":6,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":3},{"id":"GO:0032919","count":3},{"id":"GO:0060358","count":3},{"id":"GO:0017196","count":3},{"id":"GO:0019491","count":3}]},{"hash":"2089583075843892239","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0002188","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0000466","count":4}]},{"hash":"1834340181839067180","title":"Photosynthesis and Electron Transport","description":"Based on the top GO terms, the cluster is dominated by photosynthesis-related processes and electron transport (photosynthesis, photosynthetic electron transport in photosystem I, electron transport chain, light reaction). This points to a common theme of photosynthetic energy capture and electron transfer, with several other metabolic terms appearing at low frequency that may reflect broader energy metabolism annotations or cross-talk. Overall, the strongest signal is photosynthesis and related electron transport, making this a coherent energy-metabolism\u2013centered cluster.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":3},{"id":"GO:0009773","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006086","count":1},{"id":"GO:0022900","count":1}]},{"hash":"1862363103128327938","title":"RNA processing and translation initiation machinery","description":"The proteins are tied together by functions in RNA processing and translation initiation: regulation of mRNA splicing, mRNA stability under stress, assembly of the translation preinitiation complex and initiation regulation, small-subunit processome assembly, and mRNA export. A couple of terms (e.g., blastocyst formation) may reflect broader roles, but the core theme is RNA maturation/processing and the initiation of translation. ","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001825","count":2},{"id":"GO:0048025","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2}]},{"hash":"956110992987545748","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031408","count":2},{"id":"GO:0010193","count":2},{"id":"GO:0019383","count":2},{"id":"GO:0045006","count":1},{"id":"GO:0034475","count":1}]},{"hash":"689376620458979611","title":"tRNA aminoacylation and translation","description":"This cluster is dominated by GO terms for glutamyl- and glutaminyl-tRNA aminoacylation, tRNA modification, and translation, pointing to core protein synthesis machinery. The additional terms related to development and cytokine production are sparse and likely non-central annotations or multifunctional roles, but do not override the translation-focused theme.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006424","count":2},{"id":"GO:0006425","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0008584","count":2}]},{"hash":"859754252419930001","title":"Cofactor and vitamin biosynthesis","description":"The top GO terms are dominated by biosynthetic processes for cofactors and vitamins (thiamine, lipoate, biotin, and heme precursor protoporphyrinogen IX), with one term pointing to cofactor biosynthesis and a few peripheral signals (antibiotic response, lysine fermentation). This suggests the cluster groups proteins involved in cofactor/vitamin biosynthetic metabolism as a coherent theme.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0006550","count":2},{"id":"GO:0051188","count":1},{"id":"GO:0009249","count":1},{"id":"GO:0009107","count":1}]},{"hash":"308426879699485440","title":"Glycan and lipid biosynthesis with sugar response","description":"This cluster co-occurs with GO terms for glycan-related biosynthesis (GPI anchor biosynthesis, oligosaccharide-lipid intermediates, glycosylation) and sugar-associated metabolism (mycothiol biosynthesis, glycogen and sucrose pathways) as well as responses to sorbitol and sucrose. Despite several obsolete terms, the common thread appears to be glycan and lipid assembly coupled with sugar-responsive metabolic processes.","confidence":"Medium","size":6,"edges":11,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0072708","count":2},{"id":"GO:0006490","count":2},{"id":"GO:0006506","count":2}]},{"hash":"1779961257238140028","title":"Amino acid and nucleotide metabolism","description":"GO terms indicate involvement in amino acid biosynthesis (lysine/arginine pathways), peptide/protein turnover (proteolysis, peptide catabolic process), and nucleotide metabolism (uridine biosynthesis, purine/nucleobase metabolism, allantoin/ureide pathways), suggesting a cluster tied to general nitrogen metabolism spanning amino acid turnover and nucleotide synthesis/degradation.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0010136","count":2},{"id":"GO:0009089","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0009442","count":2}]},{"hash":"584487715447206324","title":"Calcium and metal ion transport","description":"The cluster\u2019s strongest signal is metal ion transport (zinc, cadmium, copper) and intracellular calcium ion homeostasis, with a possible link to fast-twitch muscle contraction via calcium signaling. A few terms (serine biosynthesis, LPS biosynthesis) are metabolic outliers, but the core theme centers on ion transport and calcium-related processes. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097755","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0006874","count":2}]},{"hash":"805635599919347051","title":"Bacterial dolichol-linked glycan biosynthesis","description":"The cluster\u2019s GO terms center on dolichyl/dolichol-based biosynthetic processes, including dolichyl diphosphate biosynthesis, dolichol-linked oligosaccharide biosynthesis, and protein N-linked glycosylation, plus O-antigen and enterobacterial common antigen biosynthesis and UDP-N-acetylglucosamine metabolism. This points to a cohesive role in assembling glycans on lipid carriers for bacterial cell envelope components, with some enrichment for related cell envelope processes. ","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006489","count":1},{"id":"GO:0009246","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0006047","count":1}]},{"hash":"466164689119048842","title":"Autophagy and Cvt/PMN vacuolar targeting","description":"The top GO terms strongly converge on autophagy-related processes: macroautophagy, piecemeal microautophagy of the nucleus, and cytoplasm-to-vacuole targeting via the Cvt pathway, signaling a shared role in autophagic/vacuolar trafficking. While other terms touch on miscellaneous processes, the autophagy/vacuolar targeting theme is the most representative for this cluster. ","confidence":"High","size":6,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002143","count":3},{"id":"GO:0016236","count":3},{"id":"GO:0018192","count":3},{"id":"GO:0006501","count":3},{"id":"GO:0034727","count":3}]},{"hash":"1430624584192871008","title":"ER protein folding and trafficking","description":"This cluster is dominated by terms tied to endoplasmic reticulum (ER) processing: protein folding in the ER, ER-to-Golgi vesicle transport, and a prolyl hydroxylation step occurring in the ER. While a couple terms point to nuclear transcription regulation or viral processes, the strongest and most representative signals are ER-based protein folding, quality control, and trafficking functions, suggesting the proteins operate in ER processing and secretion pathways.","confidence":"Medium","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0046826","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0018401","count":1}]},{"hash":"636189615934657831","title":"Mitochondrial fission and membrane dynamics","description":"The cluster\u2019s top GO terms are dominated by mitochondrial fission and membrane organization (GO:0090149, GO:0000266, GO:0007006), indicating a core role in mitochondrial membrane remodeling and fission processes. Additional terms point to ER-to-Golgi vesicle transport and Golgi organization, suggesting some association with inter-organelle trafficking, but the strongest signal remains mitochondrial dynamics. Overall, the proteins likely participate in mitochondrial membrane remodeling and fission processes.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090149","count":2},{"id":"GO:0000002","count":2},{"id":"GO:0006888","count":2},{"id":"GO:1903358","count":2},{"id":"GO:0007006","count":2}]},{"hash":"504924530229475474","title":"Diverse biosynthetic pathways","description":"This cluster\u2019s top GO terms are all biosynthetic processes spanning a range of macromolecules and cofactors, including siroheme, cobalamin, rhamnose and heptose building blocks, lipopolysaccharide core, phenylpropanoids, sporopollenin, sulfate assimilation, and amino acid metabolism. The mix covers both plant-associated biosynthesis (sporopollenin, phenylpropanoid) and bacterial cell-wall/cofactor biosynthesis (LPS precursors, siroheme, cobalamin, sulfate assimilation), suggesting a broader set of enzymes dedicated to diverse biosynthetic activities rather than a single pathway. Confidence: Medium","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019354","count":1},{"id":"GO:0080110","count":1},{"id":"GO:0009699","count":1},{"id":"GO:0000103","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1105719428671220912","title":"Unknown","description":"The GO terms describe a mix of immune signaling (TLR3), lipid regulation (SREBP), kinase signaling (PKC), neuronal/synaptic activity, mitochondrial function, and extracellular matrix remodeling, with no single unifying process evident. Because there is no coherent, shared function across the cluster, a concise, representative name cannot be assigned beyond Unknown.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1903905","count":2},{"id":"GO:0045541","count":2},{"id":"GO:0032226","count":2},{"id":"GO:0010918","count":2},{"id":"GO:0022617","count":2}]},{"hash":"548826030930094143","title":"Proteostasis and trafficking","description":"The GO terms cluster around protein assembly and oligomerization, quality-control processes such as aggresome and inclusion body assembly/disassembly, ubiquitin-related regulation, and vesicle transport between ER and Golgi, plus peroxisomal import. Together these suggest a unifying theme of proteostasis and intracellular trafficking.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0048219","count":1},{"id":"GO:0010206","count":1},{"id":"GO:0016558","count":1}]},{"hash":"2199384754326164408","title":"Diverse Transmembrane Transporters","description":"The Top Terms center on various transmembrane transport processes for vitamins, sugars, ions, xenobiotics, and neurotransmitter loading into vesicles, suggesting a group of membrane transporter proteins with broad substrate range.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0015757","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0098700","count":2}]},{"hash":"666185287906973794","title":"Unknown","description":"The Top Terms include translation, mitophagy, spindle pole body duplication, T cell proliferation, various neuronal/developmental terms, and cardiac conduction\u2014an assortment with no dominant shared function. With 0 edges and no cohesive GO signal uniting the proteins, there is no clear theme to label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0014070","count":1},{"id":"GO:1904049","count":1},{"id":"GO:0000423","count":1},{"id":"GO:0030474","count":1}]},{"hash":"2136609081830765243","title":"Calcium and potassium signaling with mechanosensation","description":"This cluster's GO terms cluster around ion homeostasis and signaling, notably intracellular potassium ion homeostasis and cellular response to calcium ion, with an additional mechanosensory (touch detection) term. While there are a few divergent terms ( xenobiotic response, bioluminescence, etc.), the strongest common theme among the proteins appears to be ion-based signaling and mechanotransduction.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:0035690","count":2},{"id":"GO:1902527","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0051343","count":1}]},{"hash":"269311086505559632","title":"RNA Processing and Translation","description":"The strongest recurring GO terms point to RNA maturation and modification (maturation of LSU rRNA, RNA guanine-N7 methylation) and protein synthesis (translation), indicating the cluster centers on RNA processing and subsequent protein production. Chromatin organization and collagen catabolic processes appear as secondary signals, but the core theme is gene expression at RNA and ribosome/translation steps; some terms are obsolete or organism-specific noise.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":2},{"id":"GO:0034396","count":2},{"id":"GO:0035551","count":2},{"id":"GO:0034724","count":2},{"id":"GO:0006412","count":2}]},{"hash":"109454024579848836","title":"Ribosome biogenesis and RNA quality control","description":"The cluster\u2019s GO terms cluster around ribosome production (ribosome biogenesis, rRNA maturation) and extensive RNA surveillance/decay pathways (nuclear mRNA surveillance, non-stop decay, TRAMP/CUT), indicating proteins tied to ribosome assembly and RNA quality control rather than a single enzymatic function. This suggests a cohesive theme of RNA processing linked to ribosome biogenesis and RNA quality control mechanisms.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006407","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0033119","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1091267904192247038","title":"Gluconeogenesis and glycolysis regulation","description":"The cluster is dominated by GO terms tied to glucose metabolism and its control, including gluconeogenesis, regulation of gluconeogenesis, fructose 1,6-bisphosphate metabolic process, and glycerol catabolic process, with a note on negative regulation of glycolysis. While there are related stress-response and signaling terms (response to axon injury, cellular response to xenobiotic stimulus, negative regulation of Ras signaling), the strongest shared theme is regulation of glucose production and utilization.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048678","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0030388","count":2},{"id":"GO:0019563","count":2},{"id":"GO:0006111","count":2}]},{"hash":"378217161053967349","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000390","count":1},{"id":"GO:1902570","count":1},{"id":"GO:0000494","count":1},{"id":"GO:0007175","count":1},{"id":"GO:0051096","count":1}]},{"hash":"947283037180702082","title":"DNA replication and mitotic machinery","description":"The top GO terms cluster around core nuclear processes tied to genome duplication, chromosome maintenance, and mitosis (DNA replication, CENP-A chromatin assembly, cell division, microtubule severing, and centromere-associated activities). There are also signals for ribosome biogenesis and rRNA maturation, common in proliferating cells, though less tightly linked to mitosis. Overall, these terms point to a theme of DNA replication and cell division with some supportive nucleolar growth functions.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0019079","count":2}]},{"hash":"1972934735729493851","title":"Ribosome Biogenesis and Translation","description":"The terms are dominated by translation and ribosome-related processes: translation, translational termination, ribosomal large subunit assembly, and mitochondrial translational initiation. These point to a cluster enriched in components of protein synthesis and ribosome biogenesis, including mitochondrial translation. The other terms (stamen formation, chlorophyll biosynthetic process, proteasome assembly, ubiquitin-dependent protein catabolic process) are likely incidental or cross-annotation noise and do not define the main function of the cluster.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006415","count":1},{"id":"GO:0015968","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0070124","count":1}]},{"hash":"1875705505908696851","title":"Unknown","description":"The listed GO terms span RNA modification, sulfur metabolism and cofactors, redox balance, basic metabolism, and developmental processes. With no clear, overrepresented functional theme linking these proteins, there isn\u2019t a single cohesive biological function to name. Therefore the cluster is best labeled Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002143","count":2},{"id":"GO:0035335","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0018192","count":2},{"id":"GO:0006071","count":2}]},{"hash":"582773508252836104","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":3},{"id":"GO:2000255","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017004","count":2}]},{"hash":"591221764561475428","title":"Unknown","description":"The Top Terms are a disparate mix: chromatin-related processes (heterochromatin formation, centromere assembly, rRNA transcription regulation) alongside reproductive development (oogenesis, single fertilization) and immune/organismal growth signals (pro-B cell differentiation, multicellular growth), with little clear overlap. There isn\u2019t a single cohesive function tying the cluster together, so a concise biological label cannot be confidently assigned.","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000973","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0051290","count":1},{"id":"GO:0071674","count":1}]},{"hash":"1691824019755215170","title":"Histone methylation and transcription regulation","description":"These proteins are enriched for GO terms related to DNA-templated transcription and histone methylation (H3-K9 and H3-K79), pointing to roles in chromatin regulation and transcription control. Additional signals for ubiquitin ligase activity regulation and RNA modifications support a broader gene-expression and DNA-damage response function. A single term about neuron projection development appears peripheral. Overall, the cluster most clearly reflects chromatin modification coupled to transcription regulation.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051567","count":2},{"id":"GO:0032466","count":2},{"id":"GO:2001162","count":2},{"id":"GO:0032995","count":2}]},{"hash":"1655119078988593262","title":"Starch, glycogen, and trehalose metabolism","description":"The top GO terms cluster around carbohydrate metabolism, including starch catabolic/biosynthetic processes, trehalose catabolism/biosynthesis, glycogen biosynthesis, and alpha-glucan metabolism. The recurring theme is metabolism of alpha-glucan-containing polysaccharides (starch, glycogen, trehalose), with both synthesis and breakdown represented, suggesting a module of polysaccharide metabolism.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0005983","count":2},{"id":"GO:0005993","count":2},{"id":"GO:0030979","count":2},{"id":"GO:0051692","count":2},{"id":"GO:0010021","count":2}]},{"hash":"724588293244705557","title":"Developmental transcription and cell cycle regulation","description":"The top GO terms include DNA-templated transcription and mitotic cell cycle, with some negative regulation of cytokinesis, suggesting regulation of gene expression during cell division. Additional terms spanning forebrain development, hepatocyte differentiation, trophoblast giant cell differentiation, and fat cell differentiation point to developmental programs across tissues. Together these imply proteins that coordinate transcriptional control with cell cycle dynamics during development rather than a single tissue-specific function.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032466","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006884","count":2},{"id":"GO:0006351","count":2}]},{"hash":"593728733734274848","title":"Unknown","description":"This cluster shows a mix of unrelated biological processes (chromatin remodeling and histone modifications, DNA replication, peroxisome protein import, snoRNP assembly, viral genome replication, ubiquitin\u2011dependent ERAD, and growth regulation), plus many obsolete GO terms, with no shared function tying the proteins together and no interaction edges to support a cohesive label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043486","count":3},{"id":"GO:0016558","count":2},{"id":"GO:0006269","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0071899","count":2}]},{"hash":"307503811331681189","title":"Unknown","description":"The Top Terms are highly diverse, spanning immune signaling (TLR3, T cell polarity), lipid metabolism (cholesterol biosynthesis, SREBP pathway), synaptic signaling (dopaminergic transmission), mitochondrial dynamics (membrane potential, inheritance), extracellular matrix remodeling, and aging. There is no single coherent biological theme uniting these functions, so a specific, representative label cannot be assigned with confidence.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903905","count":1},{"id":"GO:0045541","count":1},{"id":"GO:0032226","count":1},{"id":"GO:0010918","count":1},{"id":"GO:0022617","count":1}]},{"hash":"123875726593506616","title":"Unknown","description":"The listed GO terms span several unrelated processes (ER-to-Golgi transport, inter-Golgi vesicle transport, peroxisomal import, photosystem II repair) alongside ribosome assembly, stress granule dynamics, aggresome formation, and mitotic checkpoint signaling. This lack of a coherent, shared function among the proteins suggests no single interpretable theme for a concise cluster name. ","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:0048219","count":1},{"id":"GO:0010206","count":1},{"id":"GO:0016558","count":1},{"id":"GO:1903007","count":1}]},{"hash":"475998976916276848","title":"Unknown","description":"The terms mix vesicle trafficking, peroxisome import, ribosome and chromatin assembly, and protein quality-control structures (aggresomes, stress granules, inclusion bodies) with no clear shared function for the cluster.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0048219","count":2},{"id":"GO:0016558","count":2},{"id":"GO:1903007","count":2},{"id":"GO:0033314","count":2}]},{"hash":"202948289814541300","title":"Bacterial Metabolism and Flagellar Motility","description":"This cluster centers on bacterial energy metabolism (ETC, TCA cycle, pyruvate decarboxylation to acetyl-CoA) and on flagellar assembly/motility, suggesting a cohesive bacterial functional unit; some photosynthesis terms may reflect broader metabolic context but do not override the metabolism/motility theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009773","count":1},{"id":"GO:0022900","count":1},{"id":"GO:0006086","count":1},{"id":"GO:0044780","count":1},{"id":"GO:0006099","count":1}]},{"hash":"2112880772808925735","title":"Steroid hormone signaling in male reproduction","description":"The cluster shows GO terms centered on male reproductive development and steroid hormone signaling\u2014male sex differentiation, prostate gland development, and steroid hormone receptor complex assembly\u2014along with transcription initiation/regulation terms, suggesting involvement in hormone-driven transcriptional control in male reproduction. Some additional terms (heat response, T cell proliferation) are likely secondary annotations or broader protein roles.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046661","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0001123","count":1},{"id":"GO:0009408","count":1}]},{"hash":"375888272530862064","title":"Nuclear RNA Processing and Chromatin Regulation","description":"These proteins show a strong association with nuclear RNA metabolism (tRNA processing, RNA polymerase II transcription termination, histone mRNA metabolism) and chromatin organization (pericentric heterochromatin formation). Import into the nucleus supports their localization to these processes, suggesting the cluster captures factors coordinating transcription termination, RNA maturation, and chromatin maintenance. Some terms like P-body assembly or stress responses may be peripheral to the core theme, but the dominant signal is nuclear RNA processing and chromatin regulation.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":4},{"id":"GO:0051170","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0042633","count":3}]},{"hash":"753546063716510857","title":"Nuclear RNA Processing and DNA Maintenance","description":"The top GO terms point to core nuclear activities: spliceosome disassembly, rRNA processing, transcription-coupled nucleotide-excision repair and DNA damage recognition, DNA replication primer synthesis, and protein import into the nucleus. These indicate a shared theme of RNA maturation, DNA maintenance, and nuclear transport. A few terms related to neuronal signaling (BDNF response, exploration behavior, cold response) are present but don\u2019t strongly unify the cluster, so the central theme remains nuclear RNA/DNA processing. Confidence: Medium","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000390","count":4},{"id":"GO:0014070","count":4},{"id":"GO:0090394","count":4},{"id":"GO:0035640","count":4},{"id":"GO:1990416","count":4}]},{"hash":"151142030550369987","title":"SRP-dependent cotranslational membrane targeting (bacteria)","description":"The top GO terms are dominated by SRP-dependent cotranslational protein targeting to membrane (including translocation and signal sequence recognition), indicating a shared function in guiding nascent polypeptides to the inner membrane via the SRP pathway in bacteria. Other terms like flagellum organization and DNA replication appear less prominently and do not define the cluster, so the SRP-targeting theme is the best unifying label.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":4},{"id":"GO:0044781","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006616","count":4},{"id":"GO:0006617","count":2}]},{"hash":"2133796364744585234","title":"Viral Translation Initiation and Reinitiation","description":"The cluster centers on GO terms related to translating initiation and reinitiation, including formation of the translation preinitiation complex, regulation of translational initiation, and translation reinitiation, with specific mention of IRES-dependent viral initiation and viral termination-reinitiation. A few other terms suggest ancillary RNA processing or stability roles, but the dominant signal is initiation/reinitiation of translation, especially in viral contexts.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075522","count":3}]},{"hash":"1254809296431292203","title":"Ribosome biogenesis and transcription machinery","description":"The cluster shows strong signals for ribosome biogenesis and translation, with multiple transcription-related terms spanning RNA polymerases I, II, and III and tRNA synthesis, suggesting a cohesive module linking ribosome assembly to transcriptional processes. Anomalous terms like alpha-beta T cell differentiation appear incidental rather than core to the cluster\u2019s function. ","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0002181","count":1},{"id":"GO:0046632","count":1},{"id":"GO:0006386","count":1},{"id":"GO:0042797","count":1}]},{"hash":"1580529476998143714","title":"DNA Damage Response and Translesion Synthesis","description":"The cluster\u2019s top GO terms center on UV-C\u2013induced cellular responses and DNA damage tolerance during replication, notably both error-free and error-prone translesion synthesis, plus DNA-templated replication. This suggests a theme around coping with DNA lesions during replication (TLS pathways). Some other terms (RNA pseudouridylation, glycosylation, sperm binding) appear incidental to this core, so the label focuses on the UV damage response and TLS connection.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071494","count":2},{"id":"GO:0006261","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0042276","count":2},{"id":"GO:0031119","count":1}]},{"hash":"196456858882265526","title":"ER Protein Folding and Quality Control","description":"This cluster is dominated by terms tied to the endoplasmic reticulum (ER): post-translational targeting to the ER membrane, protein folding within the ER, and translation regulation in response to ER stress, all of which point to ER quality control and the unfolded protein response. While a few terms touch on broader or unrelated processes (e.g., axonemal assembly, neural patterning), the strongest signal centers on ER-associated folding and stress responses, making this a coherent label.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":1},{"id":"GO:0036494","count":1},{"id":"GO:1905259","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0034975","count":1}]},{"hash":"1824056522040059239","title":"Ribosome and RNA maturation proteins","description":"This cluster is strongly themed around translation and RNA metabolism. The dominant GO term is translation (GO:0006412) with multiple entries for translation-related processes, including positive regulation of translation and mitochondrial translational initiation, alongside RNA processing and rRNA maturation terms. While a few terms touch on intron splicing or transcription antitermination, the core signal points to ribosome-associated functions and RNA maturation/processing proteins.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006450","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0034337","count":1},{"id":"GO:0000372","count":1}]},{"hash":"1696754925755297591","title":"Vesicle trafficking and endomembrane sorting","description":"The top GO terms point to intracellular transport between Golgi, endosomes, and vacuoles (Cvt pathway, endocytic recycling, MVB sorting, Golgi retention), with related localization and fusion processes appearing in other terms. This suggests a cohesive theme of vesicle formation, sorting, and trafficking within the endomembrane system.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":1},{"id":"GO:0045450","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0071985","count":1},{"id":"GO:0010797","count":1}]},{"hash":"1739093676290800540","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000961","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0031426","count":1},{"id":"GO:0070129","count":1}]},{"hash":"924279953402060205","title":"Proteostasis and Mitophagy","description":"The proteins show strong enrichment for autophagy- and ubiquitin-proteasome\u2013mediated quality control: mitophagy, aggrephagy, aggresome assembly, and positive regulation of mitochondrial fusion, along with proteasomal degradation. A couple of terms (DNA repair, spindle pole duplication) seem incidental, but the core theme is protein and mitochondrial quality control.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0014070","count":2},{"id":"GO:1904049","count":2},{"id":"GO:0070911","count":2},{"id":"GO:0000423","count":2},{"id":"GO:0030474","count":2}]},{"hash":"797269971814348316","title":"Cell Cycle and Mitosis","description":"The cluster is best described by cell cycle and mitosis-related functions (cell cycle, cell division, mitotic checkpoint signaling, chromatin condensation), with a few ancillary terms likely reflecting background processes.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0099133","count":2},{"id":"GO:0016558","count":1},{"id":"GO:0033314","count":1}]},{"hash":"1721724547659699905","title":"Genome Maintenance and Ubiquitin-Proteasome Regulation","description":"The top GO terms cluster around DNA damage response and genome maintenance (global genome nucleotide-excision repair, error-prone translesion synthesis) together with ubiquitin-mediated proteostasis (free ubiquitin chain polymerization, cytoplasm protein quality control by the ubiquitin-proteasome system). Some terms are broader or multifunctional (interferon signaling, viral process, development), but the strongest consistent theme is genome maintenance linked to protein homeostasis via ubiquitination. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0070911","count":4},{"id":"GO:0016558","count":4},{"id":"GO:0042276","count":4},{"id":"GO:0060340","count":4},{"id":"GO:0070076","count":4}]},{"hash":"822508312524812858","title":"Energy metabolism and redox balance","description":"This cluster is dominated by GO terms tied to core metabolism (tricarboxylic acid cycle, anaerobic respiration, quinolinate biosynthesis for NAD synthesis) and redox-related processes (response to oxygen radicals, redox homeostasis, detoxification). While there are a few development- or neurotransmitter-related terms that may be less connected, the strongest signal across the terms points to energy production and redox balance, justifying a metabolism/redox-focused label.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0000305","count":1},{"id":"GO:0050787","count":1},{"id":"GO:0019805","count":1},{"id":"GO:0009061","count":1}]},{"hash":"584423757008315768","title":"Diverse Biosynthetic Pathways","description":"The proteins are linked to multiple biosynthetic processes across lipids (sphinganine, sphingomyelin), vitamins (cobalamin), and amino acids (aspartate, alanine), plus an entry for enterobacterial common antigen biosynthesis. The presence of a catabolic term (L-kynurenine catabolic process) alongside biosynthetic ones suggests a mix of metabolic functions rather than a single, cohesive pathway, so the label \u201cDiverse Biosynthetic Pathways\u201d best captures the cluster\u2019s broad metabolic theme.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009246","count":1},{"id":"GO:0097053","count":1},{"id":"GO:0046511","count":1},{"id":"GO:0042218","count":1},{"id":"GO:0006686","count":1}]},{"hash":"721473116848516047","title":"Leukocyte adhesion and migration","description":"This cluster centers on terms tied to immune cell adhesion and movement, including T cell activation, heterotypic cell-cell adhesion, integrin signaling, and cellular extravasation, as well as substrate-dependent migration. Additional terms point to extracellular matrix remodeling (metallopeptidase activity) and related developmental processes (cartilage morphogenesis), which are compatible with adhesion and migration themes in tissues. Overall, the dominant signal is cell adhesion/migration in an immune or vascular context, with supporting remodeling roles.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002291","count":1},{"id":"GO:0034113","count":1},{"id":"GO:0006929","count":1},{"id":"GO:0070208","count":1},{"id":"GO:0035987","count":1}]},{"hash":"1372926442263916004","title":"Unknown","description":"The top GO terms span highly diverse and seemingly unrelated processes (cell division, chromatin modification with obsolete histone methylation terms, regulation of fungal-type cell wall biogenesis, translational frameshifting, ubiquitin ligase activity, cell differentiation, signaling via phosphorelay, triglyceride homeostasis, and immune regulation). This lack of a coherent shared function, combined with the presence of obsolete terms, suggests there is no single clear theme connecting these proteins. ","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0051567","count":1},{"id":"GO:2001162","count":1},{"id":"GO:0032995","count":1},{"id":"GO:2001125","count":1}]},{"hash":"2301000235986172659","title":"ER Folding and Nuclear Transport Under Redox Regulation","description":"The terms point to ER protein folding (GO:0046826), redox homeostasis and detoxification, and regulation of nuclear processes (including nuclear import/export and transcription), suggesting these proteins may connect ER quality control with control of gene expression and nuclear transport, potentially in response to stress or viral interaction.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046826","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0018401","count":3},{"id":"GO:0000122","count":3}]},{"hash":"974355618481700443","title":"DNA replication licensing and mitotic checkpoint regulation","description":"Top terms suggest a cohesive role in initiating and regulating DNA replication (origin licensing, pre-replicative complex assembly, nuclear DNA replication) and enforcing mitotic progression (replication checkpoints, spindle/kinetochore regulation, chromatin binding). The presence of kinetochore localization and chromatin binding terms supports a function linking replication licensing with chromosome segregation, with a note of replication restart under stress via break-induced replication. This combination points to a focused cluster around DNA replication licensing and mitotic control.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030174","count":1},{"id":"GO:1905341","count":1},{"id":"GO:1905342","count":1},{"id":"GO:0033262","count":1},{"id":"GO:0000727","count":1}]},{"hash":"672057639104418576","title":"Root hair development and plant cell wall biosynthesis","description":"The top GO terms cluster around plant-specific processes: rhamnogalacturonan II biosynthesis and root hair cell development, along with general cell wall organization. This combination strongly points to proteins involved in plant cell wall biosynthesis and root hair morphogenesis, making the theme coherent despite a few unrelated annotations. ","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010306","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0051343","count":1},{"id":"GO:0034501","count":1}]},{"hash":"2246925182446488198","title":"Yeast mitotic checkpoint and cytoskeleton regulation","description":"The proteins cluster around mitotic spindle assembly checkpoint signaling, regulation of formin-nucleated actin cable assembly, and localization to the bud neck, which together point to control of cell division and cytokinesis in budding yeast. Additional annotations to ubiquitin-dependent proteolysis and organelle-related processes (peroxisome import) fit with broader proteostasis during division, but the core theme remains cell-cycle control and cytoskeletal dynamics in yeast.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046621","count":1},{"id":"GO:0031030","count":1},{"id":"GO:0044810","count":1},{"id":"GO:0090337","count":1},{"id":"GO:0016558","count":1}]},{"hash":"655106300921121123","title":"ER Protein Targeting and Sec-Mediated Transport","description":"The GO terms point to targeting and translocation of proteins to the endoplasmic reticulum membrane, including SRP-dependent cotranslational targeting and Sec complex\u2013mediated transport, plus ER-to-cytosol retrograde transport. This suggests a shared role in ER protein import/traffic, making \u201cER Targeting and Sec-Mediated Transport\u201d a concise, representative label. Some unrelated terms appear due to annotation noise, but the core function is clear.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0043952","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0007275","count":1}]},{"hash":"2251502968216472603","title":"Unknown","description":"The GO terms are diverse: pollen tube guidance contrasts with glycosylation and GPI anchor biosynthesis, and there is no clear shared function connecting the proteins. Without a cohesive theme, the cluster is best labeled Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010183","count":1},{"id":"GO:0006506","count":1},{"id":"GO:0006488","count":1}]},{"hash":"1534461272717829607","title":"ER Stress Response and Protein Folding","description":"The top GO terms cluster around handling unfolded proteins and ER stress, including cellular response to unfolded protein, negative regulation of ER-stress-induced apoptotic signaling, and chaperone-assisted refolding, plus post-translational targeting to membranes. A few terms (iron-sulfur cluster assembly, fungal cell wall biosynthesis) are less coherent with this theme, but the dominant signal points to ER quality control and protein folding. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":1},{"id":"GO:0006880","count":1},{"id":"GO:0000902","count":1},{"id":"GO:1900035","count":1},{"id":"GO:0070880","count":1}]},{"hash":"2250886973303412362","title":"Unknown","description":"The GO terms are highly diverse (touch sensing, ion homeostasis, adhesion, GPCR signaling, osmotic/stress responses, heart rate regulation, temperature response, gastric secretion), with no single dominant function linking the proteins. This makes a coherent, specific label unlikely.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":1},{"id":"GO:0030007","count":1},{"id":"GO:0016340","count":1},{"id":"GO:0097623","count":1},{"id":"GO:0008627","count":1}]},{"hash":"1304588645041045234","title":"Nuclear RNA processing and chromatin regulation","description":"These proteins cluster around nuclear functions: import into the nucleus, termination of RNA Pol II transcription, histone mRNA metabolism, and pericentric heterochromatin formation point to chromatin regulation in the nucleus. Additional RNA-centric terms (tRNA processing, P-body assembly) support a broader RNA processing/metabolism theme, while stress response terms (abscisic acid response, water deprivation) and the hair cycle are less directly tied but may reflect plant-specific regulation contexts. Overall, the dominant signal is nuclear RNA processing and chromatin regulation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0070317","count":3},{"id":"GO:0042633","count":3},{"id":"GO:0008334","count":3}]},{"hash":"1256223896627058110","title":"DNA replication and checkpoint signaling","description":"The strongest signals are around DNA biosynthesis, DNA replication, and mitotic DNA replication checkpoint signaling, indicating a core function in DNA replication and cell-cycle regulation. The other terms (vesicle transport, peroxisome import, stress granule dynamics) appear less central, suggesting these proteins may have ancillary roles beyond DNA replication.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071897","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0048219","count":2}]},{"hash":"1805295071046880398","title":"Fungal actin cytoskeleton and cytokinesis","description":"The top terms cluster around actin dynamics and cytokinesis, including Arp2/3-mediated actin nucleation, actin cortical patches, actomyosin contractile ring contraction, and mitotic cytokinesis, plus related processes like ascospore development and endocytosis regulation. This points to actin-driven remodeling of the cytoskeleton coordinating cell division and fungal-specific development, making a fungal actin/cytokinesis theme the best label.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016344","count":3},{"id":"GO:0034314","count":3},{"id":"GO:0051666","count":3},{"id":"GO:0030476","count":3},{"id":"GO:0045214","count":3}]},{"hash":"840920533915571124","title":"Nucleotide Salvage","description":"The top GO terms are strongly focused on nucleotide salvage: UMP salvage, CTP salvage, and uracil salvage, which together point to a shared role in recycling nucleotides. The other terms present (sperm-egg binding, toxin transport, cadmium response, pore complex assembly, misfolded protein detection, ATP response, virion assembly) are heterogeneous and much less coherent with the salvage theme, so the nucleotide salvage signal dominates the cluster\u2019s functional interpretation. This yields a concise, representative label, with moderate confidence due to some discordant terms.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044206","count":1},{"id":"GO:0044211","count":1},{"id":"GO:0006223","count":1},{"id":"GO:0007339","count":1},{"id":"GO:1901998","count":1}]},{"hash":"492124332026138687","title":"RNA modification and translation fidelity","description":"The top GO terms cluster around RNA modification (rRNA methylation, protein methylation) and translational control (tyrosyl-tRNA aminoacylation, maintenance and regulation of translational fidelity, and initiation regulation), suggesting these proteins participate in RNA processing/modification and ensuring accurate translation. Some terms (transcription termination/antitermination and cobalamin biosynthesis) may reflect broader RNA metabolism or incidental annotation but do not dominate the signal. Overall, a coherent theme centers on RNA modification coupled with translation accuracy.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006479","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0045903","count":1},{"id":"GO:0031564","count":1}]},{"hash":"1494408591194180734","title":"DNA Repair and Translesion Synthesis","description":"The cluster\u2019s GO terms center on DNA damage response and repair, including error-free and error-prone translesion synthesis, nucleotide-excision repair, UV-C\u2013induced cellular response, and DNA-templated processes. This points to proteins involved in DNA damage tolerance and repair pathways, with transcription-related terms possibly reflecting regulation tied to DNA damage. The absence of edges suggests limited interaction data, but the functional theme remains cohesive around DNA repair/tolerance.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":1},{"id":"GO:0042276","count":1},{"id":"GO:0006261","count":1},{"id":"GO:0006297","count":1},{"id":"GO:0071494","count":1}]},{"hash":"2064513964319443565","title":"Hypoxia-driven angiogenesis and vascular regulation","description":"This cluster centers on GO terms related to responses to low oxygen (hypoxia), promotion of angiogenesis, and vascular remodeling (including blood pressure regulation and vascular smooth muscle proliferation). Additional terms reflect broader cellular stress responses (heat, arsenic) and autophagy regulation, but the strongest common theme tying these proteins together appears to be hypoxia-associated signaling leading to vascular adaptation and angiogenesis.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043305","count":1},{"id":"GO:0071456","count":1},{"id":"GO:0045766","count":1},{"id":"GO:1904706","count":1},{"id":"GO:0034605","count":1}]},{"hash":"1893284653070359786","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":1},{"id":"GO:0070911","count":1},{"id":"GO:0042769","count":1},{"id":"GO:0043162","count":1},{"id":"GO:0016032","count":1}]},{"hash":"992104706346834769","title":"Ribosome biogenesis and translation","description":"The GO terms point to both ribosome production and function (ribosome biogenesis, small subunit assembly, and SSU rRNA maturation) as well as protein synthesis (translation). This coherence suggests the proteins are involved in ribosome assembly/processes and subsequent translation, rather than unrelated functions.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1972019163346197775","title":"Unknown","description":"The top GO terms are highly diverse, spanning cell cycle/kinetochore functions, metabolism, lipid biosynthesis, neural/myelin processes, EMT and angiogenesis, miRNA processing, and NFAT signaling. This lack of a cohesive, single-function theme across the terms makes it hard to assign a meaningful, specific label to the cluster.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051343","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0006196","count":3},{"id":"GO:0009245","count":3}]},{"hash":"1216589074378816668","title":"Mitochondrial Translation and Energy Metabolism","description":"The top GO terms include central energy pathways (glycolytic process, TCA cycle, NAD biosynthesis), redox/oxidative stress responses, cofactor and tRNA-related processes, and explicit mitochondrial translation, suggesting a cluster centered on mitochondrial energy production coupled with protein synthesis and stress defense. This supports a label like Mitochondrial Translation and Energy Metabolism.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0032543","count":1}]},{"hash":"2027994327444558146","title":"Sterol and lipid biosynthesis (mevalonate pathway)","description":"The proteins cluster around lipid metabolism and sterol production, including farnesyl diphosphate biosynthesis, ergosterol/cholesterol biosynthesis, acetyl-CoA metabolism, and the mevalonate pathway, with ER organization supporting membrane synthesis. A few terms are less connected (e.g., cell cycle regulation), but the dominant theme is sterol and lipid biosynthesis and related isoprenoid production.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010142","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0006696","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0006695","count":1}]},{"hash":"1253978341951424172","title":"Unknown","description":"The terms include clear links to mitotic progression (G1/S transition) and kinetochore localization, but also a broad mix of unrelated processes (AMP metabolism, lipid A biosynthesis, myelination, EMT, miRNA processing, vessel branching, NFAT signaling). This heterogeneity provides no single cohesive function to define the cluster, so Unknown with None confidence.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051343","count":3},{"id":"GO:0034501","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0006196","count":3},{"id":"GO:0009245","count":3}]},{"hash":"1215571470580118543","title":"Translation and Transcription Regulation","description":"This cluster is dominated by translation-related GO terms (translation, mitochondrial translational initiation, ribosomal biogenesis) and includes transcription-associated terms (transcription elongation/termination, antitermination) along with regulatory annotations (positive regulation of translation; regulation of transcription elongation) and a UV-stress\u2013related translation term. Together, these terms suggest a core function in coordinating RNA synthesis and protein synthesis machinery, i.e., regulation of both transcription and translation. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0070124","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0045727","count":1},{"id":"GO:0032784","count":1}]},{"hash":"65197575548437289","title":"Unknown","description":"The terms point to multiple, disparate processes: histone methylation (epigenetic marks), peroxisomal matrix protein import, various transcriptional regulatory events, RNA methylation, DNA damage response, neuron projection development, fungal cell wall regulation, and ubiquitin ligase regulation. The lack of a unifying biological process or pathway suggests no coherent cluster function can be inferred, so Unknown with None confidence.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051567","count":1},{"id":"GO:0016558","count":1},{"id":"GO:2001162","count":1},{"id":"GO:0032995","count":1},{"id":"GO:2001125","count":1}]},{"hash":"1227447695903549568","title":"Chromatin silencing and transcriptional repression","description":"The terms cluster around chromatin-based transcription control, with several items pointing to heterochromatin formation, transcriptional repression by RNA polymerases, and histone deacetylation. While a few terms (e.g., metabolism, cell migration) seem unrelated outliers, the dominant signal supports chromatin-mediated transcriptional silencing as the cluster's theme.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051038","count":3},{"id":"GO:0045149","count":3},{"id":"GO:0030466","count":3},{"id":"GO:0090050","count":3},{"id":"GO:0070842","count":3}]},{"hash":"853371484343475424","title":"Unknown","description":"The terms span translation, various stress/immune responses, and several unrelated synaptic or trafficking processes, with no clear shared function and no interactions tying the proteins together, so a cohesive label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046898","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0034340","count":1},{"id":"GO:0014873","count":1}]},{"hash":"1377122525318400474","title":"Lipid and Steroid Hormone Metabolism","description":"The proteins appear to participate in multiple lipid- and hormone-related biosynthetic pathways, including retinol/retinoic acid metabolism, very long-chain fatty acid and sphingolipid biosynthesis, and C21-steroid/androgen hormone metabolism; a less related acetoin term is present but does not override the dominant lipid/hormone theme. This supports labeling as lipid- and steroid-hormone metabolism.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":2},{"id":"GO:0042438","count":2},{"id":"GO:0006666","count":2},{"id":"GO:0042761","count":2},{"id":"GO:0002138","count":2}]},{"hash":"2045622113377764696","title":"Transmembrane Ion Transport and Homeostasis","description":"The GO terms point to proton transmembrane transport and intracellular ion homeostasis for Na+, K+, Ca2+, Mn2+, and Zn2+, plus specific transport/export activities, indicating proteins involved in moving ions across membranes and maintaining ionic balance; one term about vestibulocochlear nerve formation appears incidental. Overall, the cluster centers on membrane ion transport and homeostasis.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":1},{"id":"GO:0006883","count":1},{"id":"GO:0030007","count":1},{"id":"GO:0051208","count":1},{"id":"GO:0097623","count":1}]},{"hash":"1052196790913938152","title":"Unknown","description":"The terms describe diverse and largely unrelated processes (integrin regulation, DNA replication initiation, Rap signaling, transcription elongation regulation, heterochromatin formation, cerebellar layer structure, cyclic nucleotide synthesis, histone ubiquitination, spindle checkpoint signaling, and microtubule-based transport). With only singleton annotations and no cohesive signal, there is no clear shared function to assign a specific label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033624","count":1},{"id":"GO:1903468","count":1},{"id":"GO:0032487","count":1},{"id":"GO:0034244","count":1},{"id":"GO:0090055","count":1}]},{"hash":"1018742490094014086","title":"DNA Repair and Genome Maintenance","description":"The top GO terms center on base-excision repair, double-strand break repair via nonhomologous end joining, and responses to DNA-damaging conditions (gamma radiation, hyperoxia). Some terms also reference immunoglobulin gene diversification, which uses DNA repair/recombination mechanisms. Taken together, these proteins appear tied to DNA repair and genome integrity maintenance across stress conditions.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006287","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0010332","count":2},{"id":"GO:0055093","count":2},{"id":"GO:0071707","count":1}]},{"hash":"856793049739890130","title":"Unknown","description":"There are no GO terms provided to indicate a shared function among the three proteins, and the small network yields no clear functional theme, so a specific label cannot be assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"1872751722185293973","title":"Unknown","description":"The GO terms are highly diverse (chemotaxis; myelination regulation; nucleotide and amino acid metabolism; development and angiogenesis; cell cycle regulation), indicating no single coherent function ties the proteins together. ","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":1},{"id":"GO:0031641","count":1},{"id":"GO:0046104","count":1},{"id":"GO:0000162","count":1},{"id":"GO:0007275","count":1}]},{"hash":"370625792884216082","title":"Unknown","description":"The GO terms are diverse, spanning chromatin/telomere biology and meiosis, cell differentiation, plus plant hormone responses (ethylene, jasmonic acid, gibberellin) and pigment biosynthesis, with no single cohesive function tying the proteins together and no edges to support a specific label. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035390","count":1},{"id":"GO:1900386","count":1},{"id":"GO:0009723","count":1},{"id":"GO:0009739","count":1},{"id":"GO:0010380","count":1}]},{"hash":"1937978993693824458","title":"Fungal lipid biosynthesis (ergosterol and sphingolipid)","description":"The dominant GO terms cluster around lipid metabolism in fungi: unsaturated fatty acid biosynthesis, regulation of ergosterol biosynthetic process, and mannosyl-inositol phosphorylceramide metabolic process, suggesting involvement in fungal membrane lipid production. Some other terms appear noisy or unrelated, but the core pattern supports a fungal lipid biosynthesis theme.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006636","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0000001","count":1},{"id":"GO:0001949","count":1}]},{"hash":"14611065165982666","title":"Nitric Oxide Signaling and Stress Response","description":"The GO terms center on positive regulation of nitric oxide biosynthesis, responses to xenobiotic stimuli, oxidative stress, and signaling pathways like NF-kappaB, with some terms related to angiogenesis/cell migration. This suggests a functional theme around NO-mediated signaling and general stress response.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045429","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0043154","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0090050","count":1}]},{"hash":"2140367895931348207","title":"Unknown","description":"The top terms span RNA splicing, immune signaling, metabolism, circadian and developmental processes, with no clear shared function linking the proteins. The lack of edges and the diverse GO terms suggest no cohesive theme for a meaningful label.","confidence":"","size":3,"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:0050862","count":1},{"id":"GO:0046111","count":1},{"id":"GO:0042323","count":1}]},{"hash":"774936656691942175","title":"Serine/threonine and sulfur amino acid metabolism","description":"The terms are dominated by serine catabolic and threonine biosynthetic processes, plus transsulfuration and hydrogen sulfide biosynthesis, which together point to metabolism of sulfur-containing amino acids. Additional signals in 2-oxobutyrate and pyruvate biosynthesis reinforce a focus on serine/threonine\u2013linked carbon metabolism; a couple of broader catabolic terms are present but do not overturn this core theme.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:0009310","count":1},{"id":"GO:0019295","count":1},{"id":"GO:0019346","count":1},{"id":"GO:0046360","count":1}]},{"hash":"2134197981578294711","title":"Unknown","description":"The GO terms span light-response processes (regulation of photomorphogenesis; response to high fluence blue light) and a range of transport-related activities (iron, potassium, proton, water transport) plus pH and cell-volume regulation, with no single, coherent function dominating the set. This scattered signal makes it inappropriate to assign a specific, high-confidence label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010099","count":1},{"id":"GO:0055121","count":1},{"id":"GO:0080022","count":1},{"id":"GO:1904667","count":1},{"id":"GO:0034756","count":1}]},{"hash":"2285759415333669797","title":"Lipid metabolism and organelle organization","description":"The cluster shows strong signals for lipid-related processes: lipid droplet organization, galactolipid and triglyceride biosynthesis, and fatty acid catabolic process, plus ER organization and nucleus organization (endoplasmic reticulum organization; lamin depolymerization), suggesting a link between lipid metabolism and membrane/organellar remodeling. A few terms like behavioral fear response and regulation of cilium assembly are less coherent with lipid biology, but the dominant signals point to lipid metabolism coupled with organelle dynamics.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001662","count":2},{"id":"GO:0006997","count":1},{"id":"GO:0034389","count":1},{"id":"GO:0019375","count":1},{"id":"GO:0019432","count":1}]},{"hash":"2131524542204402129","title":"Lipid and steroid metabolism","description":"The top GO terms cluster around metabolism of lipid- and steroid-derived molecules: retinol/retinoic acid metabolism, sphingolipid and very long-chain fatty acid biosynthesis, and C21-steroid hormone and androgen metabolism. Additional signals include tetrahydrobiopterin biosynthesis (a cofactor for related enzymes) and a melanin biosynthetic term, with acetoin catabolism reflecting broader metabolic activity. Overall, the pattern suggests a functional grouping of proteins involved in lipid- and steroid-related metabolism, with some peripheral connections to other metabolic pathways. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":1},{"id":"GO:0042438","count":1},{"id":"GO:0006666","count":1},{"id":"GO:0042761","count":1},{"id":"GO:0002138","count":1}]},{"hash":"2026475209207045389","title":"Unknown","description":"The GO terms are very diverse and only single instances, spanning ion transport (phosphate, nitrite, formate) as well as translation regulation, sex differentiation, chromatin modification, protein modification, ciliogenesis, cell cycle, and interferon response, which together show no coherent shared function for the three proteins.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":1},{"id":"GO:0015707","count":1},{"id":"GO:0015724","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0046661","count":1}]},{"hash":"1219115567500102215","title":"Unknown","description":"The GO terms are highly diverse, including porphyrin/heme and chlorophyll biosynthesis, one-carbon metabolism, several catabolic processes, and a GPCR signaling term, with no single shared function evident. Because there are no edges connecting the proteins and no cohesive theme, this cluster cannot be confidently assigned to a specific biological role.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019353","count":1},{"id":"GO:0006730","count":1},{"id":"GO:0015995","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0046340","count":1}]}]