[{"hash":"777658436485050712","title":"Cytoskeleton remodeling and stress signaling","description":"The most represented terms are actin filament bundle assembly and cell migration, pointing to cytoskeletal remodeling. Added signaling and stress-response terms (intracellular signal transduction, regulation of JNK cascade, cellular response to misfolded protein) support a theme of signaling linked to cytoskeletal dynamics. Some terms like cell cycle, DNA repair, and X-chromosome inactivation are less central to this core, suggesting a multi-functional cluster with a primary emphasis on cytoskeleton and signaling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0009048","count":2}]},{"hash":"224863976604571380","title":"DNA replication and cell cycle","description":"Dominant GO terms revolve around nuclear processes: DNA-templated transcription, DNA replication, and mitotic cell cycle/cell division, suggesting a cohesive group of proteins involved in genome maintenance and proliferation. Some chromatin modification and stress-related terms appear but are secondary to the core replication and division functions. Confidence: High","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0070059","count":3}]},{"hash":"8419448804710724","title":"Neural development and cell cycle regulation","description":"These proteins appear to cluster around neural development themes, with terms such as myelination in the peripheral nervous system and excitatory postsynaptic potential indicating neuronal differentiation and synaptic function. At the same time, DNA replication, G1/S transition, and cell morphogenesis point to proliferative and structural remodeling processes, suggesting neural progenitor activity and morphogenesis. The inclusion of positive regulation of GTPase activity and ER-to-Golgi vesicle transport hints at coordinated signaling and intracellular trafficking necessary for neurite outgrowth and synaptic assembly. Overall, the cluster seems to reflect neural development with associated cell-cycle dynamics and vesicular trafficking rather than a single, narrow pathway.","confidence":"Medium","size":29,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000902","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0051321","count":2}]},{"hash":"876234703899446193","title":"Global gene expression and ER stress responses","description":"Based on GO terms including transcription termination, negative regulation of RNA Pol II, ribosome biogenesis, ER-to-Golgi transport, and unfolded protein response, the proteins seem tied to core gene expression and protein processing, with additional stress-related processes (UV repair, antibiotic response) and chromatin dynamics (meiotic chromosome condensation). The absence of edges indicates this is a broad, heterogeneous cluster rather than a single cohesive pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006369","count":2},{"id":"GO:0070914","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1197078298502613759","title":"Chloroplast Gene Expression and Plastid-Nucleus Signaling","description":"The cluster is driven by GO terms tied to plastid transcription, chloroplast RNA processing and modification, and chloroplast-nucleus signaling, pointing to a cohesive function in chloroplast gene expression and retrograde communication to the nucleus. Some mitochondrial RNA modification terms are present, but the dominant theme remains chloroplast RNA metabolism and signaling.","confidence":"Medium","size":29,"edges":152,"triangles":257,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0042793","count":5},{"id":"GO:0000961","count":5},{"id":"GO:0010019","count":5},{"id":"GO:0009451","count":5},{"id":"GO:0055114","count":4}]},{"hash":"1804398146807020578","title":"Unknown","description":"Unknown because the top GO terms describe disparate processes (angiotensin maturation and renin-angiotensin regulation, digestion, MHC class II antigen processing, kidney development) plus several obsolete histone modification terms, giving no cohesive functional theme for the cluster.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002003","count":3},{"id":"GO:2001040","count":2},{"id":"GO:0071440","count":2},{"id":"GO:1901674","count":2},{"id":"GO:0080182","count":2}]},{"hash":"1446369517635027870","title":"Mitotic spindle assembly and actin remodeling","description":"The most represented terms point to actin cytoskeleton remodeling and mitosis (actin remodeling; spindle assembly; mitotic cell cycle), suggesting a cluster of proteins coordinating cytoskeletal dynamics during cell division. Terms like GTPase regulation reinforce signaling to the cytoskeleton, while the other GO terms likely reflect ancillary roles rather than a core function.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0070059","count":2}]},{"hash":"1038055383128281716","title":"Retina and eye development","description":"The dominant GO signals are retina development in a camera-type eye and visual perception, with supporting links to broader developmental processes, suggesting the proteins cluster around eye/retina formation rather than a generic function. Some terms are obsolete, but the eye-related terms dominate the top terms.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0007568","count":3}]},{"hash":"1790297372432253259","title":"Mitochondrial translation and Complex IV assembly","description":"The terms point to mitochondrial gene expression and assembly of the respiratory chain: methionyl-tRNA aminoacylation, translation, and tRNA processing indicate mitochondrial translation machinery, while mitochondrial respiratory chain complex IV assembly directly ties to mitochondrial respiration. The transport terms and amino acid/ fatty acid responses fit a broader mitochondrial metabolism theme, supporting a cohesive label focused on mitochondrial translation and respiration complex assembly.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":3},{"id":"GO:0006828","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0006431","count":3},{"id":"GO:0006412","count":3}]},{"hash":"204567270064954328","title":"DNA replication and cell proliferation","description":"This cluster is dominated by GO terms related to DNA replication and DNA strand elongation, with additional terms tied to proliferation and its regulation, suggesting a core theme around genome duplication and control of cell growth. A few outliers (cell adhesion, xenobiotic response) likely reflect context-specific interactions or incidental associations rather than core function.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0008283","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0071307","count":1},{"id":"GO:1904209","count":1}]},{"hash":"2251768709800148545","title":"ER-Golgi transport and ribosome maturation","description":"Top GO terms reveal a combination of vesicle trafficking between the ER and Golgi (anterograde and retrograde), including GTPase activity regulation, together with rRNA maturation/processing, hinting at ribosome biogenesis. Additional signals for TORC1 pathway and mRNA transport suggest broader growth-regulation context. Overall, the cluster seems to group proteins involved in secretory pathway transport coupled with ribosome biogenesis processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0038202","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071560","count":2}]},{"hash":"1914720021341376084","title":"Integrin signaling and actin dynamics","description":"The cluster centers on membrane-associated signaling and cytoskeletal remodeling, highlighted by ACTIN filament bundle assembly, integrin-mediated signaling, and substrate adhesion-dependent cell spreading, along with maintaining protein localization at the plasma membrane and regulation via ubiquitination and ectodomain proteolysis. While a few terms touch on other processes, the dominant pattern is adhesion-related signaling coupled to actin dynamics. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010745","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0051044","count":2},{"id":"GO:0034446","count":2},{"id":"GO:0007229","count":2}]},{"hash":"1713329268212625545","title":"Nutrient and Metabolite Transporters","description":"The GO terms are dominated by transmembrane transport of diverse nutrients and metabolites (galactose, sialic acid, nitrite, vitamins, 4-hydroxyphenylacetate), with gluconeogenesis adding metabolic context. A single nuclear import term is an outlier. Thus, the common thread is transportators of small molecules involved in metabolism, giving a moderate confidence.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006094","count":2},{"id":"GO:0035584","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0060188","count":2}]},{"hash":"1653325810714559387","title":"Mitotic cell cycle and DNA replication","description":"Top terms center on cell division, mitotic cell cycle, DNA replication, and CENP-A chromatin assembly, indicating a mitotic/DNA-replication core. Other processes present (translation, proteolysis, RNA decay) are less defining, and the photosynthesis term appears as an outlier. Overall, the name captures the main theme of the cluster.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0000278","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0015979","count":3}]},{"hash":"2224872918518811677","title":"Neural, Visual, and Cardiac Development","description":"The top GO terms cluster around development of neural and sensory systems (nervous system development, visual perception, axon extension) and include heart development, suggesting a shared theme of tissue and organ formation in neural/visual and cardiac lineages. Some terms related to cell cycle or plant signaling may reflect broader developmental or dataset noise, but the dominant signal is neural/sensory and cardiac development. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007399","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0033138","count":3}]},{"hash":"2177783442558664806","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":340,"triangles":2663,"max_degree":26,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":16},{"id":"GO:0048026","count":16},{"id":"GO:0006369","count":12},{"id":"GO:0000398","count":12},{"id":"GO:0000464","count":12}]},{"hash":"1239971334518584672","title":"Developmental signaling and cell proliferation","description":"This cluster shows enrichment for developmental processes across multiple tissues (muscle, skin, brain region), along with regulation of transcription, signaling pathways (GTPase activity, protein autophosphorylation), and mRNA transport. The combination suggests proteins coordinating growth, tissue development, and cell-cycle-related signaling rather than a single specific pathway, hence a broad \"developmental signaling and cell proliferation\" label.","confidence":"Medium","size":27,"edges":185,"triangles":541,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048741","count":5},{"id":"GO:0021762","count":5},{"id":"GO:0043388","count":5},{"id":"GO:0043588","count":5},{"id":"GO:0000278","count":5}]},{"hash":"17149350894952158","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA maturation (spliceosome, rRNA processing) and translation initiation (preinitiation complex) plus nuclear pore localization, pointing to nuclear RNA processing and ribosome biogenesis as the core function; the other terms (muscle/skin development, ER-stress\u2013related apoptosis) are broader or pleiotropic and do not redefine the main theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0000398","count":3}]},{"hash":"756760249578830971","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030541","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0034965","count":1},{"id":"GO:0001682","count":1},{"id":"GO:0038066","count":1}]},{"hash":"1743939742573635197","title":"Intracellular transport and division signaling regulators","description":"This set centers on intracellular protein transport and localization, including SRP-dependent targeting to membranes and vesicle trafficking, alongside signals related to cell division such as kinetochore localization and septation regulation. The mix of transport and division-regulation GO terms suggests a function in coordinating trafficking with cell-cycle control; a few terms (viral process, heart development, obsolete mRNA polyadenylation) may be annotations from broader functional roles or less directly connected.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0031030","count":3},{"id":"GO:0032889","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0051534","count":3},{"id":"GO:0016032","count":2}]},{"hash":"424696295260392438","title":"Actin-driven cell migration and signaling","description":"These terms cluster around cytoskeletal dynamics and signaling related to cell movement: actin filament bundle assembly and cell migration are prominent, with supporting signals from ephrin receptor signaling, GTPase activity regulation, and Wnt pathway modulation. This suggests a cohesive theme of cytoskeletal remodeling driving migration and associated signaling cascades. Other terms such as apoptotic process and innate immune response appear less dominant and may reflect overlapping roles in specific contexts.","confidence":"High","size":27,"edges":15,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0048013","count":3},{"id":"GO:0060988","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0045087","count":3}]},{"hash":"2261551376331600342","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0000122","count":3}]},{"hash":"358900117875337927","title":"Embryonic development and tissue morphogenesis","description":"The Top Terms cluster around embryonic placenta/trophoblast differentiation, endocrine system development, cartilage morphogenesis, left-right patterning, and EMT-related morphogenesis, plus general cell and tissue morphogenesis. This points to a cohesive theme of developmental programs and tissue shaping across multiple organ systems, rather than a single specific function.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0035270","count":2},{"id":"GO:0003323","count":2},{"id":"GO:0060536","count":2}]},{"hash":"2236903194090635594","title":"Unknown","description":"The GO terms span autophagy regulation, glycogen metabolism, visual perception, replication fork processing, cardiac muscle contraction, calcium signaling, vacuole fusion, CDK activity regulation, and insulin signaling, with no single shared function tying most proteins together. This heterogeneity suggests no cohesive theme for a specific label.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016242","count":2},{"id":"GO:0005979","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0031297","count":2},{"id":"GO:0060048","count":2}]},{"hash":"1270108110484474195","title":"DNA Damage Response & Cell Cycle","description":"The top GO terms are dominated by DNA repair and cell cycle processes (double-strand break repair by homologous recombination, G1 DNA damage checkpoint signaling, mitotic cell cycle, cell division), with additional signals for ribosome biogenesis and chromatin-related acetylation that often accompany growth and division. Some development-related terms (osteoblast differentiation, pattern formation) appear as broader or incidental annotations, but the central theme across the cluster is DNA damage response coupled with cell cycle progression.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000724","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0043966","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0035264","count":4}]},{"hash":"1718543026937452041","title":"Translation Machinery and Ribosome Biogenesis","description":"GO terms are heavily centered on translation, ribosome biogenesis, and components of the translational apparatus (initiation, elongation, termination, cytoplasmic and mitochondrial translation), indicating this cluster groups proteins involved in protein synthesis machinery and ribosome assembly, with a minor association to antibiotic response under translational stress.","confidence":"High","size":26,"edges":323,"triangles":2552,"max_degree":25,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":20},{"id":"GO:0032790","count":5},{"id":"GO:0002184","count":4},{"id":"GO:0070125","count":4},{"id":"GO:0046677","count":4}]},{"hash":"154726343474578206","title":"Cell cycle and cytoskeletal remodeling","description":"The top GO terms cluster around cell division, mitotic cell cycle, and overall cell cycle, together with signals affecting cell polarity, cytoskeletal organization (podosome assembly, GTPase regulation), and EGFR signaling. This points to a group of proteins coordinating cell proliferation with dynamic cytoskeletal rearrangements and adhesion structures, hence the label.","confidence":"High","size":26,"edges":164,"triangles":446,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0051291","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0007173","count":5}]},{"hash":"218082971748887394","title":"Insect Larval Development and Innate Immunity","description":"The top GO terms point to insect-specific development (chitin-based larval cuticle pattern formation) and cell-cycle processes, alongside innate immune functions (innate immune response, defense response to virus) and stress/toxin responses. This combination suggests a cluster tied to larval development with coordinated immune/stress responses common in insects, hence the label.","confidence":"Medium","size":26,"edges":11,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0009636","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071230","count":3}]},{"hash":"1775198075657470853","title":"Development and Cell Cycle Regulation","description":"This cluster centers on developmental processes (osteoblast, brain, and monocyte differentiation) and cell cycle activities (cell division, mitotic metaphase alignment), with additional general gene expression regulators (RNA processing, chromatin modification, and protein quality control). The mix suggests broad regulation of development and cell proliferation rather than a tightly defined pathway, supporting a broad label rather than a precise function.","confidence":"Low","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0016575","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000920","count":2}]},{"hash":"1581341386029964435","title":"Fatty acid biosynthesis and transport","description":"Based on GO term enrichment, the proteins center on fatty acid metabolism, with multiple terms for fatty acid biosynthesis and transport across various chain lengths, suggesting a cohesive lipid metabolism cluster. While a few terms point to other metabolic pathways (e.g., siderophore, phenylpropanoid), the dominant signal is fatty acid synthesis and cellular transport of fatty acids.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":3},{"id":"GO:0044539","count":2},{"id":"GO:0001579","count":2},{"id":"GO:0019427","count":2},{"id":"GO:0019290","count":2}]},{"hash":"1415858443762264780","title":"Unknown","description":"The GO terms span many unrelated processes (lipid biosynthesis, tRNA methylation, ubiquitination, cell cycle, signal transduction, pain detection, etc.), with no clear shared function tying the proteins together. This lack of a cohesive theme makes a precise, representative label unreliable.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019375","count":1},{"id":"GO:0002940","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0045736","count":1},{"id":"GO:2000171","count":1}]},{"hash":"981575651484229885","title":"Rho\u2013actin remodeling under TGF-beta signaling","description":"GO terms point to cytoskeletal dynamics (positive regulation of GTPase activity, regulation of Rho signaling, actin filament polymerization, podosome assembly) and to a cellular response to TGF-beta. Neuron projection morphogenesis and interleukin-4 production hint at broader roles in development and immune contexts, while translation and spliceosome-related terms suggest coordinated gene regulation. The core theme is Rho-driven actin remodeling influenced by TGF-beta\u2013related signaling.","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0048025","count":2}]},{"hash":"825353527727123671","title":"Developmental transcription programs","description":"The cluster centers on transcription by RNA polymerase II and a variety of developmental processes (eye/morphogenesis, dorsal closure, vitellogenesis, osteoblast proliferation, microglial activation), suggesting proteins involved in regulating gene expression during development across tissues. Some terms appear orthogonal (nitrogen-starvation\u2013related transcription), but the dominant theme is transcriptional control in development.","confidence":"Medium","size":26,"edges":285,"triangles":1826,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":6},{"id":"GO:0007296","count":5},{"id":"GO:0061029","count":4},{"id":"GO:0034198","count":4},{"id":"GO:0001080","count":4}]},{"hash":"1907363224984963872","title":"Developmental Transcription and Cell Cycle Regulation","description":"The cluster centers on DNA-templated transcription and DNA repair, with additional signals for developmental processes (angiogenesis, mesoderm and neuron development) and cell-cycle transitions (G1/S, G2/M, spindle pole separation). This pattern suggests a group of proteins involved in regulating gene expression and cell division during development, with some genome maintenance context. ","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006281","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0042220","count":5},{"id":"GO:0010696","count":4}]},{"hash":"1499232977722977233","title":"Unknown","description":"The GO terms are highly heterogeneous, including pigmentation, neural tube and forebrain development, cytokinesis regulation, mitotic cell cycle, osteoblast differentiation, and stress-induced apoptosis. There is no single, coherent functional theme tying these terms together, so a concise, interpretable label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":2},{"id":"GO:0000920","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0032466","count":1}]},{"hash":"1771586896263805491","title":"DNA replication and repair with chaperone activity","description":"Cluster enriched for genome maintenance and proteostasis: DNA replication, nucleotide-excision repair, and SOS response are prominent, together with chaperone-related activities (refolding, chaperone-mediated assembly). The presence of protein complex oligomerization and ribosomal subunit export hints at broader stress-related remodeling and protein assembly. Overall, the data point to a cohesive function centered on DNA maintenance under stress, supported by chaperone systems.","confidence":"High","size":26,"edges":9,"triangles":0,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070389","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0051259","count":3}]},{"hash":"1284171222636345782","title":"Unknown","description":"The top GO terms span several distinct biological themes: transcription and gene expression; lipid metabolism (fatty acid oxidation, cholesterol biosynthesis); cell cycle regulation; responses to hormones and toxins; immune-related processes like neutrophil clearance; and viral replication regulation. The lack of a cohesive shared function and the absence of network edges suggest the cluster does not represent a single interpretable biological module.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0010467","count":2},{"id":"GO:0045071","count":2},{"id":"GO:0019395","count":2},{"id":"GO:0071372","count":2}]},{"hash":"1287881015733253821","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms for ubiquitin-mediated proteolysis (ubiquitin-dependent protein catabolic process, autoubiquitination, K48- and K6-linked ubiquitination) and processes related to turnover of signaling proteins (TNF/NF-kB signaling, Wnt receptor catabolism) as well as histone catabolism. The common thread is tagging substrates with ubiquitin to drive degradation and regulate signaling, suggesting proteins in this cluster function mainly in ubiquitin-dependent proteolysis and turnover.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0036205","count":8},{"id":"GO:1903265","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0051865","count":8}]},{"hash":"680420076488467397","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0000055","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0030433","count":3}]},{"hash":"460893355989155319","title":"Immune and Lipid Metabolism Signaling","description":"The top GO terms point to immune-related responses (cellular response to lipopolysaccharide, response to GM-CSF stimulus, T cell receptor signaling) alongside lipid metabolism processes (cholesterol biosynthetic process, fatty acid oxidation). This suggests a cluster where inflammatory signaling intersects with metabolic pathways, with additional general processes like transcription and microtubule localization likely supporting these functions. Overall, the dominant theme appears to be immune signaling coupled with lipid metabolism.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006695","count":4},{"id":"GO:0071222","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0050852","count":3}]},{"hash":"1251428793565023028","title":"Translational Initiation and Reinitiation","description":"The cluster shows strong enrichment for translation initiation and its regulation (formation of preinitiation complex, translation reinitiation, regulation of translational initiation, IRES-dependent viral translation), with other terms like cell cycle or differentiation likely secondary; the dominant signal points to initiation machinery and control of translation.","confidence":"High","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0008283","count":3}]},{"hash":"1957042885988148215","title":"Retina and kidney epithelial differentiation","description":"The cluster\u2019s top GO terms cluster around differentiation of specialized epithelial cells, notably photoreceptor (retina) differentiation and maintenance, podocyte and glomerular parietal epithelial cell differentiation, and nephron tubule epithelial differentiation. While a few terms touch on other processes (mRNA transport, autophosphorylation, endocytosis regulation), the dominant theme is epithelial cell fate specification in ocular and renal tissues, suggesting proteins involved in retina and kidney epithelial differentiation pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051028","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0060219","count":1},{"id":"GO:2000768","count":1}]},{"hash":"399562029200305224","title":"Glycosylation and receptor trafficking","description":"Several top GO terms point to protein processing and trafficking: N-linked glycosylation (GO:0006487) and dolichol-linked oligosaccharide biosynthesis (GO:0006488) indicate maturation of glycoproteins in the ER/Golgi, while receptor recycling (GO:0001881) suggests trafficking to membranes. Additional related terms such as UDP-N-acetylglucosamine metabolic process and regulation of insulin receptor signaling may modulate glycoprotein function and signaling, but the strongest shared theme is glycosylation-dependent maturation and trafficking of receptors. Therefore, a concise label is 'Glycosylation and receptor trafficking'. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0046626","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006355","count":2}]},{"hash":"327920608185415774","title":"Unknown","description":"Top terms span proteolysis, RNA splicing, translation initiation, actin depolymerization, and ciliogenesis, plus epigenetic modifications, which do not converge on a single, coherent function. Therefore I cannot assign a specific, representative label with confidence.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":5},{"id":"GO:0055114","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006349","count":2}]},{"hash":"739154953314057860","title":"Cell Cycle Control and Transcription Regulation","description":"The high-frequency GO terms cluster around mechanisms governing cell proliferation and transcription: cell division, regulation of the cell cycle, CDK activity, and negative regulation of transcription by RNA Pol II. Additional terms like canonical Wnt signaling and proteasome assembly fit into broader control of signaling and protein turnover that influence cell-cycle progression. Some terms reflect stress responses (cadmium and magnesium) and differentiation (skeletal muscle), but the core theme centers on cell-cycle control coupled with transcription regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0045737","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0035914","count":2}]},{"hash":"294624782220960801","title":"Epigenetic regulation of transcription","description":"This cluster is dominated by histone modification terms (H4-K16 acetylation, H3-K9 trimethylation, deacetylation, H3-K4 methylation, imprinting) and DNA-templated transcription, pointing to chromatin-level control of gene expression. While a few terms relate to cytoskeletal or trafficking processes, the core signal is epigenetic regulation of transcription. ","confidence":"Medium","size":25,"edges":13,"triangles":0,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0051016","count":3},{"id":"GO:0006890","count":2},{"id":"GO:0099133","count":2}]},{"hash":"328798539551503159","title":"Nuclear DNA replication and mitotic cell cycle regulators","description":"The cluster is dominated by GO terms for DNA replication, DNA-templated transcription, and mitotic cell cycle, highlighting a core set of nuclear processes driving genome duplication and cell division. Additional terms point to regulatory aspects like nuclear export and signaling pathways that may modulate transcription in proliferative or immune contexts, but the strongest signal remains nuclear replication and cell-cycle machinery.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0000278","count":7},{"id":"GO:0097011","count":6},{"id":"GO:0071222","count":6}]},{"hash":"1367660431521153266","title":"Insect morphogenesis and polarity","description":"The terms point to developmental shaping of tissues and cells in insects (antennal and chaeta morphogenesis, cuticle patterning, spermatid development) alongside cell polarity establishment and cytoskeletal restructuring (microvillus/microspike/podosome assembly, hemocyte migration). This suggests a cohesive theme of morphogenesis and polarity in an insect context, despite some term diversity. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048800","count":1},{"id":"GO:1900107","count":1},{"id":"GO:0071803","count":1},{"id":"GO:0035089","count":1},{"id":"GO:0032534","count":1}]},{"hash":"1333659494781696295","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0036265","count":2},{"id":"GO:1905289","count":2}]},{"hash":"2217079162966905262","title":"Osteogenesis and Osteoblast Differentiation","description":"Based on the Top Terms, the cluster is dominated by bone formation processes: skeletal system morphogenesis, intramembranous ossification, and osteoblast differentiation. While a few terms touch on broader cellular stress and signaling pathways, the osteogenesis-related terms are most representative of the cluster\u2019s likely function, suggesting a group of proteins involved in bone development and osteoblast activity.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0048705","count":2},{"id":"GO:0001957","count":2},{"id":"GO:0072432","count":1},{"id":"GO:2000011","count":1}]},{"hash":"1377677031096871767","title":"Unknown","description":"The top terms are widely varied (GTPase regulation, TORC1 signaling, mRNA transport, retina development, rRNA maturation, mitotic spindle assembly, transcription, dephosphorylation) with no single unifying process. There are no edges connecting proteins, suggesting a non-cohesive set or noise, so a specific functional label isn\u2019t justifiable.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0038202","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0051567","count":2}]},{"hash":"2113755306641327427","title":"Endosomal trafficking and autophagy","description":"The strongest signals are about endosomal transport (early endosome to late endosome and to Golgi) and autophagy-related pathways (Cvt/vacuole targeting), with supporting GO terms on GTPase regulation and phagocytic processes. This points to a cohesive theme of vesicle trafficking and autophagic pathways, despite a few scattered terms related to other processes.","confidence":"Medium","size":24,"edges":94,"triangles":108,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1900026","count":5},{"id":"GO:0034260","count":4},{"id":"GO:0043652","count":4},{"id":"GO:0045022","count":4},{"id":"GO:0034498","count":4}]},{"hash":"631742374008034698","title":"Signaling and Cell-Cycle Checkpoints","description":"This cluster includes GO terms across multiple signaling and regulatory processes: Hedgehog/Smoothened signaling, calcium ion transport, pinocytosis regulation, and GTPase activity control, plus developmental and immune themes (myelin assembly, thymus development, and negative regulation of T cell proliferation). It also features mitotic checkpoint signaling and DNA integrity checkpoint regulation, suggesting a broad theme of signaling regulation tied to cell-cycle control rather than a single, cohesive pathway. The lack of network edges reinforces a loose, multifaceted association.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048549","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0032288","count":2},{"id":"GO:0043087","count":2},{"id":"GO:0007224","count":2}]},{"hash":"24819871712674797","title":"ER-Golgi trafficking and mitosis","description":"This cluster centers on membrane trafficking between the ER and Golgi (SNARE complex disassembly; ER-to-Golgi vesicle transport) and mitotic processes (cell division; mitotic checkpoint signaling). Additional terms point to protein quality control (aggresome assembly; misfolded protein catabolic processes) that can intersect with division-related trafficking. A single outlier term (menaquinone biosynthetic process) may reflect annotation drift rather than core function. Overall, the themes cohere around vesicle trafficking coupled with cell-cycle regulation. ","confidence":"Medium","size":24,"edges":4,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035494","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0000122","count":3}]},{"hash":"199543475883580045","title":"Protein acetylation and related modifications","description":"The Top Terms show a clear enrichment for acetylation-related processes (N-terminal acetylation of various residues, peptidyl-lysine acetylation, spermidine acetylation, and acetylation steps in melatonin biosynthesis), suggesting the cluster centers on acetyltransferase activity and protein modification. Some terms like angiogenesis and leaf formation are peripheral or less coherent with the main theme, but the predominant signal is acetylation-based functions.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":4},{"id":"GO:2000025","count":3},{"id":"GO:0045150","count":3},{"id":"GO:0060358","count":3},{"id":"GO:0032918","count":3}]},{"hash":"856829800498264037","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by ubiquitin-related protein turnover processes (ubiquitin-dependent proteolysis, ERAD, SCF-mediated degradation, and various ubiquitin linkages). The inclusion of histone catabolic process and autoubiquitination supports a broader proteostasis theme, with peroxisome import and TNF pathway regulation possibly reflecting downstream or linked ubiquitination roles. Overall, the proteins appear to function mainly in the ubiquitin-proteasome system. ","confidence":"High","size":24,"edges":43,"triangles":31,"max_degree":16,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0030433","count":9},{"id":"GO:0031146","count":9},{"id":"GO:0070936","count":7},{"id":"GO:1903265","count":7}]},{"hash":"2160089641287723497","title":"Mitochondrial Translation and Energy Metabolism","description":"This cluster is strongly centered on mitochondrial functions: mitochondrial translation, ribosomal subunit and ATP synthase assembly, and mitochondrial electron transport, plus associated lipid metabolism like beta-oxidation and carnitine/cholesterol pathways, indicating a cohesive role in mitochondrial protein synthesis and energy production.","confidence":"High","size":24,"edges":252,"triangles":1613,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0070584","count":3},{"id":"GO:0099132","count":2},{"id":"GO:0033615","count":2},{"id":"GO:0008203","count":2},{"id":"GO:0006412","count":2}]},{"hash":"91478365418908390","title":"Immune cell cytoskeleton remodeling and endocytosis","description":"The cluster is defined by cytoskeletal processes (podosome assembly, actin polymerization) along with membrane trafficking (caveolin-mediated endocytosis) and immune-related terms (interleukin-4 production, NK T cell differentiation), suggesting a theme of immune cell adhesion/migration linked to cytoskeletal dynamics and endocytosis. Some terms about adhesion regulation further support this integrative function, though one peroxisome-related term is less connected.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071800","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0032633","count":2},{"id":"GO:1904703","count":2},{"id":"GO:0022407","count":2}]},{"hash":"2031030144766208950","title":"Cardiovascular development and cell cycle","description":"This cluster is enriched for heart development and angiogenesis, with additional broad developmental terms (multicellular organism development, skeletal system development) and proliferation-related terms (cell division, mitotic cell cycle, transcription). The prominent cardiovascular-related terms alongside cell cycle signals suggest a group of proteins involved in embryonic heart/vasculature formation and associated cellular proliferation, making \"Cardiovascular development and cell cycle\" a concise, representative label.","confidence":"High","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":4},{"id":"GO:0001525","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":3}]},{"hash":"2023864251160524763","title":"Mitotic Regulation and Nuclear Transport","description":"Top terms show a strong focus on cell cycle control and chromosome segregation, including negative regulation of CDK activity, kinetochore localization, and the mitotic cell cycle, along with regulation of protein export from the nucleus. Although neural-related GO terms appear (visual perception, cerebellar cortex formation, axon regeneration), they are less representative of the cluster than the mitosis-associated terms, so the label centers on mitotic regulation and nuclear transport.","confidence":"High","size":23,"edges":212,"triangles":1109,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":15},{"id":"GO:0034501","count":15},{"id":"GO:0007601","count":15},{"id":"GO:0000278","count":15},{"id":"GO:0046827","count":14}]},{"hash":"768019646884923309","title":"Nutrient-Responsive Metabolism","description":"The cluster shows a mix of metabolic biosynthetic processes (heme/porphyrin, biotin, amino acid catabolism) and nutrient signaling responses (cellular response to insulin stimulus, response to nutrient), plus related transcriptional activity and signaling elements (Notch pathway). This pattern points to a cohesive theme around how cells coordinate metabolism with nutrient sensing and growth signals, despite some broader or signaling-specific terms.","confidence":"Medium","size":23,"edges":140,"triangles":472,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032869","count":7},{"id":"GO:0019878","count":7},{"id":"GO:0006782","count":6},{"id":"GO:0007219","count":5},{"id":"GO:0042853","count":5}]},{"hash":"2123452365908854179","title":"Unknown","description":"The GO terms are highly diverse, spanning mitochondrial inheritance, hypoxia response, translation, sterol and fatty acid metabolism, and tissue-specific differentiation, with no clear unifying function across the cluster. This heterogeneity suggests either a mixed or non-cohesive set of proteins, so there isn\u2019t a single representative function to label. ","confidence":"","size":23,"edges":22,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0001666","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0032443","count":2}]},{"hash":"937956553167844532","title":"Telomere/Telomerase Assembly & DNA Maintenance","description":"The top GO terms cluster around telomere maintenance via telomerase, telomere-telomerase complex assembly, and related DNA/chromosome maintenance processes (including G-quadruplex DNA formation). There are also RNA processing/degradation terms (nonsense-mediated decay) that relate to nuclear RNA handling, but several unrelated terms appear as noise (e.g., visual perception). Overall, the dominant theme is nuclear genome maintenance linked to telomere biology, so the label reflects that core function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0016042","count":2},{"id":"GO:0031397","count":2},{"id":"GO:0006508","count":1}]},{"hash":"1423588766142754236","title":"Cell Growth, Chromatin, and RNA Regulation","description":"This cluster combines growth-related signals (TORC1 signaling, positive regulation of GTPase activity) with chromatin assembly and histone acetylation, plus RNA processing/transport and vesicle trafficking, suggesting a broad coordination of cell growth, gene expression, and RNA/protein handling rather than a single pathway.","confidence":"Medium","size":23,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0038202","count":2},{"id":"GO:0006335","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0070262","count":2}]},{"hash":"801834246415578198","title":"APC/C-driven mitotic proteolysis","description":"Dominant GO terms center on mitosis and ubiquitin-dependent degradation, including APC/C-dependent catabolic processes, K11-linked ubiquitination, mitotic cell cycle, and regulation of metaphase/anaphase transition. This points to a cohesive role for these proteins in controlled proteolysis during cell division, with some additional links to protein folding via peptidyl-prolyl isomerization. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000413","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0000278","count":3}]},{"hash":"2256636975574648526","title":"Protein acetylation (N-terminal and lysine)","description":"The cluster is strongly enriched for acetylation-related GO terms, including peptidyl-lysine N6-acetylation, multiple N-terminal acetylation types, and histone acetylation, suggesting a cohesive group of proteins involved in acetylation modifications. Some plant-specific terms like melatonin biosynthesis and leaf formation regulation may reflect regulatory connections via acetylation pathways, but the dominant signal is acetylation activity.","confidence":"High","size":23,"edges":24,"triangles":20,"max_degree":5,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0018003","count":6},{"id":"GO:0043967","count":6},{"id":"GO:2000025","count":5},{"id":"GO:0045150","count":5},{"id":"GO:0060358","count":5}]},{"hash":"115196052383357320","title":"Unknown","description":"This cluster has a broad and diverse mix of GO terms: cell morphogenesis, regulation of GTPase activity, cytokinesis, mitosis, transcription, apoptosis, Wnt signaling, sensory perception of sound, and lipopolysaccharide biosynthesis. The presence of both cell-cycle/morphogenesis terms and seemingly unrelated terms (lipopolysaccharide biosynthesis and sensory perception of sound) suggests there is no single coherent function or pathway defining the cluster. Therefore a single representative label is not evident.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0032465","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0090263","count":2}]},{"hash":"110376318720866508","title":"Neural Development and Transcription Regulation","description":"The cluster is enriched for neural development terms, including forebrain development and neural tube closure, alongside DNA-templated transcription and cell cycle-related terms, suggesting a group tied to neural development and its transcriptional control. While there are some stress/immune terms present, the strongest and most coherent theme centers on neurodevelopment and gene regulation.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":10},{"id":"GO:0000278","count":9},{"id":"GO:0070059","count":9},{"id":"GO:0006349","count":9},{"id":"GO:0071276","count":9}]},{"hash":"615927102363393168","title":"Rab-regulated vesicle transport","description":"Based on GO terms, this cluster is dominated by intracellular transport and vesicle fusion processes: plasma membrane to endosome transport, retrograde transport to Golgi, intracellular protein transport, and regulation of vesicle fusion and Rab signaling. These collectively point to endomembrane trafficking as the shared function. The skin and multicellular development terms appear ancillary to this core theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0048227","count":2},{"id":"GO:0035526","count":2}]},{"hash":"1330110009492058967","title":"Cell migration, polarity, and vesicle trafficking","description":"The top GO terms cluster around actin-driven remodeling (filopodium and actin filament bundle assembly), cell migration, and establishment of epithelial cell polarity, along with vesicle trafficking steps (vesicle docking in exocytosis, endosomal vesicle fusion). Ubiquitination and protein catabolic processes suggest turnover control of these components, supporting a cohesive theme of cytoskeletal dynamics coupled to vesicle trafficking in migration and polarity.","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006904","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0034058","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0046847","count":3}]},{"hash":"2084070148338518873","title":"Wnt Signaling Regulation and Ubiquitin Proteostasis","description":"The cluster centers on ubiquitin-related processes (ubiquitin-dependent ERAD, deubiquitination, and regulation of ubiquitin ligase activity) and regulation of canonical Wnt signaling (both positive and negative). This points to a common theme where ubiquitin-mediated proteostasis intersects with Wnt-driven growth and cell-cycle control (G2/M), with additional associations to immune and stress-related signaling (T cell receptor signaling and cadmium response). Confidence in this label is Medium.","confidence":"","size":23,"edges":176,"triangles":731,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0016579","count":5},{"id":"GO:0030308","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0051436","count":4}]},{"hash":"756852052030777726","title":"Cell Cycle, Transcription, and Ribosome Biogenesis","description":"The cluster is dominated by core growth-related processes: DNA-templated transcription, DNA replication, mitotic cell cycle, cell division, and ribosomal large subunit biogenesis, pointing to coordinated gene expression and proliferation. There are also stress-related terms (oxidative stress, response to antibiotic), but these appear ancillary to the main cell-cycle/gene-expression theme. Overall, this label captures the primary functional grouping.","confidence":"Medium","size":23,"edges":244,"triangles":1594,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0000902","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0051301","count":4}]},{"hash":"1822284110222617489","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":132,"triangles":365,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006283","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0048026","count":7},{"id":"GO:0006369","count":6},{"id":"GO:0048701","count":6}]},{"hash":"985159857846851453","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by ribosome biogenesis, cytoplasmic translation, ribosomal subunit export from the nucleus, and tRNA modification, indicating a cohesive group of proteins involved in ribosome assembly and protein synthesis, with supporting links to cell cycle/division. Confidence in this label is High.","confidence":"","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0009098","count":2},{"id":"GO:0000747","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0007049","count":2}]},{"hash":"617992823619390075","title":"Gene Expression Regulation and Cell Cycle","description":"This cluster centers on core processes of gene expression and cell proliferation, with the strongest terms being regulation of translational initiation, transcription initiation, and cell division (each appearing multiple times). Additional terms hint at signaling, circadian regulation, and various biosynthetic processes, which may reflect cross-species annotation noise but do not outweigh the central theme. Therefore, a label focusing on gene expression regulation and cell cycle is the most representative.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006367","count":2},{"id":"GO:0042518","count":2},{"id":"GO:0042747","count":1}]},{"hash":"2225222727243194642","title":"Cell Cycle Regulation and Transcription","description":"These proteins show a strong enrichment for cell cycle\u2013related processes: DNA-templated transcription, re-entry into the mitotic cell cycle, and G1/S and G2/M transitions, along with mitotic spindle pole body separation. A developmental term (face development) is present but appears less central; metabolic and signaling terms (glucose metabolism, calcium signaling regulation, autophagy, response to cocaine) likely reflect secondary regulatory roles or pleiotropy. Overall, the cluster is best described as focused on cell cycle control and transcriptional regulation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060324","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0010696","count":2},{"id":"GO:0000320","count":2},{"id":"GO:0000082","count":2}]},{"hash":"1179007990124765298","title":"Plant hormone signaling and chromatin remodeling","description":"These proteins show GO annotations for plant hormone responses (jasmonic acid, gibberellin), stress responses (osmotic stress), and chlorophyll regulation, coupled with chromatin-related processes (rDNA heterochromatin formation, chromatin remodeling) and regulation of secondary metabolism (flavonol and lignin biosynthesis). The combination points to a theme where hormonal signals influence chromatin state to regulate gene expression and metabolic pathways in plants.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":1},{"id":"GO:0009753","count":1},{"id":"GO:0010380","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0009739","count":1}]},{"hash":"1181678708698513347","title":"Rab-regulated vesicle trafficking and phagocytosis","description":"Proteins in this cluster predominantly map to Rab-regulated signal transduction and vesicle transport steps (intra-Golgi, plasma membrane to endosome, CVT to vacuole), alongside cytoskeleton organization, Rac signaling, cell migration, and phagocytosis. This pattern suggests a cohesive module governing membrane trafficking and actin-based remodeling critical for phagocytic and endocytic processes, with a minor outlier term related to viral genome activation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":2},{"id":"GO:0044829","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0006909","count":1}]},{"hash":"811646570717136665","title":"Histone modification and transcription regulation","description":"This cluster is dominated by GO terms for histone H3 methylation/acetylation and DNA-templated transcription, along with mitotic cell cycle involvement, pointing to a chromatin-regulatory and transcriptional control theme during cell division. Some ribosomal RNA processing terms appear but are secondary to the chromatin/transcription signals. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051568","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1638226927028899938","title":"GTPase Signaling and Cell Cycle Regulation","description":"The cluster centers on small GTPase-mediated signaling (GO:0007264) and positive regulation of GTPase activity (GO:0043547), suggesting Rho/Ras-like pathway activity. This is complemented by GO terms for transcription (GO:0006351), mitotic cell cycle (GO:0000278), and TORC1 signaling (GO:0038202), indicating a coordinated program of gene expression with cell-cycle control and nutrient/ER signaling. A couple of terms related to differentiation and pattern formation appear as outliers, which may reflect cross-species annotation breadth or multifunctional proteins. Overall, the group likely reflects a GTPase-centered signaling module linked to cell-cycle regulation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0032466","count":1},{"id":"GO:0072432","count":1}]},{"hash":"1052840320034153441","title":"Spliceosome-driven RNA processing and translation control","description":"This cluster shows strong enrichment for spliceosome-mediated mRNA processing and splicing-related terms (e.g., GO:0048026, GO:0045292, GO:0000398, GO:0006378) alongside terms tied to translation initiation and its regulation (GO:0001731, GO:0002188, GO:0075522, GO:0006446) and ncRNA-mediated gene silencing (GO:0031047). The combined signal points to a functional theme where RNA maturation (splicing) is linked to control of protein synthesis, justifying a label focused on RNA processing and translational regulation. Confidence reflects the coherent core despite some obsolete terms.","confidence":"High","size":22,"edges":203,"triangles":1100,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":14},{"id":"GO:0031047","count":13},{"id":"GO:1901407","count":11},{"id":"GO:0045292","count":10},{"id":"GO:0006378","count":9}]},{"hash":"135930045444023985","title":"Transcription and Cell Cycle Machinery","description":"This cluster\u2019s top GO terms cluster around DNA-templated transcription, regulation of transcription (including NF-kappaB signaling), and cell division, with additional hints of microtubule dynamics. While peroxisome import terms are present, the dominant signal points to transcriptional control intertwined with cell cycle and cytoskeletal processes, suggesting a coherent theme of gene expression regulation during cell division.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0051301","count":3}]},{"hash":"75799639066192379","title":"Developmental Signaling and Neural Function","description":"This cluster centers on broad developmental processes (heart, skeletal, nervous system development) with neural signaling and sensory-related activities (visual perception, excitatory postsynaptic potential, calcium-dependent exocytosis), plus some general cell-cycle terms. The combination suggests proteins involved in tissue development with emphasis on neural communication and signaling. ","confidence":"High","size":22,"edges":101,"triangles":172,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007507","count":13},{"id":"GO:0007601","count":12},{"id":"GO:0007266","count":12},{"id":"GO:0007124","count":12},{"id":"GO:0001501","count":12}]},{"hash":"900070014823785547","title":"Translational Initiation and RNA Processing Regulation","description":"The cluster is dominated by GO terms tied to translation initiation (formation of preinitiation complex, reinitiation, regulatory initiation, IRES-dependent initiation) and various RNA processing/handling steps (spliceosome-regulated splicing, ncRNA-mediated gene silencing, mRNA stability and modification). This pattern points to a coherent theme of post-transcriptional gene expression control at the level of translation and RNA processing.","confidence":"High","size":22,"edges":11,"triangles":0,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":8},{"id":"GO:0002188","count":8},{"id":"GO:0048026","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0075522","count":6}]},{"hash":"1980692971814092856","title":"Ubiquitin-Dependent Proteolysis & Cell Cycle Regulation","description":"The cluster is dominated by GO terms tied to ubiquitin-mediated protein degradation (ubiquitin-dependent proteolysis, ERAD, SCF-dependent proteasomal degradation) and regulation of ubiquitination, with a parallel emphasis on cell cycle control (mitotic G1 DNA damage checkpoint signaling). Additional terms touch on microtubule dynamics and cellular stress responses, which often intersect with proteostasis and cell cycle regulation. This core theme justifies a label centered on ubiquitin-proteasome\u2013mediated proteolysis and its connection to cell cycle control.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0030433","count":7},{"id":"GO:0031146","count":7},{"id":"GO:1902916","count":6},{"id":"GO:0031571","count":6}]},{"hash":"506685795715247516","title":"Cytoskeleton dynamics and signaling","description":"The proteins cluster around processes that remodel the cytoskeleton and regulate cell movement and division, including positive regulation of GTPase activity, sarcomere organization, pseudopodium assembly, and regulation of microtubule depolymerization. While developmental terms like hair follicle placode formation and dopaminergic neuron differentiation appear, they often involve cytoskeletal remodeling, supporting a theme of cytoskeleton dynamics and signaling as the unifying function. Confidence: Medium","confidence":"","size":22,"edges":18,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0045214","count":3},{"id":"GO:0031274","count":2},{"id":"GO:0060789","count":2},{"id":"GO:0000060","count":2}]},{"hash":"1600991206044983285","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":67,"triangles":61,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0034501","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0019079","count":3}]},{"hash":"241609367200256769","title":"Hedgehog signaling in neural development","description":"This cluster is heavily enriched for smoothened signaling (Hedgehog pathway) and nervous system development terms (brain and learning), indicating a core role in Hedgehog-driven neural development. Additional terms for ER-to-Golgi transport, cell cycle, and mitochondrial fission reflect general cellular processes supporting development, but the Hedgehog\u2013neural development theme is dominant.","confidence":"High","size":21,"edges":56,"triangles":62,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007224","count":8},{"id":"GO:0007399","count":8},{"id":"GO:0006888","count":8},{"id":"GO:0051301","count":8},{"id":"GO:0001822","count":8}]},{"hash":"1824506254662299086","title":"Unknown","description":"The GO terms for this cluster are highly diverse (viral replication, cell cycle, transcription regulation, vesicle trafficking, immune degranulation, neuronal signaling, learning), with no single dominant process connecting most members. This makes it hard to assign a concise, representative function to the cluster, so Unknown is the safest label. ","confidence":"","size":21,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0039694","count":2},{"id":"GO:1903395","count":1},{"id":"GO:0042088","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0010629","count":1}]},{"hash":"2010100579934773272","title":"Unknown","description":"The GO terms span many unrelated metabolic categories (various catabolic processes, detoxification, demethylation, biosynthesis) with no single dominant function, and there are no edges or connected terms to tie the proteins together, so there is no cohesive theme to name this cluster beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0015996","count":4},{"id":"GO:0019380","count":3},{"id":"GO:0006212","count":3},{"id":"GO:0019433","count":3}]},{"hash":"1828209126958571490","title":"Amino acid membrane transporters","description":"The cluster is enriched for GO terms describing transmembrane transport and import of several amino acids (D-alanine, methionine, lysine, ornithine, D-serine, etc.), indicating a group of proteins functioning as amino acid transporters at the plasma membrane. The presence of L-arginine catabolic process and nitric oxide production also ties to arginine metabolism and signaling related to amino acid utilization. Together, these terms point to a coherent theme of amino acid uptake and metabolism at the cell surface. ","confidence":"High","size":21,"edges":35,"triangles":8,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006527","count":2},{"id":"GO:0035826","count":2},{"id":"GO:0042941","count":2},{"id":"GO:0044690","count":2},{"id":"GO:0097639","count":2}]},{"hash":"53515730730086475","title":"Mitotic progression and development signals","description":"The cluster is dominated by mitosis- and cell-cycle-related GO terms (mitotic cell cycle, spindle orientation, cell division, cytokinesis regulation), plus GTPase activity regulation and DNA damage checkpoint signaling, pointing to a core theme of mitotic control. Some terms also invoke development/differentiation (osteoblast differentiation, adaxial/abaxial pattern formation), suggesting broader regulatory roles that connect division with cell fate decisions.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000132","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":4}]},{"hash":"2046657192292870335","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":10,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071031","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0045956","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2}]},{"hash":"1898343266911165971","title":"Lipid signaling and metabolic catabolism","description":"Based on the Top Terms, the cluster centers on lipid-related signaling (regulation of the endocannabinoid signaling pathway) and a variety of catabolic/biosynthetic processes for lipids and other small molecules (triglyceride and diacylglycerol catabolism, poly-hydroxybutyrate, cellulose), with additional detoxification and adhesion-related terms. This suggests a theme around metabolism and signaling tied to lipids, though the set includes some diverse processes, hence a Medium confidence.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0019433","count":4},{"id":"GO:2000124","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0017000","count":3}]},{"hash":"942631422945521580","title":"Translation initiation and ribosome assembly","description":"This cluster shows strong enrichment for translation-related GO terms: translation (GO:0006412), formation of translation preinitiation complex (GO:0001731), and translation reinitiation (GO:0002188), indicating components involved in initiating translation and assembling the preinitiation complex. Some minor terms (neural tube closure, iron transport, deglutamylation, folic acid metabolism) appear less connected to core translation, likely reflecting peripheral annotations or broader cellular roles. Overall, the dominant theme is translation initiation and ribosome-related processes.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0050731","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0008283","count":2}]},{"hash":"1976476060325677893","title":"Unknown","description":"The top GO terms are highly diverse, covering transcription, nuclear transport, cell cycle regulation, drug response, sensory perception, muscle structure, and ion transport, with no single dominant theme or shared cellular context. Because there isn\u2019t a cohesive function tying these terms together, a specific, meaningful label cannot be assigned beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009454","count":2},{"id":"GO:0045013","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0051447","count":2}]},{"hash":"1005857471215508455","title":"Neural development and transcriptional regulation","description":"This cluster centers on neural and embryonic development terms (forebrain development, neural tube closure, multicellular organism development) and general transcriptional activity (DNA-templated transcription), suggesting proteins that coordinate developmental gene expression and neural patterning. Some stress-related terms appear but are less representative of the main theme, so the developmental regulation signal is strongest.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0001403","count":4}]},{"hash":"124237703605392493","title":"Ribosome biogenesis and rRNA maturation","description":"The cluster is dominated by ribosome biogenesis and rRNA maturation terms (large subunit biogenesis and maturation of SSU/LSU/5.8S rRNA) and RNA processing (spliceosome). While there are scattered terms related to DNA replication and ubiquitination, the strongest signal points to proteins involved in ribosome production and RNA processing, with some potential linkage to cell-cycle-related processes. ","confidence":"Medium","size":20,"edges":69,"triangles":96,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0000209","count":2}]},{"hash":"1816345502681680076","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051321","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0000082","count":2}]},{"hash":"1663497505347134780","title":"Translation Initiation & TORC1 Signaling","description":"This cluster is dominated by translation initiation and reinitiation terms (formation of translation preinitiation complex, IRES-dependent initiation) plus nutrient-responsive growth signaling (positive regulation of TORC1, response to nutrient) and proliferation, pointing to a theme of translation control in nutrient-driven growth. A few terms related to DNA repair and mitotic cohesion appear peripheral to this core function.","confidence":"Medium","size":20,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0043547","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0000724","count":3}]},{"hash":"1508223331489592455","title":"Developmental differentiation and cell cycle control","description":"This cluster centers on proteins involved in developmental differentiation (mesoderm, skeletal muscle, neuron development) and cell cycle transitions (G1/S, meiotic). While there are also transcription termination and xenobiotic response terms, the strongest signals are development and cell cycle regulation, suggesting roles in coordinating differentiation with cell cycle progression.","confidence":"Medium","size":20,"edges":26,"triangles":9,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0032516","count":4},{"id":"GO:0000082","count":4},{"id":"GO:0007498","count":3},{"id":"GO:0001915","count":3}]},{"hash":"972623307352236525","title":"Lipid Biosynthesis and Immune Signaling","description":"The cluster centers on lipid metabolism and remodeling (phosphatidylcholine biosynthesis, ether lipids, platelet activating factor, cardiolipin remodeling) and energy production (mitochondrial ATP synthesis), with immune-oriented terms such as IL-2 production and negative regulation of activation-induced T cell death also present. A couple of terms like cerebellum morphogenesis and cutin biosynthesis appear less directly connected, possibly reflecting broader lipid-related roles or cross-species annotations. Overall, the dominant theme is lipid biosynthesis/remodeling intertwined with energy metabolism and immune signaling.","confidence":"Medium","size":20,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2001246","count":3},{"id":"GO:0008611","count":3},{"id":"GO:0006663","count":3},{"id":"GO:0070236","count":3},{"id":"GO:0070970","count":3}]},{"hash":"447577520920510300","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for ribosome biogenesis and translation (ribosomal large subunit biogenesis, ribosome biogenesis, and translation), pointing to proteins involved in ribosome assembly and protein synthesis. A few DNA repair and developmental terms are present but less frequent, suggesting they are ancillary contexts rather than the primary function. Overall, the core theme seems to be ribosome production and function with some additional roles in DNA stress response and development pathways.","confidence":"High","size":20,"edges":26,"triangles":11,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0009411","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0036297","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006412","count":2}]},{"hash":"999933132960814885","title":"Chloroplast RNA processing and plastid transcription","description":"Based on the top GO terms, the cluster centers on chloroplast/plastid gene expression: plastid transcription, chloroplast RNA processing, and chloroplast RNA modification, with supporting signals of mitochondrial RNA regulation. A few outlier terms (DNA repair, general regulation) are present but do not define the main theme. This suggests a cohesive group of proteins involved in chloroplast RNA metabolism and plastid transcription.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0005977","count":1},{"id":"GO:0043666","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0009966","count":1}]},{"hash":"1687538371537729015","title":"Unknown","description":"The top terms are scattered across stress responses (cadmium ion, ER-stress\u2013induced apoptosis), transcription and cell cycle, and diverse developmental processes (neural tube closure, forebrain and skeletal development), plus immune defense and imprinting. With no evident cohesive biological theme and no edges connecting proteins, the cluster does not map to a single functional module.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0070059","count":4}]},{"hash":"251395732638064131","title":"Mitotic cell cycle regulation and proliferation control","description":"The cluster is strongly enriched for mitosis- and cell cycle-related terms (kinetochore localization, mitotic cell cycle, negative regulation of CDK activity, and negative regulation of cell proliferation), indicating a shared theme around cell cycle control and proliferation suppression. Other terms like transcription, signaling pathways, and axon regeneration appear less central but may reflect broader regulatory networks; the dominant signal supports a cell cycle/proliferation focus.","confidence":"Medium","size":19,"edges":66,"triangles":85,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":15},{"id":"GO:0045736","count":15},{"id":"GO:0007601","count":14},{"id":"GO:0097011","count":14},{"id":"GO:0009190","count":14}]},{"hash":"658680918924057327","title":"Cell Cycle and Stress Response","description":"This cluster centers on mitotic processes and stress signaling (mitotic spindle assembly, mitotic cell cycle, G1 DNA damage checkpoint signaling) along with ubiquitin ligase regulation and ER-stress\u2013related apoptosis, suggesting a core theme of coordinating cell division with cellular stress responses. Other terms like translation initiation, actin depolymerization, and differentiation signals appear as peripheral or broader-context functions. Overall, the closest coherent theme is cell cycle control intertwined with stress responses, giving a Medium confidence.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:1904668","count":6},{"id":"GO:0032933","count":6},{"id":"GO:0030042","count":6},{"id":"GO:0090307","count":6}]},{"hash":"1196840765910679310","title":"Unknown","description":"The terms span both ER-related protein processing (ERAD, ER-to-Golgi transport) and nuclear/chromatin processes (DNA-templated transcription, CENP-A chromatin assembly, histone methylation), plus cell-cycle and cytoskeletal functions (microtubule severing, protein homooligomerization) and ER-stress\u2013related apoptosis. There is no clear, single theme tying these together, and several terms are obsolete, so a coherent, specific cluster label cannot be confidently assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0070317","count":3},{"id":"GO:0070059","count":3}]},{"hash":"1735153302086078878","title":"Neurite outgrowth and neuron morphogenesis","description":"Two terms strongly point to neuronal development, notably axon extension and dendrite morphogenesis, with accompanying processes like cell migration and transcriptional regulation, suggesting a cluster enriched for neurite growth and neuronal differentiation. Some other terms are more metabolic or broadly regulatory, so the label captures the main neuronal morphogenesis signal while acknowledging broader hints.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097350","count":2},{"id":"GO:0043433","count":2},{"id":"GO:0045773","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1341546202457906816","title":"Ubiquitination and vesicle trafficking","description":"This cluster centers on protein ubiquitination and trafficking pathways. Top GO terms include ubiquitin-dependent ERAD and protein ubiquitination, along with endosome transport, vacuolar targeting via the Cvt pathway, and localization to membranes. Despite some obsolete terms, the dominant theme is protein quality control and sorting through the endomembrane system. ","confidence":"Medium","size":19,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0006626","count":2},{"id":"GO:0007049","count":2}]},{"hash":"1756842374906747369","title":"Rab GTPase signaling and protein geranylgeranylation","description":"The top GO terms cluster around Rab protein signal transduction, activation of GTPase activity, protein transport, and specifically protein geranylgeranylation (prenylation). These point to a set of proteins involved in Rab-mediated vesicle trafficking regulated by geranylgeranylation, with supporting terms about membrane targeting. Some fish-specific developmental terms appear but are less central to the main mechanism. Confidence: Medium","confidence":"","size":19,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:2000541","count":2},{"id":"GO:0050771","count":2},{"id":"GO:0032482","count":2},{"id":"GO:0048798","count":2}]},{"hash":"530201762739167671","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":2},{"id":"GO:1904876","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0007175","count":2},{"id":"GO:0000494","count":2}]},{"hash":"515302991051701838","title":"Stress-Responsive protein turnover and trafficking","description":"The terms converge on protein quality control (ubiquitin-dependent degradation, ribophagy) and protein movement (nuclear import, endocytosis), with supporting signals from stress-related responses (antibiotic exposure, radiation) and membrane/lipid homeostasis, suggesting a cluster centered on managing protein fate and trafficking under stress.","confidence":"Medium","size":19,"edges":10,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0034517","count":2},{"id":"GO:0006606","count":2},{"id":"GO:0006898","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1471571084666855143","title":"Cell envelope polysaccharide biosynthesis","description":"This cluster is dominated by GO terms for assembling and modifying surface polysaccharides and cell walls (lipid A and LPS biosynthesis, spore wall assembly, arabinose donor biosynthesis), as well as processes linked to surface-associated lifestyles (biofilm formation) and antibiotic response. Xylan catabolism suggests carbohydrate metabolism tied to extracellular polysaccharides, while autophagosome maturation and allantoin biosynthesis appear as peripheral connections. Overall, the set points to cell envelope construction and surface carbohydrate remodeling as a common theme.","confidence":"Medium","size":19,"edges":14,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":3},{"id":"GO:0097352","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0042244","count":2},{"id":"GO:0009245","count":2}]},{"hash":"558831432423270865","title":"Organogenesis and immune cell development","description":"The top GO terms point to multiple organ development processes (otic vesicle formation, Sertoli cell development, gallbladder and trachea gland development, neural tube patterning) alongside immune differentiation (dendritic cell differentiation and plasmacytoid DC activation). The presence of translation is general, but the clustering seems to reflect a vertebrate developmental theme with some immune cell differentiation involvement, rather than a single, narrow function.","confidence":"Medium","size":19,"edges":17,"triangles":8,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0032425","count":2},{"id":"GO:0021903","count":2},{"id":"GO:0033234","count":2},{"id":"GO:2001200","count":2}]},{"hash":"1259860674519410156","title":"Actin-based cytoskeleton remodeling and cell migration","description":"The cluster is defined by lamellipodium and filopodium assembly, Rho GTPase signaling, and microtubule-driven movement, all hallmark features of actin cytoskeleton remodeling and cell motility. Additional terms about adhesion-dependent spreading and remodeling reflect motility and morphogenesis; the CNS development terms align with cytoskeletal dynamics guiding neural tissue morphogenesis.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043314","count":2},{"id":"GO:0030032","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0060313","count":2}]},{"hash":"855323659788649536","title":"Organ and tissue development","description":"These proteins cluster around GO terms tied to development of multiple organs and tissues (vascular smooth muscle differentiation, uterus development, digestive tract development, urinary bladder development, lung alveolus development). Additional terms on regulation of cell cycle and cytoskeletal changes relate to morphogenesis, supporting a general theme of organ/tissue development rather than a single specific function. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035886","count":1},{"id":"GO:0045736","count":1},{"id":"GO:0060065","count":1},{"id":"GO:0048565","count":1},{"id":"GO:1900222","count":1}]},{"hash":"243756215400877811","title":"Centromere assembly and mitotic chromatin dynamics","description":"This cluster centers on centromere-related chromatin assembly (CENP-A) and mitotic processes, including chromatin remodeling (histone acetylation) and spindle dynamics (microtubule severing, cell division, cytokinesis regulation). While a few terms (e.g., ERAD and vesicle transport) are less directly tied to mitosis, the dominant signals point to chromosome segregation and chromatin regulation during cell division.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0043966","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0061641","count":3}]},{"hash":"843375579931940798","title":"Unknown","description":"The proteins show varied GO terms from metabolism and signaling to development and stress responses, with no single shared function apparent and no edges connecting them, making a confident, cohesive label inappropriate.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010659","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0045793","count":2}]},{"hash":"221282045127510098","title":"Ribosome Biogenesis & rRNA Processing","description":"The cluster is dominated by GO terms for ribosome biogenesis and endonucleolytic cleavage in ITS1, indicating a nucleolar/ribosome assembly role. Additional terms span transcription, ubiquitination, and ER-Golgi transport, suggesting broader cellular regulation; immune-related terms may reflect cell-type specific roles or incidental annotation. Overall, the strongest signal centers on ribosome biogenesis and rRNA processing, supporting a core nucleolar function cluster.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0043029","count":2},{"id":"GO:0050830","count":2}]},{"hash":"1472894603170903995","title":"Cell Division and Mitotic Machinery","description":"Many top GO terms cluster around DNA replication, centromere (CENP-A) assembly, mitotic spindle orientation, microtubule severing, and actin cortex organization, pointing to a coordinated role in chromosome maintenance and spindle dynamics during mitosis. Some trafficking-related terms (ER-to-Golgi transport and ERAD) may reflect ancillary cellular remodeling during division, but the core signal is mitotic machinery.","confidence":"High","size":18,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1383463272734031308","title":"Cell Division and Microtubule Assembly","description":"The cluster is dominated by GO terms for cell cycle and mitosis (cell cycle, mitotic cell cycle) and microtubule organization/assembly (tubulin complex assembly), suggesting a core role in cell division and cytoskeletal dynamics; additional terms for ER-Golgi vesicle transport and development indicate broader cellular remodeling and developmental context.","confidence":"High","size":18,"edges":65,"triangles":82,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0010255","count":4}]},{"hash":"1478346887091901235","title":"Estrogen-responsive transcriptional regulation","description":"This cluster is dominated by terms for DNA-templated transcription and transcription by RNA polymerase II, together with GO terms indicating cellular response to estradiol stimulus and regulation of differentiation. The convergence on transcriptional processes and hormone-responsive signaling suggests proteins that modulate gene expression in response to estrogen, with secondary signals related to muscle differentiation and cell cycle. A few terms (MHC class II biosynthesis, macrophage apoptosis, anther development) appear more tangential or cross-species and likely reflect annotation breadth rather than core function of the group.","confidence":"Medium","size":18,"edges":122,"triangles":421,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0071392","count":3},{"id":"GO:2001016","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0051301","count":2}]},{"hash":"1310371690745951525","title":"Ribosome Biogenesis and Translation Machinery","description":"This cluster is dominated by GO terms for ribosome biogenesis, translation, and formation of translation preinitiation complex, including both small and large subunit biogenesis and translation reinitiation. Together these terms point to a core function in assembling ribosomes and initiating protein synthesis, with a secondary note of cell division coordination; the acetylation terms are ancient/obsolete and less informative. ","confidence":"High","size":18,"edges":38,"triangles":29,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0006412","count":6},{"id":"GO:0000747","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042274","count":3}]},{"hash":"742462941398893017","title":"RNA processing and ribosome biogenesis","description":"Top GO terms center on RNA processing (mRNA splicing, mRNA transport), ribosome biogenesis, and steps in translation initiation (formation of the translation preinitiation complex). The TORC1 signaling term links nutrient sensing to protein synthesis, reinforcing a theme of RNA maturation and assembly of the translation machinery. A few terms (e.g., extrinsic apoptotic signaling) may be secondary or context-specific, but the dominant signal points to RNA processing and ribosome biogenesis as the core cluster function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0038202","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0070262","count":2}]},{"hash":"773749982228795223","title":"Notch signaling and muscle lipid metabolism","description":"The cluster features Notch signaling and several lipid-related processes (sphingomyelin biosynthesis, fatty acid transport and homeostasis), along with skeletal muscle tissue regeneration. This suggests a theme around Notch-associated muscle biology tied to membrane lipid metabolism, even though some terms (like mitotic spindle assembly) are less directly connected. Overall, a muscle\u2013lipid\u2013Notch connection best fits the set.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043403","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0019551","count":1},{"id":"GO:0006686","count":1},{"id":"GO:0015908","count":1}]},{"hash":"2252182749766682818","title":"Unknown","description":"These GO terms cover a wide range of cellular processes with little overlap: cellular response to insulin stimulus; ERAD; ribosome biogenesis; microtubule severing; CENP-A chromatin assembly; heme transport; protein homooligomerization; apoptotic process; homologous recombination repair; transcription elongation by RNA polymerase II. The lack of a unifying pathway or cellular compartment suggests the cluster does not reflect a single coherent function, hence Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0061641","count":2}]},{"hash":"18574507660779540","title":"TLR-MDP Innate Immune Signaling","description":"The cluster is strongly characterized by GO terms for recognizing bacterial components (cellular response to muramyl dipeptide) and signaling through Toll-like receptors (TLR3, TLR7, TLR8) with downstream IL-1 production, plus actin remodeling and cell migration, all hallmarks of innate immune activation and response to pathogens. Some terms like RNA import into the nucleus appear peripheral, but the core theme is TLR-mediated innate immune signaling and cytokine biology.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071225","count":3},{"id":"GO:0034154","count":2},{"id":"GO:0051639","count":2},{"id":"GO:0030335","count":2},{"id":"GO:0050701","count":2}]},{"hash":"2206239979985324462","title":"DNA replication and transcription during the cell cycle","description":"This cluster is enriched for DNA-templated transcription, DNA replication, DNA repair, and mitotic cell cycle terms, pointing to a core role in genome maintenance and transcription control during cell proliferation. The additional development-related terms (cell morphogenesis and layer formation in the cerebral cortex) suggest broader involvement of these proteins in developmental processes tied to proliferation.","confidence":"Medium","size":17,"edges":78,"triangles":190,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":14},{"id":"GO:0006281","count":13},{"id":"GO:0097011","count":13},{"id":"GO:0000278","count":13},{"id":"GO:0006260","count":13}]},{"hash":"1471629453631920116","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0000398","count":7},{"id":"GO:0042273","count":7},{"id":"GO:0000466","count":7},{"id":"GO:0000463","count":7}]},{"hash":"1469577660704570767","title":"Hormone-responsive stress and DNA repair signaling","description":"This cluster groups proteins involved in hormone- and prostaglandin-related signaling (estradiol response, prostaglandin biosynthesis, female gonad development), oxidative stress/detoxification (redox homeostasis, oxidant detoxification), and DNA repair (nucleotide-excision repair), with supportive roles in cell motility and vascular/reproductive contexts (platelet aggregation, lamellipodium assembly). The common theme is cellular stress and hormone-responsive signaling pathways that intersect with DNA maintenance and detoxification processes.","confidence":"Medium","size":17,"edges":75,"triangles":163,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0070527","count":6},{"id":"GO:0008585","count":5},{"id":"GO:0001516","count":5},{"id":"GO:2000255","count":4},{"id":"GO:0098869","count":4}]},{"hash":"971506560029676797","title":"RNA processing and ribosome biogenesis","description":"The most represented GO terms cluster around spliceosome activity and mRNA splicing (spliceosome conformational changes, mRNA splicing via spliceosome), along with mRNA transport and ribosomal biogenesis including rRNA maturation. This points to a functional group focused on RNA processing and the assembly/ maturation of the ribosome. Additional terms for protein ubiquitination/degradation and retrograde vesicle transport are present but do not define the core theme, so the label highlights RNA processing and ribosome biogenesis.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000388","count":2},{"id":"GO:1990416","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2}]},{"hash":"1986615219074339257","title":"ER-Golgi vesicle transport and mitosis","description":"The cluster is strongly enriched for ER-to-Golgi trafficking terms (COPII-coated vesicle budding, vesicle transport between ER and Golgi, and retrograde Golgi-ER transport), indicating a core vesicular transport function. In addition, multiple terms point to cell division and the mitotic cell cycle, suggesting a link to cell proliferation. While ribosome biogenesis and GTPase activity regulation appear, the dominant theme appears to be vesicle trafficking with concurrent cell cycle processes.","confidence":"Medium","size":17,"edges":16,"triangles":2,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0042254","count":5}]},{"hash":"1732545593354904570","title":"Growth and division machinery","description":"This cluster centers on core cellular processes: growth signaling (growth hormone response), transcription and ribosome biogenesis (gene expression), and cell-cycle control (mitotic cycle, cytokinesis regulation, and DNA damage checkpoint signaling). These collectively point to fundamental growth and division machinery, with a few peripheral terms (defense response, osteoblast differentiation) that may reflect broader context or annotation noise rather than a cohesive functional theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060416","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":4}]},{"hash":"1286190485414131934","title":"RNA processing and translational control","description":"The cluster\u2019s top GO terms point to post-transcriptional and translational regulation, including spliceosome-mediated regulation of alternative splicing, rRNA processing, and IRES-dependent translation initiation, suggesting a shared function in RNA maturation and control of protein synthesis. Some developmental or immune-related terms may be incidental annotations, but the RNA-centric terms provide the strongest common theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0060065","count":2},{"id":"GO:0032911","count":2},{"id":"GO:0060017","count":2},{"id":"GO:0071353","count":2}]},{"hash":"846625021393128234","title":"Mitochondrial Translation and Respiratory Assembly","description":"The cluster is dominated by GO terms tied to translation in both cytosol and mitochondria, together with mitochondrial protein import and assembly of the respiratory chain (complex I) and related energy metabolism processes, suggesting a coherent theme around mitochondrial protein synthesis and respiration. Some peripheral terms (nitrogen fixation, ferredoxin, folate metabolism) may reflect broader metabolic connections but do not override the central mitochondrial translation/respiration signal.","confidence":"High","size":17,"edges":134,"triangles":651,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0009399","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070131","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0032981","count":2}]},{"hash":"2199636172280925461","title":"Unknown","description":"The terms show no single unifying function: metal and NAD transport, mitochondrial transport, RNA splicing, vision, development, retrotransposition, and stress responses. With only one edge and no clusters of related terms, the cluster lacks a coherent biological theme, so Unknown is the proper label.","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0015074","count":1}]},{"hash":"556121688157834485","title":"Membrane lipid synthesis and trafficking","description":"The top GO terms converge on lipid metabolism and membrane-related processes: unsaturated fatty acid biosynthesis, ergosterol biosynthesis and its regulation, MIPC (glycosphingolipid) metabolism, and intralumenal vesicle formation, with supportive hints from lipid-rich contexts like CNS myelin maintenance and sebaceous gland differentiation. A few terms (nitrate assimilation, nitric oxide biosynthesis) are less connected but may reflect broader metabolic signaling; overall, the dominant theme is lipid production and membrane trafficking, justifying a specific label. ","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006675","count":4},{"id":"GO:0006636","count":4},{"id":"GO:0001949","count":4},{"id":"GO:0042128","count":4}]},{"hash":"227632687725918412","title":"Lipid and Steroid Biosynthesis","description":"The cluster is dominated by GO terms tied to lipid metabolism and steroid biosynthesis, including mycolic acid biosynthesis, very long-chain fatty acid biosynthesis, fatty acid elongation, and 3-keto-sphinganine metabolism, pointing to complex lipid production and processing. In addition, there are several steroid-related terms (glucocorticoid, testosterone biosynthetic, and androgen catabolic processes), supporting a cohesive theme of lipid/steroid biosynthesis and turnover. A few terms about antibiotic response or biosynthesis are present but appear ancillary to the primary lipid/steroid metabolism theme. Confidence reflects the clear lipid/steroid metabolic connection across the top terms, with some peripheral antibiotic-related terms.","confidence":"High","size":17,"edges":21,"triangles":15,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":10},{"id":"GO:0017000","count":9},{"id":"GO:0071768","count":8},{"id":"GO:0045150","count":8},{"id":"GO:0006666","count":8}]},{"hash":"975232580257062694","title":"Mitochondrial Metabolite and Energy Carrier Transport","description":"This cluster centers on transmembrane transport of key mitochondrial metabolites and energy carriers (NAD, ATP, alpha-ketoglutarate, ornithine, pyrimidine nucleotides) and includes the malate-aspartate shuttle, suggesting a cohesive role in mitochondrial metabolite exchange and energy metabolism. The presence of a cellular response to amino acid starvation and regulation of necroptosis hints at mitochondria-linked metabolic stress and cell-death pathways, reinforcing a mitochondrial transport/metabolism theme.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090152","count":2},{"id":"GO:0035352","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0000066","count":2},{"id":"GO:1990519","count":2}]},{"hash":"1561551147644262052","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009877","count":2},{"id":"GO:0006337","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0005987","count":2}]},{"hash":"1655271429469925892","title":"Nuclear gene expression and chromatin regulation","description":"The cluster centers on nuclear processes: ribosome biogenesis, transcription (DNA-templated), and chromatin modifications (histone methylation) with associated ubiquitin-dependent protein turnover. These GO terms point to regulation of gene expression at the transcriptional and chromatin level. A few terms (ear morphogenesis, vestibular reflex, immune signaling) appear extraneous to this theme and may reflect incidental annotations, but the dominant signal is nuclear gene expression control.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006511","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0034729","count":2}]},{"hash":"1863005378739168976","title":"Nuclear proteostasis and DNA replication","description":"The cluster shows a strong enrichment for nuclear processes: DNA replication, nuclear protein quality control by the ubiquitin-proteasome system, tRNA import into the nucleus, misfolded protein transport, and translation-related terms. Redox homeostasis and protein complex oligomerization indicate broader maintenance roles; a couple of terms (mesoderm formation, iron-sulfur cluster maturation) may be less central noise. Overall, the proteins appear tied to nuclear proteostasis and DNA replication/maintenance.","confidence":"Medium","size":16,"edges":63,"triangles":103,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0097428","count":2},{"id":"GO:0001707","count":2}]},{"hash":"1181900066498258410","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":18,"triangles":5,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":9},{"id":"GO:0000398","count":9},{"id":"GO:0042273","count":9},{"id":"GO:0048026","count":9},{"id":"GO:0000466","count":9}]},{"hash":"1461064619866698521","title":"Central carbon metabolism","description":"Proteins are enriched across glycolysis, the TCA cycle, gluconeogenesis, and amino acid/fatty acid biosynthetic pathways, indicating a cohesive core metabolic cluster centered on central carbon processing and energy generation.","confidence":"High","size":16,"edges":117,"triangles":519,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":6},{"id":"GO:0006096","count":5},{"id":"GO:0033512","count":4},{"id":"GO:0006094","count":4},{"id":"GO:2001295","count":4}]},{"hash":"267527250315443951","title":"Translation and ribosome dynamics","description":"The cluster is enriched for translation-related terms (tRNA wobble uridine modification, translation, ribosome disassembly), indicating a core association with protein synthesis machinery. While metabolic processes appear among the terms, the strongest signal centers on ribosome function and translation, supporting a cohesive label. ","confidence":"High","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0009060","count":2},{"id":"GO:0019483","count":2}]},{"hash":"1869015714467032138","title":"Stress-Responsive Transcription and Growth Regulation","description":"These terms cluster around transcriptional control (DNA-templated transcription), cell cycle and proliferation (mitotic cell cycle, cell population proliferation), and multiple stress-response pathways (ER-stress\u2013induced apoptotic signaling, cadmium ion response, ubiquitin-proteasome\u2013mediated protein catabolism). The combination of gene expression, cell growth control, and stress responses suggests a module coordinating transcription with stress sensing and growth regulation, rather than a single metabolic pathway.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0006564","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0070059","count":2}]},{"hash":"202895248653511000","title":"Protein quality control and degradation","description":"The top GO terms are dominated by ubiquitin-proteasome/ERAD\u2013related processes (ubiquitin-dependent ERAD, proteasome assembly, aggresome formation) and protein folding/refolding, with several terms pointing to vesicle formation and transport. While a few terms (e.g., cilium movement, gas vesicle organization) seem less related, the core signal is proteostasis and intracellular trafficking. ","confidence":"Medium","size":16,"edges":53,"triangles":99,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0070389","count":5},{"id":"GO:0031412","count":5},{"id":"GO:0000027","count":5}]},{"hash":"924204050498965879","title":"Cranial skeleton and cerebral cortex morphogenesis","description":"The top GO terms point to developmental processes shaping the brain and skull: cerebellar cortex development, layer formation in the cerebral cortex, embryonic cranial skeleton morphogenesis, and general cell morphogenesis. There are also notes on transcription regulation and DNA replication, which suggests proliferative neural progenitors undergoing growth and differentiation. Taken together, these proteins appear to function in cranial and cerebral cortex morphogenesis during development, making this a specific and representative label.","confidence":"High","size":16,"edges":12,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0021695","count":5},{"id":"GO:0046827","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0000902","count":4}]},{"hash":"1747271786913248646","title":"Ribosome Biogenesis and rRNA Maturation","description":"The cluster shows strong signals for ribosome assembly and rRNA processing, with multiple GO terms for maturation of 5.8S, SSU, and LSU rRNA, and for ribosome biogenesis and large subunit assembly. Additional terms on protein oligomerization and GTPase activity regulation fit into the broader context of ribosome assembly cofactors. A minority of terms reference mRNA splicing and cellular fusion, which may reflect shared RNA-processing machinery or dataset noise, but the dominant theme is ribosome biogenesis and rRNA maturation.","confidence":"High","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3}]},{"hash":"443604381555342393","title":"Nuclear RNA Processing and Transcription Regulation","description":"The top GO terms include box C/D snoRNP assembly (rRNA processing in the nucleus), regulation of DNA-templated transcription, and regulation of mRNA poly(A) tail shortening, together pointing to nuclear RNA processing and gene expression control. There is also histone dephosphorylation, supporting chromatin-level regulation. Some terms (interferon response, ciliogenesis, prostate development) may be incidental annotations, but the dominant signal is nuclear RNA processing and transcription regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000492","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0060211","count":2},{"id":"GO:0016576","count":1}]},{"hash":"1712846258305389131","title":"Cell Wall Biosynthesis and Cytokinesis","description":"The top terms point to structural assembly of cell walls (cell wall polysaccharide biosynthetic process, mycolate cell wall layer assembly) and the mechanics of cell division (actomyosin contractile ring contraction, division septum site selection), with some developmental adhesion/polarity terms suggesting morphogenesis in epithelia. This combination supports a core theme around building structural components and completing cytokinesis during development, hence the label.","confidence":"Medium","size":16,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042248","count":2},{"id":"GO:0075015","count":2},{"id":"GO:0034217","count":2},{"id":"GO:0001744","count":2}]},{"hash":"2256790316389595529","title":"Axonogenesis and synaptic plasticity","description":"Top GO terms cluster around neural development and synaptic function, with clear signals for axonogenesis, neurotransmitter secretion, and long-term synaptic potentiation, plus memory. The presence of protein phosphorylation and negative regulation of protein kinase activity aligns with signaling modulation during synaptic plasticity. A few terms relate to skeletal muscle development and mitochondrial localization, but the dominant theme is neuronal connectivity and plasticity.","confidence":"High","size":16,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0048741","count":2},{"id":"GO:0033234","count":2},{"id":"GO:0006468","count":2}]},{"hash":"1789341707268772708","title":"Nucleolar ribosome biogenesis and RNA processing","description":"This cluster is driven by ribosome-related processes (ribosome biogenesis and preribosome assembly) and RNA processing activities (transcription and splicing), pointing to nucleolar roles in ribosome production and gene expression. Other chromatin-associated and DNA repair terms appear but seem secondary to the dominant nucleolar/RNA-processing signals.","confidence":"Medium","size":16,"edges":15,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006177","count":2},{"id":"GO:0001889","count":2},{"id":"GO:0045722","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0031100","count":2}]},{"hash":"781188460433094223","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":16,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:1904876","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0007175","count":2},{"id":"GO:0000494","count":2},{"id":"GO:0097309","count":2}]},{"hash":"60816739848150041","title":"Histone acetylation and transcription regulation","description":"Most of the annotated terms point to histone modification via acetylation and regulation of transcription by RNA polymerase II, indicating a chromatin-level control of gene expression. The additional terms touch on immune signaling and cytoskeleton dynamics, which may reflect broader functional connections but are not the primary theme.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043982","count":1},{"id":"GO:0043981","count":1},{"id":"GO:0006357","count":1},{"id":"GO:0043966","count":1},{"id":"GO:0043983","count":1}]},{"hash":"83491368803331272","title":"Glutamatergic Synaptic Signaling","description":"This cluster is dominated by GO terms for ionotropic glutamate receptor signaling and regulation of glutamatergic synaptic transmission, with supporting intracellular signaling and sensory/neural development terms, indicating a coherent theme of glutamatergic neuronal communication.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0052008","count":1},{"id":"GO:0009395","count":1},{"id":"GO:0001975","count":1},{"id":"GO:0035235","count":1}]},{"hash":"661883586519203814","title":"RNA processing and ribosome maturation","description":"The cluster is dominated by RNA-related functions: multiple spliceosome-associated terms (mRNA splicing, spliceosome conformational changes, regulation of splicing) and ncRNA-mediated gene silencing, plus maturation of rRNAs (5.8S, LSU, SSU), indicating roles in RNA processing and ribosome biogenesis; a secondary transport term (ER to Golgi) is present but less central. This suggests a cohesive theme around RNA processing and ribosome assembly rather than signaling. ","confidence":"Medium","size":15,"edges":17,"triangles":4,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000388","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0090394","count":3}]},{"hash":"540783642001797225","title":"Ubiquitin-Proteasome-Mediated Protein Degradation","description":"This cluster is enriched for GO terms related to ubiquitin-dependent proteolysis, SCF ubiquitin ligase activity, proteasomal degradation, ER-associated degradation, and sumoylation, pointing to a cohesive function in protein turnover and quality control. It also includes hints of regulation of deubiquitination and links to cell cycle and proliferation through turnover of regulatory proteins.","confidence":"High","size":15,"edges":37,"triangles":38,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:2000157","count":3},{"id":"GO:0034727","count":3},{"id":"GO:1903094","count":3},{"id":"GO:0016925","count":3}]},{"hash":"2229331962172741680","title":"Unknown","description":"The terms span vesicle trafficking, protein quality control, transcription initiation, DNA replication/repair, energy metabolism, and peroxisome import, with no evident single cohesive function tying all proteins together; this suggests a mixed or non-cohesive cluster rather than a unified biological theme.","confidence":"","size":15,"edges":10,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070676","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0045899","count":2},{"id":"GO:0006272","count":2},{"id":"GO:1903862","count":2}]},{"hash":"1863307667313492205","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":20,"triangles":12,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010610","count":4},{"id":"GO:0019858","count":4},{"id":"GO:0070935","count":3},{"id":"GO:0033129","count":3},{"id":"GO:0000902","count":3}]},{"hash":"1324768722958101496","title":"Unknown","description":"The terms cover TGF-beta signaling, regulation of Rho signaling, DNA repair, multiple developmental processes (neural tube patterning, Sertoli cell development, otic vesicle formation, gallbladder development) and immune cell differentiation/activation, which do not converge on a single coherent function. This makes it hard to assign a precise, representative label, so Unknown seems appropriate.","confidence":"","size":15,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0032425","count":1},{"id":"GO:0021903","count":1},{"id":"GO:0033234","count":1}]},{"hash":"974980748829440064","title":"Mitochondrial Translation and ATP Synthesis","description":"This cluster\u2019s top GO terms cluster around translation, especially mitochondrial translation, and ATP synthesis driven by the proton motive force, pointing to mitochondrial protein synthesis and energy production as the core theme. Some other terms seem unrelated or legacy annotations, but the core association is mitochondrial function. ","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042777","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0032543","count":2},{"id":"GO:0006412","count":2}]},{"hash":"2011267195118806402","title":"GTPase-driven cytoskeletal remodeling and signaling in migration","description":"The cluster\u2019s GO terms cluster around small GTPase signaling, actin cytoskeleton remodeling (filopodium/podosome assembly, cell polarity), and migration-related pathways (EGFR signaling). This points to a cohesive function in GTPase-regulated cytoskeletal dynamics that drive cell movement and polarity, with related intracellular trafficking roles.","confidence":"High","size":15,"edges":14,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0046847","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0098887","count":2},{"id":"GO:0010762","count":2},{"id":"GO:0007173","count":2}]},{"hash":"729022524678762527","title":"Mevalonate/isoprenoid and sterol biosynthesis","description":"This cluster centers on the mevalonate pathway and sterol biosynthesis, including farnesyl diphosphate biosynthesis, ergosterol biosynthetic process, and cholesterol biosynthetic process, suggesting a cohesive role in isoprenoid and sterol production. Additional terms like aromatic amino acid biosynthesis and acetyl-CoA metabolism align with broader primary metabolism, while translation and antibiotic biosynthetic terms appear less central but may reflect peripheral or overlapping functions. Overall, the data point to a metabolism-focused cluster rather than a single signaling or structural theme.","confidence":"Medium","size":15,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0009073","count":2},{"id":"GO:0010142","count":1},{"id":"GO:0006696","count":1}]},{"hash":"552500312459501797","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by ribosome-related processes, with ribosome biogenesis and cytoplasmic translation being the top GO terms, suggesting a core function in protein synthesis. The other GO terms are fewer and may reflect ancillary roles or annotation noise.","confidence":"High","size":15,"edges":9,"triangles":3,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0003351","count":2},{"id":"GO:0021692","count":1},{"id":"GO:0055088","count":1}]},{"hash":"1340421981926212921","title":"Amino Acid Metabolism and Lipid Biosynthesis","description":"The proteins cluster around multiple amino acid\u2013related pathways (lysine, alanine, tyrosine, glutamate, tryptophan/kynurenine) and lipid metabolism (sphingomyelin biosynthesis, fatty acid transport), suggesting a metabolic focus on amino acid processing with lipid biosynthetic activity. The Notch signaling term appears peripheral and does not define the main theme; some terms are obsolete, but the overall pattern points to amino acid metabolism with lipid involvement.","confidence":"Medium","size":15,"edges":89,"triangles":287,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":6},{"id":"GO:0033512","count":6},{"id":"GO:0007219","count":5},{"id":"GO:0042853","count":5},{"id":"GO:0097053","count":5}]},{"hash":"489594106682373631","title":"Ribosome biogenesis and translational machinery","description":"The top GO terms are dominated by translation, ribosome biogenesis, and rRNA processing/assembly, including cytosolic and mitochondrial translation, maturation of rRNA, and small/large subunit assembly and export. This points to a cohesive cluster of proteins involved in assembling and maintaining ribosomes and carrying out protein synthesis, with a possible ancillary link to antibiotic response through ribosome-targeting mechanisms. ","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0042254","count":4},{"id":"GO:0006407","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0000462","count":3}]},{"hash":"25580895058057421","title":"Unknown","description":"The GO terms are highly diverse and span histone modification, transcription, multiple developmental processes (brain, mesonephros), digestion, renal/angiotensin regulation, antigen processing via MHC II, and proteolysis. There isn\u2019t a single coherent biological theme tying these functions together, so a specific, descriptive label isn\u2019t supported by the available terms.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0060416","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0007586","count":2}]},{"hash":"1323220357483378359","title":"Ribosome biogenesis and RNA processing","description":"This cluster is dominated by terms tied to ribosome biogenesis, rRNA and tRNA maturation and modification, and translation regulation (including mitochondrial translation). While there are a couple of RNA processing terms (splicing, miRNA catabolism), the core signal emphasizes ribosome assembly and RNA maturation steps, suggesting a cohesive role in assembling and modifying components of the ribosome and associated RNA processing activities.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010587","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0042256","count":1},{"id":"GO:0070475","count":1},{"id":"GO:1902626","count":1}]},{"hash":"838861907037830499","title":"Nuclear transport and mitotic spindle organization","description":"The cluster is driven by GO terms for nuclear import/export (mRNA export from nucleus; NLS-bearing protein import into nucleus) and mitosis-associated processes (astral microtubule organization; regulation of centrosome duplication; mitotic metaphase chromosome alignment). This combination suggests a cohesive module coordinating nuclear transport with spindle/centrosome dynamics during cell division, hence a label reflecting both aspects.","confidence":"High","size":15,"edges":8,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":4},{"id":"GO:0030953","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0060188","count":3},{"id":"GO:0042991","count":3}]},{"hash":"1288557178217232172","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006890","count":2}]},{"hash":"1817045817638214348","title":"Yeast transcription and chromatin regulation under nutrient stress","description":"The top GO terms point to transcription-related processes (RNA polymerase II transcription and preinitiation complex assembly, splicing) and histone modifications, suggesting coordinated transcriptional control and chromatin remodeling in response to nutrient limitation. Growth-related terms (invasive/pseudohyphal growth) align with stress-induced morphological changes in yeast. Some terms appear as outliers or older annotations, but the central theme is transcription machinery and chromatin regulation under stress. ","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":2},{"id":"GO:0000398","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0009960","count":1},{"id":"GO:0007124","count":1}]},{"hash":"69226413257740898","title":"Transcriptional Regulation and Cell Signaling","description":"The cluster centers on DNA-templated transcription (2 counts) and includes TORC2 signaling, regulation of cadherin-mediated cell-cell adhesion, and fibroblast migration, suggesting a group of proteins that connect gene expression control with signaling pathways governing cell adhesion and movement. Additional terms like mRNA catabolic regulation, intracellular protein transport, glycosylation, and oxidant detoxification reflect broader regulatory roles, but do not define a single cohesive pathway beyond general regulation. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:2000049","count":1},{"id":"GO:0038203","count":1},{"id":"GO:0061014","count":1},{"id":"GO:0014068","count":1}]},{"hash":"222114982502800488","title":"Energy metabolism and growth regulation","description":"This cluster centers on central metabolism (TCA cycle, pentose phosphate shunt, pyruvate decarboxylation regulation) with accompanying signals of growth control (regulation of growth, tissue cell-number homeostasis) and stress/developmental processes (starvation response, haltere morphogenesis, oxidative detoxification). The combination points to proteins involved in energy production intertwined with growth regulation and some developmental signals, rather than a single narrow function.","confidence":"Medium","size":14,"edges":13,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0048873","count":2},{"id":"GO:0042594","count":2}]},{"hash":"727961514205314361","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000724","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0000480","count":2}]},{"hash":"1309436117337120612","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":65,"triangles":152,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1033319346795805400","title":"Mitotic machinery and protein homeostasis","description":"The cluster\u2019s prominent terms include cell division, CENP-A chromatin assembly, and microtubule severing, pointing to mitotic machinery. At the same time, there are processes related to protein quality control and trafficking (protein import into mitochondria, ER-to-Golgi transport, chaperone-mediated assembly, ubiquitin-dependent ERAD) and GTPase regulation, suggesting coordination of mitosis with protein folding, trafficking, and turnover. This combination supports a broader theme of cell-cycle progression linked to protein homeostasis rather than a single narrow function.","confidence":"Medium","size":14,"edges":84,"triangles":289,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0045041","count":2},{"id":"GO:0051131","count":2}]},{"hash":"1296448583894948714","title":"Nuclear gene expression and mitotic cell cycle","description":"This cluster centers on core nuclear processes such as DNA-templated transcription, DNA replication, mRNA export, and translation, along with mitotic cell cycle activities and kinetochore localization, plus apoptosis. These together point to a cohesive theme of gene expression regulation and cell division, with the bipolar cell polarity term being a potential minor outlier related to cell shape regulation. Overall, the proteins appear linked to nuclear functions and cell cycle control.","confidence":"High","size":14,"edges":41,"triangles":63,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0061246","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1437666866854240238","title":"Centromeric chromatin assembly and heterochromatin maintenance","description":"This cluster is enriched for CENP-A chromatin assembly and heterochromatin formation (rDNA and pericentric), pointing to centromere-related chromatin organization. The inclusion of microtubule severing suggests mitotic spindle involvement, supporting a role in chromosome segregation, with some broader terms possibly reflecting developmental contexts.","confidence":"High","size":14,"edges":15,"triangles":3,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":3},{"id":"GO:0051013","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0051290","count":2},{"id":"GO:0000183","count":2}]},{"hash":"2085052948452615234","title":"Vesicle trafficking and protein localization","description":"This cluster is dominated by GO terms related to intracellular transport and localization, including ER-to-Golgi vesicle transport, protein localization to membranes (vacuolar membrane), and protein-containing complex localization, as well as nuclear export of ribosomal subunits and GTPase activity regulation. Together these suggest a cohesive theme around vesicle trafficking and precise protein localization within the cell, despite some outlier terms related to development or chromatin. ","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:0060999","count":2},{"id":"GO:0046909","count":2},{"id":"GO:0006888","count":2},{"id":"GO:1903778","count":2}]},{"hash":"2288403586619653777","title":"Muscle and heart development with cytoskeletal signaling","description":"The enrichment is driven by terms like skeletal muscle fiber development and heart development, coupled with actin crosslink formation, indicating a muscle/cardiac developmental and cytoskeletal signaling theme. Supporting terms related to GTPase activity and protein autophosphorylation further point to signaling roles, while visual perception and NK cell regulation are present but less central. This combination supports a muscle/heart development-focused label with cytoskeletal signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0048741","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0035774","count":2},{"id":"GO:0031954","count":2}]},{"hash":"1803726266150066740","title":"Liver and Heart Metabolic Development","description":"The cluster centers on energy and substrate metabolism, including glycogen and glycolipid biosynthesis, regulation of gluconeogenesis, and catabolism of leucine, valine, and fatty acids, with tissue-development terms like liver development and cardiac muscle differentiation indicating organ-specific metabolic programs. Overall, it captures metabolism linked to liver/heart development.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0005978","count":3},{"id":"GO:0006552","count":3},{"id":"GO:0001889","count":3},{"id":"GO:0009247","count":2}]},{"hash":"2177251344640125176","title":"Developmental signaling and stress-induced apoptosis","description":"The cluster groups proteins linked to neural and immune organ development (forebrain and thymus), as well as processes tied to cell proliferation and synaptic activity, alongside stress- and apoptosis-related pathways (ER-stress\u2013driven intrinsic apoptosis, general apoptotic regulation), plus responses to metal and immune challenges. The mix points to a theme of development coupled with cellular stress and apoptotic signaling, with broader immune/metabolic context.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0006349","count":2}]},{"hash":"228705306151569550","title":"Ubiquitin-Dependent Proteostasis","description":"The cluster aggregates proteins involved in ubiquitin-mediated protein turnover and quality control, including ribosome-associated quality control, cytoplasmic proteasome degradation, and N-end rule pathway, as well as TOR signaling regulation and ER-Golgi trafficking; it also includes ubiquitin-related events in chromatin and RNAi machinery, indicating a broader role for ubiquitin signaling in proteostasis and gene expression.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0071233","count":1},{"id":"GO:1990116","count":1},{"id":"GO:0070923","count":1},{"id":"GO:0007141","count":1}]},{"hash":"786377871627662048","title":"Vesicle trafficking and pigmentation","description":"Most terms point to ER-Golgi and intra-Golgi vesicle transport (COPII coating, ER to Golgi transport, intra-Golgi transport) and melanosome assembly/pigmentation, suggesting a module of vesicle trafficking with pigment-related functions; autophagy and GTPase regulation terms further support vesicle dynamics involved in this cluster.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048208","count":1},{"id":"GO:0006914","count":1},{"id":"GO:0006891","count":1},{"id":"GO:0043473","count":1},{"id":"GO:0043547","count":1}]},{"hash":"997243348700778380","title":"Ciliary axoneme assembly and motility","description":"Top terms point to cilium movement and axoneme assembly, with intracellular signal transduction supporting ciliary signaling roles; obsolescent phosphorylation terms and DNA damage regulation appear peripheral. This suggests the cluster comprises proteins involved in ciliary structure and function.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0010569","count":1},{"id":"GO:2000002","count":1},{"id":"GO:0003341","count":1},{"id":"GO:0006174","count":1}]},{"hash":"706606757596900717","title":"DNA replication and repair with mitotic cell-cycle control","description":"Based on the top GO terms, the cluster is dominated by DNA repair (GO:0006281) and DNA replication (GO:0006260) with mitotic cell cycle (GO:0000278) and regulation of cell proliferation (GO:0008285). This points to a core function in genome maintenance and control of cell division. While cholesterol biosynthesis and some developmental terms appear, they are less central to the cluster\u2019s primary theme. Overall, the cluster reflects DNA maintenance and cell-cycle regulation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006281","count":5},{"id":"GO:0006695","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0008285","count":5},{"id":"GO:0006260","count":5}]},{"hash":"439287733160992860","title":"Developmental morphogenesis and cell migration","description":"This cluster centers on tissue and organ development (neuronal cortex layer formation, outer ear morphogenesis, glial-related processes) and on movement of cells such as macrophages and endothelial cells, plus associated transcription regulation and phosphorylation activities. The common thread is developmental morphogenesis with active cell migration/signaling, though some terms are outdated, so the connection is plausible but not perfectly tight. ","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034351","count":10},{"id":"GO:0000902","count":9},{"id":"GO:0021819","count":9},{"id":"GO:1990260","count":9},{"id":"GO:2001028","count":9}]},{"hash":"1427506133828996262","title":"Cellular Signaling and Stress Responses","description":"This cluster centers on signaling and stress-related processes, including dephosphorylation, unfolded protein response, glucocorticoid signaling, morphine (opioid) response, and interferon-alpha\u2013mediated responses. While a couple of terms touch cell cycle and metabolism, the dominant theme is regulatory signaling and cellular stress responses, with auxiliary cues like metal ion response and cilium assembly contributing to a broader stress/functional milieu.","confidence":"Medium","size":13,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016576","count":2},{"id":"GO:2000324","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0031145","count":2},{"id":"GO:0006986","count":2}]},{"hash":"1978009801115515534","title":"Mitotic cell division and chromatin modification","description":"The top GO terms cluster around mitosis and cell division (mitotic cell cycle, APC-dependent catabolic process, cell division, and cell population proliferation), indicating proteins involved in mitotic progression. Notably, there are also references to histone methylation regulation, hinting at chromatin-state control during the cycle. Some terms like cadmium response and GTPase regulation are peripheral to the core theme but do not outweigh the mitotic/chromatin signals. ","confidence":"High","size":13,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:2001162","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0061087","count":3}]},{"hash":"1692776881957261442","title":"Vertebrate Development and Organogenesis","description":"The terms cluster around neural tube closure, brain development, gonad and osteoblast differentiation, fertilization, and overall multicellular growth, indicating a vertebrate developmental program. A few terms (CENP-A chromatin assembly, defense response) are less directly related but do not override the dominant developmental theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0050830","count":2}]},{"hash":"940421232091315138","title":"Mitochondrial respiration and redox balance","description":"The GO terms converge on redox homeostasis and mitochondrial energy metabolism (oxidant detoxification, response to hydrogen peroxide, aerobic respiration, cytochrome complex assembly, proton transport), indicating a function centered on mitochondrial respiration and redox balance; a few peripheral terms (lipoprotein biosynthesis, insulin signaling) reflect broader metabolic context.","confidence":"High","size":13,"edges":23,"triangles":27,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0045454","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0070301","count":3},{"id":"GO:0009060","count":3}]},{"hash":"1817147226178106010","title":"Mitochondrial Translation and OXPHOS Assembly","description":"The cluster is dominated by mitochondrial-focused processes: protein translation within mitochondria, assembly of respiratory chain complexes (including complex IV and ATP synthase), proton-driven ATP synthesis, and cristae formation, all pointing to a cohesive module of mitochondrial protein synthesis and oxidative phosphorylation machinery.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006123","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0090305","count":1},{"id":"GO:0006259","count":1}]},{"hash":"225318803710653140","title":"Ubiquitination-Regulated Muscle Development","description":"The cluster\u2019s top GO terms center on ubiquitin-dependent protein catabolic processes, including protein K33-linked ubiquitination and regulation of ubiquitination, alongside skeletal muscle development and skeletal muscle tissue development. This suggests a cohesive module where ubiquitin signaling modulates muscle formation and maintenance. Immune-related terms (B cell receptor signaling, germinal center formation) and DNA replication appear among the hits but are less cohesive with the dominant ubiquitination\u2013muscle development theme.","confidence":"Medium","size":13,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0002467","count":2}]},{"hash":"1157361881950438566","title":"DNA Repair and Telomere Maintenance","description":"This cluster is enriched for multiple DNA repair pathways (base-excision repair, nucleotide-excision repair), mitotic DNA damage and replication checkpoint signaling, and telomere-associated regulation of end joining, pointing to a cohesive role in genome maintenance and telomere stability. A few terms related to translation and rRNA maturation appear but do not define the main function of the group.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006288","count":2},{"id":"GO:0033314","count":2},{"id":"GO:0007095","count":2},{"id":"GO:0061819","count":2},{"id":"GO:0071897","count":2}]},{"hash":"50117600390877618","title":"Plant hormone responses and chromatin remodeling","description":"This cluster centers on plant-specific signaling and chromatin dynamics: responses to jasmonic acid and gibberellin, osmotic stress, and regulation of chlorophyll biosynthesis, alongside chromatin remodeling and rDNA heterochromatin formation. Additional GO terms indicate modulation of phenylpropanoid metabolism, such as flavonol, syringal lignin, and sinapate ester biosynthesis. Taken together, the proteins likely participate in hormone-triggered stress responses coupled to chromatin-level regulation and metabolic adjustment.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":1},{"id":"GO:0009753","count":1},{"id":"GO:0010380","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0009739","count":1}]},{"hash":"1464147082081519501","title":"Immune Response and Signaling Regulation","description":"The top GO terms cluster around immune responses (cellular response to LPS, TH1 type immune response, antibacterial peptide biosynthesis) and immune signaling control (negative regulation of JAK-STAT signaling, CAMKK-AMPK pathways). While there are also terms linked to mitochondrial dynamics and development, the dominant theme is immune recognition and regulatory signaling. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0090141","count":2},{"id":"GO:1905289","count":2},{"id":"GO:0051770","count":2},{"id":"GO:0042088","count":2}]},{"hash":"27898696199941243","title":"Actin cytoskeleton remodeling and endocytosis","description":"The cluster is dominated by actin dynamics (polymerization, branching, podosome formation) and endocytic processes, with signals tied to the EGFR pathway and cell polarity, plus GTPase regulation, which together point to coordinated cytoskeletal remodeling during receptor signaling and membrane trafficking.","confidence":"High","size":12,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007173","count":4},{"id":"GO:0071963","count":4},{"id":"GO:0034260","count":4},{"id":"GO:0043652","count":4},{"id":"GO:0071803","count":4}]},{"hash":"1637160693858136464","title":"Transmembrane Transporters of Nutrients and Xenobiotics","description":"This cluster is characterized by GO terms for various transmembrane transports (vitamin, galactose, glucose, nitrite/nitrate, sialic acid, organic cations) and osmotic-stress response, indicating a set of membrane transport proteins.","confidence":"High","size":12,"edges":9,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0042128","count":4},{"id":"GO:0015757","count":3},{"id":"GO:0006970","count":3}]},{"hash":"930179167624039624","title":"Mitotic spindle orientation and cytokinesis regulation","description":"This cluster features GO terms tied to cell division and cytoskeletal dynamics, notably positive regulation of GTPase activity, establishment of mitotic spindle orientation, barbed-end actin filament capping, and regulation of cytokinesis. The combination suggests a module coordinating mitotic progression with cytoskeletal remodeling and related signaling (e.g., tyrosine phosphorylation). A single term about pattern formation is less consistent with the core theme, but the dominant signals point to mitosis and cytoskeletal control.","confidence":"High","size":12,"edges":30,"triangles":22,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0071560","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0051016","count":4}]},{"hash":"1516644704166493694","title":"Developmental cell cycle and morphogenesis","description":"The top GO terms cluster around DNA replication and mitotic cell cycle, paired with development-related processes such as multicellular organism development and cell morphogenesis, plus angiogenesis and visual perception, suggesting a theme of proliferative processes linked to development and organ/eye morphogenesis in multicellular organisms.","confidence":"Medium","size":12,"edges":30,"triangles":31,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0001525","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0007275","count":8},{"id":"GO:0007100","count":7}]},{"hash":"1665394567863102020","title":"Translational Initiation and Regulation","description":"This cluster is strongly characterized by GO terms related to translation initiation and its control: formation of the translation preinitiation complex, translation reinitiation, IRES-dependent viral translational initiation, and regulation of translational initiation. Other terms (ERAD, cytokinesis regulation, DNA damage response) appear incidental or secondary, but the dominant theme is translation initiation machinery and its regulation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0075522","count":3}]},{"hash":"671493200594473671","title":"DNA replication and chromatin dynamics","description":"The proteins are linked by processes in DNA replication, chromatin remodeling/heterochromatin formation, histone modification, nucleotide-excision repair, and ubiquitin signaling, with spindle assembly reflecting cell-cycle aspects. This combination points to a cohesive theme of genome maintenance and chromatin regulation rather than a single specialized pathway.","confidence":"High","size":12,"edges":12,"triangles":3,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":4},{"id":"GO:1904908","count":4},{"id":"GO:0051225","count":4},{"id":"GO:0043044","count":4},{"id":"GO:0006289","count":4}]},{"hash":"1674068980562141673","title":"Amino acid and cofactor biosynthesis","description":"The Top Terms show biosynthetic processes for histidine, tryptophan, p-aminobenzoate, folic acid, menaquinone, and molybdopterin cofactors, indicating a metabolic module focused on synthesizing amino acids and essential cofactors. Translation and proteolysis appear, but are likely peripheral to this core biosynthetic theme; antibiotic and food response terms may reflect regulatory links to metabolism.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0000105","count":2},{"id":"GO:0006508","count":2}]},{"hash":"2190291998234249172","title":"Bacterial cell envelope biosynthesis","description":"These proteins show a pattern of GO terms focused on synthesis of cell surface components, including lipopolysaccharide and lipid A biosynthesis, spore wall assembly, and related envelope functions, as well as antibiotic response and biofilm formation. While a few terms are peripheral, the dominant signal ties these proteins to bacterial cell envelope biosynthesis and surface-related traits.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0009231","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0042244","count":2},{"id":"GO:0009245","count":2}]},{"hash":"305670177126124542","title":"Redox Balance and Detoxification","description":"Top terms indicate a strong redox theme: oxidation-reduction processes, cellular oxidant detoxification, and removal of superoxide radicals, with menaquinone biosynthesis connected to electron transport. Despite a few unrelated or obsolete annotations, the redox/homeostasis signal is dominant, justifying this label.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009234","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0051573","count":2},{"id":"GO:0007114","count":2}]},{"hash":"32908845891673619","title":"Unknown","description":"No GO terms are listed for this cluster, and there is no obvious shared functional theme to anchor a specific label. The cluster has several connections (28 edges, 23 triangles) and a relatively high max degree (11), which might reflect a protein interaction module or a mixed set of proteins without a single cohesive function.","confidence":"","size":12,"edges":28,"triangles":23,"max_degree":11,"top_function":null,"top_go_terms":[]},{"hash":"2230468824422767327","title":"Cell Cycle and ER-Golgi Trafficking","description":"Based on the top GO terms, the cluster prominently associates with cell cycle and DNA replication (cell cycle, DNA replication) and with vesicle-mediated transport between the endoplasmic reticulum and Golgi (retrograde and ER-to-Golgi transport). A few terms related to heterochromatin, tissue homeostasis, and neuronal development appear as secondary associations, likely reflecting broader roles or annotation noise, but the core theme ties to cell proliferation processes and secretory pathway dynamics. Confidence: Medium","confidence":"","size":12,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0006348","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0060079","count":2}]},{"hash":"1793819435992179678","title":"Ubiquitin\u2013proteasome regulation of Wnt signaling and antigen processing","description":"The mix of ubiquitin-proteasome\u2013related terms (SCF-dependent proteasomal degradation, deubiquitination) alongside both positive/negative regulation of canonical Wnt signaling and antigen processing/presentation via MHC I points to a cohesive theme: ubiquitin-mediated protein turnover that modulates signaling pathways and immune peptide generation. Some cadmium response and cell-cycle regulation terms also fit as broader stress and regulatory contexts. Confidence: Medium","confidence":"","size":12,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0010950","count":2},{"id":"GO:0046686","count":2},{"id":"GO:0010972","count":2},{"id":"GO:0002862","count":2}]},{"hash":"768917470626731715","title":"RNA processing and translation regulation","description":"This cluster centers on RNA metabolism and gene expression control, including transcriptional regulation by RNA Pol II, regulation of translational initiation, mRNA stability and modification, splicing control, and miRNA-mediated silencing. The presence of small-subunit processome assembly hints at ribosome biogenesis, tying together transcription, RNA processing, and translational regulation, especially under stress contexts. Overall, these terms point to a cohesive theme of post-transcriptional regulation and RNA processing factors converging on gene-expression control.","confidence":"High","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0075522","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0010610","count":1},{"id":"GO:0016556","count":1}]},{"hash":"68134306150461503","title":"Developmental signaling and protein sumoylation","description":"This cluster features developmental processes such as heart morphogenesis and prostate gland development, alongside protein sumoylation as a key regulatory mechanism, suggesting coordinated developmental signaling with post-translational control. Additional terms like redox response and calcium release from the sarcoplasmic reticulum further tie into signaling and differentiation across tissues. Overall, the common theme points to developmentally regulated signaling with SUMO-mediated regulation, rather than a single organ-specific function.","confidence":"Medium","size":12,"edges":19,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051775","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0003007","count":2},{"id":"GO:0022417","count":2},{"id":"GO:0016925","count":2}]},{"hash":"443709937892899505","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms center on ribosome production and protein synthesis (translation; ribosome biogenesis; ribosomal subunit assembly; rRNA processing/export), indicating a cluster of ribosome-related factors involved in ribosome assembly and translation. Other terms are minor annotations and do not override the core ribosome-focused signal.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0000028","count":2},{"id":"GO:0006407","count":2}]},{"hash":"73731623043288295","title":"Innate immune signaling and ECM remodeling","description":"Most terms point to innate immune activation (LPS response, Th1 immunity, antibacterial peptide biosynthesis) and extracellular matrix remodeling (collagen fibril organization). Other terms reflect broader stress signaling (kinase activity regulation, mitochondrial fission) but are less central, and a couple neural-related terms are present but not dominant. Therefore, this label captures the main themes of the cluster.","confidence":"Medium","size":12,"edges":13,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0071222","count":2},{"id":"GO:0090141","count":2},{"id":"GO:1905289","count":2}]},{"hash":"628027419279085854","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007377","count":2},{"id":"GO:0006490","count":2},{"id":"GO:0003384","count":2},{"id":"GO:0006487","count":2},{"id":"GO:0044205","count":1}]},{"hash":"765107200387644418","title":"Developmental Signaling and Cardiovascular Growth","description":"The cluster features terms tied to development and signaling: heart development, angiogenesis, thymus development, and Rho/PI3K signaling, plus receptor clustering and cell cycle progression. This suggests proteins involved in developmental signaling networks, particularly those governing organogenesis and vascular formation, rather than a single specific process. Some terms (visual perception, cadmium response, plant ABA signaling) appear unrelated or broadly annotated, but the dominant theme centers on developmental signaling and organ development.","confidence":"Medium","size":11,"edges":18,"triangles":13,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":5},{"id":"GO:0007266","count":5},{"id":"GO:0014068","count":5},{"id":"GO:0048538","count":5},{"id":"GO:0043113","count":5}]},{"hash":"669654264923567143","title":"DNA damage response and transcriptional regulation","description":"The cluster centers on transcription (DNA-templated), DNA repair, and RNA turnover (deadenylation-dependent decapping), plus nucleotide metabolism shifts (adenosine-related catabolic processes) and epigenetic regulation (peptidyl-lysine acetylation). The presence of a p53-mediated apoptotic pathway suggests stress-induced cell fate decisions, while lipid catabolism and calcium signaling indicate broader metabolic and signaling context. Overall, the group seems linked to genome maintenance, transcription control, and apoptosis under stress.","confidence":"Medium","size":11,"edges":9,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:2000757","count":2},{"id":"GO:0000290","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006154","count":2}]},{"hash":"1312440202192111556","title":"Embryonic morphogenesis and actin dynamics","description":"The top terms cluster around developmental morphogenesis (embryonic neurocranium morphogenesis, aorta morphogenesis, planar polarity in neural tube closure) and cytoskeletal remodeling (actin polymerization and severing), suggesting a common theme of shaping tissues during development with actin-driven cell dynamics. A couple of outliers (auxin transport regulation, host-mediated suppression of symbiont invasion) may reflect annotation breadth or cross-kingdom noise, but the dominant signal is morphogenesis coupled with actin remodeling.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048702","count":1},{"id":"GO:2000012","count":1},{"id":"GO:0046597","count":1},{"id":"GO:0051014","count":1},{"id":"GO:1903906","count":1}]},{"hash":"974099693744431639","title":"Proteasome-mediated proteolysis and immune signaling","description":"The top GO terms are dominated by ubiquitin-dependent degradation pathways (ERAD and SCF-proteasomal processes), indicating a core focus on protein quality control. Immune signaling terms (T cell receptor and C-type lectin receptor pathways) suggest involvement in immune signaling. Other terms (peroxisomal protein import, cell division, translesion synthesis, cadmium response, viral process) are less central. Thus, the cluster appears to center on proteostasis with an associated immune signaling facet, with some stress-response signals contributing noise. ","confidence":"Medium","size":11,"edges":23,"triangles":26,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0016562","count":2}]},{"hash":"790560903128060983","title":"Translation initiation and cell cycle regulators","description":"The top GO terms center on regulating translation initiation (formation of preinitiation complex and initiation regulation) and cell cycle processes (cell cycle and cytokinesis), pointing to proteins that coordinate protein synthesis with cell division. Additional signals like Wnt pathway activation and differentiation terms suggest broader roles in growth and development, but the core theme remains translation control linked to proliferation. ","confidence":"Medium","size":11,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0043524","count":2}]},{"hash":"1784415146251840593","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0006564","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2}]},{"hash":"284395915777210991","title":"Unknown","description":"The top GO terms are highly diverse, spanning antibiotic and quinone biosynthesis, mRNA capping, neural development, various metabolic and catabolic processes, and a neural response term. There is no single coherent function or pathway linking these genes, suggesting a heterogeneous or annotation-mismatched cluster. ","confidence":"","size":11,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0021510","count":2}]},{"hash":"1844431813887951196","title":"Protein quality control and degradation pathways","description":"The cluster\u2019s GO terms center on ubiquitin-related processes (deubiquitination, ERAD), protein turnover and clearance (aggresome, aggrephagy), and supporting modifications (sumoylation, deglycosylation). Additional terms point to regulation of protein trafficking and signaling, all of which align with cellular protein homeostasis and degradation pathways that manage misfolded or damaged proteins and related cellular processes. ","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":8},{"id":"GO:0030433","count":6},{"id":"GO:1904049","count":5},{"id":"GO:0070842","count":5},{"id":"GO:0016925","count":5}]},{"hash":"108730576701181652","title":"Cerebellar development and cell cycle regulation","description":"The terms strongly point to cerebellar development, with cerebellar cortex formation and Bergmann glial cell differentiation highlighting neural development in the cerebellum. The presence of G1/S transition and negative regulation of CDK activity suggests a link to cell cycle control alongside differentiation. Other terms like insulin and T cell signaling may reflect broader signaling roles or annotation cross-talk, but the core theme appears to be cerebellar development with concurrent cell cycle regulation.","confidence":"Medium","size":11,"edges":24,"triangles":31,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045736","count":9},{"id":"GO:0034501","count":9},{"id":"GO:0008285","count":8},{"id":"GO:0050852","count":8},{"id":"GO:0048679","count":8}]},{"hash":"481464329802012665","title":"Mitochondrial Metabolite Transport","description":"The terms cluster around transport of metabolites across mitochondrial membranes (NAD, ornithine, alpha-ketoglutarate, pyrimidine nucleotides, malate-aspartate shuttle, manganese ions, and ATP) and associated mitochondrial metabolic processes. A few terms touch on cellular stress responses and death regulation, which can be linked to mitochondrial function, but the dominant theme is mitochondrial metabolite transport and exchange.","confidence":"Medium","size":11,"edges":13,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0090152","count":4},{"id":"GO:0035352","count":4},{"id":"GO:0034198","count":4},{"id":"GO:0000066","count":4},{"id":"GO:1990519","count":4}]},{"hash":"463769680062584357","title":"Ribosome maturation and cell cycle regulators","description":"The top GO terms cluster around ribosome maturation (5.8S and LSU rRNA processing) and cell cycle control (mitotic cell cycle, cell cycle, G1 DNA damage checkpoint signaling) with a note of cytokinesis regulation. This suggests proteins that coordinate ribosome biogenesis with cell division, even though a few terms relate to development. Overall, the core theme is coupling ribosome maturation to cell-cycle regulation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0032466","count":1},{"id":"GO:0072432","count":1}]},{"hash":"61976497658861706","title":"Ubiquitin-Mediated Turnover and Chromatin Regulation","description":"This cluster centers on ubiquitination and protein turnover (ERAD, protein ubiquitination) and also includes chromatin-related processes (histone catabolic regulation, histone acetylation regulation, X chromosome inactivation), with links to NF-kappaB/TNF signaling and receptor turnover (Wnt receptor catabolic process). The shared theme appears to be ubiquitin-dependent regulation of proteins and chromatin state influencing signaling and chromosome regulation.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0036205","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0007250","count":2},{"id":"GO:0060816","count":2}]},{"hash":"1360390498439593914","title":"Lipid Biosynthesis and Steroid Metabolism","description":"This cluster centers on lipid-related biosynthetic and metabolic processes, including fatty acid elongation, very long-chain fatty acids, mycolic acid biosynthesis, and steroid biosynthesis (glucocorticoid, testosterone) with related catabolic processes, suggesting a lipid metabolism/steroid production module. Some terms reflect broader catabolic activity, but the dominant signal is lipid and steroid pathways.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071768","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0006666","count":2},{"id":"GO:0030497","count":2},{"id":"GO:0006704","count":2}]},{"hash":"1944647633331513253","title":"Mycolic and long-chain fatty acid biosynthesis","description":"The top GO terms point strongly to lipid metabolism, especially long-chain and very long-chain fatty acid biosynthesis, including mycolic acid biosynthesis and fatty acid elongation, plus a sphingolipid precursor step (3-keto-sphinganine). These collectively define a cohesive theme of cell-envelope lipid production typical of mycobacterial or related bacteria. The other terms related to steroid biosynthesis (testosterone, glucocorticoid) and antibiotic response are less central to this lipid-focused cluster, and may reflect broader metabolic connections or annotation noise. Overall, the dominant signal is lipid and mycolic acid biosynthesis.","confidence":"High","size":11,"edges":9,"triangles":0,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0071768","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0006666","count":2}]},{"hash":"2189924448250430843","title":"Ribosome biogenesis and translation","description":"The dominant terms center on ribosome biogenesis, rRNA maturation, and translation initiation/elongation, indicating a cluster of proteins involved in assembling and operating the ribosome and translating mRNA. The presence of RNA methylation activity also fits with rRNA modification in the ribosome. The antibiotic response term likely reflects ribosome-targeting effects.","confidence":"High","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":4},{"id":"GO:0000463","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0046677","count":3}]},{"hash":"1098447519709394762","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":18,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":3},{"id":"GO:0042853","count":3},{"id":"GO:0043278","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0001701","count":2}]},{"hash":"1829291628538576976","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The top GO terms show strong enrichment for ubiquitin-dependent protein catabolic processes and protein polyubiquitination, pointing to proteasome-mediated degradation as the core function of this set. Additional terms related to ER-associated degradation and cell cycle/DNA damage checkpoints align with regulatory roles of ubiquitination in proteostasis and cell-cycle control, supporting a cohesive theme around ubiquitin-dependent proteolysis, with some developmental context.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0043966","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0007275","count":4}]},{"hash":"1934543949620014053","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010460","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0051000","count":1},{"id":"GO:0035998","count":1},{"id":"GO:0032496","count":1}]},{"hash":"1733339521728932274","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":14,"triangles":10,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":4},{"id":"GO:0000467","count":3},{"id":"GO:0071038","count":3},{"id":"GO:0034476","count":3},{"id":"GO:0031047","count":3}]},{"hash":"1923354925025066801","title":"Ubiquitin-Proteasome Regulation of the Cell Cycle","description":"This cluster is dominated by ubiquitin-dependent proteolysis (SCF and APC/C), with neddylation modulating these ligases, linking to cell cycle progression and division; additional members touch on DNA repair and redox/metal ion responses, reflecting cross-talk with proteostasis.","confidence":"High","size":10,"edges":13,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0070911","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0031145","count":3},{"id":"GO:0055114","count":2}]},{"hash":"1442458275079254488","title":"Membrane trafficking and cytoskeletal remodeling","description":"The GO terms cluster around membrane dynamics and cytoskeletal remodeling: regulation of spine/podosome formation, lysosome/endosome transport, and membrane tubulation. Some terms touch plant or reproductive processes, but the common theme is vesicle trafficking and actin remodeling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060999","count":2},{"id":"GO:0097212","count":1},{"id":"GO:1902647","count":1},{"id":"GO:0071803","count":1},{"id":"GO:0007289","count":1}]},{"hash":"2071328502629827261","title":"Cell Cycle and Vesicle Trafficking","description":"This cluster centers on mitotic cell cycle and cell division, and is complemented by vesicle trafficking and membrane localization activities (leading edge localization, endosomal transport to postsynaptic membrane, and vacuole fusion regulation). The combination suggests a module coordinating cell cycle progression with intracellular transport and signaling at membranes, with additional regulatory and stress-response terms present. ","confidence":"Medium","size":10,"edges":24,"triangles":23,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":5},{"id":"GO:1903395","count":4},{"id":"GO:0042088","count":4},{"id":"GO:0046677","count":4}]},{"hash":"675390011681921999","title":"Genome replication and transcription control","description":"This cluster is dominated by core genome maintenance and gene expression processes: DNA replication (GO:0006260), transcription regulation by RNA polymerases I and II (GO:0006363, GO:0045944, GO:0019079), and ancillary protein handling (GO:0070389, GO:0031204), suggesting a cohesive theme around genome-wide transcriptional and replicative machinery, with some developmental context terms present as broader annotations. ","confidence":"Medium","size":10,"edges":43,"triangles":104,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0000742","count":3},{"id":"GO:0006363","count":2},{"id":"GO:0019079","count":2}]},{"hash":"980645555055005556","title":"Unknown","description":"The GO terms span diverse biological areas (RNA methylation, GTPase regulation, DNA damage response, plant pattern formation, mitotic cell cycle, osteoblast differentiation, ER-stress\u2013induced apoptosis, TORC1 signaling, glial apoptosis, and male gonad development) with no clear common function or pathway. There are no edges connecting proteins, suggesting a heterogeneous set rather than a cohesive functional cluster. Therefore there\u2019s no single representative theme to give a precise, concise label.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0036265","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0072432","count":3},{"id":"GO:2000011","count":3},{"id":"GO:0000278","count":3}]},{"hash":"324338274340921612","title":"Developmental signaling and morphogenesis","description":"The top GO terms cluster around organismal development and morphogenesis across multiple tissues (heart, skeletal system, nervous system, mesoderm formation) with supporting signaling and adhesion processes (Rho signaling, cell-matrix adhesion, growth hormone receptor signaling) and calcium-dependent exocytosis. While \u201cpseudohyphal growth\u201d is a specific fungal process, the overall theme is morphogenesis and developmental signaling, making this label representative of the cluster\u2019s functions. ","confidence":"High","size":10,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":2},{"id":"GO:0007124","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0007160","count":2},{"id":"GO:0007507","count":2}]},{"hash":"31508360205379683","title":"Embryonic Organogenesis and Tissue Development","description":"The proteins are associated with embryonic organ development, spinal cord and skin development, and general multicellular growth, indicating involvement in developmental and tissue-formation processes. The presence of cell proliferation and mitotic-related terms reinforces a proliferative developmental function, justifying a label centered on organogenesis and tissue development.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035264","count":4},{"id":"GO:0072520","count":4},{"id":"GO:0048568","count":4},{"id":"GO:0021510","count":4},{"id":"GO:0008283","count":4}]},{"hash":"343851334849851018","title":"ER-Golgi vesicle trafficking","description":"This cluster is dominated by GO terms for ER-to-Golgi vesicle transport and retrograde Golgi-to-ER transport, plus general protein transport and regulation of GTPase activity. The strongest signal is vesicle trafficking within the secretory pathway, with a few additional terms (mitotic spindle assembly, development) that may reflect broader roles or annotation noise. Therefore, a concise label focusing on ER-Golgi vesicle trafficking captures the core function shared by these proteins.","confidence":"Medium","size":10,"edges":14,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0010255","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0006890","count":2}]},{"hash":"1055913474222821804","title":"Unknown","description":"The top GO terms are a mix of translation initiation and reinitiation, GTPase regulation, splicing, TORC1 signaling, centriole cohesion, and various developmental processes, with no cohesive shared function linking all terms, so a single meaningful label cannot be determined.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0048025","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:1904501","count":2}]},{"hash":"791597698512601715","title":"Epithelial cilium assembly and movement","description":"The top terms center on ciliogenesis and ciliary motility in epithelial tissues (axonemal central apparatus assembly, epithelial cilium movement, trachea development), which provides a cohesive theme despite some unrelated nucleotide biosynthesis terms that may reflect general cellular metabolism. Overall, the strongest signal is cilia-related processes in epithelia.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046940","count":1},{"id":"GO:0006241","count":1},{"id":"GO:0002064","count":1},{"id":"GO:0044209","count":1},{"id":"GO:0003351","count":1}]},{"hash":"1856671781029949880","title":"Mitochondrial Metabolite Transport","description":"The top GO terms point to transport of a variety of metabolites across mitochondrial membranes (heme, NAD, alpha-ketoglutarate, malate, ornithine, pyrimidines, ATP) and related mitochondrial localization, with a note on amino acid starvation response, indicating transporter or transport-associated functions within mitochondria.","confidence":"High","size":10,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":9},{"id":"GO:0090152","count":8},{"id":"GO:0035352","count":8},{"id":"GO:0034198","count":8},{"id":"GO:0000066","count":8}]},{"hash":"2161291463846272387","title":"Cell Cycle and Genome Maintenance with Proteostasis","description":"The cluster includes mitotic cell cycle terms (mitotic cell cycle, G2/M transition), DNA repair (NHEJ), and ubiquitin-proteasome\u2013mediated protein quality control and histone ubiquitination, indicating a focus on genome integrity and protein turnover during cell division. The ER stress\u2013linked apoptotic pathway and IL-1\u2013related cellular response reflect stress signaling that can couple to cell-cycle decisions and genome maintenance. Developmental terms (in utero embryonic development, neuron projection development) fit within broader embryogenesis where precise cell-cycle control and proteostasis are essential. Overall, these proteins appear to coordinate cell-cycle progression, DNA repair, and proteostasis in response to cellular stress and developmental cues.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071347","count":10},{"id":"GO:0001701","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0033182","count":10},{"id":"GO:0070059","count":10}]},{"hash":"468265033306343021","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by ribosome-related processes, including ribosomal subunit biogenesis (small and large subunits), ribosome export from the nucleus, and cytoplasmic translation, along with tRNA modification, pointing to a core function in assembling and using ribosomes for protein synthesis. Some energy or division-related terms appear, but the main theme centers on ribosome biogenesis and translation.","confidence":"High","size":10,"edges":10,"triangles":2,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0042254","count":3},{"id":"GO:1901001","count":3},{"id":"GO:1903833","count":3}]},{"hash":"2207591908198657086","title":"RNA processing and mRNA turnover","description":"This cluster shows strong signals for RNA processing and mRNA fate, with splicing (cis splicing via spliceosome; spliceosomal complex assembly), mRNA decay (deadenylation-dependent decapping) and P-body assembly, plus rRNA maturation and transcription termination. A couple of chromatin-related terms (pericentric heterochromatin formation, histone mRNA metabolism) suggest broader coupling with chromatin regulation, but the dominant theme is RNA processing and mRNA turnover.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:1990141","count":5},{"id":"GO:0000245","count":5},{"id":"GO:0030490","count":5},{"id":"GO:0006369","count":5}]},{"hash":"538820667389738187","title":"Ubiquitin-Dependent Inflammatory Signaling and Histone Regulation","description":"The cluster centers on ubiquitin-related processes (K6-linked ubiquitination, H2A K63-linked ubiquitination, ubiquitin-dependent proteolysis), histone turnover/regulation, and inflammatory pathways such as NF-kappaB and TNF signaling, with JNK involvement, suggesting a cohesive module linking ubiquitination, chromatin dynamics, and inflammatory signaling.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":2},{"id":"GO:0007250","count":2},{"id":"GO:2000620","count":2},{"id":"GO:1903265","count":2},{"id":"GO:1903762","count":2}]},{"hash":"1539900131684884747","title":"Fatty Acid Biosynthesis and Transport","description":"The top GO terms center on fatty acid biosynthesis, transport/import of long- and medium-chain fatty acids, and broader lipid metabolism (including retinol metabolism and LPS biosynthesis), suggesting a cohesive function in fatty acid production and intracellular lipid handling. ","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1902987","count":4},{"id":"GO:0006633","count":4},{"id":"GO:0006069","count":4},{"id":"GO:0006068","count":4},{"id":"GO:0042572","count":4}]},{"hash":"1568797030594150555","title":"Redox Metabolism and Quinone Biosynthesis","description":"The top GO terms cluster around energy metabolism and redox balance: TCA cycle, redox homeostasis, glutathione metabolism, and several quinone biosynthesis pathways (menaquinone and phylloquinone) that feed into electron transport. A few terms appear as noise (e.g., pituitary gland development, obsolete terms), but the core theme ties metabolism to redox processes and quinone biosynthesis. Confidence in this label is Medium.","confidence":"","size":9,"edges":14,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0021983","count":2}]},{"hash":"1419791819652260533","title":"Proteostasis and chaperone function","description":"This cluster shows a coherent signal around protein quality control and folding, including ubiquitin-proteasome\u2013mediated quality control, misfolded protein transport, and chaperone-assisted protein refolding, suggesting a proteostasis-focused grouping. Some annotations (e.g., mesoderm formation, tRNA import) appear unrelated and may reflect noise, but the strongest theme is proteostasis. ","confidence":"Medium","size":9,"edges":17,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071630","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0006452","count":1},{"id":"GO:1905259","count":1}]},{"hash":"2222233468949042195","title":"DNA replication, repair, and RNA processing","description":"The cluster is dominated by terms tied to DNA metabolism and RNA processing: DNA replication, DNA repair, DNA-templated transcription, mRNA processing, and phosphorylation, suggesting a nuclear genome maintenance and gene expression module. Some telomere- and wound-related terms appear but are secondary to the core DNA/RNA processing theme.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009611","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0051973","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1904355","count":2}]},{"hash":"1265909370958313587","title":"Cell growth, division, and ER-Golgi transport","description":"The cluster\u2019s top GO terms emphasize mitotic cell cycle, spindle assembly, and proliferation (cell growth), along with ribosome biogenesis and DNA-templated transcription, suggesting active growth and division. The concurrent trafficking terms (COPII vesicle budding and Golgi-ER/ER-Golgi transport) point to secretory pathway activity that supports protein synthesis and membrane dynamics during proliferation. Together, these functions reflect a cohesive theme of cellular growth and division coordinated with the ER\u2013Golgi secretory system.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0090114","count":4},{"id":"GO:0006890","count":4}]},{"hash":"2202221346269628386","title":"Multisystem Development and Differentiation","description":"The GO terms span development and differentiation across multiple tissues (lung, urogenital system, erythrocyte and eosinophil lineages, enterocytes, gonads, aortic valve morphogenesis, parathyroid secretion), plus an interleukin-4\u2013related response. There isn\u2019t a single cohesive pathway, so the label reflects a broad theme of organ/tissue development and differentiation rather than a specific function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":2},{"id":"GO:0060430","count":1},{"id":"GO:0001655","count":1},{"id":"GO:0010724","count":1},{"id":"GO:0071733","count":1}]},{"hash":"275617275095927201","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2000616","count":1},{"id":"GO:0072715","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0009307","count":1}]},{"hash":"790477660845477150","title":"Quinone biosynthesis and related metabolism","description":"The cluster\u2019s top GO terms cluster around biosynthesis of quinones (menaquinone and phylloquinone) and various small-molecule metabolism and catabolic processes (antibiotic biosynthesis, fatty acid beta-oxidation, alanine and kynurenine catabolism, oxaloacetate metabolism). This suggests a cohesive theme focused on production and turnover of key cofactors and metabolites, with quinone biosynthesis as a central motif. The presence of Notch signaling appears as an outlier, possibly due to cross-annotation or noise. ","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0006635","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0042372","count":3}]},{"hash":"1882242237669737734","title":"ER-Golgi trafficking and translation initiation","description":"The presence of ER-Golgi transport and ER retention terms (ER to Golgi, Golgi to ER, ER lumen retention) together with translation initiation signals (eIF4F assembly, translational initiation) suggests a shared theme around secretory pathway trafficking plus initiation of protein synthesis, with some development terms likely incidental.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":1},{"id":"GO:0090004","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0071340","count":1}]},{"hash":"1155230869451880903","title":"Nuclear protein quality control and folding","description":"This cluster centers on protein quality control and folding processes, especially nuclear ubiquitin-proteasome\u2013mediated QC, misfolded protein transport, and chaperone/refolding activities. While a few terms (mesoderm formation, tRNA import into nucleus, redox homeostasis) are less directly tied to QC, the dominant theme is maintaining proteome integrity and proper folding, with several terms explicitly pointing to nuclear QC and related transport.","confidence":"Medium","size":9,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071630","count":3},{"id":"GO:0097428","count":3},{"id":"GO:0001707","count":3},{"id":"GO:0006452","count":3},{"id":"GO:0035719","count":3}]},{"hash":"1155218201250568018","title":"Protein biogenesis and folding","description":"The cluster\u2019s top GO terms cluster around fundamental protein production and maturation processes (DNA-templated transcription, translation, protein folding, and protein maturation/glycosylation). While there are a few immune and developmental terms, they appear less representative of the overall theme, which points to general cellular protein biogenesis. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0019731","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0006412","count":1}]},{"hash":"2126333804763093804","title":"Actin Cytoskeleton Dynamics and Lamellipodium Formation","description":"The cluster is dominated by GO terms related to actin filament polymerization, network formation, movement, and lamellipodium assembly, pointing to actin cytoskeleton remodeling and protrusive motility as the core function. Other terms touch on broader cytoskeletal organization (e.g., stress fibers) and related processes (mitochondrial fission), but the strongest signal is actin dynamics and lamellipodium-related activity.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007121","count":2},{"id":"GO:0030032","count":1},{"id":"GO:0090140","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0051639","count":1}]},{"hash":"1620787163778455987","title":"Ubiquitin-Proteasome Regulation & DNA Damage Response","description":"This cluster centers on ubiquitination processes: ubiquitin-dependent protein degradation and regulation of polyubiquitination, along with mitotic G1 DNA damage checkpoint signaling and regulation of DNA-templated DNA replication initiation. These terms together point to a core function in ubiquitin-mediated proteolysis linked to DNA damage response and cell cycle control, with some peripheral terms related to neuronal stress responses and metal exposure that are less central to the main theme.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0031571","count":2},{"id":"GO:0030174","count":2},{"id":"GO:0060386","count":2},{"id":"GO:1903378","count":2}]},{"hash":"884835684717089872","title":"Th2-Driven MHC II Upregulation","description":"The cluster is enriched for Th2 differentiation, IL-4 signaling, and MHC class II biosynthesis regulation, pointing to a role in antigen presentation and Th2-skewed immune responses; other terms about transcription and ER stress may reflect broader regulatory contexts but do not override the core theme.","confidence":"High","size":9,"edges":35,"triangles":77,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045348","count":4},{"id":"GO:0045064","count":4},{"id":"GO:1990440","count":4},{"id":"GO:0071353","count":4},{"id":"GO:0006990","count":4}]},{"hash":"1151686084219975497","title":"Genome stability: DNA repair and telomere maintenance","description":"This cluster is dominated by terms tied to DNA metabolism (DNA recombination, DNA repair) and telomere biology (telomere maintenance and localization to telomeres) as well as mitotic checkpoint signaling, indicating a core theme of genome stability and telomere maintenance. The presence of translation and tRNA modification terms may reflect multifunctional or moonlighting roles, but the primary signal is DNA repair/ telomere-related processes.","confidence":"Medium","size":9,"edges":10,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006422","count":4},{"id":"GO:0072581","count":4},{"id":"GO:0006310","count":4},{"id":"GO:0002101","count":4},{"id":"GO:0071915","count":4}]},{"hash":"468657433594094941","title":"Glutathione-Dependent Redox Detoxification","description":"The cluster is centered on detoxification and redox balance, with GO terms like cellular oxidant detoxification, cell redox homeostasis, and glutathione metabolic process indicating a core role in oxidative stress management via glutathione pathways. Some other terms (transcriptional regulation, oligodendrocyte development, nitrogen utilization) are less central and may reflect secondary annotations or broader cellular contexts.","confidence":"High","size":9,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0006749","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0000122","count":2}]},{"hash":"648233509218964003","title":"Hematopoietic differentiation regulators","description":"The cluster\u2019s top GO terms are dominated by positive regulation of erythrocyte and megakaryocyte differentiation and related primitive erythrocyte differentiation, pointing to a hematopoietic lineage focus. Additional terms cover broader organ development, which can arise from shared developmental regulators, but the strongest signal remains blood cell lineage commitment.","confidence":"Medium","size":9,"edges":16,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045648","count":4},{"id":"GO:0045654","count":4},{"id":"GO:0010725","count":4},{"id":"GO:0021983","count":3},{"id":"GO:0008584","count":3}]},{"hash":"480182427685947760","title":"Ribosome Biogenesis and Translation","description":"Proteins in this cluster center on ribosome production and function: cytoplasmic translation, ribosome assembly (including the large subunit and overall ribosome assembly), and maturation/processing of SSU rRNA. The GO terms collectively point to ribosome biogenesis and protein synthesis, with some RNA processing aspects accompanying rRNA maturation, supporting a cohesive theme around the ribosome and translational machinery.","confidence":"High","size":9,"edges":29,"triangles":46,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0042255","count":1}]},{"hash":"672141298784103022","title":"Glyoxysome- and lipid metabolism","description":"The cluster\u2019s top GO terms center on peroxisome/glyoxysome\u2013related metabolism (glyoxysome organization; L-isoleucine and propionyl-CoA catabolic pathways) and lipid-related processes (adipose tissue development, cholesterol transport, PHB biosynthesis). Some terms also touch on hormone response and mitochondrial apoptotic regulation, suggesting a module that links metabolic pathways within peroxisomes/mitochondria to broader lipid signaling and stress responses. Overall, this points to a peroxisomal/lipid metabolism-focused cluster.","confidence":"Medium","size":8,"edges":20,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006550","count":4},{"id":"GO:0060612","count":4},{"id":"GO:0010111","count":4},{"id":"GO:0019619","count":4},{"id":"GO:1902109","count":4}]},{"hash":"381654281251787620","title":"SNARE-Driven Synaptic Vesicle Trafficking and Receptor Insertion","description":"The top GO terms point to secretory pathway trafficking (ER-Golgi, intra-Golgi, Golgi transport), SNARE complex assembly, and exocytic insertion of neurotransmitter receptors at the postsynaptic membrane, all central to SNARE-mediated vesicle fusion and synaptic plasticity (LTP). A minor autophagy term is present but does not define the cluster.","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0032258","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0048280","count":2}]},{"hash":"179373255111841353","title":"DNA replication and repair during the cell cycle","description":"Top GO terms are strongly centered on DNA replication, DNA repair, DNA-templated transcription, and mitotic cell cycle, indicating a nuclear DNA maintenance and cell-cycle regulation theme. Some cortex morphogenesis and chemotaxis terms may reflect broader annotations or secondary roles, but the core signals point to genome maintenance during cell division. This suggests a cohesive cluster of proteins involved in DNA replication/repair and associated transcription during mitosis.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006281","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0000902","count":4}]},{"hash":"772896753263122585","title":"Ubiquitin-Dependent Proteolysis and Cytoskeletal Regulation","description":"This cluster centers on ubiquitin-proteasome\u2013mediated protein degradation (SCF-dependent, ERAD, autoubiquitination, MVB sorting) and proteolysis, with supporting signals related to actin filament depolymerization and regulation of signaling pathways (GTPase activity, JNK). The shared theme is proteostasis intersecting with cytoskeletal remodeling and development. Forebrain development may reflect downstream effects or related substrates, but the core link is ubiquitin-dependent degradation coupled to cytoskeletal regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0030900","count":2}]},{"hash":"636809521452609941","title":"Unknown","description":"The top GO terms are highly diverse, spanning chromatin remodeling, regulation of DNA repair, various organ developmental processes (neural tube patterning, Sertoli cell development, otic vesicle, gallbladder, trachea glands) and dendritic cell differentiation/activation. There is no clear, shared function or pathway linking these proteins, and the cluster has no edges or triangles to suggest a cohesive mechanism. Therefore, no specific, representative label can be confidently assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0032425","count":1},{"id":"GO:0021903","count":1},{"id":"GO:0033234","count":1},{"id":"GO:2001200","count":1}]},{"hash":"1388731486204032699","title":"Oxidative stress response and redox homeostasis","description":"The cluster shows a clear enrichment for redox-related terms (cell redox homeostasis; cellular oxidant detoxification; cellular response to oxidative stress), suggesting a primary theme of managing oxidative stress. Additional terms point to proteostasis (protein folding in the ER, protein repair) and transcriptional regulation (DNA-templated transcription, RNA Pol II regulation), which together imply a coordinated response that links redox balance with gene expression and protein quality control. A few terms (e.g., viral process) may reflect broader regulatory connections rather than a core function, but the dominant signal is redox homeostasis and oxidative stress response.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0098869","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0046826","count":2},{"id":"GO:1903206","count":2}]},{"hash":"1645878305363845603","title":"Neuronal synapse signaling and organization","description":"The top GO terms point to neural communication and synaptic function, including synaptic vesicle targeting, synapse organization, and retrograde signaling by nitric oxide, as well as behavior linked to neural activity (vocalization). While some terms are broader, the shared emphasis on synaptic signaling and neuronal communication supports a cohesive label for this cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015879","count":1},{"id":"GO:0071625","count":1},{"id":"GO:0010205","count":1},{"id":"GO:0016080","count":1},{"id":"GO:0030111","count":1}]},{"hash":"2039554647936145886","title":"Unknown","description":"The GO terms here span neural-development roles (striatum, cerebellar cortex, thalamus) and several core metabolic/biosynthetic processes (glycolysis, glyceraldehyde-3-phosphate, glyoxylate, xylulose, terpenoid) plus a chloramphenicol response, with no edges connecting the proteins. This lack of a unifying function or interaction pattern suggests no single cohesive cluster function can be inferred.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021756","count":2},{"id":"GO:0021695","count":1},{"id":"GO:0046166","count":1},{"id":"GO:0072747","count":1},{"id":"GO:0052865","count":1}]},{"hash":"1324389420055455937","title":"Vesicle trafficking and secretion","description":"The Top Terms emphasize exocytic and trafficking processes: exocyst localization, exocytosis, Golgi to plasma membrane transport, endosome organization, and ECM disassembly, which together reflect the secretory pathway moving materials to the cell surface and remodeling the extracellular matrix. Other terms like spliceosomal assembly, meiosis cytokinesis, and pollen acceptance appear less central to the core theme, but may reflect broader cellular roles or species-specific processes. Overall, a vesicle trafficking/secretion theme best captures the shared functions.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":1},{"id":"GO:0007110","count":1},{"id":"GO:0045199","count":1},{"id":"GO:0007111","count":1},{"id":"GO:0051601","count":1}]},{"hash":"515319258368928854","title":"Cell cycle and ribosome biogenesis","description":"These GO terms cluster around core processes of growth and division: ribosomal biogenesis, mitotic cell cycle, and TORC1 signaling suggest protein synthesis and cell cycle progression as central roles. The DNA damage checkpoint signaling and apoptotic terms reflect stress responses linked to division, while outlier terms about development and differentiation are peripheral. Overall, the dominant theme is regulation of cell growth and division.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000920","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0072432","count":2},{"id":"GO:2000011","count":2}]},{"hash":"1101050232592963686","title":"Mitochondrial Metabolite Transport","description":"The cluster is dominated by GO terms for transport of metabolites and ions across the mitochondrial membrane (NAD, malate-aspartate shuttle, alpha-ketoglutarate, pyrimidine nucleotides, manganese, ornithine) and a cellular response to amino acid starvation, indicating proteins functioning as mitochondrial metabolite transporters and related metabolic roles; a couple of terms are ancillary, but the main theme is clear. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090152","count":1},{"id":"GO:0035352","count":1},{"id":"GO:0034198","count":1},{"id":"GO:0000066","count":1},{"id":"GO:1990519","count":1}]},{"hash":"1779128160431618473","title":"Mitotic Chromosome Alignment and Segregation","description":"The top GO terms are strongly centered on mitosis and chromosome handling (mitotic sister chromatid separation, mitotic metaphase chromosome alignment, regulation of centriole-centriole cohesion), suggesting a core theme around mitotic chromosome dynamics. A few other terms (TORC1 signaling, GTPase activity, pseudopodium and viral processes) are broader or peripheral, but do not dominate the cluster. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904501","count":1},{"id":"GO:0030997","count":1},{"id":"GO:0051306","count":1},{"id":"GO:0038202","count":1},{"id":"GO:0031274","count":1}]},{"hash":"1760938048330419452","title":"Mitochondrial and peroxisomal dynamics and metabolism","description":"The dominant GO terms center on mitochondria and peroxisomes\u2014fission, protein import into the mitochondrial matrix, and regulation of membrane permeability\u2014along with lipid metabolism (triglyceride biosynthesis) and ethanol response. This points to a cohesive theme of organelle dynamics and mitochondrial-associated metabolism, with a minor cell-cycle regulatory signal that does not obscure the main pattern.","confidence":"High","size":8,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045471","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0016559","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0010867","count":2}]},{"hash":"1888678299921775047","title":"Embryonic organogenesis","description":"The top GO terms point to morphogenesis across multiple organs\u2014midgut, optic cup, heart, neural tube, and digestive tract\u2014indicating a cohesive theme of embryonic organ development. Supporting terms include signaling and metabolic processes that can underpin developmental programs, but the dominant pattern is organogenesis during embryogenesis.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0007494","count":1},{"id":"GO:0006540","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0002072","count":1}]},{"hash":"394816202300078030","title":"Mitochondrial metabolite transport","description":"The cluster is dominated by GO terms describing transport of various metabolites across mitochondrial membranes (e.g., alpha-ketoglutarate, NAD, pyrimidines, ATP, ornithine) and related shuttle systems, pointing to a core role in mitochondrial metabolite exchange and energy metabolism; secondary terms relating to insulin signaling or amino acid starvation likely reflect metabolic state rather than defining the cluster\u2019s primary function.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0090152","count":1},{"id":"GO:0035352","count":1},{"id":"GO:0034198","count":1},{"id":"GO:0000066","count":1}]},{"hash":"199791185868665398","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0006189","count":2},{"id":"GO:0009060","count":2}]},{"hash":"512094903679748901","title":"Transmembrane transport of amino acids and metabolites","description":"Top terms are multiple transmembrane transport processes for amino acids and related metabolites (branched-chain amino acids, methionine, glycine betaine, cysteine) plus peptide export and drug/antibiotic transport. This points to a cohesive cluster of membrane transporters for amino acids and small molecules.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0000770","count":1},{"id":"GO:1900753","count":1},{"id":"GO:0090374","count":1},{"id":"GO:0042883","count":1}]},{"hash":"485190607911891248","title":"RNA Processing and mRNA Metabolism","description":"This cluster is dominated by RNA-centric processes: transcription termination, spliceosome assembly and mRNA splicing, P-body assembly, and deadenylation-dependent decapping, plus maturation of rRNA and histone mRNA metabolism. While a couple terms touch on chromatin or stress responses, the core theme is RNA processing and post-transcriptional regulation.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":4},{"id":"GO:1990141","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0030490","count":3},{"id":"GO:0045292","count":3}]},{"hash":"1992530302239846354","title":"Developmental transcription and chromatin dynamics","description":"The cluster\u2019s top GO terms center on developmental processes (multicellular growth, spermatid development, brain development) alongside nuclear transcription and RNA processing (RNA Pol III transcription, mRNA deadenylation and non-stop decay) and chromatin regulation (rDNA and pericentric heterochromatin formation). This suggests a theme of nuclear gene expression control during development, tying transcriptional activity to chromatin state, rather than a single metabolic pathway. Confidence: Medium.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0007286","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006383","count":2},{"id":"GO:0000288","count":2}]},{"hash":"1791561913424613678","title":"Unknown","description":"The GO terms are highly diverse and span animal (platelet activation), plant (lignin catabolic process), and microbial processes (FtsZ cytokinesis, sporulation, antibiotic biosynthesis) along with various metal ion transport activities. There is no clear, cohesive function linking these terms to a single biological theme, so a reliable cluster label cannot be determined.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030168","count":1},{"id":"GO:0046274","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0033215","count":1},{"id":"GO:0006825","count":1}]},{"hash":"901806188639684054","title":"Ribosome and Translation Machinery","description":"Dominant signals are translation-related GO terms (translation, translational initiation, ribosome biogenesis) and ribosomal activity (mitochondrial translation, ribosome assembly/disassembly), indicating proteins involved in ribosome function and protein synthesis. Some spliceosome-related terms appear but likely reflect broader RNA processing linked to translation.","confidence":"High","size":8,"edges":15,"triangles":11,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0070125","count":2},{"id":"GO:0032790","count":2}]},{"hash":"1709762320246115372","title":"Neurodevelopmental Transcription Regulation","description":"The cluster shows strong signals for neural/brain development (forebrain development, neural tube closure) and general developmental processes (multicellular organism development) along with DNA-templated transcription, pointing to transcriptional control during neurodevelopment as the core theme. Some stress/immune terms are present but are likely secondary annotations to a subset of proteins.","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0071276","count":3}]},{"hash":"126345856183404307","title":"ER-Golgi vesicle transport and TORC1 signaling","description":"The terms cluster around ER-Golgi trafficking, including both retrograde and anterograde transport, with GTPase regulation and ubiquitination suggesting coordination by vesicle trafficking machinery; TORC1 signaling appears as a related growth/regulatory context, making a cohesive theme of vesicle transport coupled to signaling pathways.","confidence":"Medium","size":7,"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:0051028","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0006890","count":3}]},{"hash":"1889809416873043081","title":"Golgi-mediated vesicle trafficking and secretion","description":"The GO terms are dominated by vesicle transport and targeting events\u2014Golgi vesicle fusion to membranes, Golgi-to-vacuole transport, vacuole targeting, plasma membrane localization, and neurotransmitter secretion\u2014along with related autophagy processes. This pattern suggests a cluster of proteins involved in Golgi- and vesicle\u2011mediated trafficking and secretion rather than a single metabolic pathway.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000272","count":1},{"id":"GO:0005977","count":1},{"id":"GO:0048210","count":1},{"id":"GO:0010807","count":1},{"id":"GO:0006914","count":1}]},{"hash":"1324329969699770699","title":"Unknown","description":"The GO terms span muscle development, brain structure development, fungal spore assembly, actin/patch formation, endocytosis, protein regulation (sumoylation and phosphorylation), mitochondrial localization, memory, and neurotransmitter secretion. This mix indicates no single coherent function or pathway tying all proteins together, suggesting the cluster cannot be sensibly named beyond Unknown.","confidence":"","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0030476","count":2},{"id":"GO:0000147","count":2},{"id":"GO:0030100","count":2}]},{"hash":"1136005275010792815","title":"Cell cycle and cytoskeleton regulation","description":"This cluster is dominated by GO terms about regulating the cell cycle, centrosome/centriole dynamics, chromatin-related transcription regulation, and cytoskeletal remodeling (pseudopodium assembly, GTPase activity). These reflect a common theme of controlling cell division and the cytoskeleton, with some developmental signaling terms that are likely peripheral. Hence a concise label capturing cell cycle control and cytoskeleton regulation fits best.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007050","count":5},{"id":"GO:1904501","count":4},{"id":"GO:0030997","count":4},{"id":"GO:0031274","count":4},{"id":"GO:0043547","count":4}]},{"hash":"1629752514112280932","title":"Unknown","description":"The top GO terms cover diverse areas including cell cycle control (mitotic cell cycle, G1 DNA damage checkpoint signaling), stress-induced apoptosis (ER stress\u2013related, glial apoptotic process), various developmental processes (adaxial/abaxial pattern formation, osteoblast differentiation, male gonad development), and signaling/modification processes (TORC1 signaling, GTPase activation, RNA guanine-N7 methylation). This broad and disparate mix provides no single coherent function that ties the cluster together, so a specific, representative label isn\u2019t justifiable.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0072432","count":3},{"id":"GO:2000011","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001649","count":3},{"id":"GO:0070059","count":3}]},{"hash":"2141128533323900148","title":"Hydrogen sulfide biosynthesis and transsulfuration","description":"The strongest terms are sulfur metabolism-related: L-cysteine biosynthesis via cystathionine, transsulfuration, and hydrogen sulfide biosynthetic processes, which together point to H2S production as the core function. The other GO terms are diverse developmental processes that may reflect broader or pleiotropic roles, but do not overshadow the central sulfur metabolism signal.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019343","count":3},{"id":"GO:0019346","count":3},{"id":"GO:0070814","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0007494","count":2}]},{"hash":"43484631078475960","title":"Neural development and synaptic signaling","description":"The proteins in this cluster are best characterized by terms related to nervous system development, excitatory synaptic activity, and calcium-dependent exocytosis, with a notable emphasis on dopamine-responsive signaling and neural differentiation. While a few terms touch on unrelated processes like mitotic cell cycle or heart development, the dominant signals point to neural development and synaptic communication through calcium-triggered secretion.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0045956","count":5},{"id":"GO:0007507","count":4}]},{"hash":"1315740127223941376","title":"GTPase-regulated vesicle trafficking and TORC1 signaling","description":"The top GO terms center on GTPase activity regulation, ER-Golgi vesicle transport and retrograde transport, TORC1 signaling, and related processes like mRNA transport and cell division. This suggests a cohesive theme of small GTPase\u2013driven vesicle trafficking intertwined with growth-signaling pathways, even though the proteins show no direct interactions in the graph. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0007143","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0038202","count":2}]},{"hash":"1520756749698326326","title":"Mitochondrial energy metabolism and redox regulation","description":"The prominent terms center on mitochondrial electron transport (ETC NADH to ubiquinone) and glutathione-related redox processes (glutathione metabolism and glutathionylation), with supporting amino-acid catabolism. Developmental GO terms are present but seem less central to the cluster's main metabolic theme.","confidence":"Medium","size":7,"edges":12,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":4},{"id":"GO:0006749","count":3},{"id":"GO:0006212","count":3},{"id":"GO:0006550","count":3},{"id":"GO:0042853","count":3}]},{"hash":"2014070648670327570","title":"Unknown","description":"The Top Terms are diverse and only loosely related, spanning lipid translocation and dephosphorylation, ion homeostasis and membrane electrochemical gradient maintenance, a serine biosynthesis pathway, and even neural/muscle-related terms, with no detectable shared biological process or pathway or protein\u2013protein interactions (no edges). This lack of a coherent theme makes it inappropriate to assign a meaningful label beyond Unknown.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097755","count":2},{"id":"GO:0061092","count":2},{"id":"GO:0021650","count":2},{"id":"GO:0006883","count":2},{"id":"GO:0010248","count":2}]},{"hash":"726981922998171335","title":"Amino Acid and Peptide Transporters","description":"These proteins cluster around membrane transport of small molecules and peptides: amino acids (including branched-chain and cysteine), oligopeptides, vitamins, and peptide pheromones, with notes of peptide export and transporter-related drug/g net activities. The MHC class Ib TAP-dependent peptide transport reference further supports a theme of peptide translocation into compartments. Overall, the GO terms point to a transport-focused module rather than a single discrete pathway, centered on membrane transport and peptide handling. ","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":2},{"id":"GO:0000770","count":1},{"id":"GO:1900753","count":1},{"id":"GO:0090374","count":1},{"id":"GO:0042883","count":1}]},{"hash":"226395501089436761","title":"Eye pigmentation and retinal development via organelle acidification","description":"This cluster\u2019s top GO terms center on eye biology (retina development and eye pigmentation) and on proton transport/vacuolar acidification, suggesting a role for organelle pH regulation in pigment formation and eye development. Additional terms related to cell cycle and signaling may be secondary, but do not override the core theme of eye pigmentation tied to acidification.","confidence":"Medium","size":7,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0061075","count":3},{"id":"GO:0015991","count":3},{"id":"GO:0007035","count":3},{"id":"GO:0048069","count":3},{"id":"GO:1904501","count":2}]},{"hash":"1229967740792702068","title":"Cell Cycle Regulation and Division","description":"The top GO terms cluster around cell division, mitotic cell cycle, and regulation of cytokinesis, pointing to a core theme of cell proliferation control. While some terms relate to broader growth or development (e.g., TORC1 signaling, ER stress\u2013linked apoptosis, pattern formation, osteoblast differentiation), the strongest signals are about cell cycle progression and cytokinesis regulation. This suggests the proteins collectively participate in coordinating division and growth responses.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000920","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0032466","count":1},{"id":"GO:0072432","count":1}]},{"hash":"1292183024674682526","title":"Central Metabolism & Biosynthesis","description":"This cluster shows enrichment for TCA cycle, succinyl-CoA and acetyl-CoA biosynthetic processes, and serine biosynthesis, highlighting core carbon metabolism and biosynthetic pathways. The presence of lipopolysaccharide biosynthesis and iron-sulfur cluster-related terms suggests additional biosynthetic and redox-associated roles, while transcription-related terms may reflect regulatory connections or annotation noise. Overall, the dominant theme is central metabolism with associated biosynthetic activities.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0006104","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006085","count":2},{"id":"GO:0006564","count":2}]},{"hash":"604852514703824821","title":"Unknown","description":"The top GO terms span ribosome biogenesis, RNA- and DNA-related processes, viral life cycle and membrane fusion, plant development (sepal formation, photomorphogenesis), leukocyte migration, and protein folding, with only sparse connectivity (one edge) among a highly diverse set. There isn't a single cohesive function or pathway tying these terms together, so a meaningful, specific cluster label cannot be inferred.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0042273","count":2},{"id":"GO:1902979","count":1},{"id":"GO:0019058","count":1},{"id":"GO:0006278","count":1}]},{"hash":"404136657014447892","title":"RNA processing and cell cycle regulation","description":"The proteins show enrichment for RNA processing and transcription regulation by RNA Pol II, with associations to mitotic and meiotic cell cycle steps, plus stress granule localization and IRES-dependent translation indicating stress-related RNA control. This suggests a cohesive theme of RNA metabolism coupled to cell cycle control.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903608","count":1},{"id":"GO:0006396","count":1},{"id":"GO:0075522","count":1},{"id":"GO:0007346","count":1},{"id":"GO:0060303","count":1}]},{"hash":"868661824421732407","title":"Cell Cycle Regulation and Stress-Induced Apoptosis","description":"This cluster shows enrichment in terms linked to mitotic processes (mitotic cell cycle, G1 DNA damage checkpoint signaling, negative regulation of cytokinesis) and stress-induced apoptosis (intrinsic ER stress\u2013induced apoptotic pathway, glial cell apoptotic process, TORC1 signaling). While a few terms touch on development, the dominant theme centers on controlling cell division and responding to cellular stress with apoptosis, suggesting proteins that participate in cell cycle control and stress-related apoptosis pathways.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032466","count":1},{"id":"GO:0072432","count":1},{"id":"GO:2000011","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0001649","count":1}]},{"hash":"1724119215399274651","title":"Translation Regulation and mRNA Processing","description":"The top GO terms cluster around control of translation initiation (including IRES-dependent initiation) and various facets of post-transcriptional RNA regulation, such as miRNA-mediated silencing, mRNA stability, modification, and splicing regulation, with an additional hint at ribosome biogenesis via small-subunit processome assembly. This points to a cohesive theme of RNA-level control of gene expression and translation.","confidence":"High","size":6,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0010610","count":2},{"id":"GO:0016556","count":2},{"id":"GO:1903586","count":2}]},{"hash":"754018949842828695","title":"Microtubule-based spindle orientation and polarity","description":"This cluster is dominated by GO terms describing microtubule cytoskeleton organization and spindle orientation, including meiotic spindle orientation, centrosome separation, plus- and minus-end directed microtubule sliding, and regulation of microtubule-based processes. While there are a couple tissue-context terms (cerebellar structure, epidermal stem cell homeostasis), the shared function across terms is microtubule dynamics and spindle/polarity control, suggesting a cohesive microtubule regulation theme.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051296","count":6},{"id":"GO:0007100","count":6},{"id":"GO:0021685","count":6},{"id":"GO:0036334","count":6},{"id":"GO:0031534","count":6}]},{"hash":"1692195997070630901","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099557","count":3},{"id":"GO:0070935","count":3},{"id":"GO:0001806","count":3},{"id":"GO:0071372","count":3},{"id":"GO:0051965","count":3}]},{"hash":"1305968152304460175","title":"Embryonic development and stress responses","description":"The top GO terms cluster around embryogenesis-related processes (syncytial blastoderm development, head involution, hemocyte development) and diverse stress/response pathways (DNA damage response, UV response, glucocorticoid and antibiotic responses). There isn\u2019t a single cohesive function linking all terms, so the label reflects a developmental program with associated stress responses rather than a tight module.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045736","count":1},{"id":"GO:0001700","count":1},{"id":"GO:0009411","count":1},{"id":"GO:0008258","count":1}]},{"hash":"544361393475964792","title":"Plasma membrane amino acid import","description":"The cluster\u2019s GO terms center on import/transport of amino acids across the plasma membrane (methionine, lysine, ornithine, D-alanine), suggesting a group of transporters or uptake pathways. A few outlier terms (karrikin response, symbiont-mediated disruption, phospholipid catabolism, arginine catabolism) are less representative, but the shared theme is amino acid transport.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080167","count":1},{"id":"GO:0052008","count":1},{"id":"GO:0009395","count":1},{"id":"GO:0006527","count":1},{"id":"GO:0035826","count":1}]},{"hash":"1348933889239417947","title":"Unknown","description":"The top GO terms span diverse themes from DNA repair and transcriptional responses to DNA damage to antibiotic response, plus various development processes (cerebral cortex layer formation, outer ear morphogenesis) and immune/endothelial chemotaxis. There is no clear, single function or pathway tying these proteins together, so a concise, representative label cannot be confidently assigned.","confidence":"","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0000902","count":3},{"id":"GO:0021819","count":3},{"id":"GO:1990260","count":3}]},{"hash":"115578914419579382","title":"Developmental Morphogenesis and Cell Migration","description":"The cluster shows enrichment for morphogenesis-related terms (cell morphogenesis; layer formation in cerebral cortex; outer ear morphogenesis) and for chemotaxis of immune and endothelial cells (macrophage and endothelial chemotaxis), with supporting signaling (peptidyl-threonine phosphorylation). While sperm capacitation appears, the dominant shared theme is tissue development and directed cell movement across contexts, suggesting a cohesive label around developmental morphogenesis and cell migration. ","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":5},{"id":"GO:0000902","count":3},{"id":"GO:0021819","count":3},{"id":"GO:1990260","count":3},{"id":"GO:2001028","count":3}]},{"hash":"1421497510551996091","title":"Microtubule dynamics and spindle orientation","description":"The top GO terms converge on microtubule cytoskeleton organization, including establishment of meiotic spindle orientation, mitotic centrosome separation, plus- and minus-end directed microtubule sliding, and regulation of microtubule-based processes, as well as cytoskeleton polarity. Some terms reference tissue contexts (cerebellar granular layer structure, epidermal stem cell homeostasis) that can involve microtubule organization, supporting a broader theme of microtubule dynamics in cellular architecture. Overall, the cluster appears to group proteins coordinating microtubule dynamics and spindle orientation. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051296","count":2},{"id":"GO:0007100","count":2},{"id":"GO:0021685","count":2},{"id":"GO:0036334","count":2},{"id":"GO:0031534","count":2}]},{"hash":"750342507167647734","title":"Golgi-based vesicle trafficking","description":"The top GO terms point to vesicle transport centered on the Golgi\u2014ER-to-Golgi, intra-Golgi, Golgi-to-vacuole, and retrograde endosome-to-Golgi transport\u2014plus Golgi ribbon formation, indicating a coherent cluster of Golgi-associated vesicular trafficking proteins.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006896","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0090161","count":2}]},{"hash":"1385150149296026308","title":"Unknown","description":"The terms are highly diverse, including RNA methylation, DNA replication initiation, transcriptional and chromosomal regulation (X inactivation), isotype switching, brain structure, RNA localization, and Wnt receptor turnover, with no clear shared function tying the proteins together. This makes a cohesive, specific label unlikely.","confidence":"","size":6,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0090282","count":2},{"id":"GO:1902364","count":2},{"id":"GO:1903468","count":2}]},{"hash":"1921843432717496515","title":"Cell Cycle, Telomere Maintenance, and Stress Response","description":"This cluster includes terms tied to mitotic cell cycle, telomere maintenance and capping, regulation of CDK activity, ER-stress\u2013related apoptotic signaling, plus broader processes like mRNA processing and cell migration. The common thread appears to be cellular proliferation and responses to stress rather than a single focused pathway, so the label reflects a mid-level, multi-faceted role in cell fate decisions. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0006397","count":2}]},{"hash":"988115573580311765","title":"Phosphatase-mediated lipid signaling and metal transport","description":"This cluster shows multiple dephosphorylation terms (general dephosphorylation and specifically phospholipid dephosphorylation), suggesting phosphatase-associated activity. Several terms also point to membrane-associated metal transport (cadmium and zinc transmembrane transport), with additional metabolic context (serine biosynthesis, calcium homeostasis). The common thread appears to be lipid signaling linked to dephosphorylation and coordinated ion transport/metabolism, rather than a single narrowly defined pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0006564","count":3},{"id":"GO:0006874","count":3}]},{"hash":"1076327811934957739","title":"Membrane Ion Transport and Homeostasis","description":"Consistent enrichment for membrane transport of ions (sodium/potassium), proton translocation, and vacuolar acidification, along with salt-stress and cell-volume regulation, points to a cohesive role in ionic balance and osmoregulation.","confidence":"High","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":1},{"id":"GO:0009651","count":1},{"id":"GO:0006884","count":1},{"id":"GO:1903281","count":1},{"id":"GO:0007035","count":1}]},{"hash":"1364841185000535272","title":"Proteostasis and aggrephagy","description":"These proteins show a clear enrichment for proteostasis-related processes: proteolysis, ubiquitination, sumoylation, and phosphorylation, plus aggresome assembly and aggrephagy. This points to regulation of protein quality control and degradation, including sequestration of misfolded proteins and their autophagic clearance. While a few terms touch on mitochondrial dynamics and immune signaling, the dominant theme across the cluster is proteostasis and protein turnover.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:1904049","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0070842","count":1},{"id":"GO:0016925","count":1}]},{"hash":"1831203165306527285","title":"Antibiotic response and bacterial envelope biosynthesis","description":"This cluster's top GO terms cluster around antibiotic response, LPS/Lipid A biosynthesis, spore wall assembly, and biofilm formation, which together point to bacterial envelope biogenesis and stress response; a couple of terms (liver development, mitochondrial inheritance) appear as outliers.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0001889","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0042244","count":2}]},{"hash":"1520514102878435141","title":"Unknown","description":"The top GO terms are a scattered mix: nucleotide-sugar catabolic processes (UDP/GDP/ADP/CDP), protein N-linked glycosylation, plus plant reproductive terms (anther dehiscence, pollen exine formation) and unrelated tissue development terms (fibroblast migration, smooth muscle development). There is no clear shared function tying all five proteins together, so a concise, representative label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006256","count":1},{"id":"GO:0046706","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0071405","count":1},{"id":"GO:0009901","count":1}]},{"hash":"720851276424878532","title":"RNA Biogenesis and Quality Control","description":"Top terms indicate a cluster focused on RNA maturation (transcription termination, tRNA and rRNA processing) and RNA surveillance/quality control (mRNA surveillance, non-stop decay) with links to translation readiness, suggesting a cohesive RNA metabolism/heavy RNA-processing cluster.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0030490","count":2},{"id":"GO:2000616","count":1}]},{"hash":"865451348604354899","title":"Chromatin Silencing and Transcription Regulation","description":"The top GO terms point to regulation of chromatin states (telomere and rDNA heterochromatin) and transcription control (negative regulation of RNA polymerase I transcription), with a few related stress-response/transcription terms. This pattern suggests the proteins cluster around mechanisms that govern chromatin structure and transcriptional output, rather than metabolic or signaling pathways, making a chromatin regulation-focused label appropriate.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031939","count":1},{"id":"GO:0061186","count":1},{"id":"GO:0016479","count":1},{"id":"GO:0061408","count":1},{"id":"GO:2000219","count":1}]},{"hash":"2296192568019986607","title":"Unknown","description":"The top GO terms span DNA damage response, cell cycle, apoptosis, growth signaling (TORC1), RNA methylation, and diverse developmental processes, with no clear common function. The absence of edges and the term diversity suggest no cohesive theme to name the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0072432","count":3},{"id":"GO:2000011","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001649","count":3},{"id":"GO:0070059","count":3}]},{"hash":"415088917522535578","title":"Developmental morphogenesis and signaling","description":"The top GO terms indicate morphogenesis across tissues (cell morphogenesis, cortex layer formation, outer ear morphogenesis) along with signaling-related processes (trans-synaptic signaling, peptidyl-threonine phosphorylation) and chemotaxis/differentiation (endothelial/macrophage chemotaxis, NK T cell differentiation). These collectively point to a theme of developmental tissue formation and intercellular communication, though the signals are diverse and some terms are obsolete or not tightly connected by edges. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0021819","count":2},{"id":"GO:1990260","count":2},{"id":"GO:2001028","count":2},{"id":"GO:0007070","count":2}]},{"hash":"423799370680793811","title":"Actin-driven cytoskeleton dynamics","description":"This cluster is best captured by a theme of cytoskeleton remodeling and actin-dependent processes. The top terms include actin filament polymerization and phagocytosis, both strongly supported by cytoskeletal activity, along with related processes like meiotic chromosome movement and multidimensional cell growth that can involve cytoskeletal transport and remodeling. Some terms (e.g., brain development or behavior) are more peripheral, but the recurrent emphasis on actin-mediated activities suggests this overarching theme.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030476","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0006909","count":3},{"id":"GO:0016344","count":3}]},{"hash":"2214998766240384452","title":"Cell envelope biosynthesis and biofilm formation","description":"The prominent GO terms cluster around synthesis and assembly of surface/membrane components (lipid A, LPS, spore wall), and processes linked to surface-associated growth such as biofilm formation, suggesting a core theme of envelope construction and surface lifestyle; other terms appear more peripheral, so the central theme is envelope-related biosynthesis with surface association.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080167","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0042244","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0036108","count":1}]},{"hash":"1502578223749741337","title":"Unknown","description":"The GO terms span disparate species and processes (bone, hormone signaling, plant anther development, lipid response, pigment biosynthesis, transcription, muscle atrophy, morphogenesis, neural/glial differentiation), showing no cohesive function or pathway for a specific label. Therefore a confident, specific label cannot be assigned.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045668","count":3},{"id":"GO:0060766","count":3},{"id":"GO:0048658","count":2},{"id":"GO:0071400","count":2},{"id":"GO:0031542","count":2}]},{"hash":"1940331738229076840","title":"Cell Cycle and Stress Signaling","description":"The protein set shows enrichment in mitotic cell cycle, DNA damage checkpoint signaling, TORC1 growth signaling, and intrinsic ER stress\u2013related apoptosis, together with associated apoptosis in glial cells and broader development signals. This suggests a cohesive theme around how cells regulate growth, division, and fate under stress, rather than a narrow, single-function process. The presence of RNA methylation and GTPase regulation also fits into broader regulation of gene expression and signaling during these processes, so the label \"Cell Cycle and Stress Signaling\" best captures the overarching theme.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072432","count":1},{"id":"GO:2000011","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0001649","count":1},{"id":"GO:0070059","count":1}]},{"hash":"590713189736773632","title":"Unknown","description":"The GO terms are highly diverse, spanning tissue development (striatum, uterus), mitochondrial processes (protein import into mitochondrial matrix, regulation of mitochondrial membrane permeability), lipid metabolism (triglyceride biosynthesis, omega-hydroxylase P450 pathway), and even xenobiotic/carbohydrate terms, with several obsolete entries. There are no edges or cohesive functional theme tying these proteins together, so a concise, representative label cannot be inferred beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021756","count":2},{"id":"GO:0030150","count":1},{"id":"GO:0010867","count":1},{"id":"GO:2000134","count":1},{"id":"GO:1903740","count":1}]},{"hash":"126643532567820915","title":"Nuclear proteostasis and quality control","description":"The top GO terms converge on nuclear protein quality control via the ubiquitin-proteasome system, misfolded protein handling and refolding (chaperone/cofactor-related), and redox/homeostasis processes, suggesting a proteostasis-focused cluster. Some terms appear less coherent or obsolete (mesoderm formation, frameshifting), but the core theme is protein quality control and maintenance in the nucleus.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071630","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0006452","count":1},{"id":"GO:1905259","count":1}]},{"hash":"328773989545721318","title":"Amino acid and peptide transport","description":"The GO terms cluster around transmembrane transport of amino acids (methionine, branched-chain, cysteine) and small peptides (peptide/oligopeptide export), plus vitamin and even drug (doxorubicin) transport. An outlier term relates to antigen processing, but the dominant pattern is membrane transport of amino acids, peptides, and related substrates, suggesting these proteins function as transporters.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000770","count":1},{"id":"GO:1900753","count":1},{"id":"GO:0090374","count":1},{"id":"GO:0042883","count":1},{"id":"GO:0035461","count":1}]},{"hash":"413378601397510178","title":"Unknown","description":"The GO terms are highly diverse (mesoderm and skeletal muscle development, neuron differentiation, T cell regulation, transcription termination, morphine response, NFAT signaling, synaptic activity) with no clear shared function or pathway, and there are no edges between proteins, so no cohesive cluster function emerges.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007498","count":2},{"id":"GO:0001915","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0030846","count":2},{"id":"GO:0030847","count":2}]},{"hash":"447640792820548518","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to translation and ribosome assembly/biogenesis (translation GO:0006412; ribosome assembly GO:0042255; ribosomal large subunit biogenesis GO:0042273) and rRNA processing (GO:0000448), all pointing to ribosome maturation and protein synthesis. A few peripheral terms (response to antibiotic, UV-related regulation, gamma radiation) are less representative. Overall, the functions converge on ribosome biology and translational control.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":1},{"id":"GO:0042255","count":1},{"id":"GO:0000448","count":1},{"id":"GO:0071480","count":1}]},{"hash":"1508655299305566445","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":2},{"id":"GO:0006413","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0001649","count":1}]},{"hash":"13831450451990250","title":"Ubiquitin-dependent proteolysis in meiosis","description":"Top terms indicate a core function in SCF-dependent proteasomal ubiquitin-dependent protein catabolic processes, i.e., targeted protein degradation. Coupled with terms for positive regulation of metaphase/anaphase transition and sister chromatid movement during meiosis, the cluster seems to coordinate proteolysis with meiotic cell-cycle progression. Some histone/acetylation and rRNA transcription terms appear ancillary. Therefore, a concise label emphasizing ubiquitin-mediated proteolysis linked to meiotic cell cycle control is appropriate.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0051759","count":2},{"id":"GO:1902104","count":2},{"id":"GO:0042787","count":2},{"id":"GO:1902661","count":1}]},{"hash":"63121190507181731","title":"Dopaminergic neural signaling and development","description":"The top GO terms include cellular response to dopamine, hippocampus development, and positive regulation of axon extension, pointing to neuronal signaling and growth. Additional terms reflect common neuronal signaling cascades (phosphorylation, MAPK, PI3K). Some terms are obsolete or more general, but the dominant theme centers on dopamine-responsive neural signaling and neural development. ","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043304","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0000186","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0031532","count":2}]},{"hash":"2058008013118435286","title":"Proteostasis and Neuronal Signaling Regulation","description":"This cluster is dominated by GO terms related to protein quality control and degradation (aggresome assembly, aggrephagy, proteasomal ubiquitin-dependent degradation, sumoylation) alongside terms that modulate neuronal activity (negative regulation of neurotransmitter secretion and action potential) and mitochondrial dynamics, suggesting a role in balancing proteostasis with neuronal signaling. The overlap with immune signaling terms (interferon pathway, TLR3 signaling) indicates some cross-talk but the core theme appears to be proteostasis-linked regulation in neurons.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904049","count":4},{"id":"GO:0060334","count":4},{"id":"GO:0070842","count":4},{"id":"GO:0016925","count":4},{"id":"GO:0032436","count":4}]},{"hash":"262103614764022669","title":"Microtubule organization and spindle dynamics","description":"The terms cluster around microtubule cytoskeleton regulation and mitotic/spindle processes (plus/minus-end microtubule sliding, regulation of microtubule-based processes, centrosome separation, spindle orientation, and microtubule polarity), with supporting mentions of cytoskeleton-dependent growth regulation; a cocaine response term is likely incidental. This points to a cohesive function in microtubule dynamics and spindle architecture.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":2},{"id":"GO:0051296","count":2},{"id":"GO:0007100","count":2},{"id":"GO:0021685","count":2},{"id":"GO:0036334","count":2}]},{"hash":"2107520294282952751","title":"Unknown","description":"The GO terms are a mix of developmental processes (mesoderm, skeletal muscle, neuron differentiation), meiosis (meiotic cell cycle, homologous chromosome pairing), and DNA damage/ transcription termination roles, with no single unifying function evident for the cluster. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007498","count":1},{"id":"GO:0001915","count":1},{"id":"GO:0048741","count":1},{"id":"GO:0030846","count":1},{"id":"GO:0006303","count":1}]},{"hash":"284828810019618893","title":"Proteostasis and ER stress signaling","description":"These terms cluster around proteostasis and ER stress responses: translation and phosphorylation reflect active protein regulation; aggresome assembly and sumoylation indicate handling of misfolded or damaged proteins; ERAD-related pathways and ER-stress\u2013driven apoptotic signaling point to unfolded protein response outcomes. The combination supports naming as Proteostasis and ER stress signaling.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:1904049","count":1},{"id":"GO:0070842","count":1},{"id":"GO:0016925","count":1},{"id":"GO:0006468","count":1}]},{"hash":"1125135852166584463","title":"Unknown","description":"The top terms span antifungal defense, plant cell wall loosening, reproduction, immune signaling, cell cycle regulation, drug response, and nuclear telomere maintenance, with several entries marked obsolete. The lack of a single coherent biological theme across these terms suggests the proteins do not share a common function or pathway, so a unknown, non-specific label is most appropriate.","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050832","count":1},{"id":"GO:0019953","count":1},{"id":"GO:0006949","count":1},{"id":"GO:0009828","count":1},{"id":"GO:0060334","count":1}]},{"hash":"385609973951352482","title":"Acetyltransferases and acetylation processes","description":"The top GO terms are all acetylation-related, including N-terminal peptidyl-methionine/serine/lysine acetylation, spermidine acetylation, and processes like melatonin biosynthesis and glucosamine metabolism that rely on acetyltransferase activity. This pattern suggests the cluster comprises acetyltransferases acting on diverse substrates, indicating a shared functional theme. ","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000025","count":4},{"id":"GO:0045150","count":4},{"id":"GO:0060358","count":4},{"id":"GO:0032918","count":4},{"id":"GO:0030187","count":4}]},{"hash":"2172462318151715247","title":"Cell cycle and DNA repair under stress","description":"These proteins cluster around core cellular processes involved in dividing the cell and maintaining genome integrity under stress: mitotic cell cycle regulation (G2/M), nonhomologous end joining for DSB repair, ER-stress\u2013induced apoptotic signaling, and cytoplasmic protein quality control via the ubiquitin-proteasome system. Developmental and interleukin-1\u2013response terms appear less central, suggesting a primary theme of cell cycle control and stress response rather than immune or developmental roles. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071347","count":4},{"id":"GO:0001701","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0033182","count":4},{"id":"GO:0070059","count":4}]},{"hash":"2294880537821023618","title":"Unknown","description":"Top terms are diverse and do not converge on a single process: nucleotide catabolism, chromosome organization, embryonic digit morphogenesis, and regulation of insulin signaling/glucose transport. There is no clear shared function across the cluster, so a cohesive label isn\u2019t supportable.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006193","count":1},{"id":"GO:0051276","count":1},{"id":"GO:0009213","count":1},{"id":"GO:0046325","count":1},{"id":"GO:0042733","count":1}]},{"hash":"1866994195072771482","title":"Germline small RNA silencing and piRNA processing","description":"The top GO terms cluster around RNA interference and small RNA pathways (siRNA, ta-siRNA, piRNA processing) alongside germline development processes (germarium-derived germ-line cyst formation, germ-line stem cell maintenance) and meiotic regulation, suggesting a coherent theme of germline-specific RNA silencing mechanisms that influence meiosis. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090625","count":1},{"id":"GO:0033168","count":1},{"id":"GO:0072091","count":1},{"id":"GO:0010267","count":1},{"id":"GO:0030727","count":1}]},{"hash":"1201888242499011799","title":"Translation and Transcription Regulation","description":"Dominant GO terms center on translation and transcription, including regulation of translational fidelity, negative regulation of translation, and ribosome assembly, with supporting signals from DNA-templated transcription and termination, indicating a cluster focused on gene expression control at RNA and protein synthesis levels. Some developmental terms are present but largely incidental.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006450","count":1},{"id":"GO:0060702","count":1},{"id":"GO:0017148","count":1},{"id":"GO:0046677","count":1}]},{"hash":"1239380969911886729","title":"Developmental Morphogenesis and Signaling","description":"The four proteins have GO terms focused on morphogenesis across tissues (cell morphogenesis, layer formation in cerebral cortex, outer ear morphogenesis) and on intercellular signaling or signaling-related processes (trans-synaptic signaling, phosphorylation). The set appears to reflect broad roles in developmental shaping and signaling rather than a single, narrow function, so a general label tied to development and signaling best captures the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":1},{"id":"GO:0021819","count":1},{"id":"GO:1990260","count":1},{"id":"GO:2001028","count":1},{"id":"GO:0007070","count":1}]},{"hash":"1867453607899938547","title":"Spindle Orientation and Microtubule Organization","description":"The top GO terms center on microtubule-based processes: establishment or maintenance of microtubule cytoskeleton polarity, minus- and plus-end directed microtubule sliding, and centrosome separation, as well as meiotic spindle orientation. This strongly suggests proteins involved in organizing the microtubule cytoskeleton and coordinating spindle dynamics, with some supporting signals of broader cytoskeletal regulation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051296","count":3},{"id":"GO:0007100","count":3},{"id":"GO:0021685","count":3},{"id":"GO:0036334","count":3},{"id":"GO:0031534","count":3}]},{"hash":"1772283873296153298","title":"Muscle and neural development signaling","description":"The top GO terms cluster around developmental processes (mesoderm, skeletal muscle fiber development, neuron differentiation) and signaling/transcription regulation (calcineurin-NFAT signaling, RNA Pol II transcription termination), suggesting proteins involved in developmental signaling in muscle and nervous system contexts, despite a small network connection.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007498","count":2},{"id":"GO:0001915","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0030846","count":2},{"id":"GO:0030847","count":2}]},{"hash":"2284911264038443405","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000616","count":1},{"id":"GO:0072715","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0009307","count":1}]},{"hash":"2133016636567787483","title":"Proteostasis and quality control","description":"The shared GO terms cluster around protein quality control and proteostasis, notably nuclear ubiquitin-proteasome system\u2013mediated QC, misfolded protein transport, and chaperone-related refolding. While other terms like redox homeostasis or iron-sulfur maturation are present, the proteostasis signal is most prominent, making this label representative.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071630","count":1},{"id":"GO:0097428","count":1},{"id":"GO:0001707","count":1},{"id":"GO:0006452","count":1},{"id":"GO:1905259","count":1}]},{"hash":"2063671241065857872","title":"Ubiquitination and protein quality control","description":"The cluster is dominated by GO terms related to ubiquitination (K63-linked ubiquitination, autoubiquitination, monoubiquitination) and a term involving chaperone-mediated protein complex assembly, both pointing to protein modification and proteostasis. Other terms appear incidental but do not contradict this theme. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010200","count":1},{"id":"GO:0070534","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0090035","count":1},{"id":"GO:0030579","count":1}]},{"hash":"104475749748596012","title":"Protein quality control under cellular stress","description":"The GO terms cluster around misfolded protein detection, protein stabilization, and stress responses such as cadmium exposure and ischemia, all pointing to proteostasis and cellular stress management. While some terms (e.g., sperm binding, cocaine response) appear as noise, the core theme is protein quality control and stress response mechanisms.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0014823","count":3},{"id":"GO:0050821","count":3},{"id":"GO:1903427","count":3},{"id":"GO:0002236","count":3},{"id":"GO:0042220","count":3}]},{"hash":"411386541621931810","title":"Neural development and synaptic signaling","description":"The prominent terms point to developmental morphogenesis, especially brain-related layering and synaptic signaling, with additional notes on ear morphogenesis and immune/vascular chemotaxis. This pattern supports a label focused on neural development and synaptic communication, acknowledging some non-neural roles.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000902","count":3},{"id":"GO:0021819","count":3},{"id":"GO:1990260","count":3},{"id":"GO:2001028","count":3},{"id":"GO:0007070","count":3}]},{"hash":"106477666484919415","title":"Modifications in Gene Expression Regulation","description":"These proteins cluster around diverse modification processes that govern gene expression, including transcriptional regulation (RNA polymerase II), RNA processing (mRNA capping, tRNA modification), and various post-translational and epigenetic modifications (histone methylation, arginine hydroxylation, lysine methylation). The presence of aging-related terms (cellular senescence) and polyamine biosynthesis suggests a broader context of growth and lifespan-linked regulation. Overall, the theme is gene expression control via multiple molecular modifications.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0001300","count":2},{"id":"GO:0006596","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0043985","count":2}]},{"hash":"1443008290468274476","title":"Bacterial lipid and carbohydrate biosynthesis","description":"The top GO terms cluster around biosynthetic processes for lipids (phospholipids) and carbohydrates (glycogen, starch) as well as biosynthesis of thiol-containing molecules (bacillithiol, mycothiol). This suggests the proteins share a common role in producing key biomolecules in bacteria, despite some unrelated or obsolete terms present. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009413","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0008654","count":1},{"id":"GO:0006490","count":1},{"id":"GO:0007631","count":1}]},{"hash":"1862684208642239143","title":"Unknown","description":"The top GO terms span membrane targeting, ER stress response, cell division, flagellum organization, signaling, cold response, and various metabolic processes, with no single dominant function linking the proteins. Because the terms are diverse and there's no consistent biological theme, I label this cluster Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006614","count":1},{"id":"GO:0036498","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0044781","count":1},{"id":"GO:0007165","count":1}]},{"hash":"486072441974420830","title":"Developmental Morphogenesis and Tissue Differentiation","description":"This cluster is driven by GO terms related to morphogenesis and tissue differentiation (cell morphogenesis; endodermal differentiation; salivary gland boundary specification; photoreceptor differentiation; urogenital development; ovulation cycle), suggesting proteins involved in organ and tissue development. A few terms touch on DNA replication/cell cycle processes, which may reflect proliferative states during development or annotation noise, and a single immunoregulatory term appears as an outlier. Overall, the theme centers on developmental differentiation and morphogenesis with some ancillary cell-cycle signals.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000902","count":2},{"id":"GO:0035987","count":1},{"id":"GO:0001915","count":1},{"id":"GO:0001655","count":1},{"id":"GO:0007432","count":1}]},{"hash":"590070858532025326","title":"Mitotic cycle and DNA repair with proteostasis","description":"Several top GO terms converge on cell division and genome maintenance (G2/M transition and mitotic cell cycle; nonhomologous end joining repair). Additional terms describe cytoplasmic protein quality control via the ubiquitin\u2013proteasome system and ER-stress\u2013linked apoptosis, which ties into proteostasis during mitosis and stress. A few terms touch on development or inflammatory signaling, suggesting broader cellular responses but the core themes align around mitotic progression, DNA repair, and proteostasis.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071347","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0033182","count":3},{"id":"GO:0070059","count":3}]},{"hash":"274605874838492068","title":"Ribosome biogenesis and translation","description":"The top GO terms are about cytosolic ribosome assembly, large subunit biogenesis, ribosomal subunit export from the nucleus, and rRNA maturation, along with translational initiation and translation, which together point to ribosome assembly and protein synthesis as the cluster\u2019s main function. A couple of terms related to ABA response and fatty acid biosynthesis are present but do not define the primary theme. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042256","count":1},{"id":"GO:0042304","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0000054","count":1},{"id":"GO:1902626","count":1}]},{"hash":"231941978251836059","title":"Mitochondrial respiration and ATP synthesis","description":"The top terms cluster around heme A biosynthesis (for cytochrome c oxidase) and core mitochondrial energy pathways: mitochondrial electron transport (ubiquinol to cytochrome c) and proton-motive-force\u2013driven ATP synthesis, pointing to energy metabolism in mitochondria.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006784","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0042776","count":1}]},{"hash":"1602938748334759300","title":"Viral genome integration and host cell entry","description":"These proteins are annotated with GO terms centered on viral processes: DNA recombination, RNA-templated DNA biosynthesis, DNA integration, proviral latency, and viral penetration into the host nucleus, all pointing to a viral life cycle involving entry into the host cell and integration of viral DNA into the host genome. Additional terms about symbiont-mediated host interactions support the host-pathogen context, but the dominant signal is viral infection and genome integration, making this label representative and specific.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0046718","count":1},{"id":"GO:0075713","count":1}]},{"hash":"2188626683377382611","title":"Unknown","description":"The terms span transcription, metabolism, neural/pharmacological responses, muscle structure, and sensory processes, with no shared pathway or protein interaction. The absence of edges supports the lack of a common function, so a precise, cohesive label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009454","count":1},{"id":"GO:0045013","count":1},{"id":"GO:0046827","count":1},{"id":"GO:0051447","count":1}]}]