[{"hash":"2266036722066556092","title":"RNA processing and translation initiation regulation","description":"The cluster centers on RNA-centric regulatory processes, with GO terms spanning regulatory ncRNA-mediated gene silencing, positive regulation of mRNA splicing via the spliceosome, mRNA polyadenylation and tail shortening, formation of the translation preinitiation complex, translation reinitiation, and assembly of the eIF4F complex, reflecting coordinated RNA processing and initiation of translation.","confidence":"High","size":29,"edges":398,"triangles":3444,"max_degree":28,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":18},{"id":"GO:0048026","count":18},{"id":"GO:1901407","count":15},{"id":"GO:0002188","count":11},{"id":"GO:0006378","count":11}]},{"hash":"2179337730146116597","title":"Epithelial differentiation and junctional architecture","description":"Based on the GO terms, the cluster is dominated by epithelial-related processes: epithelial to mesenchymal transition, lens fiber differentiation, microvillus and terminal web assembly, bicellular tight junction assembly, and regulation of Rho signaling and cAMP response. These collectively point to epithelial differentiation with emphasis on junctional complexes and apical cytoskeletal structures (microvilli/terminal web). Some terms like paraxial mesoderm development are less central but do not counter the main epithelial theme, so the label captures the core function of the cluster.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0001837","count":9},{"id":"GO:0070306","count":7},{"id":"GO:0046621","count":7},{"id":"GO:0035023","count":7},{"id":"GO:0071320","count":7}]},{"hash":"372192844058560643","title":"Bacterial cell wall polysaccharide biosynthesis and glycosylation","description":"This cluster\u2019s top GO terms cluster around teichoic acid biosynthesis, cellulose and hyaluronan biosynthesis, and both O- and N-linked protein glycosylation, all linked to cell wall or capsule polysaccharide construction and modification. The prevalent theme is biosynthesis of surface polysaccharides and their glycosylation, with only a few outliers (like immunoglobulin production) that do not alter the main interpretation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0075015","count":6},{"id":"GO:0019350","count":5},{"id":"GO:0030244","count":4},{"id":"GO:0018243","count":4},{"id":"GO:0071555","count":4}]},{"hash":"2143521009644662161","title":"Membrane Transport and Development","description":"The GO terms point to both membrane-associated activities (phospholipid translocation, calcium ion homeostasis, ion transport) and developmental processes (sprouting angiogenesis, nervous system development, keratan sulfate proteoglycan biosynthesis), with some stress response terms adding breadth. This suggests a broad role in membrane signaling/transport linked to development rather than a single narrow function, justifying a label that reflects both aspects.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045332","count":4},{"id":"GO:0006874","count":3},{"id":"GO:0070574","count":3},{"id":"GO:0006486","count":3},{"id":"GO:0018146","count":3}]},{"hash":"479752642056882109","title":"cGMP signaling and sensory response cluster","description":"This cluster is dominated by cGMP-related signaling (cellular response to cGMP; negative regulation of receptor guanylyl cyclase signaling) and sensory perception elements (olfaction), with additional terms spanning TGF-beta signaling, dopamine metabolism, LPS response, and basic transcription/DNA processes. The common thread appears to be stimulus-induced signaling pathways that can lead to transcriptional changes, with a particular emphasis on cGMP signaling and sensory signaling. ","confidence":"Medium","size":29,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071321","count":9},{"id":"GO:0007608","count":9},{"id":"GO:0010754","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0071560","count":8}]},{"hash":"198516189426164972","title":"Cardiovascular development and signaling regulation","description":"The terms cluster around heart development (cardiac right atrium morphogenesis, Notch signaling in heart field proliferation) and venous endothelial differentiation, with broader signaling regulation themes (NF-kappaB negative regulation, ubiquitination, kinase activity control). Some items (e.g., NOD2 signaling, obsolete terms) are less directly linked, but the dominant theme points to cardiovascular development and its signaling regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032088","count":10},{"id":"GO:0007275","count":9},{"id":"GO:0016567","count":9},{"id":"GO:0070431","count":9},{"id":"GO:0003213","count":8}]},{"hash":"512605153210073880","title":"Chromosome segregation and TORC1 signaling","description":"The top GO terms center on sister chromatid cohesion and separation in both meiotic and mitotic contexts, plus positive regulation of kinase activity and TORC1 signaling, suggesting a cluster of proteins involved in chromosome handling during cell division and its regulation by nutrient-sensing pathways. Additional terms like mRNA transport and GTPase regulation hint at supporting roles in cellular logistics and signaling, but the strongest signal is for chromosome segregation intertwined with TORC1-driven growth control.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0051754","count":9},{"id":"GO:0051028","count":8},{"id":"GO:0070262","count":8},{"id":"GO:0038202","count":8}]},{"hash":"578365175911409026","title":"Developmental morphogenesis","description":"The cluster\u2019s top GO terms center on embryo development and tissue/organ formation, including cartilage morphogenesis, left-right patterning, endocardial cushion formation, endocrine system development, and pancreatic cell development. These collectively point to a developmental morphogenesis theme; a few terms relate to general cellular processes (RNA processing/export, transcriptional regulation) that are common in many gene sets but do not override the morphogenesis signal. Overall, the cluster appears to represent proteins involved in developmental morphogenesis and organogenesis.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0060536","count":25},{"id":"GO:1903026","count":25},{"id":"GO:0003323","count":25},{"id":"GO:0000055","count":25},{"id":"GO:0000398","count":25}]},{"hash":"1038951101927882506","title":"Ubiquitin-Dependent Immune Signaling","description":"The cluster is dominated by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, ERAD, autoubiquitination) and specific Ub linkages (K63, K6), with strong signals for innate immunity and antiviral defense (innate immune response, defense response to virus, NF-kappaB regulation). This points to a cohesive role of ubiquitination in regulating immune signaling pathways, rather than non-immune functions; the vitamin D response term may reflect immune modulatory context. Confidence that this label captures the cluster\u2019s function is High.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":22},{"id":"GO:0030433","count":21},{"id":"GO:0051865","count":21},{"id":"GO:0033280","count":20},{"id":"GO:0045087","count":20}]},{"hash":"1331996260219121693","title":"Neuronal development and synaptic vesicle regulation","description":"The top GO terms cluster around neuronal development and synaptic function, including brain and hippocampus development, excitatory postsynaptic potentials, and regulation of synaptic vesicle exocytosis and endocytic recycling, suggesting a module involved in neural development and synaptic transmission. A few terms (mating projection growth regulation, multivesicular body size regulation, mitotic cell cycle) are less aligned with this theme, but the dominant signal points to neural differentiation and synaptic activity.","confidence":"Medium","size":29,"edges":42,"triangles":10,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031384","count":7},{"id":"GO:0032456","count":7},{"id":"GO:0010796","count":7},{"id":"GO:0071260","count":7},{"id":"GO:2000300","count":7}]},{"hash":"857804976600496590","title":"Neuron development and synaptic signaling","description":"The most represented terms relate to neuron development and synaptic function (dendritic spine morphogenesis, excitatory postsynaptic potential), with related developmental processes like neural tube closure and signaling pathways (JNK, cocaine response). This suggests a cluster of proteins involved in neuronal development and synaptic signaling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000289","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0046330","count":3},{"id":"GO:0042220","count":3}]},{"hash":"1430539172781969938","title":"Protein and rRNA Methyltransferases","description":"Dominant GO terms are rRNA methylation and multiple protein methylations (peptidyl-lysine, arginine, glycine N-terminal), plus rDNA heterochromatin formation, pointing to enzymes that transfer methyl groups to RNA and proteins, often involved in chromatin regulation and ribosome biogenesis. Other terms (cobalamin/antibiotic biosynthesis, responses) are minor by comparison, consistent with a methyltransferase-centered cluster.","confidence":"High","size":29,"edges":171,"triangles":428,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":18},{"id":"GO:0031167","count":18},{"id":"GO:0018027","count":17},{"id":"GO:0018013","count":16},{"id":"GO:0018023","count":16}]},{"hash":"1001878340280556493","title":"Drosophila Embryogenesis and Oogenesis Development","description":"The top GO terms cluster around early embryonic processes (regulation of the preblastoderm mitotic cell cycle and syncytial nuclear migration) and ovary/germline development (follicle cells, germarium-derived cyst encapsulation, egg chamber stalk formation), with additional signals pointing to differentiation programs (macrophage/granulocyte differentiation) in a Drosophila context. This suggests a cohesive theme of developmental regulation during Drosophila embryogenesis and oogenesis.","confidence":"High","size":29,"edges":5,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0048706","count":6},{"id":"GO:0030225","count":6},{"id":"GO:0030851","count":6},{"id":"GO:0035190","count":6}]},{"hash":"338994981496598055","title":"Neural perception and dopaminergic signaling","description":"Top terms are dominated by sensory and neural signaling functions (pain perception, visual perception and learning, dopaminergic synaptic transmission, cocaine response) with ERK cascade regulation, pointing to neuronal perception and dopamine-related signaling as the core. While some terms pertain to non-neural processes (heart development, macrophage chemotaxis, prostaglandin response, electron transport), the strongest cohesive theme is neural sensing and dopaminergic communication.","confidence":"High","size":29,"edges":47,"triangles":1,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":18},{"id":"GO:0007601","count":17},{"id":"GO:0007507","count":17},{"id":"GO:0070374","count":16},{"id":"GO:0048148","count":16}]},{"hash":"2013605322430073072","title":"Immune Signaling and Receptor Pathways","description":"The cluster\u2019s top GO terms are dominated by innate immune response and T cell receptor signaling, along with ERK cascade regulation, ephrin receptor signaling, and mast cell degranulation, pointing to a cohesive group of proteins involved in immune signaling networks and receptor-mediated pathways; associations with focal adhesion and PI3K signaling also fit with immune cell communication and movement during responses.","confidence":"High","size":29,"edges":71,"triangles":48,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045087","count":27},{"id":"GO:0070374","count":27},{"id":"GO:0000186","count":27},{"id":"GO:0050852","count":27},{"id":"GO:0006260","count":27}]},{"hash":"115225556059020549","title":"Brain and Neural Development","description":"Top terms point to brain and neural development (forebrain, spinal cord, brain development, multicellular organism development) and cell migration, suggesting a neural-development-focused cluster. Other terms on protein oligomerization or signaling are less defining, so Brain and Neural Development is the best representation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051092","count":5},{"id":"GO:0030900","count":4},{"id":"GO:0070208","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0021510","count":4}]},{"hash":"2126878136654826179","title":"Embryonic eye and neural organogenesis","description":"The cluster is dominated by terms tied to embryonic development, especially eye morphogenesis (camera-type eye development, embryonic eye morphogenesis) and neural tissues (cerebellum development, motor neuron axon guidance, pituitary gland development). The presence of broader transcriptional regulation by RNA polymerase II also fits a regulatory program guiding organogenesis. This points to a cohesive theme of embryonic eye and neural development, with gene regulation as a supporting motif.","confidence":"High","size":29,"edges":19,"triangles":0,"max_degree":4,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":16},{"id":"GO:0006366","count":13},{"id":"GO:0043010","count":13},{"id":"GO:0060441","count":13},{"id":"GO:0048048","count":13}]},{"hash":"2199749445882145148","title":"Heart development and immune/coagulation pathways","description":"The top GO terms point to developmental signaling (including midbrain and general development via Wnt), EMT in heart development (endocardial cushion formation), ECM remodeling (collagen catabolic process), and immune/coagulation activity (complement activation pathways, blood coagulation, LPS response). This suggests a cluster of proteins involved in cardiovascular development with linked inflammatory and coagulation roles.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030901","count":8},{"id":"GO:0016055","count":7},{"id":"GO:0032496","count":7},{"id":"GO:0000122","count":7},{"id":"GO:0003198","count":6}]},{"hash":"1134401138462934565","title":"Branched-chain amino acid biosynthesis and central metabolism","description":"This cluster is dominated by GO terms for biosynthesis of isoleucine, leucine, and valine, plus related catabolic processes, the TCA cycle, and redox homeostasis, suggesting a core module for branched-chain amino acid production and energy metabolism. Some terms like translation, embryonic development, and sporulation may reflect broader cellular roles or annotation noise rather than a single cohesive function.","confidence":"Medium","size":29,"edges":80,"triangles":173,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":5},{"id":"GO:0006550","count":4},{"id":"GO:0001701","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0006099","count":4}]},{"hash":"373575965156506435","title":"Neural sensory perception and dopaminergic signaling","description":"This cluster is dominated by GO terms related to sensory perception (pain, vision) and dopaminergic synaptic transmission, with related behavioral and signaling context such as cocaine response and ERK pathway regulation. The presence of brain-related terms like the brain renin-angiotensin system and visual learning suggests a cohesive theme around neural processing, perception, and reward signaling, despite a few peripheral terms (e.g., heart development). Overall, it points to a brain/spinal cord\u2013centered signaling module governing sensation, perception, and dopaminergic signaling.","confidence":"Medium","size":29,"edges":212,"triangles":478,"max_degree":19,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":24},{"id":"GO:0007601","count":22},{"id":"GO:0048148","count":22},{"id":"GO:0071380","count":22},{"id":"GO:0002035","count":22}]},{"hash":"395176062279559890","title":"GPCR-driven cardiovascular and sensory signaling","description":"This cluster centers on GPCR signaling with links to blood pressure regulation, heart development, and prostaglandin responses, suggesting a cardiovascular signaling theme. The presence of terms related to visual perception and cocaine response points to broader GPCR-mediated neural pathways, which complements the general signaling/metabolic context (e.g., electron transport). Overall, the common thread is GPCR-mediated signaling impacting cardiovascular and sensory processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045777","count":12},{"id":"GO:0022900","count":12},{"id":"GO:0010579","count":12},{"id":"GO:0035025","count":11},{"id":"GO:0071380","count":10}]},{"hash":"989420759242144833","title":"Vascular signaling and development","description":"This cluster centers on signaling pathways that regulate cardiovascular function (adenylate cyclase\u2013activating GPCR signaling, blood pressure regulation, smooth muscle contraction, coagulation) and developmental processes (multicellular development, synapse assembly, Rho signaling). While energy metabolism and broader signaling terms appear, the most representative common theme is signaling and regulation in vascular development and function, making this label a concise summary of the dominant terms. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":10},{"id":"GO:0010579","count":9},{"id":"GO:0045777","count":8},{"id":"GO:0035025","count":7},{"id":"GO:0051965","count":7}]},{"hash":"917597218617265454","title":"Wnt signaling and cell cycle regulation","description":"The top GO terms center on cell cycle transitions (G1/S, G2/M), transcription, and a canonical Wnt signaling pathway, with additional developmental context (mammary gland and Leydig cell development). This pattern suggests a coordinated role in regulating cell proliferation through Wnt signaling, making the label a coherent summary of the cluster's function.","confidence":"High","size":29,"edges":45,"triangles":10,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000082","count":17},{"id":"GO:0060749","count":17},{"id":"GO:0006351","count":17},{"id":"GO:0033327","count":17},{"id":"GO:0033601","count":16}]},{"hash":"1979216775552581995","title":"Innate and Adaptive Immune Response","description":"The proteins cluster around core immune functions: phagocytosis, complement activation, T cell costimulation, NK cell cytotoxicity, and regulation of IL-10, spanning both innate and adaptive immunity, with a minor outlier related to spermatid development.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006910","count":13},{"id":"GO:0006958","count":13},{"id":"GO:0007157","count":13},{"id":"GO:0002250","count":12},{"id":"GO:2001181","count":12}]},{"hash":"1869157151861648175","title":"Neural development and innate immune signaling","description":"Top terms show neural development (axonogenesis, corpus callosum development) alongside innate immune pathways (LPS signaling, dsRNA response, interferon-\u03b2 production) and neuromodulatory/pain-related processes, suggesting a cluster tied to neurodevelopment with brain immune signaling. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007409","count":14},{"id":"GO:0045087","count":12},{"id":"GO:0071222","count":11},{"id":"GO:0014068","count":11},{"id":"GO:0045359","count":11}]},{"hash":"1741008208327005456","title":"Membrane Ion Transport and Excitability","description":"Top GO terms are dominated by ion transmembrane transport (sodium, potassium, calcium), membrane depolarization, and neuromuscular signaling, indicating a cluster of proteins involved in membrane transport and regulation of excitability. Additional terms such as blood coagulation and sensory mechanotransduction appear as minority associations and may reflect distant or multifunctional roles of a subset of members rather than a single cohesive function.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0007596","count":3},{"id":"GO:1990966","count":2}]},{"hash":"614831294291615093","title":"Mitosis and gene expression regulation","description":"The cluster is driven by mitotic cycle and spindle orientation terms (mitosis, spindle orientation, cell proliferation) alongside transcription and translation initiation processes (DNA-templated transcription, translation reinitiation, preinitiation complex formation) and epigenetic regulation (histone deacetylation). Developmental terms (male gonad and skeletal system development) suggest broader roles in growth, but the shared core theme appears to be coordinating cell division with gene expression control.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0008584","count":4},{"id":"GO:0016575","count":4},{"id":"GO:0000132","count":4}]},{"hash":"1493537215817204612","title":"RNA splicing and translation control","description":"The cluster is enriched for mRNA splicing regulation, spliceosome activity, mRNA export, translation initiation/reinitiation, and stress-granule localization, plus ncRNA-mediated gene silencing, indicating proteins involved in RNA maturation and controlling gene expression at the translation level.","confidence":"High","size":28,"edges":362,"triangles":2900,"max_degree":27,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":16},{"id":"GO:0031047","count":16},{"id":"GO:0002188","count":13},{"id":"GO:0001731","count":13},{"id":"GO:1901407","count":13}]},{"hash":"747634467862990246","title":"Spliceosome-driven mRNA processing and regulation","description":"The top GO terms point to mRNA processing and regulation: mRNA splicing via spliceosome, spliceosome-regulated alternative splicing, mRNA polyadenylation, and mRNA stability regulation in stress. The terms also include translation initiation factor complex assembly, suggesting coupling between RNA maturation and translation. Together, these proteins appear to form a module centered on RNA processing and splicing regulation.","confidence":"High","size":28,"edges":377,"triangles":3250,"max_degree":27,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":24},{"id":"GO:0006378","count":16},{"id":"GO:0031047","count":15},{"id":"GO:0048026","count":15},{"id":"GO:0045292","count":15}]},{"hash":"1893413210474041330","title":"Post-transcriptional mRNA processing and stability regulation","description":"The top GO terms cluster around mRNA processing and turnover: regulation of mRNA stability in response to stress, splicing via the spliceosome, polyadenylation, tail shortening, mRNA modification, and mRNA stabilization, with links to translation initiation complex assembly and regulatory ncRNA\u2013mediated silencing. This points to a cohesive theme of post-transcriptional control of gene expression, including splicing, polyadenylation, stability, and translation readiness under stress.","confidence":"High","size":28,"edges":378,"triangles":3276,"max_degree":27,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":20},{"id":"GO:0045292","count":19},{"id":"GO:0006378","count":19},{"id":"GO:0060211","count":16},{"id":"GO:1905663","count":16}]},{"hash":"689258440165173635","title":"Endothelial and neuronal signaling and growth regulation","description":"These proteins cluster around signaling pathways: VEGF signaling affecting endothelial cells, EGFR signaling, JUN and STAT phosphorylation, and regulation of endothelial chemotaxis, plus neuronal signaling indicated by excitatory postsynaptic potential. Together, they suggest a coherent theme of growth-related signal transduction across vascular and neural contexts. Some terms like mitotic checkpoint or visual perception are more peripheral but do not overturn the central signaling/growth focus.","confidence":"Medium","size":28,"edges":319,"triangles":2040,"max_degree":27,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":28},{"id":"GO:0048010","count":28},{"id":"GO:0007258","count":28},{"id":"GO:2001028","count":28},{"id":"GO:0070849","count":28}]},{"hash":"686047146524967135","title":"Xenobiotic and nutrient transporter proteins","description":"The cluster is dominated by transmembrane transport GO terms for xenobiotics, vitamins, and sugars (including D-glucose) and includes potassium ion transport, pointing to a common role in membrane transport of nutrients and small molecules. Some host- and cell state\u2013related terms are present but do not outweigh the clear transporter theme.","confidence":"High","size":28,"edges":7,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":27},{"id":"GO:0035461","count":27},{"id":"GO:0042891","count":22},{"id":"GO:0042908","count":19},{"id":"GO:0071805","count":18}]},{"hash":"718452930344536340","title":"Innate Immune Response and Transcriptional Regulation","description":"The cluster is heavily enriched for innate immune terms, including defense against Gram-positive bacteria, cellular and systemic responses to lipopolysaccharide and dsRNA, and general innate immune signaling. The presence of DNA-templated transcription suggests linked transcriptional regulation during immune activation. A few development terms appear as potential outliers or broad annotation overlap, but the dominant theme is innate immune signaling and stress-responsive transcription.","confidence":"Medium","size":28,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050830","count":28},{"id":"GO:0001501","count":27},{"id":"GO:0006351","count":27},{"id":"GO:0045087","count":27},{"id":"GO:0043330","count":27}]},{"hash":"1444567680221907780","title":"Neural development and synaptic signaling","description":"This cluster is dominated by neural-related terms: axonogenesis, substantia nigra development, astrocyte activation, and regulation of synaptic plasticity, along with calcium channel regulation and protein phosphorylation, all pointing to neural development and neuronal signaling. While some terms like cell cycle and cardiac contraction are broader or less specific, the neural themes are strong and represent the cluster\u2019s core function. ","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":13},{"id":"GO:0048143","count":11},{"id":"GO:1901387","count":11},{"id":"GO:0006468","count":11},{"id":"GO:0008284","count":11}]},{"hash":"1862732004739944737","title":"Cardiac muscle contraction and sarcomere organization","description":"The top GO terms are dominated by cardiac-related processes: cardiac muscle contraction and sarcomere organization, with multiple terms about regulation of heart rate and sarcomere assembly. While there are a few terms related to visual perception and nervous system development, the strongest signals point to cardiac muscle function and sarcomere structure, making this the most representative theme for the cluster.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060048","count":17},{"id":"GO:0045214","count":16},{"id":"GO:0034609","count":14},{"id":"GO:0003065","count":14},{"id":"GO:1904706","count":14}]},{"hash":"145680583066544304","title":"Neural development and synaptic signaling","description":"The top GO terms point to nervous system development, CNS development, synapse organization, and glutamatergic synaptic transmission, with supporting pathways in BMP signaling, Rho regulation, and phosphatidylinositol signaling. While a few terms like angiogenesis or salivary gland boundary specification appear, the dominant signal is neural development and synaptic function. This suggests the cluster functions primarily in neural patterning, synapse formation, and neurotransmission.","confidence":"High","size":28,"edges":362,"triangles":2893,"max_degree":27,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0001525","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0035023","count":7},{"id":"GO:0001778","count":7},{"id":"GO:0048015","count":7}]},{"hash":"187098469533561672","title":"Metabolic and Nutrient Signaling","description":"This cluster shows enrichment in glycolysis, oxaloacetate and amino acid metabolism (L-alanine, L-kynurenine), and responses to nutrients and signaling cues (response to cAMP, Notch signaling). The mix of central metabolism with nutrient- and signal-responsive terms suggests a group involved in energy generation and nutrient-regulated processes rather than a single isolated pathway.","confidence":"Medium","size":28,"edges":344,"triangles":2738,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051591","count":9},{"id":"GO:0006107","count":8},{"id":"GO:0007584","count":8},{"id":"GO:0017000","count":7},{"id":"GO:0007219","count":7}]},{"hash":"450440288139213883","title":"Cerebellar Neurodevelopment and Cell Cycle","description":"The top GO terms reveal a blend of cerebellar-specific development (cerebellar cortex formation; Bergmann glial cell differentiation) with core cell cycle and mitotic machinery (cell cycle; microtubule nucleation; mitotic spindle pole body duplication; spindle midzone assembly). This pattern suggests proteins that participate in cerebellar neural development while coordinating mitotic processes, reflecting proliferation-differentiation dynamics in cerebellar cells. Confidence in this label is High.","confidence":"","size":28,"edges":148,"triangles":389,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007049","count":13},{"id":"GO:0007020","count":12},{"id":"GO:1903087","count":12},{"id":"GO:0060020","count":11},{"id":"GO:0048679","count":11}]},{"hash":"1343898228877096823","title":"Developmental signaling and cytoskeletal regulation","description":"This cluster centers on signal transduction affecting the cytoskeleton (Rho, actin remodeling) and key pathways (ERK/JNK, Wnt), with links to angiogenesis and brain development, suggesting proteins that coordinate signaling with cytoskeletal changes during development and vascular/neural formation.","confidence":"Medium","size":28,"edges":232,"triangles":718,"max_degree":22,"top_function":"wound healing","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0070374","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0031532","count":5},{"id":"GO:0071222","count":5}]},{"hash":"1834388309500135827","title":"Septin ring assembly at the bud neck during mitosis","description":"This cluster is dominated by GO terms related to septin ring assembly, bud neck organization, and division septum formation, all tied to mitotic progression and cytokinesis. The strongest signals (septin ring assembly, bud neck localization, division septum assembly, exit from mitosis) point to septin-driven processes governing cytokinesis at the bud neck, with some secondary terms reflecting broader developmental processes.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000921","count":10},{"id":"GO:0032186","count":10},{"id":"GO:0097271","count":10},{"id":"GO:0000278","count":8},{"id":"GO:0030154","count":8}]},{"hash":"2011824426794447850","title":"ER stress and apoptosis regulation","description":"This cluster centers on proteins that negatively regulate stress- and apoptosis-related pathways, including negative regulation of apoptotic processes, JNK signaling, Fas signaling, and unfolded protein response components. The common theme is modulation of ER stress\u2013linked signaling and downstream cell fate decisions, with some association to broader stress responses (e.g., hypoxia and immunoglobulin-related regulation). Overall, they appear to function as regulators dampening stress-induced apoptosis and related pathways.","confidence":"Medium","size":28,"edges":35,"triangles":8,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:1990441","count":4},{"id":"GO:0006915","count":3},{"id":"GO:1904780","count":3},{"id":"GO:0046329","count":3},{"id":"GO:1902065","count":3}]},{"hash":"1682277467654278076","title":"Dopaminergic Neuron Development and Dendrite Regulation","description":"The cluster centers on neuronal development and dendrite morphogenesis, highlighted by substantia nigra development and regulation of dendrite morphogenesis, along with synaptic activity signals such as excitatory postsynaptic potentials. While other terms point to broader cell biology (Golgi organization, transcription) and stress-related responses (xenobiotic, epinephrine), the strongest signal is neuronal development and synaptic function with a dopaminergic context.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050774","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006517","count":4},{"id":"GO:0019310","count":4},{"id":"GO:0060079","count":3}]},{"hash":"1709872139517078596","title":"Nuclear transcription and chromatin regulation","description":"This cluster is driven by GO terms linked to transcriptional control and chromatin modification (DNA-templated transcription, RNA polymerase II regulation, histone methylation) and includes a ribosome biogenesis note (rRNA processing). The dominant theme appears to be nuclear gene expression regulation, with some outlier terms reflecting broader roles or annotation noise (heart development, B cell proliferation, SREBP signaling). Overall, a cohesive label is about transcription and chromatin regulation in the nucleus.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":3},{"id":"GO:0030890","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0035023","count":3}]},{"hash":"880293414255555902","title":"Rho GTPase\u2013driven actin remodeling and endocytosis","description":"The cluster is enriched for small GTPase signaling and actin dynamics, including ruffle, filopodium, and podosome assembly, as well as endocytosis and cell spreading. The presence of terms related to epithelial polarity and T cell receptor signaling suggests these actin-driven processes are coordinated with membrane trafficking and cell-surface signaling, indicating a cohesive role in cytoskeletal remodeling and endocytic pathways regulated by Rho-family GTPases.","confidence":"High","size":28,"edges":25,"triangles":3,"max_degree":20,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007264","count":23},{"id":"GO:0030838","count":22},{"id":"GO:0097178","count":22},{"id":"GO:0006897","count":22},{"id":"GO:1900026","count":22}]},{"hash":"1629881054880204538","title":"Ubiquitin-Proteasome-Mediated Proteolysis in Oocyte Meiosis","description":"Based on GO terms, the cluster is enriched for ubiquitin-dependent protein catabolic process, protein polyubiquitination, and SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, indicating a core theme of proteostasis via the ubiquitin-proteasome system. The presence of terms related to spindle assembly, microtubule polymerization, and oocyte maturation suggests a functional link to meiotic progression and oogenesis, where timely protein degradation governs cell-cycle transitions. While some terms like third ventricle development and circadian rhythm regulation are broader or less obviously connected, the dominant signal points to regulated proteolysis during female meiosis. Therefore the proposed label captures both the degradation machinery and its role in meiosis/oocyte maturation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":18},{"id":"GO:0042752","count":11},{"id":"GO:0021678","count":10},{"id":"GO:0000209","count":10},{"id":"GO:0031146","count":10}]},{"hash":"1709964077618291933","title":"GPCR Signaling and Sensory Perception","description":"The top GO terms are dominated by GPCR-related signaling (adenylate cyclase activation/inhibition, GPCR signaling pathways) and sensory perception (visual perception). Additional terms include regulatory processes (blood pressure, GTPase activity) and responses to peptides/xenobiotics, which fit the broad GPCR-mediated signaling and sensory-response theme. An electron transport chain term appears as an outlier, but does not override the central GPCR/sensory pattern.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":26},{"id":"GO:0045777","count":26},{"id":"GO:0010579","count":26},{"id":"GO:0042493","count":25},{"id":"GO:0007190","count":25}]},{"hash":"468628577381153238","title":"Mitochondrial Electron Transport Chain Proteins","description":"The cluster is dominated by the GO term electron transport chain (enriched in 20 proteins), suggesting a core set of mitochondrial respiration components. While there are additional GO terms related to signaling (GPCR-cAMP pathways, prostaglandin response) and physiological processes (blood pressure regulation, pain perception, bone remodeling), these may reflect regulatory roles or annotation cross-talk rather than a single shared function beyond mitochondrial respiration. Overall, the ETC signature best fits the primary theme of this cluster.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":20},{"id":"GO:0045777","count":20},{"id":"GO:0010579","count":20},{"id":"GO:0035025","count":18},{"id":"GO:0051930","count":17}]},{"hash":"164220994747839060","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0070651","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070370","count":3}]},{"hash":"1123205381674382434","title":"Developmental differentiation and gene regulation","description":"The cluster is enriched for differentiation and developmental processes (lens fiber and osteoblast differentiation), along with gene expression control (DNA-templated transcription, mRNA splicing, genomic imprinting regulation) and developmental signaling (TGF-beta response) plus related cellular processes (spindle orientation, cilium assembly). These together point to a cohesive theme of development and differentiation with associated gene regulation.","confidence":"Medium","size":28,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000132","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0070306","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0007338","count":4}]},{"hash":"2285635019123607292","title":"Developmental transcription and signaling","description":"This cluster centers on vertebrate development and growth signaling, with terms like neural tube closure, forebrain development, and skeletal system development, along with core regulatory processes such as mitotic cell cycle and DNA-templated transcription. Additional terms indicate broader stress and metabolic responses (ER stress\u2013related apoptosis, cadmium response, insulin signaling). The common thread appears to be developmental regulation intertwined with signaling and transcriptional control, with ancillary stress-response aspects.","confidence":"Medium","size":28,"edges":126,"triangles":243,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0008286","count":5},{"id":"GO:0001501","count":4},{"id":"GO:0001843","count":4}]},{"hash":"1325696130433056481","title":"Ribosome biogenesis and translation with ubiquitin regulation","description":"This cluster is driven by translation (GO:0006412) and ribosome biogenesis (GO:0042254), indicating a core role in protein synthesis. The accompanying ubiquitin-related terms (GO:0030433, GO:0051865) point to protein quality control and turnover, suggesting a theme of coordinated synthesis and regulation of proteins. A few developmental, circadian, and immune differentiation terms are present but appear ancillary to the main translational/ubiquitin-focused functions. ","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0072156","count":5}]},{"hash":"2282733008318207812","title":"Embryonic morphogenesis and lineage differentiation","description":"This cluster centers on developmental processes, with prominent terms for embryonic tissue morphogenesis (cartilage morphogenesis, left-right patterning, EMT in heart development) and lineage differentiation (placental trophoblast differentiation, pancreatic cell development, endocrine system development). While a few regulatory terms appear, the dominant theme is embryonic development and tissue specification, supporting this label.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060536","count":19},{"id":"GO:0003323","count":19},{"id":"GO:0060806","count":19},{"id":"GO:0060972","count":19},{"id":"GO:0060707","count":19}]},{"hash":"352926657883143560","title":"Inflammation-Driven Angiogenesis and ECM Remodeling","description":"Top GO terms point to inflammatory response and classical complement activation alongside angiogenesis and collagen fibril organization. Additional signals regulate ERK cascade and smooth muscle proliferation, indicating coordinated immune activation, vascular remodeling, and extracellular matrix changes during development. Taken together, the cluster seems to capture inflammation-associated blood vessel formation and ECM dynamics rather than a single isolated function.","confidence":"Medium","size":28,"edges":5,"triangles":1,"max_degree":3,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045766","count":9},{"id":"GO:0030199","count":9},{"id":"GO:0006958","count":8},{"id":"GO:0042346","count":7},{"id":"GO:0014068","count":7}]},{"hash":"985345474680378203","title":"Translation and Protein Oligomerization","description":"The cluster\u2019s top GO terms are dominated by translation and protein oligomerization (homotetramerization/heterooligomerization), indicating roles in protein synthesis and assembly. Additional terms for protein turnover (protein catabolic process) and stress-related responses (apoptotic process, response to cold) suggest broader proteome maintenance under stress, with a peripheral hint of membrane-associated transport. Overall, the recurring theme centers on protein production and assembly with stress-linked quality control.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":4},{"id":"GO:0006412","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006915","count":2}]},{"hash":"653164541500497850","title":"Immune signaling and vascular development","description":"The top GO terms cluster around innate/adaptive immune responses (cellular response to lipopolysaccharide, defense against Gram-positive bacteria, positive regulation of T cell proliferation, IFN and IL-4 production) and vascular/hemostatic processes (cell-matrix adhesion, endothelial migration, blood microparticle formation), suggesting a functional grouping of immune signaling with vascular-related roles. Some reproductive terms are present but likely less central to the core function of this cluster.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":3},{"id":"GO:0007160","count":2},{"id":"GO:0042102","count":2},{"id":"GO:0048599","count":2},{"id":"GO:0032729","count":2}]},{"hash":"313184060501372165","title":"Ubiquitin-Dependent Degradation and Innate Immunity","description":"The dominant GO terms cluster around ubiquitin-dependent protein degradation (ERAD, autoubiquitination, K6-linked ubiquitination) and related chromatin associations (histone catabolic process), with concurrent signals for innate immune response and defense against virus. This suggests a group of proteins linked to ubiquitin-proteasome\u2013mediated turnover that interfaces with immune signaling and chromatin regulation. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":23},{"id":"GO:0030433","count":16},{"id":"GO:0051865","count":15},{"id":"GO:0045087","count":15},{"id":"GO:0051607","count":15}]},{"hash":"395271332805607163","title":"Lipid Signaling in Angiogenesis and Brain Development","description":"The GO terms point to lipid-mediated signaling (triglyceride catabolic process, sphingosine-1-phosphate receptor signaling, GPCR signaling, phosphorylation regulation) that co-occurs with vascular/neuronal development (angiogenesis, blood vessel development, brain development). This suggests proteins in this cluster coordinate lipid signaling to promote vascular and brain development, with ancillary roles in inflammatory cytokine regulation and hormone biosynthesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019433","count":7},{"id":"GO:0007205","count":6},{"id":"GO:0048146","count":6},{"id":"GO:0045766","count":6},{"id":"GO:0010800","count":6}]},{"hash":"19889296254281952","title":"Stress-Response and Genome Maintenance","description":"The top GO terms cluster around stress-related processes (response to heat, cellular response to glucose stimulus) and genome integrity functions (DNA repair, telomere capping, telomere maintenance via telomerase, mRNA processing). Ubiquitination is a key regulatory link among these processes, supporting stress responses and genome maintenance. Some terms also touch on adipogenesis and cell migration, but they appear less central, so the core theme centers on stress response coupled with genome maintenance rather than a single differentiated pathway.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0009408","count":5},{"id":"GO:0071333","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0045444","count":5},{"id":"GO:1904355","count":5}]},{"hash":"1521457788536411412","title":"Signaling and proliferation regulators","description":"This cluster shows enrichment for phosphorylation and regulation of signaling pathways that control cell proliferation, including endothelial proliferation, TGF-beta receptor signaling, p38 MAPK cascade, and regulation of GTPase activity. Although some terms (like mammary gland involution and ER organization) appear less directly related, the central theme across the top terms is regulatory roles in signaling and proliferation rather than a single structural process. Confidence in this thematic label is Medium.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:0001938","count":3},{"id":"GO:0001937","count":3},{"id":"GO:0030512","count":3},{"id":"GO:0060056","count":3}]},{"hash":"1682920512902215332","title":"Integrin-Rho Cytoskeleton Signaling in Heart Development","description":"The cluster centers on cytoskeleton remodeling and integrin signaling (actin cytoskeleton reorganization, integrin activation, and Rho pathway regulation) with heart development as a common context, aligning with cell adhesion and cytoskeletal dynamics; apoptosis appears less central.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0007205","count":4},{"id":"GO:1902896","count":3}]},{"hash":"1843341131758411080","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":9,"triangles":0,"max_degree":5,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0007157","count":24},{"id":"GO:0007156","count":23},{"id":"GO:0043931","count":23},{"id":"GO:0007399","count":22},{"id":"GO:0051965","count":20}]},{"hash":"941812954572897726","title":"Embryonic organogenesis and placental development","description":"The top GO terms cluster around development of multiple organs (heart, face, placenta, vagina) and related transcriptional regulation, with DNA-templated transcription and retinoic acid response highlighting embryogenic gene regulation. While some terms touch on other processes, the dominant theme is coordinated embryonic organ development and placentation.","confidence":"High","size":28,"edges":77,"triangles":84,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":23},{"id":"GO:0001890","count":23},{"id":"GO:0060324","count":23},{"id":"GO:0006351","count":23},{"id":"GO:0071300","count":23}]},{"hash":"493180381980245611","title":"Neuronal development and synapse formation","description":"The cluster centers on nervous system processes: neuron development, migration, synapse assembly, and transmission of nerve impulses, with cell adhesion and ERK signaling terms supporting synaptic connectivity and neuronal differentiation; while an innate immune term appears, the predominant theme is neural development and synaptic signaling.","confidence":"Medium","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":8},{"id":"GO:0048671","count":7},{"id":"GO:0051965","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0019226","count":7}]},{"hash":"227548796048650117","title":"Organ development and transcription regulation","description":"The top GO terms show involvement in development across multiple organs (retina, inner ear, pituitary, locus ceruleus, osteoblasts, gonads, ureteric bud), suggesting a broad role in organogenesis. The additional transcription-related terms (transcription by RNA polymerase II and its negative regulation) indicate these proteins are linked to controlling gene expression during these developmental processes. This combination points to a cluster of proteins associated with organ development governed by transcriptional regulation.","confidence":"High","size":28,"edges":366,"triangles":2977,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":18},{"id":"GO:0060041","count":18},{"id":"GO:0002087","count":16},{"id":"GO:0002076","count":16},{"id":"GO:0008584","count":15}]},{"hash":"2236320804195149248","title":"Unknown","description":"The GO terms cover neural development, organ growth, cellular processes (mitochondrial fission, chromatin assembly), reproduction, plasmid maintenance, and immune defense, with no clear common function linking all proteins and no network edges, so there is no cohesive theme to name.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:1904693","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0035264","count":3}]},{"hash":"1587584743172715023","title":"Embryonic Development and Placental Differentiation","description":"This cluster shows strong enrichment for embryogenesis- and placental-related processes (trophoblast giant cell differentiation, endocrine system development, placenta-related differentiation, left-right patterning) and tissue morphogenesis (cartilage morphogenesis, EMT in heart cushion). While a few terms reflect general transcription or ribosome export, the dominant signal is developmental differentiation and morphogenesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0060707","count":13},{"id":"GO:0003323","count":12},{"id":"GO:0035270","count":11},{"id":"GO:0060536","count":11},{"id":"GO:0060806","count":11}]},{"hash":"650195748451280938","title":"Developmental cell adhesion and signaling","description":"The terms cluster around tissue development and adhesion (kidney, skeletal, multicellular development) with structural (sarcomere) and signaling/immune pathways (T cell costimulation, Fc-epsilon receptor signaling, neutrophil extravasation, homophilic adhesion), implying proteins that coordinate cell interactions and communication during development.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001822","count":5},{"id":"GO:0031175","count":5},{"id":"GO:0001736","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0007275","count":4}]},{"hash":"2267034812768260126","title":"Actin Cytoskeleton Dynamics and Rho Signaling","description":"The cluster\u2019s top GO terms strongly point to actin cytoskeleton organization and regulation of Rho-mediated signaling, with related processes in focal adhesion regulation, membrane targeting, and cell spreading. This suggests proteins that coordinate cytoskeletal remodeling and adhesion, rather than a single isolated function; heart development and synaptic plasticity hints reflect broader tissue-specific roles of actin regulators.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0043113","count":3},{"id":"GO:0051895","count":3},{"id":"GO:0090315","count":3}]},{"hash":"1127931986744396394","title":"Gene Expression and Ribosome Assembly","description":"Most frequent GO terms center on transcription, ribosome biogenesis, and the formation of translation preinitiation complex, pointing to a core program of gene expression and protein synthesis. Additional terms hint at chromatin regulation via histone acetylation and broader growth/stress responses (actin dynamics, invasive growth under glucose limitation, and defense against Gram-positive bacteria). Overall, the cluster seems to group genes involved in transcriptional control, ribosome biogenesis, and translation readiness, i.e., the cellular machinery for gene expression and growth. Confidence is Medium.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035264","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0034316","count":5},{"id":"GO:0043966","count":5}]},{"hash":"490448611119250616","title":"Ribosome Biogenesis and Translation Initiation","description":"Based on the top GO terms, the cluster centers on translation machinery and ribosome maturation: translation reinitiation; formation of translation preinitiation complex; maturation of SSU- and LSU-rRNA; regulation of translational initiation. These point to ribosome assembly and control of protein synthesis as the core shared function. Other terms like ER-Golgi transport and cell division describe cellular context but are likely secondary. Therefore the label summarizes the main theme: Ribosome biogenesis and translation initiation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0006890","count":5},{"id":"GO:0000462","count":5}]},{"hash":"1133668823727645558","title":"Ubiquitin-regulated Signaling and Transcription","description":"This cluster is enriched for protein ubiquitination along with key signaling pathways (Wnt, NF-\u03baB, TGF-\u03b2, ephrin receptor) and transcription-related activity, suggesting a module where ubiquitination modulates signal transduction and downstream gene expression. Additional terms for interferon signaling and DNA-templated transcription support a broader regulatory role, while a few terms like sensory perception of sound may reflect peripheral associations rather than core function.","confidence":"Medium","size":27,"edges":6,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0090263","count":5},{"id":"GO:0048013","count":5},{"id":"GO:0051092","count":5},{"id":"GO:0006351","count":4}]},{"hash":"1736463787996181260","title":"Broad Signaling Pathway Regulators","description":"This cluster centers on multiple signaling pathways (Wnt canonical, Hippo, growth hormone receptor, T cell receptor) and differentiation processes (keratinocyte differentiation, dendrite morphogenesis) as well as apoptosis, suggesting proteins that broadly regulate signaling cascades to influence cell fate across tissues.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":20},{"id":"GO:0030216","count":19},{"id":"GO:0060044","count":19},{"id":"GO:0006915","count":19},{"id":"GO:0035329","count":19}]},{"hash":"2238768232274102156","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000472","count":9},{"id":"GO:0000447","count":9},{"id":"GO:0000480","count":9},{"id":"GO:0034316","count":9},{"id":"GO:0035264","count":9}]},{"hash":"642888923431207295","title":"Translational initiation and ribosome biogenesis","description":"This cluster is dominated by GO terms for initiating and reinitiating translation, forming preinitiation complexes, and IRES-dependent viral translation, with additional signals for ribosome biogenesis and related RNA processing (mRNA export/splicing). Together, these point to a cohesive role in assembling and controlling the protein synthesis machinery, with broader RNA processing context. ","confidence":"High","size":27,"edges":11,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006446","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0045292","count":4},{"id":"GO:0075525","count":4}]},{"hash":"500397162080081528","title":"Adaptive Immune Activation and IL-2 Signaling","description":"This cluster centers on adaptive immunity: multiple terms point to B cell receptor signaling, Fc-epsilon receptor signaling, adaptive immune response, and cytokine-related activity (IL-2 production and IL-2 response). The inclusion of a lipopolysaccharide response supports immune activation as well, though a couple of terms (melanocyte differentiation, epigenetic methylation processes) are less directly connected to adaptive immunity. Overall, the proteins appear enriched for immune signaling and activation pathways.","confidence":"High","size":27,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0070669","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0030318","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0048681","count":3}]},{"hash":"1366476913751053067","title":"Neural signaling and synaptic plasticity","description":"The strongest signals point to neuronal communication and adaptation: excitatory postsynaptic potential, long-term synaptic potentiation, and axonogenesis suggest synaptic signaling and plasticity, while DNA replication/transcription and phosphorylation regulation imply accompanying gene expression and signaling control in neurons. The abscisic acid pathway is an outlier (plant signaling) and may reflect annotation noise or conserved kinase elements, but it does not override the dominant neural theme. Overall, the cluster seems centered on neural signaling and plasticity with gene regulation aspects.","confidence":"Medium","size":27,"edges":30,"triangles":8,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0007601","count":10},{"id":"GO:0060079","count":10},{"id":"GO:0006351","count":10},{"id":"GO:0009738","count":10}]},{"hash":"1517117778653263081","title":"Craniofacial neural crest and heart development","description":"The top GO terms cluster around craniofacial patterning and neural crest biology (roof of mouth development, embryonic cranial skeleton morphogenesis, neural crest cell migration, cartilage development) with strong representation of heart and cochlear morphogenesis, indicating a coherent program of craniofacial neural crest\u2013driven development and associated organogenesis.","confidence":"High","size":27,"edges":18,"triangles":8,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0060021","count":17},{"id":"GO:0048701","count":13},{"id":"GO:0001764","count":12},{"id":"GO:0001755","count":12},{"id":"GO:0051216","count":12}]},{"hash":"1497066215107644974","title":"Telomere maintenance and PARP activity","description":"This cluster centers on GO terms related to maintaining telomeres (telomere capping, telomerase regulation, telomeric localization, and telomere maintenance via telomeres) and on ADP-ribosylation processes (auto- and poly-ADP-ribosylation), suggesting a group of proteins involved in telomere biology and PARP-mediated modification. The recurring telomere-associated terms dominate the list, making this a coherent telomere/PARP cluster despite a few unrelated terms.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021707","count":4},{"id":"GO:0051225","count":4},{"id":"GO:1904355","count":4},{"id":"GO:1904357","count":4},{"id":"GO:0032212","count":4}]},{"hash":"1214672189389325193","title":"Embryonic Skeletal and Cardiac Morphogenesis","description":"The top GO terms cluster around early embryonic development of mesoderm-derived tissues: bone and skeletal lineages (osteoblast differentiation, skeletal muscle differentiation, trachea cartilage development) alongside heart development (outflow tract morphogenesis, secondary heart field specification, primitive streak formation). TGF-beta signaling also features, indicating a common regulatory axis. Together, these suggest a cohesive developmental program governing skeletal and cardiac organogenesis, with craniofacial skeletal elements involved as well.","confidence":"Medium","size":27,"edges":309,"triangles":2093,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":16},{"id":"GO:0060021","count":13},{"id":"GO:0035914","count":12},{"id":"GO:0045669","count":11},{"id":"GO:0003151","count":10}]},{"hash":"322551611355321604","title":"Plant cell wall glycosylation and polysaccharide biosynthesis","description":"The cluster shows strong representation of plant cell wall\u2013related processes, including multiple glycosylation pathways (protein O-linked glycosylation via mannose and via N-acetyl-galactosamine), galactose metabolism, and key polysaccharide biosynthesis like homogalacturonan and glucuronoxylan, plus mucilage production and plant-type secondary cell wall biogenesis. This points to a cohesive role in assembling and modifying cell wall polysaccharides and related glycoproteins.","confidence":"High","size":27,"edges":150,"triangles":309,"max_degree":21,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006486","count":5},{"id":"GO:0010417","count":5},{"id":"GO:0071555","count":5},{"id":"GO:0010192","count":5},{"id":"GO:0009834","count":5}]},{"hash":"1288859647804427246","title":"Neural development and sensory system formation","description":"The dominant GO terms cluster around development with a strong emphasis on neural and sensory contexts: forebrain development, retinal ganglion cell axon guidance, synapse assembly, and sensory perception of pain. Supporting terms about broader organismal development and signaling (PI3K/AKT pathway, peptidyl-serine phosphorylation) align with developmental and connectivity processes. While there are also terms for keratinocyte and skeletal development, the recurring theme centers on nervous system formation and sensory pathways.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007275","count":10},{"id":"GO:0051965","count":7},{"id":"GO:0019233","count":7},{"id":"GO:0030216","count":6},{"id":"GO:0001501","count":6}]},{"hash":"1634216127026235786","title":"Melanocyte and Hair Follicle Development","description":"Based on the top GO terms, the cluster centers on pigment cell development and hair follicle morphogenesis, notably melanocyte differentiation and migration, with related neural crest\u2013derived morphogenesis (CNS and cochlea). Additional signals like Rho pathway regulation and axonogenesis fit the broader morphogenetic context, while serotonin uptake and hepatocyte apoptosis are less central but do not negate the main theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031069","count":4},{"id":"GO:0007417","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0045636","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1508603363679173513","title":"Cell cycle and developmental signaling","description":"The enriched terms point to mitotic cell cycle and cell division, combined with growth/differentiation signals (JNK, GTPase regulation, TGF-beta), transcriptional activity, and selective development processes (lens fiber differentiation, skeletal development). The inclusion of ubiquitin-dependent proteolysis suggests coordinated protein turnover during proliferation and differentiation. Altogether, the cluster seems to group proteins involved in balancing cell proliferation with developmental signaling and tissue differentiation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1656080105773820044","title":"Mitochondrial Stress Response and Metabolism","description":"These proteins show a clear mitochondrial focus, covering genome maintenance, membrane permeability regulation, and apoptotic changes, along with transport of iron and nucleotides into mitochondria, and responses to oxidative stress, amino acid starvation, fatty acids, and adaptive thermogenesis. Together, the terms delineate a cohesive mitochondrial maintenance and stress/metabolic program.","confidence":"High","size":27,"edges":7,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000002","count":18},{"id":"GO:0034198","count":17},{"id":"GO:0000303","count":17},{"id":"GO:0048250","count":17},{"id":"GO:0070542","count":17}]},{"hash":"1626854636939558608","title":"Actin Cytoskeleton Dynamics and Morphogenesis","description":"The cluster is dominated by GO terms related to actin dynamics (barbed-end capping, polymerization, lamellipodium assembly) and dendritic spine morphogenesis, indicating a core theme of actin cytoskeleton remodeling across cell types. Innate immune response and IFN signaling terms suggest actin remodeling during immune activation, while bone/uterus development and pattern specification reflect broader developmental contexts but are less central to the main motif.","confidence":"High","size":27,"edges":37,"triangles":3,"max_degree":20,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051016","count":18},{"id":"GO:0060997","count":18},{"id":"GO:0030041","count":18},{"id":"GO:0030032","count":18},{"id":"GO:1900029","count":18}]},{"hash":"90740473747134847","title":"Proteasome-mediated degradation and circadian regulation","description":"Top GO terms are dominated by ubiquitin-dependent proteolysis and protein turnover (ubiquitin-dependent protein catabolic process, protein polyubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process). The strong signal for regulation of circadian rhythm indicates temporal control of these proteolytic processes. Additional terms related to microtubule polymerization and spindle assembly suggest coordination with cell-cycle events. Taken together, these terms point to a cluster of proteins involved in proteasome-mediated degradation with circadian- and cell-cycle\u2013linked regulation.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":18},{"id":"GO:0042752","count":15},{"id":"GO:0000209","count":11},{"id":"GO:0031146","count":11},{"id":"GO:0006516","count":10}]},{"hash":"451728899192028960","title":"Ubiquitin-Dependent Proteolysis and NF-\u03baB/TNF Signaling","description":"The cluster is dominated by GO terms for ubiquitin-dependent protein catabolic processes (ERAD, autoubiquitination) and for TNF-mediated signaling and NF-\u03baB activation, suggesting proteins involved in ubiquitin-proteasome regulation and inflammatory signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":20},{"id":"GO:0030433","count":15},{"id":"GO:0051865","count":15},{"id":"GO:1903762","count":13},{"id":"GO:1901253","count":13}]},{"hash":"78534436130211896","title":"Inflammatory and stress signaling","description":"The cluster is enriched for cellular response to lipopolysaccharide, TNF signaling, NF-kappaB regulation, and p53-mediated apoptotic pathways, indicating a core theme of inflammatory and stress-responsive signaling. Rho-regulated cytoskeletal signaling and transcriptional regulation appear as supplementary connections; developmental GO terms (bone, midbrain morphogenesis, male gonad development) are less central but compatible with broad signaling roles.","confidence":"Medium","size":27,"edges":53,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":4},{"id":"GO:0035023","count":3},{"id":"GO:0042771","count":3},{"id":"GO:0042347","count":3},{"id":"GO:0033209","count":3}]},{"hash":"1279383910489043289","title":"Immune and Developmental Signaling","description":"These proteins cluster around signaling and response to stimuli, spanning immune responses (interferon, biotic stimulus, viral-related activity) and developmental/metabolic processes (bone/CNS development, glucose transport, neuromuscular control, endosomal trafficking). The common thread is broad cell signaling coordinating defense, growth, and differentiation rather than a single pathway.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019076","count":2},{"id":"GO:0051898","count":2},{"id":"GO:0007417","count":2},{"id":"GO:0035455","count":2},{"id":"GO:0060349","count":2}]},{"hash":"1899171748559773937","title":"Keratinocyte differentiation and growth signaling","description":"This cluster is dominated by keratinocyte differentiation along with key growth-regulatory pathways, including canonical Wnt signaling and Hippo signaling, indicating control of epidermal cell proliferation and differentiation. Additional terms like apoptotic process, cell migration, hyaluronan metabolism, and VEGF response suggest coordinated signaling for epidermal development, ECM interaction, and tissue remodeling. Overall, it represents an epidermal differentiation module with growth-control signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030216","count":23},{"id":"GO:0090263","count":23},{"id":"GO:0060044","count":23},{"id":"GO:0035329","count":23},{"id":"GO:0006915","count":23}]},{"hash":"1558091453846673216","title":"NF-kappaB Signaling in Immune Response","description":"Most top GO terms point to canonical NF-kappaB signal transduction with positive regulation, alongside responses to lipopolysaccharide and signaling pathways in B cells and NOD2. This indicates a cluster of proteins involved in NF-kappaB\u2013mediated immune signaling across innate and adaptive immunity, with some ancillary links to Rho signaling and mechanotransduction. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043123","count":7},{"id":"GO:0007249","count":5},{"id":"GO:0071222","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0035023","count":4}]},{"hash":"2203560057909077001","title":"Spliceosome-mediated mRNA splicing and processing","description":"These proteins are enriched for GO terms centered on mRNA splicing and post-transcriptional processing via the spliceosome, including regulation of splicing, mRNA capping, export, and stabilization, with a note of circadian rhythm involvement. The common theme is RNA maturation and processing rather than other cellular processes, indicating a cohesive spliceosome/processing-focused cluster.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0000381","count":4},{"id":"GO:0006370","count":4},{"id":"GO:0048255","count":3},{"id":"GO:0007623","count":3}]},{"hash":"1887480593567668808","title":"Developmental Processes and Stress Responses","description":"This cluster is dominated by development-related GO terms (multicellular organism development, skeletal system development, neural tube closure) but also shows signals of cellular stress and immune-response pathways (ER-stress\u2013related apoptosis, responses to LPS and Gram-positive bacteria) alongside DNA replication/transcription activity. The name reflects the central developmental theme with notable inclusion of stress- and immune-related processes.","confidence":"Medium","size":26,"edges":218,"triangles":1164,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0032436","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0001501","count":5},{"id":"GO:0006351","count":5}]},{"hash":"1974822210106792489","title":"Signaling and cytoskeletal remodeling in muscle and vessels","description":"GO terms point to GPCR signaling, mechanical nociception, actin filament assembly, cell migration, muscle regeneration, and vascular remodeling, indicating a theme of signaling-driven cytoskeletal dynamics governing tissue remodeling in muscle and endothelial contexts. While spindle assembly and SA node action potential reflect broader cellular organization, the overall pattern centers on signal transduction shaping the cytoskeleton and tissue remodeling.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007205","count":8},{"id":"GO:0050966","count":8},{"id":"GO:0051225","count":8},{"id":"GO:0098907","count":8},{"id":"GO:0043547","count":7}]},{"hash":"1600566277177330987","title":"Chromatin Organization and Transcriptional Regulation","description":"The GO terms point to chromatin maintenance and transcription control, including nucleosome assembly, chromatin localization, histone modification regulation (H3K27/H3K4), and heterochromatin formation, with additional involvement in transcriptional attenuation and RNA processing, suggesting a cohesive chromatin-modifying/maintaining cluster.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":5},{"id":"GO:0006334","count":4},{"id":"GO:0061086","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0080182","count":3}]},{"hash":"482184819001901114","title":"Vertebrate Embryonic Skeletogenesis and Neural Development","description":"The top GO terms point to embryonic cranial skeleton morphogenesis, chondrocyte differentiation, and collagen fibril organization, indicating skeletogenesis and ECM remodeling. Additional terms cover neural development (myelination, synapse assembly) and growth signaling (RTK signaling), suggesting a developmental program coordinating skeletal and neural tissue formation, with some immune-related terms likely reflecting broader developmental signaling environments.","confidence":"Medium","size":26,"edges":5,"triangles":0,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048701","count":15},{"id":"GO:0002062","count":13},{"id":"GO:0030097","count":13},{"id":"GO:0045087","count":12},{"id":"GO:0030199","count":12}]},{"hash":"316353647070197065","title":"Developmental transcription and morphogenesis","description":"Based on the top GO terms, this cluster centers on transcriptional control during development, including negative regulation of RNA polymerase II transcription, chromatin remodeling, and DNA-templated transcription. It also features diverse embryonic morphogenesis programs such as neural crest cell migration, pancreas and digestive tract development, neural tube patterning, and organ bud formation. Together, these suggest a cohesive role in regulating gene expression to drive embryogenesis and tissue morphogenesis.","confidence":"High","size":26,"edges":233,"triangles":1116,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":23},{"id":"GO:0043044","count":18},{"id":"GO:0090190","count":17},{"id":"GO:0001755","count":17},{"id":"GO:0048557","count":17}]},{"hash":"874374219023452228","title":"Unknown","description":"The top GO terms cover brain development, cartilage morphogenesis, DNA repair, aging, transcription regulation, and even teichoic acid biosynthesis, plus defense against fungus. This mix spans developmental, genomic maintenance, immune, and apparently bacterial biosynthesis processes, with no clear unifying function for the protein cluster. Consequently, there isn\u2019t a coherent, specific label that accurately represents the cluster\u2019s common biology.","confidence":"","size":26,"edges":35,"triangles":18,"max_degree":12,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0001302","count":4},{"id":"GO:0050832","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006289","count":3}]},{"hash":"970033396369941734","title":"Embryogenesis and Tissue Patterning","description":"The proteins are enriched for GO terms spanning embryonic development, placenta formation, mesoderm development, left-right patterning, EMT-related endocardial cushion formation, endocrine system development, and cartilage morphogenesis, indicating a broad developmental/tissue-patterning role rather than a single mature function.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003323","count":13},{"id":"GO:0060806","count":13},{"id":"GO:0060972","count":13},{"id":"GO:0060707","count":13},{"id":"GO:0003198","count":13}]},{"hash":"1739574774688599065","title":"Neural Signaling and Metabolic Regulation","description":"This cluster combines GO terms for sensory perception (pain, vision), GPCR-mediated signaling and calcium release, Rho/GTPase modulation, and energy/metabolic processes (electron transport, thermogenesis). The common thread appears to be cellular signaling, particularly GPCR-driven pathways with calcium dynamics, that intersect with metabolic regulation in neural or sensory-related contexts. While diverse, these terms collectively point to a theme of signal transduction coupled with energy management, rather than a single isolated pathway.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":10},{"id":"GO:0045777","count":10},{"id":"GO:0010579","count":10},{"id":"GO:0019233","count":9},{"id":"GO:0035025","count":9}]},{"hash":"216451026697866038","title":"Mitochondrial metabolism and stress response","description":"The cluster centers on mitochondrial-associated processes: maintenance/import into mitochondria (including nucleotides and iron), membrane permeability regulation, and apoptotic mitochondrial changes, along with various stress responses such as to superoxide, fatty acids, and amino acid starvation. These collectively point to mitochondrial metabolism and stress-response roles, despite some obsolete GO terms.","confidence":"High","size":26,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":6},{"id":"GO:0097274","count":6},{"id":"GO:0034198","count":5},{"id":"GO:0000303","count":5},{"id":"GO:0048250","count":5}]},{"hash":"1945535882265540074","title":"Unknown","description":"The top GO terms span mitochondrial energy production, GPCR-cAMP signaling, membrane potential regulation, sensory and visual perception, immune defense, and more, with no clear single function uniting them. This diversity suggests the cluster cannot be confidently labeled with a specific, cohesive biological role.","confidence":"","size":26,"edges":9,"triangles":0,"max_degree":4,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":16},{"id":"GO:0045777","count":16},{"id":"GO:0010579","count":16},{"id":"GO:0007190","count":15},{"id":"GO:0042391","count":15}]},{"hash":"1413840607985381356","title":"T cell activation and cell\u2013cell adhesion signaling","description":"The cluster is rich in GO terms for T cell costimulation and proliferation, coupled with homophilic and heterophilic cell\u2013cell adhesion, indicating a role in immune cell activation and intercellular communication. Additional signaling-related terms (PI3K and calcium signaling) point to broader intracellular signaling connections accompanying these processes.","confidence":"High","size":26,"edges":132,"triangles":298,"max_degree":21,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045663","count":10},{"id":"GO:0031295","count":9},{"id":"GO:0042102","count":9},{"id":"GO:0007157","count":9},{"id":"GO:0019226","count":8}]},{"hash":"1561544429094369210","title":"Mitochondrial energy production and dynamics","description":"The top GO terms point to mitochondrial functions: proton motive force-driven ATP synthesis, mitochondrial translation, and positive regulation of mitochondrial fusion, along with mitochondrial genome maintenance. These together suggest a core theme of mitochondrial energy metabolism and organelle dynamics, with related processes like cell cycle/division and ion transport that relate to mitochondrial function. Some terms (e.g., sensory perception of sound) appear peripheral and not central to the main theme.","confidence":"High","size":26,"edges":226,"triangles":924,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0099132","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0010636","count":2}]},{"hash":"1033736499876760590","title":"Mitochondrial translation and cardiac calcium signaling","description":"This cluster prominently features mitochondrial tRNA aminoacylation terms (mitochondrial aspartyl- and asparaginyl-tRNA aminoacylation), indicating mitochondrial protein synthesis as a core theme. It also includes several GO terms for calcium ion transport and regulation of cardiac muscle contraction/heart rate, pointing to involvement in cardiac calcium signaling. Some terms ( xenobiotic response, telomere capping) are less central, but the dominant signal is mitochondrial translation linked to cardiac calcium regulation.","confidence":"Medium","size":26,"edges":150,"triangles":260,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0035690","count":3},{"id":"GO:0086004","count":3},{"id":"GO:0010459","count":3},{"id":"GO:0010881","count":3}]},{"hash":"1125098095575344370","title":"Cell adhesion and GPCR signaling","description":"This cluster is dominated by terms related to cell adhesion (hemidesmosome assembly, substrate adhesion-dependent spreading, heterophilic cell-cell adhesion) and receptor signaling (GPCR acetylcholine receptor pathway, receptor clustering), with additional links to processes like apoptotic-cell engulfment and developmental morphogenesis, suggesting a cohesive theme around adhesion-mediated signaling and cell communication in tissue organization.","confidence":"Medium","size":26,"edges":282,"triangles":1722,"max_degree":25,"top_function":"wound healing","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0031581","count":9},{"id":"GO:0034446","count":9},{"id":"GO:0043113","count":8},{"id":"GO:0070527","count":7}]},{"hash":"164843552523505660","title":"Prenatal Immune and Metabolic Development","description":"The GO terms point to embryonic development and immune system maturation (e.g., in utero development, T cell differentiation, germinal center regulation) alongside metabolic signaling (insulin receptor signaling, glucose homeostasis) and inflammation regulation, suggesting a cohesive role in early-life developmental processes that couple immunity with metabolism.","confidence":"Medium","size":26,"edges":160,"triangles":607,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":17},{"id":"GO:0002635","count":17},{"id":"GO:0008286","count":17},{"id":"GO:0061470","count":17},{"id":"GO:0042593","count":17}]},{"hash":"1228155044990976668","title":"Transcription Regulation and Chromatin Remodeling","description":"The top GO terms cluster around transcription control and chromatin state: negative regulation of transcription by RNA polymerase II, regulation of DNA-templated transcription, chromatin remodeling, and histone acetylation. While some developmental terms appear, the strongest signals are transcriptional regulation and chromatin dynamics, suggesting a cohesive function in controlling gene expression rather than a single developmental pathway.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0070306","count":6},{"id":"GO:0090009","count":6},{"id":"GO:0048935","count":5},{"id":"GO:0008584","count":5}]},{"hash":"1767460517555860974","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0045087","count":5},{"id":"GO:0010863","count":5},{"id":"GO:0043552","count":5},{"id":"GO:0007507","count":5}]},{"hash":"1985696976745092804","title":"Neuronal Development and Calcium Signaling","description":"This cluster is dominated by brain- and neuron-specific terms (brain development, substantia nigra development, EPSP) and calcium- and signaling-related processes (detection of calcium ion, calcineurin-NFAT signaling, guanylate cyclase/cGMP involvement), suggesting a theme of neuronal development coupled with calcium-dependent signaling in brain circuits. Some terms are broader ( xenobiotic response, chromatin regulation), but the core appears to be neuronal development and calcium-dependent pathways.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:0060079","count":6},{"id":"GO:0031284","count":6},{"id":"GO:0005513","count":6},{"id":"GO:0035690","count":6}]},{"hash":"1009473787773011925","title":"ECM remodeling and bone development in reproduction","description":"This cluster is dominated by extracellular matrix remodeling signals (collagen catabolic process, basement membrane disassembly) alongside bone-related processes (bone resorption, intramembranous ossification) and decidualization, suggesting tissue remodeling in reproductive contexts, with additional developmental signals (lung branching) enriching the developmental theme.","confidence":"High","size":26,"edges":262,"triangles":1513,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0001913","count":23},{"id":"GO:0051603","count":23},{"id":"GO:0030574","count":23},{"id":"GO:0060448","count":23},{"id":"GO:0046697","count":23}]},{"hash":"1359489092912441841","title":"Embryonic organogenesis and patterning","description":"The terms cluster around broad developmental processes across multiple tissues\u2014pancreatic beta cell development, placental and endocrine system development, cartilage morphogenesis, EMT in heart structures, and left-right patterning, plus associated transcriptional regulation and eye development. This suggests a general embryonic organogenesis/patterning theme rather than a single specific pathway, yielding a cohesive label of embryonic development and organ formation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0003323","count":6},{"id":"GO:0060707","count":5},{"id":"GO:0035270","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060806","count":5}]},{"hash":"1376456651320962719","title":"Axon guidance and neural crest migration","description":"This cluster is dominated by terms related to neuron development, axon pathfinding, and neural crest migration (e.g., branchiomotor neuron axon guidance, semaphorin-plexin signaling in axon guidance, neural crest migration, sympathetic neuron projection extension). A few terms about skeletal development appear peripheral, but the core signal is neural development and guidance.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0001501","count":11},{"id":"GO:0007157","count":11},{"id":"GO:0048661","count":11},{"id":"GO:0030913","count":11},{"id":"GO:0042511","count":11}]},{"hash":"678664095512466067","title":"Embryogenesis and placental development","description":"The cluster's GO terms cluster around developmental processes, especially embryonic and placental lineages (trophoblast giant cell differentiation, placenta-related development, EMT in heart formation, cartilage morphogenesis, endocrine system development). Supporting terms about gene expression regulation and RNA processing appear, but the dominant theme is embryonic/placental development and differentiation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0060707","count":23},{"id":"GO:0060536","count":22},{"id":"GO:1903026","count":22},{"id":"GO:0003323","count":22},{"id":"GO:0000055","count":22}]},{"hash":"1905665837393054463","title":"Developmental Signaling Regulators","description":"The cluster is enriched for terms that regulate signaling pathways (ERK cascade, GPCR signaling, Rho signaling) and developmental processes (heart development, pollen tube guidance, exploration behavior, growth hormone secretion), suggesting a shared role in modulating signaling networks that drive development and behavior. Some terms about membrane and post-translational protein processing (GPI anchor biosynthesis, dolichol-linked glycan biosynthesis) support signaling protein maturation. Given the broad, connective theme but no specific single function, Developmental Signaling Regulators is a concise, representative label.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0070374","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0035023","count":4},{"id":"GO:0006506","count":3},{"id":"GO:0010183","count":3}]},{"hash":"1291067203185054434","title":"Neural Development and Myelination","description":"The cluster is dominated by neural-related terms (neurogenesis, nervous system development, myelination) and includes signaling-associated GO terms (ERK/MAPK cascade regulation), indicating a cohesive neural development function; a few terms like spermatid development or angiogenesis may reflect broader expression but do not alter the core theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0022008","count":8},{"id":"GO:0007399","count":8},{"id":"GO:0007286","count":8},{"id":"GO:0070374","count":8},{"id":"GO:0048661","count":8}]},{"hash":"1421695310056597556","title":"Membrane trafficking and remodeling","description":"The cluster is dominated by GO terms related to membrane dynamics and vesicle trafficking, including plasma membrane tubulation, regulation of SNARE complex assembly, and pinocytosis, suggesting a core function in vesicle trafficking and membrane remodeling. While there are cell cycle and neuronal differentiation terms present, the strongest cohesive signal is membrane trafficking processes, with supportive links to cell division and immune-related regulation that may reflect broader cellular activity in these proteins.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0097320","count":2},{"id":"GO:0051044","count":2},{"id":"GO:0035544","count":2},{"id":"GO:0006907","count":2}]},{"hash":"2047841037113983028","title":"NF-kappaB transcription regulation and innate immune signaling","description":"These proteins cluster around transcriptional control and innate immune signaling: multiple GO terms point to DNA-templated transcription and RNAP II regulation, plus NF-kappaB\u2013related signaling and defense responses to bacteria/LPS. A few terms (tRNA methylation, tight junction assembly) are peripheral but may reflect broader cellular signaling. Overall, the dominant theme is NF-kappaB\u2013mediated transcriptional regulation in immune responses.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0033138","count":3}]},{"hash":"1432780456210205930","title":"Mitotic Spindle and Microtubule Dynamics","description":"The terms cluster around mitosis and microtubule cytoskeleton functions: spindle pole separation, metaphase chromosome recapture, plus-end\u2013directed transport and sliding along microtubules, microtubule depolymerization, polarity of the microtubule array, cytokinesis, and related nuclear migration roles. Together these indicate a cohesive module of proteins that regulate spindle assembly, chromosome segregation, and microtubule dynamics during cell division.","confidence":"High","size":25,"edges":157,"triangles":537,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":25},{"id":"GO:0000073","count":25},{"id":"GO:0072383","count":25},{"id":"GO:0031535","count":25},{"id":"GO:0000743","count":25}]},{"hash":"1946002649941002370","title":"Cellular stress responses and apoptosis","description":"The proteins show GO terms centered on environmental stress and cell fate: cellular response to hypoxia and response to cold indicate stress signaling; positive regulation of release of cytochrome c from mitochondria and neuron apoptotic process point to mitochondrial-mediated apoptosis. There are also mentions of innate immune response and cell division, but these are less dominant relative to the stress/apoptosis themes. Overall, the cluster seems to group proteins involved in stress signaling leading to apoptosis rather than a single cohesive pathway. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0009409","count":2}]},{"hash":"2033066561863981566","title":"Developmental transcriptional regulation","description":"The top GO terms combine core transcription by RNA polymerase II and regulation with multiple tissue- and development-related processes (pancreas, muscle, nervous system, interneuron differentiation, bronchiole development) and circadian entrainment, suggesting a cohort of factors coordinating transcriptional control to drive diverse developmental programs.","confidence":"Medium","size":25,"edges":294,"triangles":2166,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":11},{"id":"GO:0006351","count":10},{"id":"GO:0031018","count":10},{"id":"GO:0035914","count":9},{"id":"GO:0000122","count":8}]},{"hash":"1073639377624177798","title":"Mitotic signaling and developmental processes","description":"This cluster is dominated by mitotic cell cycle terms and regulation of signaling activities (GTPase and serine/threonine kinase), with several development-related GO terms (multicellular organism development, skeletal system development, neural tube closure). The combination points to proteins involved in cell-cycle\u2013driven developmental signaling, justifying a name focused on both mitosis and development.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":15},{"id":"GO:0043547","count":14},{"id":"GO:0071902","count":14},{"id":"GO:0071456","count":14},{"id":"GO:0030433","count":14}]},{"hash":"1200996296513442745","title":"Immune differentiation and transcription regulation","description":"The cluster\u2019s top GO terms center on transcriptional control (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) alongside immune-related differentiation signals (positive regulation of dendritic cell differentiation; B cell receptor signaling; defense response to Gram-positive bacterium) and ubiquitin-dependent protein turnover. Developmental terms (nervous system development; skeletal muscle and myoblast differentiation) suggest broader differentiation roles, but the strongest coherent theme ties transcriptional regulation to immune cell differentiation. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0050830","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0042787","count":6},{"id":"GO:2001200","count":5}]},{"hash":"1900891718521221532","title":"Protein and RNA Methyltransferases","description":"Most of the prevalent terms are methylation-related (protein N-terminal methylation, arginine dimethylation, rRNA methylation, and histone methylation), pointing to methyltransferase enzymes acting on proteins and RNA as a core theme; other biosynthetic terms seem ancillary.","confidence":"High","size":25,"edges":292,"triangles":2121,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0036068","count":3},{"id":"GO:0018013","count":3}]},{"hash":"1491742380338450730","title":"Signaling and cell cycle regulation","description":"The top GO terms include immune signaling (cellular response to lipopolysaccharide; T cell receptor signaling), cell migration and cytoskeletal dynamics (positive regulation of pseudopodium assembly), neural and skin development (midbrain dopaminergic neuron differentiation; hair follicle placode formation; prostate gland development), and cell cycle control (regulation of cell cycle; cytokinesis; PKA signaling). This pattern suggests a general signaling/cell-cycle regulatory role affecting proliferation, differentiation, and movement rather than a single, tightly defined pathway. ","confidence":"Medium","size":25,"edges":49,"triangles":81,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071222","count":9},{"id":"GO:0050852","count":7},{"id":"GO:0031274","count":7},{"id":"GO:1904948","count":7},{"id":"GO:0060789","count":7}]},{"hash":"1383342415525661692","title":"Neuronal development and ER-Golgi trafficking regulation","description":"The cluster features terms centered on nervous system development, dendrite morphogenesis, Rac signaling, ERK cascade activation, and ER-to-Golgi vesicle transport, along with actin cytoskeleton remodeling and membrane-related processes. This combination points to a cohesive module governing neuronal morphogenesis and associated membrane trafficking/signaling pathways, making the proposed label a specific reflection of the cluster\u2019s core functions.","confidence":"High","size":25,"edges":219,"triangles":957,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0010628","count":5},{"id":"GO:0006998","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0007399","count":5},{"id":"GO:0031532","count":5}]},{"hash":"1702215168137976738","title":"Integrin signaling and cytoskeletal dynamics","description":"Top terms cluster around integrin-mediated signaling, cell-matrix adhesion, and actin filament bundle assembly, with supporting processes like exocytosis, endocytic recycling, and platelet aggregation. While some endocrine signaling terms appear, the dominant theme is surface signaling coupled to adhesion and cytoskeletal remodeling, justifying a label focused on integrin signaling and the cytoskeleton.","confidence":"Medium","size":25,"edges":145,"triangles":296,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:2001046","count":25},{"id":"GO:2000691","count":25},{"id":"GO:0006887","count":25},{"id":"GO:0007160","count":25},{"id":"GO:0070527","count":25}]},{"hash":"2107443479752367517","title":"Neuronal Synaptic Transport and Receptor Regulation","description":"This cluster is dominated by GO terms tied to neuronal/synaptic function, including retrograde synaptic vesicle transport, AMPA receptor activity regulation, and JUN phosphorylation, which are central to synaptic signaling and plasticity. Additional terms touch on neural differentiation and CNS-related processes, supporting a theme of neuronal development and synaptic regulation, even though some terms are broader. Overall, the label captures the core connection around synaptic transport and receptor modulation, with a Medium confidence due to some non-neuronal terms present.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048491","count":3},{"id":"GO:0060487","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0070940","count":3},{"id":"GO:0035026","count":2}]},{"hash":"46136530752502591","title":"Chromatin silencing and chromosome maintenance","description":"The enriched GO terms point to chromatin-state regulation (heterochromatin formation, chromatin localization, histone methylation modulation) and chromosome dynamics (cohesion maintenance, dosage compensation, telomere-associated localization), indicating a coherent theme of chromatin organization and chromosome maintenance. A single term about mRNA surveillance appears ancillary. Overall, these proteins likely function together in nuclear chromatin regulation and chromosome stability.","confidence":"High","size":25,"edges":102,"triangles":129,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":21},{"id":"GO:0071169","count":21},{"id":"GO:0061086","count":20},{"id":"GO:0070481","count":20},{"id":"GO:0045618","count":20}]},{"hash":"584406189937632633","title":"Lens development and light-stress signaling","description":"Top GO terms indicate lens fiber morphogenesis and light/UV responses, accompanied by stress-activated MAPK signaling and cytoskeletal dynamics (microtubule polymerization/depolymerization). Hormonal responsiveness (estradiol) and growth regulation further frame the context as developmental and stress-adaptive rather than a single pathway. Overall, these terms converge on eye lens formation intertwined with light-induced stress signaling and cytoskeletal remodeling.","confidence":"High","size":25,"edges":296,"triangles":2211,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0070309","count":7},{"id":"GO:0051403","count":7},{"id":"GO:0032355","count":7},{"id":"GO:0032463","count":7},{"id":"GO:0009644","count":7}]},{"hash":"276512866334297707","title":"Immune signaling and inflammatory response","description":"This cluster's top GO terms center on defense and inflammatory processes (defense response to bacterium, acute inflammatory response, T cell chemotaxis, response to xenobiotic stimulus) and are strongly supported by GPCR/Adenylate cyclase signaling and protein phosphorylation motifs (positive regulation of GTPase activity, receptor signaling). The mixture suggests a cohesive theme of immune activation and signaling regulation, with GPCR-mediated pathways guiding chemotaxis and inflammatory responses. The visual perception term appears as an outlier and does not drive the cluster's core theme.","confidence":"High","size":25,"edges":276,"triangles":1807,"max_degree":24,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":25},{"id":"GO:0042742","count":25},{"id":"GO:0043547","count":25},{"id":"GO:0007197","count":25},{"id":"GO:1901652","count":25}]},{"hash":"149307403483047961","title":"Vertebrate Development and Keratan Sulfate Proteoglycan Biosynthesis","description":"The cluster prominently includes terms tied to vertebrate development (heart development, spinal cord motor neuron differentiation, multicellular organism development) and extracellular matrix components via keratan sulfate proteoglycan biosynthesis, suggesting a theme of developmental processes coupled with ECM biosynthesis. Some terms (like sulfate assimilation and visual learning) may reflect annotation noise or broader cross-species mappings, but the core signal points to developmental and ECM-related functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000103","count":4},{"id":"GO:0008542","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0018146","count":3},{"id":"GO:0042403","count":3}]},{"hash":"104981099502356465","title":"ER-Associated Ca2+ Signaling and GPCR/TGF-\u03b2","description":"This cluster centers on proteins linked to endoplasmic reticulum processes and calcium signaling\u2014evidenced by GO terms for Ca2+ release from the ER/SR, ER tubular network organization, and protein targeting to the ER\u2014as well as signaling pathways commonly associated with the ER milieu, including GPCR signaling and TGF-\u03b2 receptor signaling. The presence of terms related to xenobiotic response, inflammation/angiogenesis regulation, and nuclear pore assembly suggests broader cellular homeostasis roles that intersect ER function and signaling. Overall, the label reflects an ER-centric signaling/trafficking theme, with calcium and membrane-associated pathways tying the terms together.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035584","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0007179","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0050728","count":2}]},{"hash":"117016322759319295","title":"Glucocorticoid-responsive immune and vascular signaling","description":"The cluster centers on steroid-triggered immune modulation and signaling pathways, including dexamethasone response, NF-kappaB signaling, chemokine signaling, angiogenesis regulation, PI3K/AKT signaling, and smooth muscle proliferation, pointing to a coordinated inflammatory-vascular remodeling program.","confidence":"High","size":25,"edges":255,"triangles":1771,"max_degree":24,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0009636","count":7},{"id":"GO:0045071","count":7},{"id":"GO:0071549","count":5},{"id":"GO:0016525","count":5}]},{"hash":"1641291971039317134","title":"Prostaglandin Biosynthesis and Inflammatory Response","description":"The top GO term is prostaglandin biosynthetic process, paired with several inflammatory/immune-related terms (response to lipopolysaccharide, neutrophil aggregation) and oxidative/chemical stress terms (response to toxic substance, cellular oxidant detoxification). This points to a cluster of proteins involved in prostaglandin signaling and inflammatory responses, with supporting roles in detoxification and stress responses. ","confidence":"High","size":25,"edges":45,"triangles":47,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":8},{"id":"GO:0009636","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0045471","count":4},{"id":"GO:0071222","count":4}]},{"hash":"2234234381472923947","title":"Ubiquitin-Dependent Degradation and NF-kappaB Signaling","description":"The prominent terms are ubiquitin-dependent proteolysis, various ubiquitination processes (including K6-linked ubiquitination and autoubiquitination), and histone turnover, complemented by regulators of NF-kappaB signaling (I-kappaB phosphorylation and NIK activation) and TNF-mediated pathways, with some apoptosis-related terms. This points to a coherent theme: a cluster centered on the ubiquitin-proteasome system and its control of NF-kappaB signaling and cell fate, with supporting links to chromatin remodeling and immune gene rearrangements. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":19},{"id":"GO:0085020","count":11},{"id":"GO:0051865","count":11},{"id":"GO:0036205","count":10},{"id":"GO:1903265","count":10}]},{"hash":"325037969344012582","title":"Cell junctions and actin cytoskeleton","description":"GO terms point to formation and maintenance of cellular junctions (endothelial barrier, tight and adherens junction localization) and the organization of the actin cytoskeleton, with related signals to centrosome localization. This suggests a module of proteins coordinating cell\u2013cell contacts and cytoskeletal architecture rather than a single signaling pathway. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0090557","count":10},{"id":"GO:0006470","count":10},{"id":"GO:0070830","count":9},{"id":"GO:1903760","count":9},{"id":"GO:2000821","count":9}]},{"hash":"694834311497447150","title":"Viral Translation Initiation and Translational Regulation","description":"The most prominent GO terms are centered on translation initiation and regulation (translation initiation, translation reinitiation, formation of translation preinitiation complex, regulation of translational initiation) and IRES-dependent viral translation (IRES-dependent viral translational initiation, viral translational termination-reinitiation). This points to a functional cluster focused on controlling protein synthesis at the initiation stage, including viral contexts. Other terms like hypoxia response, multicellular development, exocytosis, and endothelial barrier are present but less directly tied to this core function, suggesting they reflect broader cellular context rather than defining the cluster.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043547","count":9},{"id":"GO:0007275","count":8},{"id":"GO:0071456","count":8},{"id":"GO:0075522","count":8},{"id":"GO:0006446","count":8}]},{"hash":"513230739620514081","title":"Ribosome biogenesis and endomembrane trafficking","description":"Most represented GO terms cluster around ribosome biogenesis and translation initiation (formation of translation preinitiation complex; ribosome biogenesis) together with endomembrane trafficking steps (endosome transport to Golgi; Cvt pathway). The inclusion of positive regulation of GTPase activity further supports involvement of small GTPases in trafficking processes. While some developmental terms appear, the dominant signal is basic cellular machinery linking protein synthesis assembly and vesicle transport, suggesting a cohesive group of proteins participating in these core processes. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0032258","count":3},{"id":"GO:0045022","count":3},{"id":"GO:0034499","count":3}]},{"hash":"691570641598934584","title":"Muscle development and contraction signaling","description":"Top GO terms are dominated by cardiac and skeletal muscle development and contraction, suggesting a muscle-focused cluster. Additional terms reflect broader signaling (TORC2, PI3K-Akt) and regulation like protein dephosphorylation, which can influence muscle function; a few terms are less directly related (B cell signaling, telomere maintenance). Overall, label as muscle development/contraction signaling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0060048","count":5},{"id":"GO:0048741","count":5},{"id":"GO:0050853","count":5},{"id":"GO:0038203","count":4}]},{"hash":"1260374725630255436","title":"Innate Immune Signaling","description":"These proteins cluster around innate immune functions: responses to lipopolysaccharide and dsRNA, innate immune activation, and interferon-\u03b2 and IL-2 production, indicating a module of pathogen sensing and antiviral/inflammatory signaling. Some terms like collagen fibril organization and axonogenesis are less connected to immunity but likely reflect multi-functional proteins in the group; the dominant signal is innate immune activation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071222","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0030199","count":5},{"id":"GO:0032743","count":4},{"id":"GO:0009992","count":4}]},{"hash":"2032622490557694309","title":"Innate immune phagocytosis and cytoskeleton remodeling","description":"This cluster centers on innate immune functions, especially phagocytosis, and features strong signals for cytoskeletal dynamics driven by Rho and GTPase activity (podosome assembly, cleavage furrow formation). These terms together point to immune cells reorganizing their cytoskeleton to engulf targets and migrate, with some bone-development related terms likely reflecting shared signaling pathways in osteoclasts or developmental contexts. Overall, the dominant theme is innate immune\u2013mediated phagocytosis supported by cytoskeleton remodeling.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0043547","count":3},{"id":"GO:1904888","count":3},{"id":"GO:1904179","count":3}]},{"hash":"1453792067003751313","title":"Cell signaling and tissue homeostasis","description":"The top GO terms cover diverse yet related aspects of cellular signaling and tissue maintenance, including Rho-mediated signaling, thrombin receptor pathways, endothelial barrier establishment, synaptic vesicle exocytosis, and regulation of tissue cell numbers, suggesting a core theme of coordinated signaling that preserves tissue integrity. Some terms (defense response, gonad development) appear peripheral to the main network, indicating broader or context-specific roles in this cluster. Confidence in this label is Medium.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0090557","count":3},{"id":"GO:0070493","count":3}]},{"hash":"2046681470036116388","title":"Nervous system development and signaling","description":"The cluster is heavily enriched for neural-related processes: nervous system development, transmission of nerve impulses, and both homophilic and heterophilic cell\u2013cell adhesion, which support neural connectivity and network formation. Signaling elements like positive regulation of STAT phosphorylation and MAPK activity align with neuronal differentiation and response pathways, while auxiliary terms such as collateral sprouting point to neural plasticity. Some outliers (ossification and megakaryocyte development) suggest broader developmental roles, but the dominant theme centers on neural development and communication through adhesion and signaling mechanisms.","confidence":"Medium","size":25,"edges":25,"triangles":1,"max_degree":5,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0042511","count":12},{"id":"GO:0019226","count":12},{"id":"GO:0007157","count":12},{"id":"GO:0043931","count":12},{"id":"GO:0048672","count":12}]},{"hash":"1675044790509323245","title":"Trichome development and cuticle wax biosynthesis","description":"This cluster is dominated by GO terms for trichome branching and papilla formation, as well as wax and very long-chain fatty acid biosynthesis, pointing to plant epidermal differentiation involved in trichome formation and cuticle wax production. A few steroid-related terms may be noise, but the core signal supports trichome and wax biosynthesis functions.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"lipid metabolic process","top_go_terms":[{"id":"GO:0010091","count":4},{"id":"GO:0042761","count":4},{"id":"GO:0006702","count":4},{"id":"GO:0010025","count":4},{"id":"GO:0030539","count":4}]},{"hash":"928691645804267329","title":"Immune Activation and Antigen Presentation","description":"The terms cluster around innate immunity (complement activation, phagocytosis, LPS response) and adaptive immunity (B cell receptor signaling, regulation of B cell activation, antigen processing and presentation via MHC I and II). This suggests a cohesive module coordinating pathogen recognition with antigen presentation to T cells and B cell activation.","confidence":"High","size":25,"edges":138,"triangles":275,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":11},{"id":"GO:0006910","count":10},{"id":"GO:0006911","count":10},{"id":"GO:0050853","count":10},{"id":"GO:0045087","count":10}]},{"hash":"183568915996733579","title":"Lens development and eye differentiation","description":"The top GO terms cluster around lens fiber cell differentiation, lens morphogenesis, camera-type eye development, and visual perception, indicating a core association with lens/eye formation and function, despite some peripheral immune-related terms.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0070306","count":7},{"id":"GO:0050830","count":5},{"id":"GO:0014068","count":5},{"id":"GO:0045648","count":5}]},{"hash":"1684204843491047051","title":"Neural crest migration and axon guidance","description":"The cluster is dominated by terms related to nervous system development, neural crest cell migration, axon guidance (including semaphorin-plexin signaling), and neural tissue organization, with supporting cell adhesion terms. A secondary note is ossification, but the prominent theme is neural crest\u2013driven migration and neuronal wiring. ","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043931","count":15},{"id":"GO:0007157","count":14},{"id":"GO:0007399","count":14},{"id":"GO:0007156","count":13},{"id":"GO:0036486","count":13}]},{"hash":"1208494841484385773","title":"Embryonic organogenesis and patterning regulators","description":"The cluster shows strong representation of developmental processes (cartilage morphogenesis, left-right pattern formation, endocardial cushion EMT, endocrine system and placenta development), suggesting a focus on embryonic organogenesis and body plan patterning. Additional GO terms related to transcriptional regulation and RNA processing imply coordinated gene expression control during development.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0060536","count":21},{"id":"GO:1903026","count":21},{"id":"GO:0003323","count":21},{"id":"GO:0000055","count":21},{"id":"GO:0000398","count":21}]},{"hash":"1414313486995805995","title":"Xenobiotic and nutrient transmembrane transporters","description":"This cluster is dominated by GO terms for transmembrane transport of xenobiotics, vitamins, glucose, phosphate, and ions, indicating proteins that function as membrane transporters for diverse small molecules and nutrients. The inclusion of vitamin and glucose transport supports a transporter-centric group, while potassium and phosphate transport reinforce the membrane transport theme.","confidence":"High","size":24,"edges":140,"triangles":292,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042908","count":23},{"id":"GO:0006855","count":23},{"id":"GO:0035461","count":23},{"id":"GO:0071805","count":22},{"id":"GO:0052106","count":13}]},{"hash":"2262855817395583482","title":"RNA splicing and mRNA processing regulation","description":"Most frequent GO terms cluster around spliceosome-mediated splicing (mRNA cis splicing via spliceosome; negative regulation of splicing via spliceosome), regulation of mRNA stability in response to stress, mRNA tail shortening, mRNA modification, ncRNA-mediated gene silencing, and translation initiation factor complex assembly. This points to a cohesive function in RNA processing and regulation of mRNA fate, including splicing, stability, and translation, especially under stress. Therefore, the label captures the cluster\u2019s central theme.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":19},{"id":"GO:0045292","count":18},{"id":"GO:0048025","count":17},{"id":"GO:1901407","count":17},{"id":"GO:0060211","count":16}]},{"hash":"820523241530494455","title":"Mitochondrial metabolism and translation","description":"Top terms cluster around central energy metabolism (malonyl-CoA biosynthesis, fatty acid biosynthesis, TCA cycle, glycolysis, 2-oxoglutarate metabolism) together with protein synthesis activities, notably translation and mitochondrial translational elongation, plus selenocysteine incorporation. This combination points to a group of proteins involved in mitochondrial energy production linked to the translation machinery. Some terms like viral genome replication and antibiotic response are atypical but do not override the overall theme.","confidence":"High","size":24,"edges":171,"triangles":731,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:2001295","count":8},{"id":"GO:0042759","count":8},{"id":"GO:0006099","count":8},{"id":"GO:0006412","count":7},{"id":"GO:0006096","count":7}]},{"hash":"1915795674480453640","title":"Adaptive immune signaling and lymphoid development","description":"The top terms cluster around adaptive immunity and lymphoid tissue development: T cell proliferation, B cell homeostasis, and lymph node development, with NF-kappaB transcription factor activity and signaling pathways such as vitamin D and retinoic acid receptor signaling. This points to immune regulation and transcriptional control in lymphocytes. Negative regulation of apoptosis and DNA-templated transcription further support a theme of immune cell survival and gene regulation. The mammary gland alveolus development term is related to developmental signaling rather than core immune function, but can be linked through common developmental pathways. ","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051092","count":7},{"id":"GO:0042098","count":5},{"id":"GO:0000185","count":5},{"id":"GO:0001782","count":5},{"id":"GO:0033280","count":5}]},{"hash":"2223637498333510758","title":"Tyrosine Kinase Signaling and ERK Activation","description":"The cluster is dominated by GO terms tied to receptor-mediated signaling and downstream MAPK/ERK activation, including T cell and B cell receptor signaling, integrin signaling, peptidyl-tyrosine autophosphorylation, and growth hormone receptor signaling. Additional terms like cellular response to nitric oxide and transcytosis point to related signaling and trafficking processes, while cerebellar cortex formation indicates developmental contexts where these pathways operate. Overall, the proteins likely function in receptor tyrosine kinase\u2013driven signaling and ERK cascade regulation.","confidence":"Medium","size":24,"edges":53,"triangles":32,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070374","count":24},{"id":"GO:0071732","count":24},{"id":"GO:0045056","count":24},{"id":"GO:0021697","count":24},{"id":"GO:0007229","count":24}]},{"hash":"888729158291390439","title":"Angiogenic Signaling and DNA Maintenance","description":"The top GO terms show strong representation of endothelial cell signaling and angiogenesis (VEGF receptor signaling, endothelial chemotaxis, EGF response, JUN phosphorylation) alongside core nuclear processes (DNA-templated transcription, DNA replication, DNA repair). This suggests a cluster of proteins involved in both angiogenic signaling and DNA maintenance, possibly with multifunctional roles or shared components. ","confidence":"Medium","size":24,"edges":137,"triangles":353,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051973","count":24},{"id":"GO:0006351","count":24},{"id":"GO:0006260","count":24},{"id":"GO:0006281","count":24},{"id":"GO:0007601","count":23}]},{"hash":"395525754372185865","title":"Vertebrate development and cell signaling","description":"The GO terms point to vertebrate development and associated signaling: multicellular and skeletal development, neural tube closure, DNA replication and transcription, along with ERK1/ERK2 cascade regulation and GTPase activity, indicating a cluster of developmentally oriented, proliferative signaling processes; a defense-response term is present but does not define the overall theme.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0001501","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0070374","count":3}]},{"hash":"699411613871319138","title":"Developmental Signaling and Growth Control","description":"The cluster centers on developmental signaling and growth regulation, with strong representation of Wnt and Hippo pathways, differentiation (keratinocytes), vascular development, and signaling in immune and receptor pathways, plus apoptosis and DNA replication, suggesting a core theme of coordinated signaling controlling growth and cell fate.","confidence":"High","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":16},{"id":"GO:0030216","count":15},{"id":"GO:0060044","count":15},{"id":"GO:0035329","count":15},{"id":"GO:0006915","count":15}]},{"hash":"2240343746492952425","title":"Neurovascular Development Signaling","description":"The cluster\u2019s prominent terms center on signaling pathways that drive nervous system and vascular development, including VEGF receptor signaling, EGFR response, JUN and STAT phosphorylation, and endothelial chemotaxis, with supporting references to nervous system and visual development. Some terms (B cell receptor signaling, mitotic cycle, skeletal muscle development) are broader or outliers, but the overarching theme is developmentally oriented signaling in neural and vascular tissues.","confidence":"Medium","size":24,"edges":216,"triangles":1103,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":24},{"id":"GO:0000278","count":24},{"id":"GO:0050853","count":19},{"id":"GO:0007519","count":19},{"id":"GO:0007399","count":19}]},{"hash":"2201920587891993481","title":"Signaling Pathway Inhibitors","description":"The top GO terms show widespread negative regulation across diverse signaling pathways (T cell receptor, ERK/MAPK, insulin receptor, IL-6, prolactin) plus related developmental and vascular processes. This pattern suggests the proteins act as inhibitors of multiple signaling pathways rather than a single specific pathway, making \u201cSignaling Pathway Inhibitors\u201d an appropriate, cohesive label.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0050860","count":18},{"id":"GO:0070373","count":18},{"id":"GO:0000200","count":18},{"id":"GO:0046627","count":15},{"id":"GO:0035855","count":14}]},{"hash":"1962022498898633686","title":"Stress-Responsive Signaling and Apoptosis","description":"The top GO terms cluster around signaling pathways (Hippo, TRK/neurotrophin signaling; NF-kappaB regulation; CDK activity) and responses to hormones and environmental stimuli (estradiol, xenobiotics, cobalt ion) with apoptotic outcomes (nurse cell apoptosis, intrinsic osmotic-stress\u2013induced apoptosis). This points to proteins that coordinate signaling networks governing cell fate under stress or hormonal cues, with a possible neuronal/signaling context hinted by sensory perception of sound. Overall, a theme of stress- and hormone-responsive signaling leading to apoptosis or cell fate decisions. ","confidence":"Medium","size":24,"edges":35,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0051092","count":2},{"id":"GO:0032355","count":2},{"id":"GO:0042493","count":2}]},{"hash":"1870444084580904571","title":"Neural development and cell adhesion","description":"This cluster is dominated by terms tied to nervous system development and synapse assembly, with many proteins linked to cell\u2013cell adhesion (heterophilic/homophilic). Those themes point to neural tissue formation and neuronal connectivity, supported by broader development terms like multicellular organism development and kidney development, but with some outliers (bone ossification, complement activation, host-cell entry) that are less central. Therefore, a neural development and cell adhesion label best captures the core signal.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":14},{"id":"GO:0051965","count":13},{"id":"GO:0007399","count":13},{"id":"GO:0007275","count":12},{"id":"GO:0043931","count":12}]},{"hash":"1122109418323936394","title":"Brain development and neuronal signaling","description":"This cluster is enriched for brain-development terms (hippocampus and substantia nigra development) and neural processes (neuronal apoptotic regulation, response to mechanical stimuli), with links to ERK/MAPK signaling and vesicle trafficking (Golgi to plasma membrane). While there is some diversity, the predominant theme centers on neural development and neuron signaling pathways.","confidence":"High","size":24,"edges":113,"triangles":146,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032729","count":7},{"id":"GO:0007420","count":7},{"id":"GO:0070374","count":6},{"id":"GO:0043001","count":6},{"id":"GO:0043525","count":6}]},{"hash":"367206916159893263","title":"Mitotic growth and translation machinery","description":"This cluster centers on cell division and mitotic processes (cell cycle, mitotic cytokinesis, exit from mitosis) and is strongly linked to protein synthesis pathways (ribosome biogenesis, tRNA modification). The presence of development-related terms (neuron projection development, regulation of embryonic cell shape) suggests roles in growth and developmental contexts as well. Taken together, the dominant theme is cellular proliferation coupled with translation machinery, with supportive developmental signals.","confidence":"High","size":24,"edges":142,"triangles":344,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":10},{"id":"GO:0042254","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0000747","count":9},{"id":"GO:0031175","count":9}]},{"hash":"968481990595204618","title":"T Cell Signaling and Cytokine Regulation","description":"The cluster is dominated by GO terms for IL-27 signaling, Th2 cytokine production, MAPK and PI3K/AKT signaling, and apoptotic/proliferation regulation, which together indicate a cohesive immune signaling module centered on T cell activation and cytokine control. Some terms like neurogenesis or vagina development may be annotation noise but do not override the main immune-related themes.","confidence":"High","size":24,"edges":271,"triangles":1918,"max_degree":23,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0008284","count":14},{"id":"GO:0042517","count":14},{"id":"GO:0022008","count":14},{"id":"GO:0060068","count":14},{"id":"GO:0070106","count":14}]},{"hash":"779444054662742978","title":"Immune receptor signaling and migration","description":"The top GO terms cluster around T cell and B cell receptor signaling (TCR/BCR pathways), activated T cell proliferation, and integrin-mediated signaling, along with innate immune response. Tyrosine phosphorylation events (JUN phosphorylation, peptidyl-tyrosine autophosphorylation) support signaling activity downstream of immune receptors. Additional terms for cellular migration and nitric oxide response fit leukocyte movement and inflammatory responses, with transcytosis indicating transport processes. Overall, this points to a cohesive set of proteins involved in immune signaling and leukocyte migration.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0007258","count":3},{"id":"GO:0071732","count":3},{"id":"GO:0045056","count":3},{"id":"GO:0007229","count":3}]},{"hash":"833483825325367404","title":"Ubiquitin-mediated muscle development and circadian regulation","description":"The cluster prominently features ubiquitin-dependent proteolysis and K6-linked ubiquitination terms, together with skeletal muscle tissue and fiber development as well as circadian rhythm regulation, pointing to a cohesive theme around ubiquitin-regulated protein turnover that impacts muscle development and circadian biology. A minority of terms such as B cell receptor signaling appear tangential, but do not outweigh the core connection. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":17},{"id":"GO:0085020","count":9},{"id":"GO:0051260","count":9},{"id":"GO:0007519","count":8},{"id":"GO:0072156","count":8}]},{"hash":"403136089049753531","title":"Rho-Integrin Cytoskeletal Signaling in Immune Cells","description":"This cluster centers on signaling pathways linking Rho GTPase activity to integrin signaling and actin remodeling (lamellipodium assembly), regulating adhesion and migration in immune contexts. The mix of terms on Rho signaling, integrin activation, lamellipodium formation, ERK cascade regulation, and immune-related responses (T cell signaling, microglial migration, LPS response) points to a cohesive theme of cytoskeletal signaling modulating immune cell movement and signaling.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":14},{"id":"GO:0007229","count":13},{"id":"GO:0050860","count":11},{"id":"GO:0043552","count":10},{"id":"GO:0030032","count":10}]},{"hash":"104824775283704274","title":"Ubiquitin-Driven Antiviral Innate Immunity","description":"The cluster is driven by ubiquitin-related processes (ubiquitin-dependent protein catabolic process, K63-linked ubiquitination) and innate antiviral responses (defense response to virus, suppression of viral release), suggesting a unified function in ubiquitin signaling that modulates antiviral defense. Additional terms related to NF-kappaB activity and vitamin D response imply immunomodulatory signaling layers accompanying this antiviral Innate immune function.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":17},{"id":"GO:0045087","count":15},{"id":"GO:0051607","count":14},{"id":"GO:0070534","count":11},{"id":"GO:0033280","count":10}]},{"hash":"1095509514283740992","title":"Developmental ECM and Synaptic Signaling","description":"The cluster shows strong representation of extracellular matrix interactions (cell-matrix adhesion) and developmental processes (cartilage condensation, skeletal system development) alongside neural connectivity terms (cerebellar Purkinje cell layer development, synapse maturation, glutamatergic transmission), suggesting a cohesive theme of development guided by ECM with neural synaptic formation. Immune-related terms like complement activation appear less central to the main pattern.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0001867","count":16},{"id":"GO:0007160","count":12},{"id":"GO:0051968","count":12},{"id":"GO:0021680","count":11},{"id":"GO:0007338","count":11}]},{"hash":"56735070776856357","title":"Unknown","description":"The top GO terms span cold response, redox, proteasome assembly, several metabolism pathways and cell cycle; no single unifying function stands out. The mix and inclusion of obsolete GO terms imply diverse, possibly noisy annotations, so there isn't a coherent cluster function to name.","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009409","count":4},{"id":"GO:0070682","count":3},{"id":"GO:0045329","count":3},{"id":"GO:0007049","count":3}]},{"hash":"2108912784042455685","title":"Ubiquitin-regulated mitophagy","description":"This cluster is enriched for ubiquitin-related processes (deubiquitination, autoubiquitination, ERAD) along with mitochondrial quality control (mitophagy and both positive and negative regulation of mitochondrial fusion), indicating a cohesive module centered on ubiquitin-mediated regulation of mitochondrial homeostasis and proteostasis.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016579","count":14},{"id":"GO:0010637","count":13},{"id":"GO:0000423","count":13},{"id":"GO:1902283","count":13},{"id":"GO:0070842","count":13}]},{"hash":"1712981332819257117","title":"Transcriptional Repression and Cell Cycle Regulation","description":"The top GO terms cluster around negative regulation of transcription by RNA polymerase II, negative regulation of apoptotic processes, DNA damage response modulation, and mitotic cell cycle control, with ubiquitination as a common regulatory mechanism. While there are some outliers (e.g., infection structure formation, some obsolete terms), the dominant theme ties gene expression control to cell cycle and stress signaling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0075015","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0043066","count":4},{"id":"GO:2000327","count":3}]},{"hash":"178791489863174654","title":"Innate and Adaptive Immune Activation","description":"Top GO terms cluster around immune response activation, spanning innate processes (complement activation, phagocytosis) and adaptive signaling (B cell receptor signaling, immunoglobulin production, T cell costimulation) with associated cell adhesion, indicating a coherent immune activation module.","confidence":"High","size":24,"edges":239,"triangles":1324,"max_degree":23,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045087","count":12},{"id":"GO:0006958","count":12},{"id":"GO:0006911","count":12},{"id":"GO:0050853","count":12},{"id":"GO:0006910","count":11}]},{"hash":"1497660357913538315","title":"GPCR-cAMP signaling and Rho GTPase regulation","description":"The cluster is dominated by GO terms for GPCR signaling, including adenylate cyclase-activating/inactivating pathways and activation of adenylate cyclase, plus positive regulation of Rho GTPase signaling, indicating a cohesive group of GPCR-mediated signal transduction components that regulate cAMP and Rho pathways. Some terms like visual perception and defense response appear as peripheral annotations, possibly due to broad GPCR or tissue-specific annotations, but the core theme centers on GPCR-driven signaling and GTPase regulation. Edges are absent in this dataset, so this label reflects functional enrichment rather than interaction structure.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":23},{"id":"GO:0045777","count":23},{"id":"GO:0010579","count":23},{"id":"GO:0007190","count":21},{"id":"GO:0035025","count":18}]},{"hash":"24082189384234203","title":"Embryonic development and steroid/stress response","description":"Proteins in this cluster associate with broad embryonic developmental processes across multiple organs (kidney ureteric bud branching, left/right asymmetry, digestive tract development, gonad development, pregnancy) and with hormonal/stress signaling (response to xenobiotic stimulus and dexamethasone stimulus, immobilization stress). The pattern suggests a developmental module modulated by steroid/hormone and stress pathways, rather than a single narrow function.","confidence":"Medium","size":24,"edges":95,"triangles":146,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":4},{"id":"GO:0071549","count":3},{"id":"GO:0035902","count":3},{"id":"GO:0001938","count":3},{"id":"GO:0046676","count":3}]},{"hash":"1258971038578249918","title":"Unknown","description":"The top GO terms span metal ion homeostasis (cadmium, cobalt), ion transport, nitrate assimilation, nitric oxide biosynthesis, sterol/ fatty acid biosynthesis, and even mitochondrion inheritance and nervous system/skin differentiation. This mix does not point to a single cohesive function or pathway, suggesting a functionally heterogeneous cluster.","confidence":"","size":24,"edges":39,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":6},{"id":"GO:0006876","count":4},{"id":"GO:0006877","count":4},{"id":"GO:0070574","count":4},{"id":"GO:0032443","count":4}]},{"hash":"2290513108812113632","title":"GPCR Signaling Across Tissues","description":"The cluster's top GO terms are dominated by GPCR-related signaling activities spanning multiple tissues: tachykinin receptor signaling, adrenergic receptor pathways, GPCR internalization, and opsin-mediated visual perception. Additional terms point to GPCR-regulated downstream processes like GTPase activity and adenylate cyclase inhibition, with cardiovascular (heart development, relaxation of cardiac muscle) and neural/sensory (synaptic plasticity, visual perception) contexts. This pattern supports a cohesive theme around GPCR signaling networks operating across tissues.","confidence":"High","size":24,"edges":53,"triangles":17,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":8},{"id":"GO:0007507","count":7},{"id":"GO:0002031","count":7},{"id":"GO:0007601","count":6},{"id":"GO:0031914","count":6}]},{"hash":"1899543255867771300","title":"Glutathione-Mediated Detox and DNA Repair","description":"The cluster is dominated by GO terms linked to oxidative stress defense and chemical detoxification, including cellular oxidant detoxification, glutathione metabolic process, response to toxic substance, and toxin catabolic process, plus aromatic amino acid metabolism. The presence of nucleotide-excision repair suggests a link to DNA damage repair under stress. Together, these points indicate a cohesive module focused on detoxification and maintenance of genomic integrity under chemical/oxidative stress. Some terms about calcium signaling and platelet aggregation appear less central and may reflect broader multifunctionality or annotation noise, but do not override the core detox/repair theme.","confidence":"Medium","size":24,"edges":177,"triangles":954,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0009072","count":17},{"id":"GO:0098869","count":16},{"id":"GO:0009636","count":15},{"id":"GO:0060316","count":15},{"id":"GO:0006749","count":15}]},{"hash":"968315245928373096","title":"Mitotic Chromosome Assembly and Spindle Dynamics","description":"The GO terms point to core mitotic machinery: mitotic cell cycle, establishment of mitotic spindle orientation, CENP-A-containing chromatin assembly, cell division, and microtubule severing, all of which reflect chromosome organization and spindle-driven segregation. Additional terms on chromatin modification and protein oligomerization align with structural chromosome components and protein complexes involved in mitosis. Some unrelated terms (ER-Golgi transport, skeletal morphogenesis, obsolete terms) likely reflect broader annotations, but the dominant signal is a mitotic chromosome and spindle function module.","confidence":"High","size":24,"edges":8,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0000132","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0048705","count":4},{"id":"GO:0061641","count":4}]},{"hash":"995123106200366445","title":"Chromatin Assembly and Transcription Regulation","description":"The top GO terms emphasize transcriptional control (negative regulation of transcription by RNA polymerase II) and chromatin assembly (CENP-A containing chromatin assembly), with supporting signals from development/differentiation terms, suggesting this cluster centers on gene expression regulation through chromatin dynamics rather than a single metabolic pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0045618","count":3},{"id":"GO:0071333","count":3},{"id":"GO:0007420","count":3}]},{"hash":"524907550029388361","title":"Striatal neuron differentiation and excitatory synaptic signaling","description":"The cluster prominently features terms tied to striatal medium spiny neuron differentiation, axonal guidance, and modulation of excitatory synaptic activity (AMPA receptor activity and EPSP regulation), pointing to neuronal development and excitatory synaptic signaling. While immune-related and chromosomal localization terms appear, the dominant theme is neuronal differentiation and synaptic function in the striatum.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007413","count":4},{"id":"GO:1901187","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0070198","count":3},{"id":"GO:0045087","count":3}]},{"hash":"1654374476018026875","title":"Fatty acid biosynthesis and lipid metabolism","description":"The top GO terms are dominated by fatty acid biosynthetic and metabolic processes, including fatty-acid-CoA metabolism, long-chain fatty acid metabolism, and import of long-chain fatty acids, pointing to a cohesive lipid-centric metabolic module. While there are some additional, less central terms (menaquinone biosynthesis, siderophore biosynthesis, seed coat development), the prevailing theme is lipid metabolism, supporting a focused label around fatty acid synthesis and related lipid pathways.","confidence":"High","size":24,"edges":140,"triangles":375,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":10},{"id":"GO:0036112","count":8},{"id":"GO:0009234","count":8},{"id":"GO:0010124","count":8},{"id":"GO:0019427","count":8}]},{"hash":"1370382251068064165","title":"ER Stress Signaling and Cytoskeleton Remodeling","description":"The cluster centers on stress-activated signaling (apoptosis, JUN phosphorylation) and ER-stress\u2013driven translation control, coupled with cytoskeletal dynamics (actin organization/bundle assembly, cell migration). While some terms touch on neuronal or developmental contexts, the recurring themes are stress-response signaling and cytoskeletal remodeling, which likely reflect the shared functional core of this protein group.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006915","count":20},{"id":"GO:0007258","count":19},{"id":"GO:0036493","count":19},{"id":"GO:0016191","count":19},{"id":"GO:0043547","count":19}]},{"hash":"2184504135806554527","title":"Immune Activation and NK Cell Regulation","description":"Based on the GO terms, the cluster is enriched for innate immune response, phagocytosis recognition, cytokine production, IL-10 regulation, T cell costimulation, and NK cell cytotoxicity modulation, suggesting a core theme of immune signaling and cytotoxic control. Some outlier terms (spermatid development, lens morphogenesis) may reflect multi-function annotations or unrelated associations, but the dominant signal is immune-related.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006910","count":9},{"id":"GO:0045087","count":8},{"id":"GO:0002374","count":8},{"id":"GO:2001181","count":8},{"id":"GO:0031295","count":8}]},{"hash":"2119588006204240613","title":"Eye and hindbrain development","description":"Top terms cluster around embryonic eye morphogenesis, camera-type eye development, retinal ganglion cell axon guidance, brain segmentation, and rhombomere patterning, with transcriptional regulation terms also present. This points to a coherent vertebrate developmental module coordinating eye formation and hindbrain patterning via transcription control. ","confidence":"Medium","size":24,"edges":69,"triangles":24,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":15},{"id":"GO:0048048","count":14},{"id":"GO:0043010","count":13},{"id":"GO:0060441","count":13},{"id":"GO:0000122","count":11}]},{"hash":"45683869393051440","title":"Mitochondrial apoptosis and stress signaling","description":"The terms cluster around mitochondrial involvement in apoptosis (cytochrome c release, mitochondrial fragmentation), hypoxia and ROS-related stress responses, and stress-induced signaling (including mechanical stimulus). This points to a cohesive pathway where mitochondrial dynamics and oxidative stress regulate apoptotic and stress signaling pathways, justifying a label centered on mitochondrial apoptosis and stress responses.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090200","count":4},{"id":"GO:0071456","count":4},{"id":"GO:0043653","count":4},{"id":"GO:0071260","count":4},{"id":"GO:2000378","count":4}]},{"hash":"1629021480243123475","title":"Neural axon guidance and vascular development","description":"The cluster centers on processes linking neural development (neuron development, axonogenesis, axon extension) with cardiovascular remodeling (heart development, endothelial chemotaxis, smooth muscle migration) and signaling pathways (MAPK/ERK, integrin signaling, tyrosine phosphorylation). This points to a coordinated role of MAPK-driven signaling in both neural patterning and vascular development.","confidence":"Medium","size":24,"edges":9,"triangles":0,"max_degree":3,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0050731","count":7},{"id":"GO:0048666","count":6},{"id":"GO:0000187","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0060385","count":5}]},{"hash":"691493874615797655","title":"Circadian Proteostasis","description":"Top GO terms indicate a strong link between circadian rhythm regulation and ubiquitin-dependent protein degradation, suggesting a module where the circadian clock governs protein turnover. The presence of circadian-related terms (circadian rhythm, circadian sleep/wake cycle) supports this theme, while other terms likely reflect annotation noise or pleiotropy. Confidence is high that the cluster represents circadian proteolysis.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":20},{"id":"GO:0042752","count":14},{"id":"GO:0051260","count":10},{"id":"GO:0007519","count":9},{"id":"GO:0072156","count":9}]},{"hash":"2071418150441794270","title":"Embryonic organogenesis","description":"This cluster is dominated by developmental processes across multiple organs (eye, heart, hindlimb, habenula, prostate, gonad) with several terms explicitly describing embryogenesis and morphogenesis. The presence of eye-related development terms, along with heart and limb morphogenesis, suggests a module of genes driving embryonic organ formation. Transcriptional regulation terms (RNA polymerase II\u2013mediated transcription) indicate these proteins either regulate or participate in developmental transcription programs, reinforcing the interpretation as an embryonic development cluster.","confidence":"High","size":24,"edges":112,"triangles":82,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048048","count":11},{"id":"GO:0000122","count":10},{"id":"GO:0007507","count":10},{"id":"GO:0021986","count":10},{"id":"GO:0006366","count":9}]},{"hash":"25378467945842907","title":"Craniofacial development and neural crest organogenesis","description":"The top GO terms point to craniofacial morphogenesis and neural crest\u2013driven organogenesis, including palate/roof of mouth development, neural crest migration, odontogenesis, dentin formation, and pharyngeal system development, with additional signals for inner ear and midbrain development. The inclusion of negative regulation of RNA polymerase II transcription suggests these proteins regulate transcription to coordinate these developmental programs. Overall, the cluster represents transcriptionally regulated craniofacial and related organogenesis processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0060021","count":7},{"id":"GO:0001755","count":6},{"id":"GO:0042475","count":6},{"id":"GO:0048839","count":6}]},{"hash":"633311501543627031","title":"Photoreceptor signaling and visual perception","description":"The top GO terms are dominated by photoreceptor-related processes: rhabdomere development, visual perception, and opsin-mediated signaling, with supporting annotations for GPCR signaling and intracellular signal transduction. While terms like heart development and cardiac contraction also appear, they likely reflect shared signaling components (e.g., GTPase and calcineurin\u2013NFAT pathways) used in multiple tissues. Overall, the common theme is photoreceptor/opsin signaling and visual perception, suggesting the proteins function together in phototransduction rather than cardiac processes.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042052","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0033173","count":2}]},{"hash":"2224187443828509511","title":"Rho GTPase signaling and lamellipodium formation","description":"This cluster\u2019s top GO terms cluster around Rho family GTPase activity and actin cytoskeleton dynamics, including lamellipodium assembly and Rho-mediated signaling, indicating a shared role in actin remodeling and cell migration. Some terms (thymus development, thrombin receptor signaling) are peripheral, but the dominant theme is Rho-driven cytoskeleton organization.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0030032","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0007266","count":3},{"id":"GO:0007205","count":3}]},{"hash":"1889527146371230870","title":"Neuronal transport and cytoskeletal regulation","description":"Based on the top GO terms, the cluster is enriched for microtubule-based movement, vesicle trafficking (Golgi to ER, synaptic vesicle budding), and regulation of cytoskeletal dynamics (Arp2/3, GTPase activity). The presence of spinal cord development and adult locomotory behavior terms further suggests a neuronal context. While a few terms touch cell cycle, the dominant signals point to neuronal transport and cytoskeletal regulation as the cluster's core function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007018","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0016185","count":4},{"id":"GO:0008344","count":4},{"id":"GO:0007205","count":4}]},{"hash":"1855455889423483555","title":"Midbrain neural development and epigenetic regulation","description":"These proteins show annotations centered on neural development, especially midbrain and dopaminergic neuron differentiation, with supporting signals from Wnt pathways. They also feature transcriptional and epigenetic control (RNA Pol II regulation, histone methylation, mRNA regulation), suggesting a theme of neural development governed by transcriptional/epigenetic mechanisms. Some outlier terms exist, but the dominant signal points to midbrain neural development with regulatory control.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0051569","count":2},{"id":"GO:0030901","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0034052","count":2}]},{"hash":"595531855720000635","title":"Neural development and synaptic plasticity","description":"Derived from GO terms dominated by nervous system functions: social behavior, long-term synaptic depression, calcium signaling, and ion transport, with additional nervous system development terms such as sympathetic nervous system development and multicellular organism development. While a couple terms related to adipose tissue development and ossification appear, the majority indicate neural development and synaptic plasticity as the core theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035176","count":4},{"id":"GO:0060292","count":4},{"id":"GO:0035725","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0060612","count":2}]},{"hash":"2299373317579605134","title":"Protease-Activated GPCR Signaling and ECM Remodeling","description":"The dominant GO terms point to protease-triggered GPCR signaling (thrombin-activated receptor signaling), PKC and Rap signaling pathways, along with collagen catabolic remodeling of the extracellular matrix, suggesting a cohesive theme of protease-driven signal transduction affecting ECM dynamics.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030574","count":3},{"id":"GO:0019933","count":3},{"id":"GO:0070528","count":3},{"id":"GO:0032486","count":3},{"id":"GO:0070493","count":3}]},{"hash":"1851775269862660254","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007155","count":3},{"id":"GO:0045214","count":3},{"id":"GO:0032402","count":2},{"id":"GO:0070121","count":2},{"id":"GO:0051877","count":2}]},{"hash":"267507534522068981","title":"Angiogenesis and heart development","description":"The top GO terms cluster around blood vessel formation and remodeling (branching in blood vessel morphogenesis, regulation of angiogenesis), together with heart development and endothelial cell guidance. Additional terms about cell-cell adhesion/junctions and mesodermal fate support a vascular/cardiovascular development theme. This makes a cohesive, specific label that captures the dominant function of the proteins in this cluster.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032516","count":5},{"id":"GO:0001569","count":4},{"id":"GO:0045765","count":4},{"id":"GO:0007157","count":4},{"id":"GO:0007507","count":4}]},{"hash":"1324199191235533303","title":"Muscle development and Wnt signaling regulation","description":"The cluster is enriched for mesoderm development and skeletal muscle fiber development, plus a term for positive regulation of canonical Wnt signaling, suggesting a theme around muscle differentiation and developmental signaling. Other terms\u2014such as transcriptional regulation and control of proteasomal degradation\u2014fit with gene expression and protein turnover during development. Some terms (response to morphine, lipid A biosynthesis) appear peripheral and likely reflect noise, but the dominant signals support a muscle-development/Wnt-regulation theme.","confidence":"High","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043278","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009245","count":3},{"id":"GO:0010951","count":3},{"id":"GO:0007498","count":3}]},{"hash":"564424756065835535","title":"Post-transcriptional RNA regulation","description":"The proteins are tied to post-transcriptional controls: regulation of mRNA stability under stress, translation initiation and reinitiation, formation of the translation preinitiation complex, and regulation of spliceosome-mediated splicing, including IRES-dependent viral translation and poly(A) tail regulation. This cohesion centers on RNA fate decisions after transcription.","confidence":"High","size":23,"edges":78,"triangles":64,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":14},{"id":"GO:0002188","count":13},{"id":"GO:0001731","count":13},{"id":"GO:0048026","count":12},{"id":"GO:0006446","count":12}]},{"hash":"994288019783571527","title":"Embryonic tissue morphogenesis and differentiation","description":"This cluster centers on developmental processes and tissue morphogenesis across multiple lineages, including heart valve and septum formation, muscle morphogenesis, and neuronal differentiation (GABAergic interneurons, oligodendrocytes) as well as hemangioblast differentiation. The variety of lineage- and tissue-specific developmental terms suggests a general theme of embryonic tissue specification and morphogenesis rather than a single pathway, with circadian regulation of gene expression appearing as a broad regulatory layer and a plant-related term (stomatal complex development) contributing to the diversity of developmental contexts.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090128","count":23},{"id":"GO:0010374","count":23},{"id":"GO:2000793","count":23},{"id":"GO:0048715","count":23},{"id":"GO:0021892","count":23}]},{"hash":"12110798702785542","title":"mRNA Stability and Translation Regulation","description":"The cluster is dominated by GO terms focused on post-transcriptional control of gene expression, including mRNA polyadenylation and tail shortening, mRNA modification and stabilization, regulation of mRNA stability in response to stress, and assembly of the eIF4F translation initiation complex. Together with regulatory ncRNA-mediated gene silencing and ubiquitination-related processes, these proteins appear to coordinate mRNA maturation, stability, and translation initiation, pointing to a cohesive post-transcriptional regulatory module.","confidence":"High","size":23,"edges":187,"triangles":898,"max_degree":22,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":9},{"id":"GO:0060211","count":8},{"id":"GO:1905663","count":8},{"id":"GO:0016567","count":8},{"id":"GO:0097010","count":8}]},{"hash":"1047540752278315319","title":"Unknown","description":"The GO terms span diverse functions, including transcription, multiple biosynthetic pathways (porphyrin, biotin, histidine, cobalamin, lysine, sphingomyelin), redox processes, and signaling (salicylic acid defense, Notch). This lack of a cohesive, single theme makes it unclear what a representative label would be.","confidence":"","size":23,"edges":32,"triangles":32,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006782","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0000105","count":6},{"id":"GO:0055114","count":5}]},{"hash":"1336647657878769340","title":"Stimulus-Responsive Neural Signaling","description":"The cluster is enriched for responses to various stimuli (glucose, dsRNA, prostaglandin, cocaine) and associated signaling pathways (ERK cascade), with strong representation of neural functions such as visual perception, visual learning, and dopaminergic synaptic transmission. While some terms touch on immune and cardiac processes, the dominant theme appears to be stimulus-triggered signaling in neural contexts.","confidence":"Medium","size":23,"edges":200,"triangles":896,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071333","count":22},{"id":"GO:0043330","count":22},{"id":"GO:0055119","count":13},{"id":"GO:0007601","count":12},{"id":"GO:0070374","count":12}]},{"hash":"1844021682808169924","title":"Calcium-Driven Signaling in Muscle and Nervous System","description":"The dominant terms cluster around calcium ion detection and calcium-regulated muscle contraction (skeletal and cardiac), indicating a core theme of calcium signaling controlling muscle force. Additional terms related to visual perception and neural activity (excitatory postsynaptic potential, astrocyte activation) reflect calcium's role in neural signaling, while kinase and GTPase regulation suggest broader signal transduction. Overall, the cluster seems to represent calcium-mediated signaling integrating muscle contraction and neural processes.","confidence":"High","size":23,"edges":170,"triangles":634,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0005513","count":17},{"id":"GO:0048741","count":17},{"id":"GO:0010881","count":17},{"id":"GO:0098735","count":17},{"id":"GO:0007601","count":16}]},{"hash":"2148461812493666621","title":"Embryonic eye and brain morphogenesis","description":"Top GO terms cluster around embryonic development and organ morphogenesis, with strong emphasis on eye morphogenesis (camera-type eye development, embryonic eye morphogenesis) and hindbrain patterning (brain segmentation, rhombomere development), plus related organ development (pituitary gland, lung morphogenesis). This suggests a cohesive theme of early developmental morphogenesis across tissues.","confidence":"High","size":23,"edges":162,"triangles":479,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":9},{"id":"GO:0001701","count":8},{"id":"GO:0043010","count":7},{"id":"GO:0060441","count":7},{"id":"GO:0048048","count":7}]},{"hash":"980442125873772618","title":"GPCR Signaling and Second Messenger Pathways","description":"The cluster is dominated by G protein-coupled receptor (GPCR) signaling terms, including dopamine, adrenergic, and acetylcholine receptor pathways, as well as downstream second messengers such as cAMP and phospholipase C signaling. Additional terms like Rho signaling and phototransduction reinforce a theme of GPCR-driven signal transduction and its diverse second-messenger outputs, with heart development likely reflecting GPCR roles in cardiac signaling. Overall, the proteins appear to form a GPCR-centered signaling module rather than a single specialized process.","confidence":"High","size":23,"edges":236,"triangles":1446,"max_degree":22,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007507","count":23},{"id":"GO:0043547","count":20},{"id":"GO:0010513","count":20},{"id":"GO:0007603","count":20},{"id":"GO:0071880","count":20}]},{"hash":"1676194854060675940","title":"Developmental gene regulation and differentiation","description":"This cluster includes GO terms centered on transcription by RNA polymerase II and a broad array of differentiation and development processes across neural, glial, cardiac, muscle, and plant contexts, plus circadian regulation of gene expression. The common thread is regulation of gene expression guiding cell fate and tissue development, so the label Developmental gene regulation and differentiation is appropriate.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":18},{"id":"GO:0048712","count":17},{"id":"GO:2001038","count":17},{"id":"GO:0090128","count":14},{"id":"GO:0010374","count":14}]},{"hash":"1078926659710508747","title":"ER stress response and protein trafficking","description":"The cluster centers on processes related to how cells handle stress in the ER, protein quality control via ubiquitination, and intracellular trafficking (Golgi localization), with supporting signals and junction-related terms. While developmental terms appear (dendrite/kidney development), the strongest cohesive theme is ER stress response together with protein processing and trafficking pathways.","confidence":"Medium","size":23,"edges":46,"triangles":0,"max_degree":15,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:1903206","count":7},{"id":"GO:0034976","count":7},{"id":"GO:0016358","count":6},{"id":"GO:0016567","count":6},{"id":"GO:0070374","count":6}]},{"hash":"1218904173324601603","title":"Angiogenesis and vascular remodeling","description":"This cluster is dominated by terms related to blood vessel formation and remodeling, including angiogenesis, endothelial cell migration, vasoconstriction regulation, cell-matrix adhesion, and ERK signaling\u2014patterns pointing to vascular development and remodeling, with supporting notes from plasminogen activation and immune-related processes. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045907","count":12},{"id":"GO:0001867","count":12},{"id":"GO:0007171","count":11},{"id":"GO:0007160","count":11},{"id":"GO:0043536","count":10}]},{"hash":"1106657698309446441","title":"Neural development and organogenesis","description":"The top GO terms point to neural differentiation (cerebral cortex GABAergic interneuron differentiation; subpallium neuron fate; spinal cord neuron and oligodendrocyte specification) as well as development of other organs (eye, pancreas, bronchioles, gonads). This suggests a cluster centered on developmental fate specification across multiple tissues, with a neural emphasis. ","confidence":"Medium","size":23,"edges":252,"triangles":1750,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":14},{"id":"GO:0021892","count":9},{"id":"GO:0060435","count":9},{"id":"GO:0060163","count":9},{"id":"GO:0021520","count":9}]},{"hash":"1288518927781894195","title":"Ubiquitin-Dependent Protein Degradation and Autophagy","description":"The top terms center on ubiquitin-related proteolysis (ubiquitin-dependent protein catabolic process, protein ubiquitination, polyubiquitination, ERAD), plus autophagy and links to cell cycle, transcriptional regulation, and apoptosis. The combination suggests a proteostasis-focused cluster where ubiquitination tags proteins for degradation via the proteasome or autophagy, with ancillary roles in immune defense. Confidence in this label is High.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":14},{"id":"GO:0016567","count":11},{"id":"GO:0030433","count":11},{"id":"GO:0071157","count":10},{"id":"GO:0000122","count":10}]},{"hash":"472287076285035817","title":"DNA Damage Response and Transcription Regulation","description":"The top terms cluster around DNA metabolism and damage response (DNA replication, DNA biosynthesis, UV-damage excision repair, DNA damage\u2013related apoptotic signaling) along with regulation of transcription by RNA polymerase II and protein interactions. A stress-response (oxidative stress) signal and a competence-related term are present, but the dominant theme ties DNA replication/repair to transcription control, suggesting a cohesive DNA-damage\u2013response/transcription regulatory module.","confidence":"Medium","size":23,"edges":33,"triangles":24,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0008630","count":3},{"id":"GO:0071897","count":3},{"id":"GO:0070914","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1355732399238741815","title":"Genome maintenance and proteostasis","description":"This cluster shows strong enrichment for DNA replication and repair processes (DNA replication, leading strand elongation, mitotic checkpoint signaling, UV-damage repair) and, separately, protein quality control and stress responses (protein processing, ER unfolded protein response, aggresome assembly, SNARE disassembly). Together they suggest a role in preserving genome integrity while maintaining proteostasis under cellular stress.","confidence":"Medium","size":23,"edges":8,"triangles":0,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0016485","count":8},{"id":"GO:0019079","count":7},{"id":"GO:0070914","count":7},{"id":"GO:0033314","count":7}]},{"hash":"1570381943100191739","title":"Embryonic Development and Morphogenesis","description":"The dominant GO terms indicate embryonic tissue development and morphogenesis across heart, skeletal muscle, cranial skeleton, neurons, and retinal axons, suggesting proteins function in multicellular development. Some immune signaling terms appear but do not define the cluster.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007507","count":6},{"id":"GO:0007519","count":5},{"id":"GO:0001764","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0007275","count":5}]},{"hash":"764996609837820107","title":"Multitissue Development Across Organs","description":"This cluster is dominated by GO terms for development across multiple tissues\u2014forebrain and nervous system, skeletal muscle, spleen, uterus, and roof of mouth\u2014along with axis specification and transcription regulation, suggesting a broad developmental program rather than a single tissue-specific function. A few terms for ubiquitin-dependent proteolysis and B cell signaling appear but do not define a single tissue; overall the cluster best fits a cross-tissue developmental category.","confidence":"Medium","size":23,"edges":52,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":4},{"id":"GO:0050853","count":4},{"id":"GO:0007519","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0007399","count":3}]},{"hash":"1108853665143724996","title":"Dopaminergic Visual GPCR Signaling","description":"The cluster is dominated by terms tying GPCR signaling to neuronal processes, including visual perception/opsin signaling and dopaminergic synaptic transmission, along with ERK cascade modulation and GPCR internalization. The presence of cocaine-related behavioral response and prostaglandin-linked signaling suggests a cohesive module of GPCR-driven signaling and phosphorylation that influences both vision-related processing and reward pathways.","confidence":"High","size":23,"edges":223,"triangles":1240,"max_degree":22,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":23},{"id":"GO:0043547","count":23},{"id":"GO:0006468","count":23},{"id":"GO:0048148","count":23},{"id":"GO:0071380","count":23}]},{"hash":"444437205170897646","title":"Cell Cycle and Energy Metabolism","description":"This cluster shows enrichment for cell cycle and cell division terms along with ATP synthesis/electron transport, pointing to proteins involved in growth-related energy production. Additional signals for translation and protein quality control suggest general housekeeping tied to proliferation, with peroxisomal protein import hinting at broader metabolic maintenance. Overall, the shared theme appears to be proliferation-associated energy management and proteostasis rather than a single specific pathway.","confidence":"Medium","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0034599","count":2},{"id":"GO:0006515","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0016558","count":2}]},{"hash":"2119049701216332024","title":"Embryonic Development and Morphogenesis","description":"This cluster is dominated by GO terms tied to developmental processes: cartilage morphogenesis, left-right pattern formation, placental and endocrine system development, EMT in cardiac development, trophoblast differentiation, and pancreatic cell development. While a few terms point to general cellular processes like RNA splicing and DNA replication regulation, the overarching theme is embryonic development and tissue morphogenesis, suggesting these proteins collectively participate in developmental programs rather than a single enzymatic function.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032298","count":19},{"id":"GO:0060536","count":19},{"id":"GO:1903026","count":19},{"id":"GO:0003323","count":19},{"id":"GO:0000398","count":19}]},{"hash":"479017307443599723","title":"Proteoglycan Biosynthesis and Cell Adhesion","description":"Top terms indicate proteoglycan biosynthesis (heparin and chondroitin sulfate), UDP-xylose metabolism, and glycosylation, coupled with cell adhesion processes (leukocyte tethering/rolling and heterotypic adhesion) and developmental contexts like lens and kidney morphogenesis. This points to an ECM-centric theme where proteoglycans drive adhesion and tissue morphogenesis.","confidence":"High","size":23,"edges":37,"triangles":1,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006486","count":7},{"id":"GO:0036438","count":5},{"id":"GO:0050901","count":5},{"id":"GO:0060352","count":5},{"id":"GO:0060993","count":5}]},{"hash":"1984987652740385220","title":"Carbohydrate biosynthesis and glycosylation","description":"The top GO terms cluster around glycogen and starch biosynthesis, glucose metabolism, and GPI anchor biosynthesis, indicating a shared focus on carbohydrate production and protein/lipid glycosylation. Some terms reflect energy/nutrient status (feeding behavior, response to water deprivation), but the dominant theme is carbohydrate biosynthesis and glycosylation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005978","count":4},{"id":"GO:0009405","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0006506","count":3},{"id":"GO:0007631","count":3}]},{"hash":"930985986941072343","title":"Developmental signaling and cytoskeletal remodeling","description":"The cluster highlights Wnt signaling, GTPase regulation, actin remodeling, and development-related terms (heart and substantia nigra), with neural plasticity hints, suggesting a theme of developmental signaling linked to cytoskeletal dynamics; ribosome biogenesis and mRNA capping may reflect broader cellular activity. ","confidence":"Medium","size":23,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0042254","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0034115","count":2}]},{"hash":"2040141266136535524","title":"Innate immune actin remodeling","description":"The top GO terms show emphasis on actin-based structures (actin cortical patches, podosomes, ruffles) and innate immune response, indicating a cluster of proteins involved in cytoskeleton remodeling during innate immune activities. Some neuronal and developmental terms (synapse/dendritic spine, bone development) appear, but they likely reflect shared actin regulation rather than primary functions.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0000147","count":3},{"id":"GO:0006368","count":2},{"id":"GO:1903679","count":2},{"id":"GO:0007416","count":2}]},{"hash":"1633492169090038665","title":"Broad-spectrum solute transporters","description":"The GO terms show transmembrane transport of a wide range of substrates (nitrite, nitrate, various sugars, sialic acid, phosphate, vitamins, xenobiotics), indicating proteins functioning as membrane transporters for diverse solutes, justifying this label.","confidence":"High","size":23,"edges":55,"triangles":6,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":9},{"id":"GO:0035461","count":9},{"id":"GO:1900754","count":9},{"id":"GO:0015739","count":9},{"id":"GO:0035435","count":9}]},{"hash":"805594342050052941","title":"Neurovascular development and inflammation","description":"This cluster centers on nervous system development (motor neuron axon guidance, axonogenesis), vascular/heart development (angiogenesis, heart development), and immune/inflammatory signaling (monocyte activation, IL-1 and TNF responses, inflammatory response), indicating a coherent neurovascular-immune development theme. The obsolete oxidation-reduction term is not informative for this cluster.","confidence":"High","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0007160","count":4},{"id":"GO:0008045","count":4},{"id":"GO:0048936","count":4},{"id":"GO:0042117","count":3}]},{"hash":"1309656900776682238","title":"Neuronal signaling and synaptic plasticity","description":"The GO terms emphasize neuronal communication and synaptic dynamics (glutamatergic transmission, synapse structural plasticity, GPCR/MAPK signaling, Rac regulation). Additional terms touch on cell adhesion and cytoskeletal aspects (integrin regulation) and neural development (photoreceptor differentiation), suggesting a theme centered on signaling that governs synaptic function and connectivity. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051497","count":4},{"id":"GO:0035021","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0000161","count":4},{"id":"GO:0051968","count":3}]},{"hash":"418807176921983843","title":"Neuronal calcineurin-NFAT signaling","description":"This cluster centers on neuronal calcium signaling: excitatory postsynaptic potential, regulation of postsynaptic calcium, and the calcineurin-NFAT signaling cascade. The presence of brain-related terms like substantia nigra development supports a neuronal context, while some terms ( xenobiotic response, vascular branching) may be less central or incidental. Overall, the core theme is calcium-dependent signaling and NFAT activation in neurons.","confidence":"Medium","size":23,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060079","count":5},{"id":"GO:0005513","count":5},{"id":"GO:0035690","count":5},{"id":"GO:0033173","count":5},{"id":"GO:0021762","count":5}]},{"hash":"1116391896535262899","title":"Immune activation and antigen presentation","description":"These proteins show enrichment for both adaptive (T cell costimulation, dendritic cell differentiation) and innate (innate immune response, complement activation) immune processes, with accompanying roles in cell adhesion and regulation of macrophage activity, suggesting a module involved in initiating and regulating inflammation and antigen presentation.","confidence":"High","size":23,"edges":148,"triangles":394,"max_degree":18,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0031295","count":14},{"id":"GO:1904597","count":14},{"id":"GO:0045087","count":14},{"id":"GO:0071639","count":14},{"id":"GO:2001200","count":14}]},{"hash":"440397143761463127","title":"RNA Pol II Transcription Regulation","description":"This cluster is dominated by GO terms for transcriptional regulation by RNA polymerase II (both negative and positive regulation), suggesting a core function as transcriptional regulators. The presence of development-related terms (digestive system and midbrain development) and ECM-related terms (extracellular matrix disassembly, cell-matrix adhesion) indicates additional roles in development and tissue morphogenesis, but the strongest signal centers on RNA Pol II\u2013mediated transcription control.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0045944","count":7},{"id":"GO:0055123","count":6},{"id":"GO:0030901","count":6},{"id":"GO:1903142","count":6}]},{"hash":"2110922800865411162","title":"NF-\u03baB and GPCR immune signaling","description":"The terms cluster around regulation of NF-\u03baB activity and canonical NF-\u03baB signaling, together with G protein-coupled receptor signaling (acetylcholine receptor) and processes like clathrin-mediated endocytosis and B cell homeostasis, suggesting a theme of immune signaling networks where NF-\u03baB control integrates with GPCR cues and membrane trafficking.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":5},{"id":"GO:0007026","count":4},{"id":"GO:0043123","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0010765","count":4}]},{"hash":"1651332467333878299","title":"Heart development and vascular remodeling","description":"The top GO terms center on cardiac development (right atrium morphogenesis, SA node electrophysiology), ephrin signaling, and vascular-related remodeling (endothelial delamination, cell migration, actin assembly), suggesting a cohesive theme around heart formation and associated vascular changes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":7},{"id":"GO:0098907","count":7},{"id":"GO:0051017","count":5},{"id":"GO:0097497","count":5},{"id":"GO:0035544","count":5}]},{"hash":"1050563792389341665","title":"Embryonic Development and Organogenesis","description":"The top GO terms cluster around embryonic and organ development (in utero embryonic development, spinal cord development, metanephric collecting duct development), suggesting a common theme of developmental programs across tissues. Additional terms touch on related signaling and regulatory processes (phosphorylation, necroptosis regulation) that commonly accompany development. Some items (e.g., B cell homeostasis, acetylcholine biosynthetic process) are broader nervous/immune functions but can be related to developmental contexts, supporting a developmental theme overall.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":2},{"id":"GO:0070584","count":2},{"id":"GO:0072205","count":2},{"id":"GO:0032000","count":2},{"id":"GO:0008292","count":2}]},{"hash":"1290590425870571556","title":"Membrane transporters and signaling proteins","description":"Based on the recurring GO terms, the proteins cluster around membrane-associated functions: transmembrane and sodium ion transport, bile acid transport, and cell surface receptor signaling, including Hedgehog/Smoothened pathway regulation. While some terms appear as outliers (visual perception, plant hypersensitive response), the dominant pattern points to membrane transport and signaling roles, justifying the label.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0030321","count":3},{"id":"GO:0015721","count":2},{"id":"GO:0009626","count":2},{"id":"GO:0007166","count":2}]},{"hash":"2033775267699736636","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000398","count":9},{"id":"GO:0002188","count":8},{"id":"GO:0001731","count":8},{"id":"GO:0000447","count":7},{"id":"GO:0000132","count":7}]},{"hash":"1669480930718876873","title":"Translation initiation and neural development","description":"The top GO terms cluster around translation initiation (translation reinitiation; formation of translation preinitiation complex) and neural development (brain development; spinal cord development), suggesting proteins tied to the translation machinery with links to neurodevelopmental processes. Additional terms point to broader cellular roles, but the dominant pattern is translation initiation together with neural development cues.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0045071","count":6},{"id":"GO:0001649","count":5}]},{"hash":"129545098129192161","title":"RNA processing and translation regulation","description":"This cluster centers on post-transcriptional control, with GO terms spanning regulatory ncRNA-mediated gene silencing, mRNA splicing regulation, mRNA stability under stress, poly(A) tail regulation, mRNA modification and stabilization, and translational initiation (including EIF4F complex assembly and initiation control). Together these terms indicate a cohesive RNA metabolism/translation regulation program, rather than DNA-level transcriptional processes.","confidence":"High","size":22,"edges":160,"triangles":588,"max_degree":21,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":11},{"id":"GO:0048026","count":11},{"id":"GO:0010610","count":8},{"id":"GO:0060211","count":7},{"id":"GO:1905663","count":7}]},{"hash":"28963546174846601","title":"Unknown","description":"The top GO terms include neural development and signaling (cerebellar cortex formation, Bergmann glial differentiation, axon regeneration, glutamatergic transmission) alongside seemingly unrelated pathways (T cell receptor signaling, insulin signaling, and plant hormone signaling), indicating a highly heterogeneous set with no single coherent function tying all proteins together. Therefore there isn\u2019t a clear, representative theme for the cluster.","confidence":"","size":22,"edges":170,"triangles":906,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0021697","count":12},{"id":"GO:0050852","count":12},{"id":"GO:0060020","count":12},{"id":"GO:2001275","count":12},{"id":"GO:0048679","count":12}]},{"hash":"97031068077743898","title":"Ribosome biogenesis and gene expression","description":"The cluster is dominated by translation, ribosomal subunit assembly, and DNA-templated transcription terms, indicating a core module of protein synthesis and gene-expression machinery with supporting cell-growth/metabolic processes; a few unrelated terms (lactation, vasculogenesis) likely reflect broader annotations rather than shared function.","confidence":"High","size":22,"edges":144,"triangles":451,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1754390484622939976","title":"Metabolism and stress response cluster","description":"The GO terms cluster around core metabolism\u2014carbohydrate metabolism, transsulfuration and serine/cysteine pathways, GMP nucleotide biosynthesis\u2014and glycine betaine transport, alongside a cellular response to glucose starvation. These together point to metabolic functions with an adaptive stress-response role; the lone lymphocyte proliferation term appears as an outlier rather than a defining theme. Overall, the cluster seems to reflect metabolism with a stress-adaptation angle.","confidence":"Medium","size":22,"edges":80,"triangles":137,"max_degree":20,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0031460","count":7},{"id":"GO:0019346","count":6},{"id":"GO:0005975","count":6},{"id":"GO:0006177","count":6},{"id":"GO:0046651","count":6}]},{"hash":"1981994856939409348","title":"Angiogenic Growth Factor Signaling","description":"This cluster is dominated by VEGF receptor signaling, EGF response, JUN and STAT phosphorylation, and endothelial cell chemotaxis, pointing to growth-factor\u2013driven signaling in angiogenesis. The neural terms (visual perception, excitatory postsynaptic potential) are less central and could reflect shared signal-transduction components or pleiotropy. Spindle checkpoint signaling and growth regulation terms add cell-cycle context, but the core theme remains endothelial growth signaling.","confidence":"Medium","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":22},{"id":"GO:0048010","count":22},{"id":"GO:0007258","count":22},{"id":"GO:2001028","count":22},{"id":"GO:0070849","count":22}]},{"hash":"1474170108255599248","title":"Developmental cell migration and adhesion","description":"This cluster is dominated by GO terms related to cell migration, calcium-dependent cell-cell adhesion, and regulation of GTPase activity, along with developmental contexts like cranial skeletal system development and mesenchymal proliferation in lung development, plus Wnt signaling modulation. Together these point to a mesenchymal morphogenesis program driven by adhesion and cytoskeletal signaling; a minor outlier term (proton transmembrane transport) does not alter the overall theme.","confidence":"High","size":22,"edges":216,"triangles":1280,"max_degree":21,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0016477","count":14},{"id":"GO:0008285","count":14},{"id":"GO:0043065","count":14},{"id":"GO:0015991","count":14},{"id":"GO:0090090","count":14}]},{"hash":"639917421136802797","title":"Cell Cycle and Transcriptional Regulation","description":"This cluster is dominated by nuclear processes: DNA-templated transcription, mitotic cell cycle, cell division, and chromatin modification (H3K9 methylation), pointing to coordinated regulation of gene expression and proliferation. While there are also signals related to GTPase activity, tyrosine phosphorylation, actin nucleation, and Golgi-ER trafficking, the strongest theme centers on cell-cycle progression and transcriptional control.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0043547","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0050731","count":6}]},{"hash":"331507768828613854","title":"STAT/Cytokine Signaling in Development and Neurogenesis","description":"The cluster centers on cytokine- and STAT-driven signaling (notably IL-27-mediated signaling and tyrosine phosphorylation of STAT) and is enriched for neurodevelopmental terms (neurogenesis and CNS development), with additional developmental patterning terms such as salivary gland boundary specification and vagina development, plus regulation of cell proliferation and apoptosis.","confidence":"Medium","size":22,"edges":211,"triangles":1185,"max_degree":21,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0070106","count":12},{"id":"GO:0042517","count":12},{"id":"GO:0022008","count":12},{"id":"GO:0060068","count":12},{"id":"GO:0035745","count":12}]},{"hash":"164042320173418942","title":"Phosphatase-regulated MAPK signaling","description":"This cluster is dominated by GO terms for peptidyl-tyrosine and peptidyl-threonine dephosphorylation and negative regulation of kinase activity, especially MAPK/JNK pathways, plus notes on cell-cycle and developmental signaling. The pattern suggests a set of protein phosphatases and regulators that dampen signaling and influence developmental and cell-division processes.","confidence":"High","size":22,"edges":205,"triangles":1203,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035335","count":14},{"id":"GO:0051895","count":13},{"id":"GO:0001701","count":12},{"id":"GO:0031031","count":12},{"id":"GO:0098783","count":12}]},{"hash":"1153498464633502990","title":"Heart and vascular development","description":"The top GO terms center on heart morphogenesis (cardiac right atrium morphogenesis, Notch signaling in heart field) and endothelial differentiation/delamination, pointing to cardiovascular development; other terms relate to cytoskeleton and vesicle processes involved in morphogenesis, and mechanical signaling relevant to vascular formation. Overall, the cluster is best described as cardiovascular development.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071651","count":7},{"id":"GO:0003270","count":7},{"id":"GO:0060843","count":7},{"id":"GO:0071901","count":7},{"id":"GO:0033280","count":7}]},{"hash":"398237621258613084","title":"Vertebrate eye and hindbrain morphogenesis","description":"The top GO terms cluster around eye/retina development (camera-type eye development, embryonic eye morphogenesis, retina development) and hindbrain patterning (brain segmentation, rhombomere 5 development), suggesting a developmental module coordinating vertebrate head structures like the eye and hindbrain, with transcriptional regulation terms reflecting gene expression control during this morphogenesis.","confidence":"High","size":22,"edges":200,"triangles":1012,"max_degree":21,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":12},{"id":"GO:0000122","count":10},{"id":"GO:0043010","count":9},{"id":"GO:0060441","count":9},{"id":"GO:0048048","count":9}]},{"hash":"1133386574805266387","title":"Steroid Hormone Signaling and Male Development","description":"The cluster is dominated by GO terms tied to steroid hormone receptor activity and nuclear receptor signaling, including male sex differentiation and prostate gland development, pointing to a core theme of steroid hormone signaling driving male development. Other terms present (cytokinin signaling, stress responses, ubiquitination) are less central, suggesting this label captures the primary function with some peripheral annotations.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046661","count":10},{"id":"GO:0006463","count":10},{"id":"GO:0030850","count":10},{"id":"GO:0051301","count":10},{"id":"GO:2000324","count":8}]},{"hash":"1008526358860895962","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms show strong enrichment for chromatin-related processes and transcription control (negative regulation of transcription by RNA Pol II, DNA-templated transcription, chromatin remodeling, nucleosome assembly). Some outliers pertain to telomere protection and plant hormone responses, but the overall pattern centers on regulating gene expression via chromatin state.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":11},{"id":"GO:0006351","count":6},{"id":"GO:0043044","count":5},{"id":"GO:0006334","count":5},{"id":"GO:1902262","count":5}]},{"hash":"1389257471229356738","title":"ER protein folding and redox homeostasis","description":"The cluster is dominated by GO terms for ER-associated protein folding (including chaperone-mediated refolding) and redox balance/detoxification, indicating proteins involved in ER quality control and managing oxidative stress. Additional terms about ER stress\u2013driven translation initiation and membrane targeting support a cohesive theme around ER function and protein processing, with a few outliers like DNA replication that may reflect unrelated associations. Overall, the group centers on ER protein folding and redox homeostasis.","confidence":"High","size":22,"edges":97,"triangles":168,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045454","count":16},{"id":"GO:0034975","count":14},{"id":"GO:0070389","count":9},{"id":"GO:0098869","count":9},{"id":"GO:0055114","count":9}]},{"hash":"1076141604086484276","title":"Chromatin Assembly and Transcription Regulation","description":"The top GO terms cluster around chromatin biology\u2014CENP-A containing chromatin assembly, establishment of protein localization to chromatin, and negative regulation of transcription by RNA polymerase II\u2014along with protein heterotetramerization. This points to a cohesive theme of chromatin organization and transcriptional control, possibly linked to centromere/chromatin maintenance and regulation of gene expression, with a few outliers that are less central to the cluster.","confidence":"High","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0051290","count":20},{"id":"GO:0000122","count":20},{"id":"GO:0071169","count":20},{"id":"GO:0061641","count":19},{"id":"GO:0007338","count":19}]},{"hash":"2154438063140804312","title":"LPS/O-antigen and storage polymer biosynthesis","description":"The top GO terms point strongly to synthesis of lipopolysaccharides and O-antigen (cell envelope components), along with poly-hydroxybutyrate (PHB) biosynthesis, suggesting a cohesive theme around bacterial surface polysaccharide production and storage polymer biosynthesis. While other terms like antibiotic biosynthesis and retinoid metabolism appear, they are less central to the core envelope/polyer biosynthesis function, which is why this label captures the primary shared activity.","confidence":"Medium","size":22,"edges":6,"triangles":4,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0009243","count":6},{"id":"GO:0009103","count":6},{"id":"GO:0042619","count":6}]},{"hash":"259047556584991042","title":"Fe-S Cluster Biogenesis and Mitochondrial Respiration","description":"The top GO terms emphasize iron-sulfur cluster assembly, protein maturation, and mitochondrial electron transport (NADH dehydrogenase and cytochrome c to oxygen pathways), which together point to Fe-S biogenesis feeding into mitochondrial respiration. Translation-related terms appear but do not dominate, so the core theme is Fe-S cluster biosynthesis linked to respiratory function.","confidence":"Medium","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0006123","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0006880","count":2}]},{"hash":"1463112086872806872","title":"Eye and craniofacial development","description":"The top GO terms cluster around head and sensory organ development, notably eye-related processes (lens fiber differentiation, visual perception) and craniofacial morphogenesis (midbrain-related structures, cranial skeleton morphogenesis, roof of the mouth, pituitary development). ECM disassembly supports tissue remodeling during morphogenesis, while transcription regulation is a broader background process. Together they point to a module focused on eye and head development rather than a single signaling pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":8},{"id":"GO:0030901","count":7},{"id":"GO:0021983","count":5},{"id":"GO:0007601","count":5},{"id":"GO:0070306","count":5}]},{"hash":"1026291313992887669","title":"Innate Immune Signaling and Chemokine Production","description":"Top GO terms cluster around innate immune response and inflammatory signaling, including regulation of Rho GTPase signaling and cytoskeletal dynamics that enable immune cell movement, plus chemokine and IL-8 production, LPS-mediated signaling, and JNK/NF-kB\u2013related pathways. The combination suggests a module of proteins that coordinate immune activation, chemokine-driven recruitment, and associated cytoskeletal remodeling.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0090197","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0043087","count":5},{"id":"GO:0045087","count":4}]},{"hash":"2282122204449667810","title":"Embryonic tissue differentiation","description":"The cluster is dominated by GO terms tied to development of embryonic tissues (trophoblast/placenta, cartilage, pancreatic endocrine cells) and morphogenetic processes (EMT in heart development). While a few terms relate to general cellular processes like RNA processing, the common thread is differentiation of diverse embryonic tissues, justifying a label centered on embryonic tissue differentiation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0060707","count":19},{"id":"GO:0035270","count":19},{"id":"GO:0060536","count":19},{"id":"GO:0032298","count":19},{"id":"GO:1903026","count":19}]},{"hash":"2106104932341794675","title":"Thiamine Biosynthesis and Redox/Xenobiotic Stress Response","description":"The cluster is dominated by thiamine biosynthesis (GO:0009228) with a strong association to redox homeostasis and xenobiotic response terms (e.g., response to xenobiotic stimulus, response to ethanol), suggesting a metabolic module connected to redox balance and detoxification. Some obsolete or development-related annotations appear as noise and do not define the core function.","confidence":"Medium","size":22,"edges":123,"triangles":364,"max_degree":20,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009228","count":11},{"id":"GO:0051573","count":11},{"id":"GO:0045454","count":11},{"id":"GO:0043046","count":11},{"id":"GO:0055114","count":11}]},{"hash":"62911450733624883","title":"Collagen ECM Remodeling","description":"Top GO terms such as collagen fibril organization, cellular response to mechanical stimulus, bone development, and angiogenesis point to connective tissue remodeling and extracellular matrix dynamics, spanning cartilage/bone formation, vascularization, and fibroblast regulation. These collectively suggest a cohesive function in ECM organization and tissue remodeling.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030199","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0014068","count":4},{"id":"GO:0048147","count":3},{"id":"GO:0007596","count":3}]},{"hash":"1160930520906873343","title":"Unknown","description":"The cluster shows a mix of tRNA processing, DNA repair/recombination, translation, histone demethylation, and energy metabolism terms (glycolysis, aerobic respiration, mitochondrial potential) with no single unifying function, so there isn\u2019t a robust common theme to label; thus Unknown is the safest, most representative choice.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0008033","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0010917","count":2}]},{"hash":"920298351970760004","title":"Nervous System and Inner Ear Development","description":"The cluster is dominated by GO terms related to neural and sensory organ development (inner ear development, brain development, nervous system development) and functions like positive regulation of synapse assembly, pointing to a cohesive theme of neural/sensory development. A few terms about immune responses and inflammation appear but are less representative of the main function, suggesting some annotation noise rather than a core immune role for the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048839","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0006958","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0007286","count":4}]},{"hash":"1354387728910843268","title":"SNARE-mediated Golgi and synaptic vesicle trafficking","description":"This cluster centers on vesicle transport through the Golgi network (ER-to-Golgi, intra-Golgi, retrograde Golgi transport) and SNARE complex assembly, plus exocytic delivery of neurotransmitter receptors to the postsynaptic membrane and related synaptic plasticity processes. The combination of Golgi trafficking and receptor localization to the plasma membrane suggests a cohesive module coordinating intracellular vesicle routing with synaptic receptor placement.","confidence":"High","size":22,"edges":23,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0048280","count":6},{"id":"GO:0060291","count":6},{"id":"GO:0006891","count":6}]},{"hash":"152355629132991593","title":"Xenobiotic Detoxification and Lipid Metabolism","description":"The cluster is dominated by xenobiotic-related processes (dibenzo-p-dioxin catabolic, insecticide metabolic) and environmental response (response to ozone), with supporting lipid/sterol pathways (cholesterol catabolic, oxylipin biosynthesis) and inflammation modulation, suggesting a theme around detoxification and lipid-mediated signaling. Some terms (cell cycle regulation) are less connected but do not override the overall detox/metabolism signal.","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019341","count":20},{"id":"GO:0002677","count":20},{"id":"GO:0010193","count":20},{"id":"GO:1900087","count":20},{"id":"GO:0017143","count":20}]},{"hash":"1636051043838662534","title":"Steroid and lipid biosynthesis cluster","description":"The top GO terms cluster around androgen metabolism (testosterone biosynthesis, androgen catabolic processes) and lipid/sterol pathways (sphingolipid biosynthesis, fatty acid elongation, phylloquinone catabolic process), indicating a core theme of steroid and lipid metabolism. Some terms like lung development or antibiotic response appear tangential, possibly due to broad or cross-species annotations.","confidence":"Medium","size":22,"edges":36,"triangles":2,"max_degree":15,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0016310","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0008209","count":4},{"id":"GO:0061370","count":4}]},{"hash":"523660758815401765","title":"Eye and craniofacial morphogenesis","description":"Reason: The top GO terms cluster around embryonic development of sensory and craniofacial structures\u2014camera-type eye development, embryonic eye morphogenesis, cochlea morphogenesis, neural crest cell migration, cartilage development, pituitary gland development, and forebrain proliferation\u2014indicating a cohesive theme of craniofacial/eye morphogenesis with transcriptional regulation as a supporting layer.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":10},{"id":"GO:0043010","count":8},{"id":"GO:0001755","count":8},{"id":"GO:0021983","count":8},{"id":"GO:0006366","count":7}]},{"hash":"1323351107791009740","title":"Ubiquitin-Dependent Antiviral Defense","description":"Top GO terms cluster around ubiquitin-dependent protein catabolic processes and various ubiquitination types (polyubiquitination, K63- and K6-linked), alongside innate immune and antiviral responses, including suppression of viral release by the host. This suggests a cohesive theme where ubiquitin signaling governs protein turnover and antiviral defense, with histone catabolic processes hinting at chromatin-level regulation as part of the response. Confidence in this label is high due to the clear linkage between ubiquitination pathways and antiviral/innate immune terms across the top terms.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":14},{"id":"GO:0045087","count":11},{"id":"GO:0051607","count":11},{"id":"GO:1903265","count":9},{"id":"GO:0070534","count":8}]},{"hash":"841325315473190840","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0070534","count":11},{"id":"GO:1903265","count":10},{"id":"GO:0045087","count":10},{"id":"GO:0051607","count":9}]},{"hash":"1936924815917233835","title":"Cardiac development and hypoxia-responsive transcription","description":"This cluster\u2019s terms point to cardiac-specific processes (ventricular cardiac muscle morphogenesis, regulation of muscle filament sliding speed) alongside hypoxia response and EMT, suggesting a set of proteins involved in cardiac development and the transcriptional/regulated remodeling that occurs under hypoxic or developmental conditions. The presence of DNA-templated transcription and protein turnover/tight regulation supports a broader regulatory network that governs cardiac muscle formation and adaptation, making this theme plausible, though not exclusively cardiac.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071456","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000466","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0001837","count":2}]},{"hash":"1484580226155504328","title":"Neurovascular development and signaling","description":"This cluster shows strong signals for neural connectivity and signaling (long-term synaptic potentiation, axonogenesis, cAMP response, GPCR pathway) alongside vascular/heart development (angiogenesis, heart development, endothelial survival). The overlap suggests a neurovascular development and signaling theme, with xenobiotic response and mRNA processing as supportive processes.","confidence":"Medium","size":22,"edges":18,"triangles":7,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035690","count":7},{"id":"GO:0060291","count":6},{"id":"GO:0051591","count":6},{"id":"GO:0007205","count":5},{"id":"GO:1902042","count":5}]},{"hash":"2089410804008228730","title":"Rho GTPase\u2013driven actin remodeling and migration","description":"The terms cluster around regulation and activation of Rho GTPase signaling, including lamellipodium assembly and cell migration, supported by related endosome organization and vesicle priming. This points to a cohesive theme of cytoskeletal remodeling and motility governed by Rho family signaling, with some vesicle trafficking associations strengthening the link to dynamic membrane\u2013cortex interfaces.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0043547","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0007032","count":3},{"id":"GO:0030032","count":3}]},{"hash":"1284628655892119485","title":"NF-\u03baB\u2013driven innate immune signaling","description":"This cluster centers on NF-\u03baB\u2013related signaling and immune defense: I-kappaB phosphorylation and non-canonical NF-\u03baB signaling indicate NF-\u03baB pathway involvement; responses to LPS, defenses against viruses and Gram-negative bacteria, TH1-type responses, and interferon production all flag innate/adaptive immune activation. A few terms like axonogenesis and negative regulation of kinase activity are peripheral, but the core pattern is robustly immune/NF-\u03baB\u2013driven.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0016525","count":7},{"id":"GO:0007252","count":7},{"id":"GO:0071222","count":7},{"id":"GO:0045078","count":7},{"id":"GO:0051607","count":7}]},{"hash":"1163831287933329002","title":"Neural crest migration and axon guidance","description":"The top GO terms strongly point to neural development, especially neural crest cell migration and various axon guidance/pathfinding processes (including trigeminal nerve organization, branchiomotor neuron guidance, sympathetic neuron projection guidance, and semaphorin-plexin signaling), as well as nerve fiber organization (paranodal junction assembly and axonal fasciculation). Ossification and embryonic hematopoiesis appear less related, likely noise. Overall, this cluster is best described by neural crest\u2013related development and axon guidance.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030913","count":11},{"id":"GO:0043931","count":11},{"id":"GO:0036486","count":10},{"id":"GO:1902287","count":10},{"id":"GO:0021637","count":10}]},{"hash":"1138008091981927086","title":"Ribosome biogenesis and protein turnover","description":"The cluster's terms cluster around ribosome biogenesis and cytoplasmic translation, alongside ubiquitin-dependent protein degradation via the multivesicular body pathway, suggesting a focus on protein production and quality control.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007507","count":2}]},{"hash":"772818532203616415","title":"Ribosome biogenesis and RNA maturation","description":"The cluster shows enrichment for terms tied to ribosome production (ribosome biogenesis, ribosomal large subunit biogenesis, maturation of SSU- and 5.8S rRNA) and translation-related processes (translation reinitiation), with additional RNA processing (mRNA splicing via spliceosome). This points to a coherent theme around ribosome assembly and RNA metabolism, with some broader cell-cycle references, suggesting a core of ribosome/RNA-processing proteins rather than a single signaling pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0042254","count":4}]},{"hash":"2171687815007388412","title":"Nervous system development with collagen ECM","description":"Top terms indicate neural development processes (axonogenesis, axonal fasciculation, synapse assembly) and peripheral nervous system myelination, alongside collagen biosynthesis and fibril organization. This suggests a cluster of proteins involved in nervous system morphogenesis with an extracellular matrix (collagen) framework guiding neurite outgrowth and connectivity.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:0030199","count":6},{"id":"GO:0016525","count":6},{"id":"GO:0007409","count":5},{"id":"GO:0014068","count":5}]},{"hash":"685328296199196042","title":"Neural Synaptic Plasticity and Behavior","description":"The top GO terms point to neural communication and plasticity (long-term potentiation and depression, chemical synaptic transmission) and to behavioral aspects (social and grooming behaviors). Although a couple terms reference junction components, these can relate to synaptic adhesion and junctions in neuronal tissue. Together, the proteins seem centered on synaptic signaling and plasticity with behavioral readouts, justifying this label.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060292","count":4},{"id":"GO:0007268","count":3},{"id":"GO:0035176","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0070830","count":2}]},{"hash":"1268259416029482757","title":"Developmental angiogenesis and tissue differentiation","description":"The cluster is dominated by terms tied to multicellular development, angiogenesis, and skin development, suggesting a focus on tissue formation and vascularization. IL-6 production hints at inflammatory signaling integrated with development, while RNA processing terms appear as peripheral components rather than core functions. Overall, developmental angiogenesis and tissue differentiation best describes the shared theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0045766","count":3},{"id":"GO:0043588","count":3},{"id":"GO:2000778","count":3},{"id":"GO:0002188","count":2}]},{"hash":"17314050126218832","title":"Neurodevelopmental signaling and transcriptional regulation","description":"The top GO terms cluster around neural development (neuron projection development, neural tube closure), broad multicellular development (multicellular organism development, skeletal system development), and growth/signaling pathways (TORC1 signaling, positive regulation of GTPase activity). Additionally, there are terms for gene expression control (DNA-templated transcription) and mRNA transport, suggesting coordination of transcriptional and post-transcriptional regulation during development. While there are a few outliers (innate immune response), the dominant theme points to proteins involved in neurodevelopment and associated signaling and gene regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0038202","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0070262","count":4}]},{"hash":"1875777895325171123","title":"Blood coagulation and angiogenesis","description":"The top GO terms are dominated by coagulation, fibrinolysis, and positive regulation of angiogenesis, pointing to a vascular-hemostasis and remodeling theme. Additional terms like cell migration and signaling pathways (Wnt, PKC-related) fit with wound healing and vascular dynamics, while residual terms such as mRNA processing and glucose response suggest broader regulatory roles. Overall, the vascular/hemostatic core is the strongest cohesive thread.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0042730","count":4},{"id":"GO:0007596","count":4},{"id":"GO:0016477","count":3},{"id":"GO:0007205","count":3}]},{"hash":"222859236055839183","title":"Circadian Transcription in Neural Development","description":"The cluster is dominated by DNA-templated transcription and mRNA processing terms, with multiple neurodevelopmental terms (cerebellar cortex development, hippocampus development) and a rhythmic process term, pointing to transcriptional regulation linked to brain development and circadian rhythms. While some terms are broader or legacy (obsolete annotations), the cohesive theme appears to be neural transcriptional regulation with rhythmic control.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0048511","count":3},{"id":"GO:0021695","count":3},{"id":"GO:0033138","count":3},{"id":"GO:0043433","count":3}]},{"hash":"23395558685339148","title":"Angiogenesis and Endothelial Cytoskeletal Signaling","description":"These proteins show a cohesive focus on endothelial cell function, highlighted by terms for endothelial tube lumen extension and blood vessel remodeling, and supported by small GTPase\u2013mediated signaling (Rac/Rho) and stress fiber regulation. IGF receptor signaling and apoptotic regulation further fit endothelial growth and survival during angiogenesis. While some terms touch on immune signaling, the dominant theme centers on endothelial angiogenesis and cytoskeletal dynamics, making this label representative of the cluster.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0035021","count":2},{"id":"GO:0035024","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0007264","count":2}]},{"hash":"509879597796898293","title":"Axon Guidance and Neural Crest Migration","description":"The top GO terms cluster around axon pathfinding and neural development (axonal fasciculation, axon extension/guidance, trigeminal and branchiomotor neuron axon guidance, sympathetic neuron projections, and semaphorin-plexin signaling), indicating a cohesive set of proteins involved in directing neural connections and neural crest\u2013derived cellular movements; a secondary term on angiogenesis regulation is present but likely peripheral to the main theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007413","count":10},{"id":"GO:0014068","count":9},{"id":"GO:1902287","count":8},{"id":"GO:0036486","count":8},{"id":"GO:0021637","count":8}]},{"hash":"1545934971660584406","title":"Rho GTPase Signaling and Morphogenesis","description":"The cluster centers on signaling pathways involving GTPase activity and Rho signaling (positive regulation of GTPase activity; regulation of Rho protein signal transduction) and thrombin-activated receptor signaling, alongside developmental and morphogenetic processes (cartilage morphogenesis; endocrine system development; EMT in endocardial cushion formation; placenta development), suggesting a cohesive theme of signaling-driven development and tissue morphogenesis with supporting exocytosis activity.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0070493","count":3},{"id":"GO:0060536","count":2},{"id":"GO:0003323","count":2}]},{"hash":"183980659551882864","title":"RNA processing and post-transcriptional regulation","description":"Many GO terms point to RNA processing steps (splicing, polyadenylation, mRNA modification) and post-transcriptional regulation (mRNA stability, ncRNA-mediated silencing, translation initiation factor assembly), indicating a cohesive RNA maturation/regulation theme.","confidence":"High","size":21,"edges":87,"triangles":208,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":11},{"id":"GO:0010610","count":10},{"id":"GO:0045292","count":10},{"id":"GO:0048025","count":10},{"id":"GO:0060211","count":9}]},{"hash":"1630779996874542814","title":"Developmental transcriptional regulation","description":"This cluster centers on transcription-related GO terms (DNA-templated transcription, negative regulation of transcription by RNA polymerase II) and encompasses diverse developmental themes (forebrain, retina/visual system, brain, heart, skeletal muscle, and multicellular development), pointing to transcriptional programs guiding development across tissues.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0030900","count":5},{"id":"GO:0060041","count":5},{"id":"GO:0007420","count":5}]},{"hash":"116891146330119952","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by translation (GO:0006412) and ribosome biogenesis (GO:0042254), with supporting terms for rRNA and tRNA processing and even mitochondrial translation, pointing to a cluster of proteins involved in ribosome assembly and protein synthesis. Some stress-related terms (response to toxic substance, antibiotic) appear but do not define the core function. ","confidence":"High","size":21,"edges":191,"triangles":1140,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0008033","count":4},{"id":"GO:0006364","count":4},{"id":"GO:0070126","count":4},{"id":"GO:0006407","count":4}]},{"hash":"1618982857772019877","title":"Phospho-Signaling and Cell-Cycle Regulation","description":"The top GO terms point to phosphorylation-driven signaling pathways (JUN and STAT phosphorylation, CDK regulation) and growth factor signaling (EGF, VEGF) that coordinate cell-cycle control (kinetochore localization, spindle checkpoint). The presence of neural-related terms (visual perception, excitatory postsynaptic potential) suggests these signaling networks also operate in neuronal contexts. Together, they indicate a cluster of phosphorylation-based signal transduction regulating cell-cycle progression and growth-factor responses across tissues.","confidence":"Medium","size":21,"edges":161,"triangles":623,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":21},{"id":"GO:0045736","count":21},{"id":"GO:0007601","count":20},{"id":"GO:0048010","count":20},{"id":"GO:0007258","count":20}]},{"hash":"795763227902654962","title":"RNA Pol II transcription regulation and processing","description":"The top GO terms cluster around RNA polymerase II transcription, including elongation, preinitiation complex assembly, and transcription fidelity, with additional signals for transcription regulation via deubiquitination, DNA binding regulation, and downstream RNA processing such as splicing and mRNA stability under stress. This points to a cohesive role in coordinating Pol II\u2013mediated transcription with RNA processing steps.","confidence":"High","size":21,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":5},{"id":"GO:0032968","count":4},{"id":"GO:0045899","count":3},{"id":"GO:0042981","count":3},{"id":"GO:0016579","count":3}]},{"hash":"2205380380859975378","title":"Neuronal Signaling and Membrane Remodeling","description":"The cluster features multiple neural-related terms such as glutamatergic synapses, neurotransmitter secretion, and regulation of synaptic plasticity, suggesting a central role in neuronal communication. Coupled with membrane repair, myoblast fusion, and Rho-mediated cytoskeletal signaling, the group also emphasizes membrane dynamics and structural remodeling that support synapse formation and maintenance.","confidence":"Medium","size":21,"edges":136,"triangles":400,"max_degree":20,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007520","count":9},{"id":"GO:0001778","count":8},{"id":"GO:0001324","count":8},{"id":"GO:0016525","count":8},{"id":"GO:0035249","count":8}]},{"hash":"1890295540570696523","title":"Cardiac Development and Calcium Signaling","description":"The top GO terms cluster around heart development and morphogenesis (multicellular organism development, outflow tract, left ventricular morphogenesis) plus calcium handling in cardiomyocytes (release of sequestered Ca2+ from the SR), and excitation-contraction\u2013related signaling (Purkinje-to-ventricular signaling, atrial action potential regulation), with additional notes on hypertrophy response to stress. While ossification and skin development appear, the dominant theme is cardiogenesis and Ca2+-mediated cardiac signaling, suggesting the proteins function together in cardiac development and function.","confidence":"High","size":21,"edges":31,"triangles":16,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903244","count":15},{"id":"GO:0007275","count":14},{"id":"GO:0043931","count":14},{"id":"GO:0003151","count":13},{"id":"GO:0043588","count":13}]},{"hash":"1637931597595783509","title":"Embryonic neuroendocrine and CNS development","description":"The cluster is enriched for GO terms spanning development of multiple organs (pituitary, thyroid, pancreas) and neural structures (habenula, cerebral cortex, spinal cord), plus cranial skeletal morphogenesis and transcriptional regulation during development, suggesting a broad embryonic organogenesis program with emphasis on neuroendocrine and CNS contexts.","confidence":"Medium","size":21,"edges":209,"triangles":1311,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":10},{"id":"GO:0090190","count":10},{"id":"GO:2000288","count":10},{"id":"GO:0048701","count":10},{"id":"GO:0021986","count":10}]},{"hash":"1086097218019091120","title":"Diverse tissue development","description":"Top GO terms indicate differentiation and development across multiple tissues (muscle, glial, hair follicle) with supporting signaling processes (calcium import, apoptotic regulation). The common thread is involvement in developmental programs rather than a single tissue, justifying a label centered on multi-tissue differentiation.","confidence":"Medium","size":21,"edges":20,"triangles":0,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:1990000","count":2},{"id":"GO:0060670","count":2},{"id":"GO:0048709","count":2},{"id":"GO:1902042","count":2},{"id":"GO:0001942","count":2}]},{"hash":"2136248034437085312","title":"Notch-regulated epidermal differentiation","description":"The cluster features multiple terms tied to Notch signaling (Notch receptor processing; negative regulation of Notch signaling) and keratinocyte differentiation, pointing to Notch\u2019s role in epidermal cell maturation. Other terms like inflammatory responses and oxidative stress appear but are less central to the core theme, which is Notch-driven epidermal differentiation. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0055114","count":13},{"id":"GO:0034612","count":7},{"id":"GO:0030216","count":7},{"id":"GO:0007220","count":7},{"id":"GO:0010042","count":7}]},{"hash":"170641768757383945","title":"Ubiquitin-Dependent Proteolysis and Cell Cycle Regulation","description":"This cluster centers on ubiquitin-mediated protein degradation (ubiquitin-dependent catabolic processes, polyubiquitination, SCF-dependent pathways) and includes links to cell cycle control (DNA replication initiation, G1/S regulation, G1 DNA damage checkpoint) as well as circadian rhythm regulation, suggesting a cohesive set of proteins coordinating proteostasis with cycle and clock control.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:0042752","count":9},{"id":"GO:0031146","count":8},{"id":"GO:0000209","count":7},{"id":"GO:0008285","count":7}]},{"hash":"775337624158764712","title":"Cell Migration and Cytoskeletal Dynamics","description":"This cluster is enriched for GO terms tied to cell movement and cytoskeletal organization, including cell migration, adherens junction assembly, and intermediate filament bundle assembly, along with regulators of GTPase activity and nuclear import, which supports coordinated signaling, adhesion, and cytoskeletal remodeling during movement. The inclusion of centriole cohesion regulation and endodermal fate commitment hints at cell division control and developmental context. A few terms like proton transport and vacuole fusion are less central but do not override the dominant migration/adhesion theme.","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":7},{"id":"GO:0015991","count":7},{"id":"GO:0043547","count":6},{"id":"GO:0007050","count":6},{"id":"GO:0006607","count":6}]},{"hash":"1708499563465983146","title":"Immune activation, phagocytosis, and T cell regulation","description":"The top GO terms cluster around innate and adaptive immune processes: phagocytosis and bacterial defense, monocyte extravasation, T cell costimulation and proliferation, regulation of NK T cell activity, and IL-10 production. While a couple of terms (neuron-related) may be peripheral or noisy, the dominant signal points to leukocyte-mediated defense and immune signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006910","count":8},{"id":"GO:0042102","count":8},{"id":"GO:2001181","count":7},{"id":"GO:0042742","count":7},{"id":"GO:0086072","count":7}]},{"hash":"213533866371920327","title":"Multimodal sensory perception and GPCR signaling","description":"This cluster centers on sensory modalities (visual perception, pain, temperature stimulus response) and neural signaling, including regulation of membrane potential and GPCR-mediated pathways (adenylate cyclase-inhibiting signaling, GTPase activity). The strongest and most consistent themes are multimodal sensory processing and GPCR signaling in neurons, making this label representative. Outlier terms like defense response to bacterium and an obsolete protein-chromophore linkage do not undermine the core theme. ","confidence":"High","size":21,"edges":149,"triangles":499,"max_degree":20,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002024","count":21},{"id":"GO:0042391","count":21},{"id":"GO:0071502","count":21},{"id":"GO:0019233","count":21},{"id":"GO:0018298","count":21}]},{"hash":"742116226974012889","title":"Carbohydrate Metabolism and Sugar Catabolism","description":"This cluster's signature terms center on the pentose phosphate shunt (oxidative branch) and broader carbohydrate metabolism, with several entries mapping to catabolic steps of amino sugars such as N-acetylglucosamine and N-acetylneuraminate, and the UDP-N-acetylglucosamine biosynthetic pathway. Together these suggest a group of enzymes involved in interconverting and degrading sugar substrates and producing UDP-sugars. A couple of terms like lung development or xenobiotic response appear peripheral.","confidence":"High","size":21,"edges":8,"triangles":1,"max_degree":5,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009051","count":3},{"id":"GO:0006098","count":3},{"id":"GO:0005975","count":3},{"id":"GO:0019262","count":3},{"id":"GO:0006043","count":3}]},{"hash":"1522214620948821565","title":"Neuronal signaling and axon development","description":"The top GO terms cluster around neural function: excitatory postsynaptic potential, clustering of voltage-gated potassium channels, axonogenesis, and visual perception, all pointing to neurons and synaptic connectivity. Additional terms involve Rho signaling and apoptotic regulation, which can relate to neuronal development and cytoskeletal dynamics. Some terms like heart development and mitotic cell cycle are broader/developmental and may reflect multisystem roles or annotation overlap. Overall, the dominant theme appears to be neuronal signaling and axon development.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":5},{"id":"GO:0038095","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0045163","count":5},{"id":"GO:0007601","count":4}]},{"hash":"1760154053783137640","title":"DNA repair and cellular stress response","description":"The cluster\u2019s top GO terms center on DNA maintenance (base-excision repair, DNA recombination), cell-cycle regulation (positive regulation of G1/S transition), and redox/homeostatic responses, which together point to genome integrity maintenance under stress. A few terms (xenobiotic response, insulin response, renal water transport, infection structure formation) are more peripheral and do not define the core theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0075015","count":3},{"id":"GO:0032869","count":2},{"id":"GO:0006310","count":2},{"id":"GO:1900087","count":2}]},{"hash":"947417370899062291","title":"Plant cell wall glycoprotein and mucilage biosynthesis","description":"The cluster is dominated by terms for arabinogalactan proteins, mucilage biosynthesis, and related O-glycosylation processes, all characteristic of plant cell wall glycoproteins and seed mucilage. While a few terms touch on insect or infection-structure concepts that seem out of place, the strongest signal is plant-specific glycoprotein and mucilage biosynthesis and root hair development, suggesting a cohesive theme around cell wall glycoprotein metabolism.","confidence":"High","size":21,"edges":100,"triangles":206,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":12},{"id":"GO:0030311","count":10},{"id":"GO:0080147","count":10},{"id":"GO:0010493","count":10},{"id":"GO:0048354","count":10}]},{"hash":"510579220067685288","title":"Unknown","description":"The proteins show diverse functions from potassium transport and heart conduction to vascular development, ossification, apoptosis, and sensory perception, with no clear single theme linking them. This makes a cohesive, specific label unlikely.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0043931","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0097497","count":2}]},{"hash":"2234618001898001812","title":"Mitochondrial respiration and Fe-S cluster assembly","description":"This cluster is dominated by mitochondrial functions: mitochondrial translation, electron transport components such as succinate dehydrogenase, and regulation of iron-sulfur (Fe-S) cluster biology (Fe-S cluster assembly and iron incorporation into metallo-sulfur clusters), as well as regulation of ferrochelatase activity and cytochrome c release, plus a response to hydrogen peroxide. The convergence of ETC activity, Fe-S cluster biogenesis, and mitochondrial apoptosis signaling points to a cohesive theme centered on mitochondrial energy metabolism and Fe-S cluster maintenance under oxidative stress.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0032543","count":2},{"id":"GO:0042542","count":1},{"id":"GO:0090201","count":1},{"id":"GO:0006121","count":1}]},{"hash":"1471490374119526410","title":"Mitochondrial translation and respiration complex assembly","description":"The top terms combine translation with mitochondrial energy metabolism, including mitochondrial electron transport, respirasome assembly, and aerobic respiration. This pattern points to proteins involved in mitochondrial protein synthesis that supply components of the electron transport chain and the assembly of oxidative phosphorylation complexes, as well as proton translocation. The coexistence of a translation term with mitochondria-specific respiration terms strongly supports a mitochondrion-centered cluster focused on mitochondrial translation and OXPHOS complex assembly.","confidence":"High","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0006123","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0009060","count":2},{"id":"GO:0097250","count":2}]},{"hash":"1538015407510443379","title":"Mitochondrial Translation and Energy Metabolism","description":"This cluster is enriched for mitochondrial translation and respiration processes, including mitochondrial translational termination, mitochondrial electron transport, proton transmembrane transport, and aerobic respiration, pointing to roles in mitochondrial protein synthesis and energy production. Some terms (tryptophan catabolic and cobalamin biosynthesis) are peripheral and may reflect broader metabolic annotations rather than core functions.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006569","count":2},{"id":"GO:0019878","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0009060","count":2}]},{"hash":"1286981422026310811","title":"Cardiac Mitochondrial Complex IV Assembly","description":"The strongest GO signal is mitochondrial respiratory chain complex IV assembly, with supporting heart development and oxygen transport terms, suggesting the proteins cluster around mitochondrial function in cardiac tissue. Other terms like endocytosis and platelet aggregation are present but less defining; thus the label emphasizes the core mitochondrial\u2013cardiac theme.","confidence":"High","size":21,"edges":88,"triangles":168,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0006898","count":4},{"id":"GO:0009636","count":4},{"id":"GO:0070527","count":4}]},{"hash":"407558068844506364","title":"Unknown","description":"The top GO terms are scattered across detox responses, various catabolic and biosynthetic pathways, and even plant hormone-related processes, with some terms marked obsolete. There is no coherent shared function or pathway tying all 21 proteins together, and the network has no edges, suggesting the cluster is not functionally cohesive.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":4},{"id":"GO:0009086","count":4},{"id":"GO:0097755","count":4},{"id":"GO:0019740","count":4},{"id":"GO:2000124","count":4}]},{"hash":"2157731922792455216","title":"Unknown","description":"GO terms span development, immune signaling, stress responses, RNA processing, hormone signaling, and sensory biology with no single cohesive function tying the proteins together.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001822","count":4},{"id":"GO:0070301","count":3},{"id":"GO:0046661","count":3},{"id":"GO:0071357","count":3},{"id":"GO:0043278","count":3}]},{"hash":"130461848669824754","title":"Ubiquitin-Dependent Proteolysis and Immune Regulation","description":"The top GO terms show a strong enrichment for ubiquitin-dependent protein catabolic process and innate immune response, suggesting a core theme around protein turnover linked to immune signaling. While other terms indicate tissue development and circadian aspects, these can be connected to how ubiquitination modulates signaling and timing in immune and developmental contexts, justifying a label that centers on ubiquitin-mediated degradation and immune regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0045087","count":7},{"id":"GO:0072156","count":6},{"id":"GO:0007519","count":6},{"id":"GO:0045497","count":6}]},{"hash":"2088893096778479630","title":"Unknown","description":"The terms span brain and gonadal development, bone differentiation, immune defense, multicellular growth, chromatin/centromere assembly, fertilization, and even plasmid partitioning, yielding no single cohesive function for the cluster. This heterogeneity makes a specific, reliable label infeasible.","confidence":"","size":21,"edges":63,"triangles":54,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":8},{"id":"GO:0035023","count":7},{"id":"GO:0061641","count":6},{"id":"GO:0007338","count":6},{"id":"GO:0008584","count":6}]},{"hash":"2283288463722079361","title":"Developmental signaling and tissue differentiation","description":"The top GO terms are dominated by developmental processes (brain development, skeletal system development, lens fiber cell differentiation, cardiac muscle cell differentiation, multicellular organism development) and by signaling regulators (regulation of Rho protein signal transduction, positive regulation of peptidyl-tyrosine phosphorylation). This points to a cluster of proteins involved in coordinating tissue development through signaling pathways, with one incidental immune-related term present but not central to the core theme.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0007420","count":4},{"id":"GO:0001501","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0070306","count":4}]},{"hash":"1458001683713032296","title":"Developmental differentiation with immune signaling","description":"The top GO terms cover developmental differentiation across neural (axon extension regulation, cerebellar granule cell differentiation), kidney development, bone ossification, and Th1 differentiation, plus immune/inflammatory responses (inflammatory response, complement activation). This mix suggests a cluster of proteins involved in developmental processes linked to immune signaling rather than a single pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030516","count":3},{"id":"GO:0001822","count":3},{"id":"GO:0006954","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0021707","count":3}]},{"hash":"732990779632546587","title":"Eye and Brain Morphogenesis","description":"The cluster is enriched for embryonic development terms focused on ocular and neural tissues, including embryonic eye morphogenesis, camera-type eye development, brain segmentation, rhombomere development, and interneuron differentiation, indicating a coherent theme around vertebrate eye and brain morphogenesis, with some additional organogenesis terms broadening the scope.","confidence":"Medium","size":21,"edges":150,"triangles":480,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":13},{"id":"GO:0048048","count":9},{"id":"GO:0035284","count":8},{"id":"GO:0021571","count":8},{"id":"GO:0043010","count":8}]},{"hash":"1831225751971902223","title":"Developmental transcriptional regulation","description":"The cluster is enriched for GO terms tied to transcriptional control (DNA-templated transcription, circadian regulation of gene expression, regulation of transcription factor activity) and multiple developmental processes (heart development, neuron axonogenesis, vagina development, enamel mineralization), suggesting a shared role in coordinating gene expression during development. ","confidence":"High","size":21,"edges":91,"triangles":176,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032922","count":14},{"id":"GO:0043433","count":14},{"id":"GO:0045872","count":14},{"id":"GO:0006351","count":14},{"id":"GO:0060068","count":14}]},{"hash":"1104620443718850420","title":"Immune signaling and cytoskeletal remodeling","description":"The top GO terms point to both innate and adaptive immune responses alongside actin-based cytoskeletal reorganization (lamellipodium and podosome assembly), Rho signaling, and cell adhesion/ centrosome localization, suggesting proteins involved in immune-related cell migration, adhesion, and signaling dynamics.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":6},{"id":"GO:0006915","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0002250","count":5},{"id":"GO:0070830","count":4}]},{"hash":"1108564086372376022","title":"Endosome\u2013Golgi Vesicle Trafficking","description":"The top GO terms cluster around endocytic transport (endosome to lysosome; early to late endosome) and Golgi localization, plus positive regulation of GTPase activity, suggesting Rab-regulated vesicle trafficking between endosomal compartments and the Golgi/lysosome system. Despite no observed edges, these terms point to a cohesive trafficking module rather than isolated functions. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0008333","count":4},{"id":"GO:0045022","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0035264","count":3}]},{"hash":"968164148363991744","title":"Rho/Rac GTPase Signaling and Actin Remodeling","description":"The top GO terms cluster around regulation of Rho/Rac/Ras GTPase signaling, general GTPase activity regulation, and downstream cytoskeletal processes like lamellipodium assembly and cell migration, suggesting a core theme of GTPase-mediated actin remodeling. Additional terms touch on synaptic plasticity and immune signaling, which can be downstream contexts where GTPase-driven cytoskeletal changes influence cell motility, synaptic function, and T cell signaling, reinforcing a unifying role in cytoskeletal dynamics driven by small GTPases.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0046580","count":5},{"id":"GO:0060291","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0060313","count":4}]},{"hash":"1071457698362067365","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046626","count":3},{"id":"GO:0048680","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0000086","count":3}]},{"hash":"1511729900204092701","title":"Histone methylation and chromatin silencing","description":"The top GO terms are dominated by histone modification and chromatin silencing processes (e.g., histone H3-K27, H3-K9, H3-K4 methylation, rDNA heterochromatin formation, chromatin silencing), indicating the proteins in this cluster are linked to epigenetic regulation of chromatin structure. While some annotations are marked obsolete or relate to other pathways (Notch signaling, DNA damage response), the recurring theme centers on chromatin modification and silencing.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045746","count":3},{"id":"GO:1900477","count":2},{"id":"GO:1902231","count":2},{"id":"GO:0098532","count":2},{"id":"GO:0000183","count":2}]},{"hash":"1502249839162044363","title":"Diverse Vitamin and Lipid Metabolism","description":"The GO terms point to multiple, distinct metabolic processes: biosynthesis of vitamins (biotin, menaquinone), lipid biosynthesis and catabolism (phosphatidylcholine, phosphatidylserine), and even chlorophyll breakdown, plus some broad stress-response signals. This spread suggests a collection of proteins involved in varied metabolic transformations rather than a single, cohesive pathway, so a broad label like \"Diverse Vitamin and Lipid Metabolism\" is most representative.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0009636","count":4},{"id":"GO:0032026","count":3},{"id":"GO:0006656","count":3}]},{"hash":"2193622644361409605","title":"Stress Response and Transcription Regulation","description":"Primarily links stress response and transcriptional regulation, with metabolic detoxification and growth-related terms; additional associations with cell cycle and symbiont interactions reflect a broad environmental-response program rather than a single pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009636","count":6},{"id":"GO:0006351","count":5},{"id":"GO:0000086","count":5},{"id":"GO:0007155","count":5},{"id":"GO:0046718","count":5}]},{"hash":"172877760255379721","title":"Immune activation and phagocytosis","description":"This cluster is enriched for immune-related GO terms, including phagocytosis recognition and engulfment, innate immune response, complement activation, and regulatory signaling in B and T cells, indicating a cohesive theme of immune activation and phagocytic/adaptive immune processes.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006910","count":6},{"id":"GO:0045087","count":6},{"id":"GO:0002859","count":6},{"id":"GO:0090138","count":6},{"id":"GO:0043318","count":6}]},{"hash":"2106714455025439023","title":"Nuclear transcription regulation and redox control","description":"The top GO terms cluster around negative regulation of RNA polymerase II transcription, regulation of DNA binding, and nuclear transport processes, pointing to a core function of controlling transcriptional activity in the nucleus. Redox-related terms (cell redox homeostasis, deglutathionylation) suggest redox modulation of these nuclear processes, with a few outlier terms (like prolyl hydroxylation) that may reflect broader protein modification roles. Overall, the theme centers on nuclear transcriptional regulation with redox influence.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016242","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0033158","count":2},{"id":"GO:0046826","count":2}]},{"hash":"460047676931113286","title":"Transmembrane sugar and ion transporters","description":"The top GO terms are dominated by various transmembrane transport activities for sugars and ions (arabinose, galactose, sialic acid, nitrate, potassium, phosphate, etc.), indicating a shared function as membrane transport proteins. A couple of development terms appear but are less representative and likely incidental. Overall, the transport theme is strong, justifying this label with a Medium confidence.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007458","count":2},{"id":"GO:0048536","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0015751","count":1},{"id":"GO:1900754","count":1}]},{"hash":"119436950941492584","title":"Sperm Flagellum Axoneme and Cilium Motility","description":"This cluster is dominated by GO terms related to sperm axoneme assembly, flagellated sperm motility, and cilium movement, including axoneme/cilium dynamics and microtubule-based processes like microtubule severing and tubulin post-translational modifications (polyglutamylation, polyglycylation). The presence of protein transport and GTPase regulation terms aligns with axonemal assembly and movement pathways, supporting a cohesive focus on the structure and motility of sperm flagella/cilia.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007288","count":3},{"id":"GO:0015031","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0003351","count":2},{"id":"GO:0030516","count":2}]},{"hash":"1636762384370691319","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":170,"triangles":873,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":19},{"id":"GO:0006260","count":19},{"id":"GO:0000398","count":18},{"id":"GO:0010501","count":17},{"id":"GO:0071051","count":17}]},{"hash":"471054385785638076","title":"mRNA maturation and translation initiation regulation","description":"This cluster centers on post-transcriptional control of gene expression, integrating mRNA processing (polyadenylation and tail shortening), mRNA modification and stabilization, and assembly of the eIF4F translation initiation complex, with some ncRNA-mediated silencing terms.","confidence":"High","size":20,"edges":181,"triangles":984,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":16},{"id":"GO:0006378","count":11},{"id":"GO:1901407","count":11},{"id":"GO:0060211","count":10},{"id":"GO:1905663","count":10}]},{"hash":"738957560018663270","title":"mRNA processing and translation initiation regulation","description":"This cluster centers on RNA-level control of gene expression, with frequent GO terms for mRNA stability regulation in stress, translation initiation and preinitiation complex formation, mRNA polyadenylation/modification, and ncRNA-mediated gene silencing, indicating a coherent module coordinating mRNA processing and the start of translation.","confidence":"High","size":20,"edges":19,"triangles":0,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":12},{"id":"GO:0002188","count":12},{"id":"GO:0006378","count":12},{"id":"GO:0001731","count":12},{"id":"GO:0060211","count":11}]},{"hash":"1473419850068370652","title":"Neurovascular development and angiogenic signaling","description":"The cluster is strongly enriched for angiogenesis and endothelial signaling terms (angiogenesis, VEGF receptor signaling, endothelial cell chemotaxis) and also includes neurodevelopmental terms (telencephalon development, neural tube closure, visual perception), suggesting proteins that coordinate blood vessel formation with brain/eye development. Signal transduction and cell cycle regulation terms (JUN phosphorylation, negative regulation of CDK activity) fit into developmental control pathways, supporting a cohesive neurovascular development theme.","confidence":"High","size":20,"edges":33,"triangles":54,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001525","count":15},{"id":"GO:0050830","count":12},{"id":"GO:0001843","count":12},{"id":"GO:0045736","count":12},{"id":"GO:0008286","count":12}]},{"hash":"1330708636617874760","title":"TCA Cycle and Acetyl-CoA Metabolism","description":"Most terms cluster around central energy metabolism: the TCA cycle, acetyl-CoA biosynthesis, and succinyl-CoA metabolism, pointing to mitochondrial carbohydrate and energy production as the unifying function. There are also ancillary signals for nucleotide biosynthesis and protein complex oligomerization, and a few obsolete or non-metabolic annotations, but the dominant theme remains central metabolism related to acetyl-CoA and the TCA cycle.","confidence":"High","size":20,"edges":178,"triangles":952,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006099","count":10},{"id":"GO:0006085","count":7},{"id":"GO:0006104","count":7},{"id":"GO:0055114","count":5},{"id":"GO:0006187","count":4}]},{"hash":"1060171179064367218","title":"Translation Initiation Machinery","description":"Enrichment across GO terms centers on eukaryotic translation initiation, including regulation of initiation, translation reinitiation, IRES-dependent initiation, and preinitiation complex/eIF4F assembly. A distant splicing term is present but not defining, so the dominant theme is the translation initiation machinery.","confidence":"High","size":20,"edges":34,"triangles":22,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006446","count":9},{"id":"GO:0075525","count":9},{"id":"GO:0002188","count":9},{"id":"GO:0075522","count":9},{"id":"GO:0001731","count":9}]},{"hash":"1577437919315727964","title":"Cell Cycle and RNA Metabolism","description":"The cluster\u2019s top GO terms converge on cell cycle processes (cell cycle, cell division) and DNA repair regulation, alongside RNA metabolism and translation control (mRNA decay pathways, translational elongation/fidelity, deadenylation-dependent decay). Protein homooligomerization also fits into coordinated, multi-subunit complex assembly needed for replication and division, while glial cell proliferation mirrors the proliferation theme. The apparent inclusion of viral genome replication likely reflects shared replication machinery or motifs rather than a viral-specific function, reinforcing a core theme around nucleic acid metabolism and cell-cycle\u2013linked processes. ","confidence":"Medium","size":20,"edges":15,"triangles":3,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0070651","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0010569","count":4}]},{"hash":"464991774506652268","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":118,"triangles":366,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0000480","count":4}]},{"hash":"198366896371185752","title":"Immune and Cardiovascular Signaling","description":"The proteins cluster around immune receptor signaling (T cell receptor signaling, neutrophil homeostasis, LPS response, TGF-beta response) and cardiovascular signaling (epinephrine response, regulation/relaxation of cardiac muscle contraction, cAMP/cGMP pathways). This pattern suggests a cohesive module of signal transduction linking immune activation with cardiovascular responses.","confidence":"Medium","size":20,"edges":24,"triangles":5,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050852","count":9},{"id":"GO:0071560","count":9},{"id":"GO:0019933","count":8},{"id":"GO:0071222","count":7},{"id":"GO:0043949","count":7}]},{"hash":"1622737681374154500","title":"Multisystem development and morphogenesis","description":"The top GO terms point to developmental processes across multiple tissues (cardiac septum morphogenesis, heart valve development, muscle morphogenesis, neural differentiation and synapse maturation, stomatal development, circadian regulation of gene expression). This suggests the cluster represents proteins involved in broad developmental and morphogenic pathways across systems rather than a single, specific pathway.","confidence":"Medium","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0090128","count":19},{"id":"GO:0010374","count":19},{"id":"GO:2000793","count":19},{"id":"GO:0048715","count":19},{"id":"GO:0021892","count":19}]},{"hash":"1955867930388241980","title":"Developmental processes and cellular stress responses","description":"The Top Terms include several developmental processes (forebrain development, neural tube closure, skeletal system development) and transcription/mitosis terms (DNA-templated transcription, mitotic cell cycle), plus stress-related terms (ER stress\u2013induced apoptosis, cadmium ion response, invasive growth in response to glucose limitation). This pattern suggests proteins tied to developmental regulation with accompanying cellular stress and environmental response roles, rather than a single isolated function. Therefore, a label that reflects both development and stress responses is appropriate.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048549","count":6},{"id":"GO:0001501","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0001843","count":5},{"id":"GO:0006351","count":5}]},{"hash":"531796850995180837","title":"Developmental and Immune Signaling Network","description":"The cluster centers on multiple signaling pathways (TCR, Hedgehog/SMO, ROBO, PI3K-Akt, MAPK) alongside developmental processes (kidney and nervous system development) and immune-related regulation (T cell cytotoxicity), suggesting a broad network of signaling modules coordinating development and immune responses across tissues.","confidence":"High","size":20,"edges":178,"triangles":952,"max_degree":19,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0050852","count":7},{"id":"GO:0007224","count":7},{"id":"GO:0001822","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0035385","count":7}]},{"hash":"1737226967707339750","title":"Negative Regulation of Signaling and Cell Cycle","description":"This cluster shows strong enrichment for negative regulation across several signaling pathways (MAPK/ERK, insulin receptor, T cell receptor) and for inhibition of cyclin-dependent kinase activity, in addition to tyrosine dephosphorylation and mitotic/kinetochore-related localization. The common thread is suppression of signaling to control proliferation and differentiation, with neural context hints (glial differentiation, axon regeneration) adding breadth to the regulatory theme. ","confidence":"Medium","size":20,"edges":137,"triangles":510,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035335","count":12},{"id":"GO:0070373","count":9},{"id":"GO:0045736","count":9},{"id":"GO:0034501","count":9},{"id":"GO:0000200","count":9}]},{"hash":"2230114859085784543","title":"Adaptive immune signaling and hematopoiesis","description":"The dominant GO terms center on B cell and Fc receptor signaling, adaptive immune response, and downstream ERK/MAPK activation, with additional terms for interleukin-2 production, negative regulation of TCR signaling, megakaryocyte development, and angiogenesis. Together these points suggest a cluster of proteins involved in immune receptor signaling pathways and hematopoietic development.","confidence":"High","size":20,"edges":67,"triangles":90,"max_degree":16,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0043552","count":14},{"id":"GO:0050853","count":13},{"id":"GO:0038095","count":12},{"id":"GO:0002250","count":12},{"id":"GO:1900042","count":12}]},{"hash":"1362036555685113641","title":"TGF-beta/BMP Signaling Inhibition Cluster","description":"This cluster centers on terms that negatively regulate TGF-beta and BMP signaling, including negative regulation of TGF-beta receptor signaling, negative regulation of BMP signaling, and cellular response to TGF-beta stimulus, with SMAD-related assembly regulation also appearing. The dominant theme is modulation (inhibition) of TGF-\u03b2/BMP pathways, suggesting a coherent functional group despite a few unrelated terms that may reflect annotation noise or cross-species data.","confidence":"Medium","size":20,"edges":86,"triangles":240,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":11},{"id":"GO:0030512","count":10},{"id":"GO:0010991","count":8},{"id":"GO:0080005","count":8},{"id":"GO:0000173","count":8}]},{"hash":"1913534087974886175","title":"Vesicle trafficking and autophagy","description":"This cluster is enriched for GO terms tied to intracellular transport and vesicle dynamics: cytoplasm-to-vacuole targeting (autophagy-related transport), positive regulation of the secretory pathway, and microtubule-mediated mitochondrial movement. While there are developmental and tissue-specific terms (dendrite development, heart contraction, osteoclast development, mast cell chemotaxis), the common thread appears to be vesicle trafficking and autophagic/secretory transport that underpins these processes.","confidence":"Medium","size":20,"edges":105,"triangles":272,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032258","count":20},{"id":"GO:0060079","count":20},{"id":"GO:0016358","count":20},{"id":"GO:0036035","count":20},{"id":"GO:0060047","count":20}]},{"hash":"1182049120284590190","title":"Rho/Ras GTPase signaling and cytoskeletal remodeling","description":"The top GO terms center on regulation and signaling of Rho and Ras (small GTPases), plus general small GTPase\u2013mediated signaling and lamellipodium assembly, pointing to actin cytoskeleton remodeling downstream of GTPases. Immune signaling terms (NK T cell differentiation, B cell maturation, IL-4 production) also appear, suggesting involvement in immune cell signaling. Overall, the cluster seems to reflect GTPase-driven signaling linked to cytoskeletal dynamics and immune processes.","confidence":"High","size":20,"edges":42,"triangles":10,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0046580","count":4},{"id":"GO:0060065","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0038028","count":3}]},{"hash":"199106816910118229","title":"Neuronal Signaling and Sensory Perception","description":"Dominant terms point to neuronal communication and sensation (excitatory postsynaptic potential, regulation of synaptic plasticity, sensory perception of touch). Other terms (smoothened signaling, ossification, spermatid development, mast cell chemotaxis) reflect broader developmental processes but do not outweigh the neural theme. ","confidence":"Medium","size":20,"edges":24,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":4},{"id":"GO:0043931","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0048169","count":4},{"id":"GO:0007224","count":4}]},{"hash":"1550321436046974811","title":"Ubiquitin-Dependent Regulation of Degradation and Transcription","description":"This cluster is dominated by GO terms tied to ubiquitination and deubiquitination (K48-, K11-, and K63-linked deubiquitination), along with ubiquitin-dependent protein catabolic processes and regulation of transcription. The convergence on histone and protein turnover pathways plus transcriptional regulation points to proteins that modulate ubiquitin signaling to control protein stability and gene expression, with occasional links to phenotype terms like adult feeding behavior and differentiation. Overall, the label captures the core shared function of ubiquitin-mediated regulation.","confidence":"High","size":20,"edges":113,"triangles":299,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0070537","count":5},{"id":"GO:0035871","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0008343","count":4},{"id":"GO:1903070","count":4}]},{"hash":"1930409170987239522","title":"Actin Cytoskeleton Remodeling and Cell Motility","description":"Top terms are dominated by actin-related processes (polymerization, bundle formation, crosslinking), ruffle assembly, endocytosis, and substrate-dependent cell spreading, all pointing to dynamic actin remodeling driving cell movement. Regulatory signals like positive regulation of GTPase activity further support this theme, with a few outliers (apoptosis, heterochromatin formation) likely reflecting broader annotations. Overall, the cluster centers on actin dynamics and motility.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0006897","count":3}]},{"hash":"791997708833528491","title":"Neural development and MAPK signaling with trafficking","description":"Top terms indicate strong involvement in nervous system development, dendrite/axon development, and activation of ERK/JNK cascades, along with small GTPase\u2013mediated signaling and early endosome-to-Golgi trafficking. This pattern suggests a cohesive role in neural development and signal transduction, coordinated by vesicular transport; the spermatid development term appears less central to the cluster\u2019s core theme.","confidence":"High","size":20,"edges":6,"triangles":1,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":11},{"id":"GO:0010628","count":10},{"id":"GO:0007286","count":10},{"id":"GO:0007264","count":10},{"id":"GO:0055091","count":10}]},{"hash":"523558990465030540","title":"Immune signaling and inflammatory responses","description":"This cluster shows strong enrichment for defense and inflammatory terms (defense response to bacterium, acute inflammatory response, T cell chemotaxis, response to xenobiotic stimulus) as well as signaling processes (positive regulation of GTPase activity, GPCR-linked pathways, protein phosphorylation) and vascular effects (vascular smooth muscle contraction). The visual perception term appears unrelated and may be annotational noise; overall, the cluster aligns with immune signaling and inflammatory responses.","confidence":"Medium","size":20,"edges":155,"triangles":641,"max_degree":19,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":20},{"id":"GO:0042742","count":20},{"id":"GO:0043547","count":20},{"id":"GO:0007197","count":20},{"id":"GO:1901652","count":20}]},{"hash":"2072354783921585441","title":"GPCR-Driven Immune and Inflammatory Signaling","description":"The terms point to signaling via GPCR pathways (adenylate cyclase-inhibiting GPCR signaling; regulation of GTPase activity) coupled with immune and inflammatory responses (defense against bacteria, T cell chemotaxis, acute inflammatory regulation, xenobiotic response, vascular contraction). Although one term mentions visual perception, the prevailing pattern suggests GPCR-mediated communication coordinating immunity and inflammation, with phosphorylation as a common downstream process.","confidence":"Medium","size":20,"edges":63,"triangles":54,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":20},{"id":"GO:0042742","count":20},{"id":"GO:0043547","count":20},{"id":"GO:0007197","count":20},{"id":"GO:1901652","count":20}]},{"hash":"886960220074597951","title":"Brain Visual and Dopaminergic Signaling","description":"This cluster is enriched in neural functions: visual perception/learning and dopaminergic synaptic transmission, plus cocaine-related behavioral response and ERK signaling, suggesting a brain-centered module of vision and reward pathways. Additional terms about GTPase regulation and GABAergic synaptic regulation fit general neuronal signaling within this context.","confidence":"High","size":20,"edges":51,"triangles":11,"max_degree":15,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":17},{"id":"GO:0043547","count":17},{"id":"GO:0048148","count":17},{"id":"GO:0071380","count":17},{"id":"GO:0002035","count":17}]},{"hash":"1511542398969758850","title":"Dopaminergic Visual Signaling and Plasticity","description":"This cluster is dominated by GO terms linking dopaminergic synaptic transmission, visual perception/learning, GPCR internalization, and ERK/MAPK signaling with protein phosphorylation, all pointing to signaling dynamics in retinal/dopaminergic circuits and associated plasticity. While some terms (vasoconstriction, prostaglandin response) are broader, the core theme centers on dopamine-mediated neural signaling affecting vision and plasticity.","confidence":"High","size":20,"edges":76,"triangles":64,"max_degree":12,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0070374","count":17},{"id":"GO:0007601","count":16},{"id":"GO:0043547","count":16},{"id":"GO:0006468","count":16},{"id":"GO:0048148","count":16}]},{"hash":"954561117939617525","title":"Thermoception and Nociception with Chemokine Regulation","description":"The cluster is enriched for temperature sensing (thermoception, response to cold) and pain-related detection (chemical and mechanical nociception), along with regulation of chemokine production (CXCL1/CXCL5), suggesting a core theme of sensory detection tied to inflammatory signaling. Peripheral terms like endothelial delamination and brown fat differentiation appear as secondary associations rather than defining the main function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097497","count":4},{"id":"GO:0050955","count":4},{"id":"GO:2000340","count":4},{"id":"GO:1903444","count":4},{"id":"GO:0071651","count":4}]},{"hash":"1139971845713950800","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006382","count":4},{"id":"GO:0009561","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0050992","count":2}]},{"hash":"403386068879438246","title":"Ribosome and Organellar Assembly Machinery","description":"The cluster is dominated by translation and ribosome-related terms (translation, ribosomal large subunit assembly) and includes assembly processes for mitochondrial respiratory chain complexes and photosynthesis light reactions, indicating a core function in protein synthesis machinery and organelle biogenesis. Peripheral terms such as cellular response to interleukin-4 and transport may reflect multifunctional proteins or broader annotations, but do not override the central theme.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0000027","count":3},{"id":"GO:0071353","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0032981","count":2}]},{"hash":"765807059415618347","title":"Translation machinery and calcium transport","description":"The top GO terms show a strong emphasis on translation and ribosome biogenesis, suggesting core protein synthesis machinery. The presence of multiple calcium ion transport terms (including transmembrane and ER-specific transport) indicates additional involvement in calcium signaling or homeostasis. Taken together, the cluster appears to combine ribosomal/translation components with calcium transport processes, perhaps reflecting proteins functioning in calcium-regulated translation contexts or a mixed set of ribosomal and ion-transport proteins.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0070588","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0033574","count":2},{"id":"GO:0045579","count":2}]},{"hash":"9330292546922506","title":"Genome Maintenance and Stress Response","description":"The cluster is enriched for DNA repair (base-excision repair), DNA recombination, and cell-cycle regulation (positive regulation of G1/S transition), plus stress-related terms (response to xenobiotic stimulus, redox homeostasis). Together, these point to genome integrity maintenance and cellular stress signaling; minority terms like brain development or aging are likely peripheral annotations. ","confidence":"Medium","size":20,"edges":107,"triangles":247,"max_degree":19,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:1900087","count":7},{"id":"GO:0007420","count":5},{"id":"GO:0042493","count":5},{"id":"GO:0006284","count":5},{"id":"GO:0007568","count":5}]},{"hash":"1750955368695870378","title":"Membrane Transporters and Secretory Pathway Components","description":"The top GO terms are dominated by various membrane transport activities (potassium, nitrite, vitamin, hydroxyphenylacetate, sialic acid transport) and include secretory granule organization, which together point to membrane transport and secretory pathway functions. Additional terms related to salt stress and kidney-related development align with transport and osmoregulation contexts. A few outliers (e.g., nonsense-mediated decay) may reflect broader annotations, but the shared theme is transport across membranes and secretion. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":4},{"id":"GO:0033363","count":3},{"id":"GO:0072205","count":3},{"id":"GO:0071472","count":3},{"id":"GO:0000184","count":2}]},{"hash":"975100755754768660","title":"Neural development and axon guidance","description":"The cluster is centered on neural development terms, including peripheral nervous system neuron axonogenesis, motor neuron axon guidance, lateral motor column neuron migration, and cell-matrix adhesion, suggesting a cohesive role in nervous system development and axon pathfinding; a few terms (e.g., PHB biosynthesis, sporulation) may be incidental or cross-species noise.","confidence":"High","size":20,"edges":109,"triangles":180,"max_degree":15,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0070527","count":9},{"id":"GO:0097477","count":9},{"id":"GO:0007160","count":9},{"id":"GO:0048936","count":9}]},{"hash":"378432127930524048","title":"Xenobiotic Detoxification and Lipid Metabolism","description":"This cluster is enriched for metabolism and breakdown of xenobiotics (e.g., dibenzo-p-dioxins, insecticides) and lipid/steroid pathways (cholesterol catabolism, oxylipins, aldosterone biosynthesis), with additional stress-related responses (ozone, copper ion) and some cell-cycle/inflammatory terms suggesting a broader metabolic-stress context. The dominant signal points to detoxification and lipid-related metabolism as the core theme.","confidence":"Medium","size":20,"edges":140,"triangles":508,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0019341","count":17},{"id":"GO:0002677","count":17},{"id":"GO:0010193","count":17},{"id":"GO:1900087","count":17},{"id":"GO:0017143","count":17}]},{"hash":"1514804298137071855","title":"Embryonic Development and Tissue Morphogenesis","description":"The top GO terms point to developmental processes across tissues and organs: palatal roof development, mesoderm development, left-right patterning, hair follicle morphogenesis, placental lineage differentiation (trophoblast giant cells), EMT in endocardial cushion formation, and endocrine system development. Together these suggest a cohesive theme of embryonic tissue formation and organ morphogenesis, with a minor regulatory note on vitamin D biosynthesis that does not change the main pattern. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":7},{"id":"GO:0007498","count":6},{"id":"GO:0003323","count":6},{"id":"GO:0010957","count":6},{"id":"GO:0060806","count":6}]},{"hash":"1962059900858397488","title":"Innate Immune Response and Complement Activation","description":"The top GO terms strongly center on innate immunity and host defense: innate immune response, defense against bacteria, phagocytosis, and classical complement activation. Additional terms about immune signaling (STAT phosphorylation) and cell\u2013cell interactions fit with immune cell communication, while an outlier skeletal development term is likely incidental. Overall, the cluster appears to represent proteins involved in immediate immune defense and complement-mediated responses.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":11},{"id":"GO:0000187","count":10},{"id":"GO:0007157","count":10},{"id":"GO:0045087","count":10},{"id":"GO:0042742","count":9}]},{"hash":"1854512093524340437","title":"Innate immune signaling repression and LPS tolerance","description":"These proteins cluster around the theme of dampening innate immune signaling and promoting immune tolerance, as indicated by GO terms for negative regulation of NOD2 and TLR5 signaling, negative regulation of chronic inflammatory response, and tolerance induction to LPS. The inclusion of B-1 B cell homeostasis and ubiquitin-related regulation supports broader immune homeostasis rather than a single pathway. Some terms also touch on growth factor signaling and smooth muscle dynamics, suggesting coordinated modulation of immune responses with tissue remodeling in inflammatory contexts.","confidence":"High","size":20,"edges":35,"triangles":4,"max_degree":15,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0070433","count":17},{"id":"GO:0048745","count":14},{"id":"GO:0048008","count":14},{"id":"GO:0060368","count":14},{"id":"GO:0002677","count":12}]},{"hash":"187731753750613780","title":"Neural actin cytoskeleton remodeling","description":"Most Top Terms center on actin cytoskeleton dynamics and neural development (regulation of Rho signaling, negative regulation of stress fiber assembly, actin cytoskeleton reorganization, dendrite extension, nervous system development, brain-derived neurotrophic factor response). This suggests the cluster represents proteins coordinating cytoskeletal remodeling critical for neurite outgrowth and neural development. A few terms (megakaryocyte development, subtelomeric heterochromatin formation, insulin signaling regulation) are less central but may reflect broader signaling roles or cross-talk with cytoskeletal processes in different tissues.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0051497","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0007399","count":4}]},{"hash":"1354042648620511116","title":"Unknown","description":"The top GO terms cover a broad range of processes across different tissues (neural, cardiac, glial) and cellular activities (trafficking, autophagy, signaling) with no clear, unifying function linking the proteins. Terms include visual perception, excitatory postsynaptic potential, heart development and contraction, astrocyte activation, tight junction assembly, Golgi to plasma membrane transport, microautophagy, and NF-kappaB signaling, along with GTPase activity regulation. Because there isn\u2019t a cohesive theme that ties these together, the cluster is best labeled Unknown with no confidence.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0016237","count":4},{"id":"GO:0043001","count":4},{"id":"GO:0043123","count":4},{"id":"GO:0007601","count":4}]},{"hash":"1943245572838809196","title":"Synaptic signaling and cytoskeletal regulation","description":"The top GO terms emphasize modulation of neuronal signaling components (endosome-to-postsynaptic transport, dendritic spine modification) and cytoskeletal/cell-migration processes (focal adhesion, sprouting angiogenesis, GTPase activity). Although there are also terms about BMP, osteoclasts, and apoptosis, the strongest clustering appears around regulation of synaptic signaling and structural remodeling, suggesting a theme of signaling modulation coupled to cytoskeletal dynamics.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060268","count":2},{"id":"GO:1900144","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0045671","count":2},{"id":"GO:0060313","count":2}]},{"hash":"2147484294774388697","title":"Brush border cytoskeleton and glucose absorption","description":"The top terms cluster around the intestinal epithelial brush border: actin filament bundle assembly, terminal web assembly, and regulation of microvillus length point to cytoskeletal organization of microvilli, while intestinal glucose absorption links directly to brush border function. Other terms like macroautophagy, embryonic development, and complement activation are present but less central, suggesting a core theme of brush border structure and nutrient uptake with some broader cellular roles.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0016525","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0051017","count":3},{"id":"GO:1902896","count":3}]},{"hash":"1257748505580824289","title":"Neural MAPK signaling and synaptic regulation","description":"The top GO terms cluster around neural signaling and MAPK pathways, including ERK1/ERK2 cascade and stress-activated MAPK cascade, as well as regulation of synaptic transmission (glutamatergic) and innervation, with some terms indicating glial involvement (astrocyte differentiation). These coherently point to a neural signaling module governed by MAPK signaling, justifying the proposed label. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein maturation","top_go_terms":[{"id":"GO:0048711","count":4},{"id":"GO:0010757","count":3},{"id":"GO:0051403","count":3},{"id":"GO:0034104","count":3},{"id":"GO:0035009","count":3}]},{"hash":"1590947635701711960","title":"Actin Cytoskeleton Regulation and Cell Adhesion","description":"This cluster is dominated by terms about regulation of Rho signaling, GTPase activity, stress fiber assembly, and cell spreading, pointing to actin cytoskeleton remodeling and adhesion dynamics that drive migration and development, with immune-related processes like phagocytosis reflecting cytoskeletal roles in those contexts.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035024","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0051497","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0060348","count":2}]},{"hash":"1639843801145493467","title":"Cardiac development and insulin signaling","description":"The Top Terms show a strong focus on heart development (GO:0007507) and insulin receptor signaling (GO:0008286), complemented by metabolic regulation (fatty acid beta-oxidation, glycogen biosynthesis) and membrane trafficking phenomena (clathrin-dependent endocytosis, GPCR internalization). This pattern suggests a cardiogenic program intertwined with metabolic signaling and endocytic regulation, rather than a random assortment of functions. While placental development appears among terms, the core signal centers on cardiogenesis and insulin-mediated metabolic control, supporting a cardiometabolic and endocytic theme for the cluster.","confidence":"High","size":20,"edges":4,"triangles":0,"max_degree":4,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007507","count":15},{"id":"GO:2001275","count":15},{"id":"GO:0002031","count":15},{"id":"GO:0072583","count":15},{"id":"GO:0001893","count":14}]},{"hash":"822588174795404554","title":"Embryonic organogenesis and neural development","description":"Top terms indicate broad embryonic development and tissue differentiation across neural and non-neural organs (brain, spinal cord, pancreas, thyroid, digestive tract).","confidence":"Medium","size":20,"edges":11,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":10},{"id":"GO:0002070","count":10},{"id":"GO:0030878","count":10},{"id":"GO:0021892","count":10},{"id":"GO:0007501","count":10}]},{"hash":"258919471722120463","title":"Eye and Visual System Development","description":"The cluster is enriched for terms tied to eye/visual system formation and function (camera-type eye development, visual perception, lens fiber cell differentiation, inner ear development). While some terms span broader organ morphogenesis (midbrain, pancreas, pituitary), the strongest signals point to eye-related development and sensory system formation.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0043010","count":8},{"id":"GO:0007601","count":6},{"id":"GO:0030901","count":6},{"id":"GO:0003148","count":5}]},{"hash":"1485531555272992910","title":"Neural development and synapse assembly","description":"The top GO terms are dominated by neural-related processes: positive regulation of synapse assembly, nervous system development, myelination, and cell adhesion (both homophilic and heterophilic), which together point to formation and maturation of neural connections. Some terms about bone ossification and smooth muscle proliferation appear, but they do not define the cluster; the strongest signal remains neural development and synapse organization.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051965","count":10},{"id":"GO:0007156","count":9},{"id":"GO:0043931","count":9},{"id":"GO:0007157","count":9},{"id":"GO:0007399","count":9}]},{"hash":"1002489073766966392","title":"Unknown","description":"The top GO terms span nerve branching and embryonic development, germinal center formation, spindle assembly, PKC signaling, hypoxia response, transcription regulation, chromatin remodeling, and even renin secretion. This mix shows no single cohesive function or pathway tying all proteins together, so a precise, representative label can't be confidently assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048755","count":2},{"id":"GO:0048706","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0070528","count":2},{"id":"GO:0001666","count":2}]},{"hash":"1593395705076381126","title":"Ubiquitin-Dependent NF-\u03baB Innate Immunity","description":"The cluster is dominated by GO terms for ubiquitination and ubiquitin-dependent protein catabolic processes, as well as components of the NF-\u03baB signaling axis (activation of NIK, I\u03baB phosphorylation, TNF-mediated signaling) and innate immune response. This indicates a cohesive role in ubiquitin-mediated regulation of inflammatory NF-\u03baB signaling in innate immunity, with a minor nod to vitamin D response. Confidence: High.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0016567","count":9},{"id":"GO:0042787","count":8},{"id":"GO:0045087","count":7},{"id":"GO:0090073","count":7},{"id":"GO:1903265","count":7}]},{"hash":"2283943818326634318","title":"Golgi-ER and endosome vesicle transport","description":"The top terms cluster around intracellular protein transport between the ER, Golgi, and endosomal systems, including ER-to-Golgi vesicle transport, retrograde and recycling endosome pathways, and plasma membrane-to-endosome routes, as well as vesicle fusion regulation. This points to a cohesive function in vesicle trafficking within the Golgi-ER-endosome network, with lens-specific terms possibly reflecting tissue context. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0070309","count":5},{"id":"GO:0034499","count":5},{"id":"GO:0035526","count":5},{"id":"GO:0071955","count":5},{"id":"GO:0006886","count":5}]},{"hash":"1415450808944702896","title":"Membrane signaling and cell adhesion","description":"GO terms in this cluster converge on membrane-associated signaling and adhesion processes, including bicellular tight junction assembly, integrin-mediated signaling, B cell receptor signaling, and eisosome/membrane organization. The presence of related immune and adhesion terms, alongside broader signaling and structural roles, supports a cohesive theme of membrane-mediated communication and cell-cell interactions, though the diversity of terms (e.g., neuronal plasticity and apoptotic signaling) prevents a single narrowly defined function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070830","count":5},{"id":"GO:2001046","count":4},{"id":"GO:0035208","count":3},{"id":"GO:0090038","count":3},{"id":"GO:0050861","count":3}]},{"hash":"2157258656280353931","title":"RNA processing and mRNA metabolism","description":"Top GO terms center on mRNA processing and stabilization (splicing, poly(A) tail regulation, mRNA modification) and extend to translation initiation factor complex assembly, indicating a cluster of proteins involved in RNA maturation and post-transcriptional control, especially under stress.","confidence":"Medium","size":19,"edges":5,"triangles":0,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":10},{"id":"GO:0006376","count":9},{"id":"GO:0060211","count":8},{"id":"GO:1905663","count":8},{"id":"GO:0097010","count":8}]},{"hash":"1827538600160818775","title":"Actin cytoskeleton remodeling and epithelial polarity","description":"The cluster is dominated by terms related to cytoskeletal dynamics and small GTPase signaling (positive regulation of GTPase activity, Rac signaling regulation, podosome and actin filament reorganization, cytokinesis-related processes) together with establishment of epithelial cell polarity and proliferation in epithelial contexts. This points to a cohesive theme of actin-driven control of cell shape, adhesion, and polarity in epithelial cells, with a few broader cell cycle/apoptosis references as less central contributors.","confidence":"High","size":19,"edges":69,"triangles":208,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0061000","count":5},{"id":"GO:0033601","count":4},{"id":"GO:1990386","count":4},{"id":"GO:0071803","count":4}]},{"hash":"369373081376478723","title":"Neural signaling and synaptic plasticity","description":"The dominant terms point to neuronal communication and plasticity, including excitatory postsynaptic potentials, long-term potentiation, and signaling regulation via phosphorylation and GTPases. Some terms (Schwann cell development, visual perception) are less directly related, but the core cluster centers on neural signaling and synaptic remodeling.","confidence":"Medium","size":19,"edges":79,"triangles":148,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":12},{"id":"GO:0006607","count":12},{"id":"GO:0060079","count":11},{"id":"GO:0014044","count":11},{"id":"GO:0035690","count":11}]},{"hash":"719946846505502092","title":"Unknown","description":"The GO terms present a mix of unrelated processes (cytoskeletal regulation and filopodium assembly; folate metabolism; RNA quality control including TRAMP, NMD, and mRNA decay), with several obsolete terms, offering no single unifying function for the cluster. Therefore a coherent, specific label isn\u2019t supported.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0046654","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0033274","count":2}]},{"hash":"1705303742392441656","title":"Mitochondrial transcription and redox regulation","description":"This cluster's top GO terms cluster around DNA-templated transcription and circadian gene expression, coupled with mitochondrial-related processes (axonal transport of mitochondrion, regulation of aerobic respiration, intracellular oxygen homeostasis) and redox response. Together, they suggest a shared theme of transcriptional control tied to mitochondrial metabolism and cellular redox state. Some terms (histone deacetylation, immune or synaptic terms) appear tangential but do not negate the main pattern.","confidence":"Medium","size":19,"edges":169,"triangles":936,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":19},{"id":"GO:1903715","count":19},{"id":"GO:0001922","count":18},{"id":"GO:0017006","count":18},{"id":"GO:0032922","count":18}]},{"hash":"821012564109012475","title":"TLR and NOD2 Innate Immune Signaling","description":"The GO terms cluster around innate immune sensing and cytokine regulation, including TLR4 and TLR10 signaling, NOD2\u2019s muramyl dipeptide detection, and modulation of IL-6, IL-18, chemokine production, and dendritic cell cytokines, with ubiquitination tying into signaling control.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034142","count":11},{"id":"GO:0032498","count":10},{"id":"GO:0016567","count":10},{"id":"GO:0046827","count":10},{"id":"GO:0070431","count":10}]},{"hash":"25159543529619791","title":"Mechanotransduction Signaling and Endosomal Transport in Development","description":"The terms cluster around mechanosensitive signaling (cellular response to mechanical stimulus; regulation of NF-kappaB, ERK, and JNK cascades) and vesicular trafficking (early endosome to Golgi/late endosome transport), with developmental contexts such as heart development and ossification. This suggests a cohesive theme of mechanotransduction-linked signaling integrated with endosomal trafficking in development, though the set spans multiple related processes. ","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071260","count":6},{"id":"GO:0043123","count":5},{"id":"GO:0032258","count":5},{"id":"GO:0070374","count":5},{"id":"GO:0043931","count":4}]},{"hash":"1711966638100882241","title":"Unknown","description":"The GO terms are diverse, including insulin response, TGF-beta regulation, Rho signaling, ubiquitin-dependent protein catabolism, carbohydrate phosphorylation, fructose metabolism, and renin secretion, plus dendrite morphogenesis regulation. There is no single dominant function or pathway linking all proteins, making a concise, representative label not feasible.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":4},{"id":"GO:0032911","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0043950","count":3},{"id":"GO:0050774","count":3}]},{"hash":"1906426099603739164","title":"Calcium signaling in neural development","description":"This cluster centers on GO terms related to calcium ion detection and brain development, with additional signals tied to growth factor responses (EGF), Rho signaling, and membrane repair. While a few terms are broader (miRNA processing, TNF regulation, blood pressure), the recurring themes point to Ca2+-dependent signaling pathways active during neural development and neuronal responses to growth cues, justifying a label focused on calcium signaling in neural development.","confidence":"Medium","size":19,"edges":25,"triangles":0,"max_degree":16,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0005513","count":4},{"id":"GO:0007420","count":4},{"id":"GO:1904468","count":4},{"id":"GO:0001778","count":4},{"id":"GO:1903799","count":4}]},{"hash":"374976905641750999","title":"Ubiquitin-ERAD Proteostasis under Stress","description":"This cluster centers on ubiquitin-dependent ERAD pathways and autoubiquitination, along with aggresome formation, indicating a shared role in protein quality control and proteostasis. Associated stress responses include cadmium exposure and heat acclimation, with some links to broader cellular stress signaling. While a few terms (e.g., nucleotide-excision repair or action potential regulation) are peripheral, the dominant theme is ubiquitin-mediated protein quality control and stress response.","confidence":"High","size":19,"edges":153,"triangles":712,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":13},{"id":"GO:0070911","count":13},{"id":"GO:0051865","count":12},{"id":"GO:0071276","count":8},{"id":"GO:1903071","count":8}]},{"hash":"1450471975759242720","title":"Neural development and apoptosis regulation","description":"The top GO terms point to neural development (substantia nigra development; excitatory postsynaptic potential) and processes governing cell fate and morphology (apoptotic processes, protein ubiquitination, and polarity). While some terms touch on non-neural contexts (epithelial polarity, angiogenesis-related regulation), the strongest signal is toward neuronal development and regulation of cell death, with ubiquitination as a common regulatory mechanism. ","confidence":"Medium","size":19,"edges":7,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071260","count":6},{"id":"GO:0016567","count":4},{"id":"GO:0033028","count":4},{"id":"GO:0097284","count":4},{"id":"GO:0090162","count":4}]},{"hash":"585376421179196235","title":"Developmental signaling and sensory differentiation","description":"This cluster shows a convergence on developmental processes (skeletal system development, mesodermal fate regulation, endothelial chemotaxis during development) and sensory neuron guidance (photoreceptor axon guidance, mechanoreceptor differentiation), with involvement in Rho-mediated signal transduction, suggesting roles in cytoskeletal signaling and cell movement during development. Some terms like triglyceride catabolism and response to toxic substances appear peripheral to the core theme.","confidence":"Medium","size":19,"edges":16,"triangles":0,"max_degree":6,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0019433","count":6},{"id":"GO:0035023","count":6},{"id":"GO:0042102","count":6},{"id":"GO:0009636","count":5},{"id":"GO:0055114","count":5}]},{"hash":"457671925494053045","title":"Phototransduction GPCR signaling","description":"Reasoning: The top GO terms group around visual processes (phototransduction, visual perception) and GPCR-mediated signaling cascades (adenylate cyclase and PLC pathways via dopamine/adrenergic receptors, GTPase regulation, and cAMP signaling). This points to a coherent module of GPCR-driven signal transduction in the visual system. Some outliers like heart development or defense response are broader annotations and less central to the cluster\u2019s core theme.","confidence":"High","size":19,"edges":170,"triangles":952,"max_degree":18,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043547","count":18},{"id":"GO:0010513","count":18},{"id":"GO:0007603","count":18},{"id":"GO:0071880","count":18},{"id":"GO:0060158","count":18}]},{"hash":"796383901160950398","title":"Dopaminergic Reward Signaling and Drug Response","description":"This cluster is enriched for dopaminergic synaptic transmission and behavioral responses to cocaine and morphine, plus ERK1/ERK2 cascade regulation, supporting a brain reward/learning module tied to drug responsivity; other terms such as visual perception/learning and prostaglandin signaling suggest broader neural processing and neuromodulatory context rather than a peripheral function.","confidence":"High","size":19,"edges":154,"triangles":733,"max_degree":18,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":17},{"id":"GO:0048148","count":17},{"id":"GO:0071380","count":17},{"id":"GO:0002035","count":17},{"id":"GO:0070374","count":17}]},{"hash":"2055722993572112321","title":"GPCR-cAMP Signaling and Peptide Response","description":"This cluster is dominated by GO terms tied to GPCR signaling and cAMP regulation (activation/inhibition of adenylate cyclase, GPCR pathways) and includes a peptide-response term, suggesting a core theme of GPCR-mediated signal transduction with downstream cAMP effects, despite the presence of a few metabolism-related terms.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":16},{"id":"GO:0045777","count":16},{"id":"GO:0007190","count":16},{"id":"GO:0010579","count":16},{"id":"GO:0033861","count":15}]},{"hash":"625401390576019471","title":"Cardiac and smooth muscle contraction signaling","description":"This cluster shows enrichment for terms related to muscle electrical activity and contraction, including atrial repolarization, bundle of His depolarization, calcium ion response, and smooth muscle contraction in micturition, suggesting a shared theme of cardiac and smooth muscle signaling and function; other terms (mechanosensation, skin development) are present but less central.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":7},{"id":"GO:0051592","count":7},{"id":"GO:0098914","count":7},{"id":"GO:0060083","count":6},{"id":"GO:0043588","count":6}]},{"hash":"187528031464377709","title":"Immune Activation and Apoptotic Signaling","description":"The cluster centers on immune-related processes (platelet activation, B cell proliferation, chemokine production) and signaling pathways (calcineurin-NFAT), with several terms tied to apoptotic signaling and glucocorticoid response, suggesting an overall theme of immune activation linked to apoptosis regulation. Some metabolic terms appear but do not redefine the main theme.","confidence":"Medium","size":19,"edges":5,"triangles":0,"max_degree":4,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0030168","count":4},{"id":"GO:0030730","count":4},{"id":"GO:0046325","count":4},{"id":"GO:0006919","count":4},{"id":"GO:0051384","count":4}]},{"hash":"1945020273010830166","title":"Cell Adhesion and Synapse Organization","description":"The cluster is dominated by GO terms for cell-cell adhesion (homophilic/heterophilic), general cell adhesion, and synapse-related processes (synapse assembly and organization). This pattern points to proteins involved in establishing and organizing neural connections, aligning with CNS development and synaptic formation. While there are additional terms related to broader developmental processes such as mesoderm specification and endothelial chemotaxis, the central theme is adhesion-driven neural connectivity.","confidence":"High","size":19,"edges":10,"triangles":1,"max_degree":3,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007156","count":13},{"id":"GO:0007157","count":13},{"id":"GO:0016337","count":12},{"id":"GO:0051963","count":12},{"id":"GO:0046718","count":12}]},{"hash":"1528435988736964063","title":"DNA Replication and Damage Response","description":"This cluster centers on DNA replication and repair pathways, including base-excision repair and DNA biosynthesis, with multiple stress-response signals (gamma radiation, camptothecin, UV protection), suggesting a cohesive role in maintaining genome integrity under genotoxic stress.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006284","count":4},{"id":"GO:0071897","count":4},{"id":"GO:0010332","count":3},{"id":"GO:0051106","count":2}]},{"hash":"138208230204607576","title":"Mitochondrial Redox Balance and Apoptosis","description":"The cluster is dominated by GO terms centered on redox homeostasis, mitochondrial electron transport, and detoxification of reactive oxidants, plus apoptosis-related processes involving cytochrome c and its heme linkage. While a few terms (e.g., endothelial cell migration and photosynthesis) are less directly connected, the core signal ties to mitochondrial redox regulation and intrinsic apoptotic signaling, suggesting proteins involved in managing oxidative stress and programmed cell death.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0045454","count":14},{"id":"GO:0043535","count":12},{"id":"GO:0098869","count":6},{"id":"GO:0006470","count":3},{"id":"GO:0006122","count":3}]},{"hash":"686351074266218118","title":"Polysaccharide biosynthesis and cell wall assembly","description":"This cluster centers on sugar nucleotide biosynthesis (UDP-N-acetylglucosamine, GDP-mannose), glycogen biosynthesis, and general cell wall-related processes (cell wall organization, O antigen biosynthesis), indicating a cohesive theme of polysaccharide production and cell wall construction; a gravity-detection term appears incidental and not central to the main theme.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0005978","count":4},{"id":"GO:0009228","count":3},{"id":"GO:0009298","count":3},{"id":"GO:0009243","count":3}]},{"hash":"435765916048223817","title":"DNA transcription and cell-cycle regulation under stress","description":"This cluster is enriched for DNA-templated transcription, DNA replication, and cell-cycle transitions (G1/S, cell division), plus an unfolded protein response, indicating a theme of transcriptional control intertwined with cell-cycle progression and stress signaling. The LPS and insulin signaling terms suggest broader regulatory cues, but the core appears to be transcriptional regulation linked to the cell cycle and stress responses.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0071222","count":7},{"id":"GO:0046626","count":6},{"id":"GO:0006260","count":6},{"id":"GO:2000775","count":5}]},{"hash":"2056049419159055181","title":"Ubiquitin-mediated protein degradation","description":"Based on GO terms, the cluster is dominated by ubiquitination and ubiquitin-dependent proteolysis (protein ubiquitination, ubiquitin-dependent protein catabolic process, protein polyubiquitination), suggesting a shared role in protein turnover. Other terms point to regulatory roles in transcription and apoptosis, with some developmental processes appearing, but ubiquitination-related processes appear to be the central theme. This label best captures the most represented function among the cluster\u2019s GO terms.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0033280","count":7},{"id":"GO:0098907","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0042787","count":6}]},{"hash":"353953407920016798","title":"Innate immunity and phagocytic signaling","description":"The top GO terms point to innate immune response, phagocytosis/engulfment, and cytoskeletal signaling via Rho and Rac pathways, which together suggest a unit focused on immune cell activation and engulfment. Some developmental terms appear as minor outliers, but the core signal centers on innate immunity and phagocytic dynamics. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010765","count":5},{"id":"GO:0007296","count":5},{"id":"GO:0006911","count":5},{"id":"GO:2000973","count":4},{"id":"GO:0007266","count":4}]},{"hash":"522536115099561818","title":"Neural cell adhesion molecules and synapse assembly","description":"Several top GO terms center on cell-cell adhesion with both homophilic and heterophilic binding, plus processes tied to nervous system development and axonal fasciculation, and a GO term related to synapse assembly. This pattern suggests a cluster of membrane proteins functioning as cell adhesion molecules (CAMs) that guide neural connectivity and synapse organization. Some immune-related and bone formation terms appear, which can occur because CAMs and related signaling pathways participate in immune cell interactions and osteogenesis, but the dominant signal here is neural adhesion and synaptic assembly.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":14},{"id":"GO:0046718","count":11},{"id":"GO:0051965","count":10},{"id":"GO:0032516","count":10},{"id":"GO:0043931","count":10}]},{"hash":"1616625677523614809","title":"Craniofacial morphogenesis and ECM remodeling","description":"The top GO terms point to craniofacial development (midbrain region, roof of mouth development, odontogenesis, embryonic cranial skeleton morphogenesis, endoderm) and extracellular matrix remodeling (ECM disassembly, collagen catabolic process), with some coagulation regulation (plasminogen activation). This suggests a coherent theme of tissue remodeling and morphogenesis in the head/face region, supported by transcriptional regulation as an accompanying layer.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":7},{"id":"GO:0030901","count":5},{"id":"GO:0042475","count":4},{"id":"GO:0048701","count":4},{"id":"GO:0007492","count":4}]},{"hash":"439115130827611612","title":"Innate Immune and Cardiovascular Remodeling","description":"The top GO terms point to innate immune response and heart-related processes (heart development, blood vessel remodeling), with additional hints of cytoskeletal regulation, cell adhesion, apoptosis, ER stress response, and Fc receptor signaling. This suggests a cluster of proteins involved in immune signaling that also interfaces with cardiovascular remodeling and stress responses, rather than a single narrow function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0007507","count":3},{"id":"GO:2000251","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0032355","count":2}]},{"hash":"781384961883401494","title":"Telomere Maintenance and Telomere Localization","description":"The dominant GO signals are telomere-related: negative regulation of telomere maintenance via lengthening, protein localization to the telomeric region, and regulation of telomere-associated mitotic cohesion. Although there are some outliers (mRNA processing, signaling), the strongest pattern points to nuclear telomere biology and chromosome-telomere dynamics, supporting a cohesive label centered on telomere maintenance and localization.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0006469","count":2},{"id":"GO:2000778","count":2},{"id":"GO:2000667","count":2},{"id":"GO:1901187","count":2}]},{"hash":"1959026117203263211","title":"Ubiquitin-mediated antiviral immunity","description":"Based on the top GO terms, the cluster is enriched for ubiquitination processes (ubiquitin-dependent protein catabolic process, protein ubiquitination, polyubiquitination) and innate immune defense against virus, indicating roles in tagging proteins for degradation and antiviral signaling. While a few terms (vitamin D response, cardiac development) are present, the dominant theme links ubiquitin regulation to innate antiviral defense.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0000209","count":4}]},{"hash":"1188186254598133177","title":"Unknown","description":"The cluster's terms span apoptosis, neuron development/behavior, transcription and mRNA processing, vesicle transport, cytoskeletal remodeling (lamellipodium), and even symbiont entry, with no reported interactions among proteins (Max Degree 0). This lack of a cohesive functional theme or connectivity suggests no single interpretable function for the cluster.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097284","count":4},{"id":"GO:0035641","count":3},{"id":"GO:0048666","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006397","count":3}]},{"hash":"810133875992064483","title":"ECM remodeling and skin/connective tissue development","description":"The proteins show strong signals for collagen biosynthesis and fibril organization, integrin-mediated signaling, and regulation of cell growth, with accompanying themes of tissue remodeling, skin development, and inflammatory clearance. This combination strongly points to extracellular matrix remodeling and connective tissue/skin development as the core function of the cluster.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001558","count":5},{"id":"GO:0016525","count":4},{"id":"GO:0007229","count":4},{"id":"GO:0010757","count":3},{"id":"GO:0002544","count":3}]},{"hash":"1415368453461442160","title":"RNA splicing and processing regulation","description":"Proteins in this cluster are enriched for regulation of mRNA splicing (both positive and negative via the spliceosome), mRNA export, stability, and poly(A) tail processing, plus ncRNA-mediated gene silencing and stress-related regulation. This combination points to a cohesive group involved in post-transcriptional RNA processing and control of gene expression.","confidence":"High","size":18,"edges":114,"triangles":391,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":11},{"id":"GO:0048026","count":11},{"id":"GO:0006378","count":11},{"id":"GO:0010610","count":10},{"id":"GO:0045292","count":10}]},{"hash":"1295063936833424155","title":"Unknown","description":"The terms include RNA processing (polyadenylation), cell cycle, cell growth, immune signaling (monocyte differentiation, interferon production), microtubule localization, osmotic stress response, calcium detection, and development (outflow tract morphogenesis). This mix does not converge on a single clear function or pathway, suggesting diverse roles or noisy annotations. Therefore, a specific, representative label cannot be confidently assigned.","confidence":"","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045657","count":3},{"id":"GO:0006378","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0032479","count":2}]},{"hash":"1107762733594409558","title":"Wnt/Hippo signaling and apoptosis regulation","description":"Top GO terms center on modulation of canonical Wnt and Hippo signaling, along with regulation of ERK cascades, keratinocyte differentiation, and apoptotic processes, suggesting a cluster of proteins coordinating development, proliferation control, and cell survival through signaling pathway regulation.","confidence":"High","size":18,"edges":48,"triangles":20,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":13},{"id":"GO:0030216","count":11},{"id":"GO:0060044","count":11},{"id":"GO:0006915","count":11},{"id":"GO:0035329","count":11}]},{"hash":"474373785186925922","title":"Angiogenic Growth Factor Signaling","description":"This cluster centers on VEGF and EGF-related signaling, endothelial cell chemotaxis, and growth-related phosphorylation (JUN, STAT), pointing to a cohesive theme of angiogenic signaling and endothelial cell behavior. Some terms (visual perception, excitatory postsynaptic potential) may reflect broader or pleiotropic roles, but the dominant pattern ties to growth factor\u2013driven endothelial signaling.","confidence":"Medium","size":18,"edges":142,"triangles":673,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":18},{"id":"GO:0048010","count":18},{"id":"GO:0007258","count":18},{"id":"GO:2001028","count":18},{"id":"GO:0070849","count":18}]},{"hash":"1764123845708128148","title":"Cell Cycle Control and Developmental Signaling","description":"GO terms indicate a focus on regulation of cell cycle-related processes (kinetochore localization, negative regulation of CDK activity, and cell proliferation) along with neural development (cerebellar cortex formation, Bergmann glial differentiation). Additional signaling contexts (T cell receptor and insulin signaling) and a cadmium stress response suggest broader, coordinated signaling control across mitosis, development, and metabolism. Overall, a cohesive theme around regulated signaling for division and development with peripheral immune/metabolic inputs.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":16},{"id":"GO:0045736","count":16},{"id":"GO:0021697","count":11},{"id":"GO:0050852","count":11},{"id":"GO:0060020","count":11}]},{"hash":"1868413142564457857","title":"Neural development and embryogenesis","description":"This cluster is dominated by neural development terms (forebrain development, neural tube closure, neural crest cell migration) and related embryogenic processes (single fertilization, male gonad development). Additional terms point to transcriptional regulation and protein turnover/epigenetic modulation, suggesting a set of genes involved in regulating neurodevelopment during embryogenesis. Confidence: High","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0030900","count":6},{"id":"GO:0000209","count":6},{"id":"GO:0000278","count":5},{"id":"GO:0001843","count":5}]},{"hash":"1068182045967481552","title":"Innate Immune Signaling and TNF/NF-kappaB","description":"The cluster is characterized by strong representation of innate immune response and defense against virus terms, with key connections to TNF signaling and NF-kappaB activation. Ubiquitin-dependent protein turnover (including ERAD-related processes) suggests coordinated regulation of immune signaling via the ubiquitin-proteasome system, tying degradation to signaling. A vitamin D response annotation appears as a modulatory link, but the dominant theme is innate immune signaling and inflammatory pathways.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045087","count":9},{"id":"GO:0051607","count":9},{"id":"GO:0042787","count":9},{"id":"GO:0033280","count":8},{"id":"GO:0090073","count":8}]},{"hash":"2247540862729027958","title":"Signaling, Trafficking, and Actin Dynamics","description":"The cluster shows a cohesive theme of intracellular signaling pathways (T cell receptor, Ephrin, Wnt) coupled with membrane trafficking processes (Golgi-to-endosome transport, endocytosis) and actin cytoskeleton remodeling (actin polymerization, podosome assembly, cell spreading), suggesting coordinated signaling-driven regulation of trafficking and adhesion during cell movement.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0006895","count":7},{"id":"GO:0030838","count":7},{"id":"GO:0071803","count":7},{"id":"GO:0050852","count":7}]},{"hash":"1717677987205574487","title":"Epithelial Morphogenesis and Hair/Gland Development","description":"These proteins appear linked to developmental signaling and morphogenesis in epithelial/ectodermal tissues, with emphasis on Wnt and MAPK signaling and regulation of GTPase activity. Specific terms point to hair follicle morphogenesis and proliferation, submandibular gland formation, and lung morphogenesis, suggesting a cohesive theme of organ development and differentiation rather than a single neural process.","confidence":"Medium","size":18,"edges":36,"triangles":14,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0070374","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0031069","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0090263","count":4}]},{"hash":"1939861470948447260","title":"Cell adhesion and migration signaling","description":"This cluster is dominated by GO terms related to cell adhesion, integrin signaling, and substrate-dependent migration (cellular extravasation, heterotypic cell-cell adhesion, integrin-mediated signaling, substrate-dependent cell migration). Developmental terms like skin development and endodermal differentiation suggest tissue formation context. A T cell activation term appears but the overall pattern points to adhesion and movement processes and their signaling rather than a single immune or developmental pathway. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0070208","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0002291","count":6},{"id":"GO:0035987","count":6}]},{"hash":"1808713498647426747","title":"Neural development and sensory signaling","description":"The dominant GO terms are axonogenesis, visual perception, excitatory postsynaptic potential, and Schwann cell development, which together indicate neural development and sensory neuronal signaling. While there are some broader developmental terms and an odd plant signaling entry, the neural/sensory-related roles best explain the cluster\u2019s core function.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007409","count":16},{"id":"GO:0007601","count":15},{"id":"GO:0060079","count":15},{"id":"GO:0000278","count":15},{"id":"GO:0043065","count":15}]},{"hash":"2045966652516857270","title":"Trigeminal neural development and axon guidance","description":"The top GO terms cluster around neural development and axon pathfinding, especially for the trigeminal/sensory neuron systems: trigeminal ganglion development, sensory neuron axon guidance, axonogenesis, axonal fasciculation, and trigeminal nerve organization, with semaphorin-plexin signaling supporting axon guidance. There are a few broader developmental terms (roof of mouth development, GnRH neuronal migration) that reflect shared developmental signaling contexts, but the dominant theme is neural development and axon guidance in the trigeminal/sensory domain.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061551","count":3},{"id":"GO:0060021","count":3},{"id":"GO:0060707","count":3},{"id":"GO:0097374","count":2},{"id":"GO:0036486","count":2}]},{"hash":"1167293191084175917","title":"Unknown","description":"The top GO terms span metabolism (L-threonine biosynthesis), DNA replication and cell division, chromatin assembly, protein folding/unfolding, oligomerization, vesicle trafficking, and proteostasis (aggresome assembly), indicating a mix of unrelated core cellular processes without a single cohesive function.","confidence":"","size":18,"edges":75,"triangles":186,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009088","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0051260","count":5},{"id":"GO:0046835","count":5},{"id":"GO:1903007","count":4}]},{"hash":"139919181532994202","title":"NF-kappaB signaling regulators","description":"This cluster\u2019s top GO terms center on canonical NF-kappaB signaling regulation and transcription factor activity, pointing to a core function in modulating NF-kappaB pathways. The accompanying development-related terms (multicellular development, nervous system development, ossification) and cellular processes (actin polymerization, ER-Golgi transport) suggest broader roles in development and intracellular trafficking that can intersect with NF-kappaB signaling. Overall, the proteins likely participate in regulating NF-kappaB activity, with additional developmental and cellular-transport contexts.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051092","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0043931","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0043552","count":4}]},{"hash":"79166139925222754","title":"ER-Golgi trafficking and signaling regulation","description":"Top GO terms indicate ER to Golgi vesicle transport and endosome-to-Golgi transport, along with regulation of NF-kappaB and ERK signaling and GTPase activity. This points to proteins that coordinate intracellular trafficking with modulation of signaling pathways, rather than a single enzyme or structural role. Some terms like ossification or dendritic cell differentiation are broader developmental connections, but the core theme remains trafficking-linked signaling regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0043123","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0043931","count":3}]},{"hash":"699294960752450211","title":"GPCR Signaling in Vision and Cardiac Tissues","description":"This cluster centers on G protein-coupled receptor (GPCR) signaling, with terms pointing to dopamine and adrenergic receptor pathways that activate cAMP and PLC/PI signaling, plus phototransduction and visual perception. The inclusion of heart development reinforces GPCR roles in cardiac signaling, making GPCR-mediated pathways the unifying theme across sensory (vision) and cardiac contexts.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043547","count":18},{"id":"GO:0010513","count":18},{"id":"GO:0007603","count":18},{"id":"GO:0071880","count":18},{"id":"GO:0060158","count":18}]},{"hash":"1627301882914240931","title":"Innate and Adaptive Immune Response","description":"This cluster shows strong enrichment for complement activation, phagocytosis, and innate immune response, along with B cell activation/signaling, indicating involvement in both innate defense and adaptive humoral responses, with notes of regulatory effects on cytotoxic lymphocytes and cell\u2013cell adhesion in immune contexts.","confidence":"High","size":18,"edges":110,"triangles":313,"max_degree":16,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":14},{"id":"GO:0006910","count":13},{"id":"GO:0045087","count":13},{"id":"GO:0050871","count":11},{"id":"GO:0006911","count":11}]},{"hash":"634729450676708659","title":"Potassium Ion Homeostasis and Nervous System Development","description":"The cluster centers on potassium ion transport and homeostasis (intracellular/extracellular, transmembrane, and cell volume regulation) and includes neural context terms like nervous system development and visual perception, plus a mechanosensitive feel from the muscle stretch response. This suggests proteins that coordinate potassium balance with neural/sensory functions and related transcriptional regulatory roles.","confidence":"Medium","size":18,"edges":101,"triangles":269,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035994","count":9},{"id":"GO:0006813","count":9},{"id":"GO:0006884","count":7},{"id":"GO:0030007","count":7},{"id":"GO:0071805","count":7}]},{"hash":"1609862835156786528","title":"GPCR-cAMP-ERK Signaling in Inflammation and Vascular Response","description":"The cluster shows strong enrichment for GPCR signaling pathways that activate adenylate cyclase and cAMP, leading to ERK1/2 cascades, with related terms such as prostaglandin response and blood pressure regulation, plus Rho signaling and dopamine receptor pathways. This points to a coherent set of proteins involved in GPCR-driven signaling that modulates vascular tone, cell proliferation, and inflammatory responses; the electron transport chain term may be incidental. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":13},{"id":"GO:0045777","count":13},{"id":"GO:0010579","count":13},{"id":"GO:0035025","count":12},{"id":"GO:0042742","count":9}]},{"hash":"1331114108806932992","title":"GPCR signaling and Rho GTPase regulation","description":"The cluster\u2019s top GO terms cluster around G protein-coupled receptor signaling and downstream GTPase/Rho pathways, including activation/inhibition of adenylate cyclase and positive regulation of Rho GTPase activity, indicating a coherent GPCR-mediated signal transduction theme. Some terms like electron transport chain or visual perception may be incidental annotations, but the dominant signal is GPCR-driven signaling with Rho GTPase regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045777","count":15},{"id":"GO:0022900","count":15},{"id":"GO:0010579","count":15},{"id":"GO:0007190","count":14},{"id":"GO:0035025","count":14}]},{"hash":"531971080645962626","title":"Transmembrane Transport of Nutrients and Xenobiotics","description":"The top GO terms are all transmembrane transport activities for diverse substrates (nitrite, nitrate, vitamins, sugars, sialic acid, phosphate, xenobiotics), indicating a shared membrane transport function. This cluster likely groups proteins involved in importing/exporting a variety of nutrients and xenobiotics across membranes, rather than a single substrate. The coherence across multiple related transport processes supports a cohesive label centered on membrane transport.","confidence":"High","size":18,"edges":25,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":6},{"id":"GO:0035461","count":6},{"id":"GO:1900754","count":6},{"id":"GO:0015739","count":6},{"id":"GO:0035435","count":6}]},{"hash":"2095339715338692120","title":"Unknown","description":"This set shows a broad mix of functions: translation is the most represented term, but there are neural development, osteoblast differentiation, signaling regulation, DNA repair, deubiquitination, and stress response terms. The lack of a single unifying process makes a cohesive label unlikely.","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0007605","count":3},{"id":"GO:0001649","count":2},{"id":"GO:0035023","count":2},{"id":"GO:1904693","count":2}]},{"hash":"2272758379627377690","title":"Ribosome biogenesis and translational fidelity","description":"The most frequent GO terms center on protein synthesis and ribosome assembly, including translation, ribosome biogenesis, and translational fidelity regulation. These signals suggest a cluster dominated by components of the protein synthesis machinery and its quality control. A few terms about cofactor biosynthesis (menaquinone, ubiquinone) and antibiotic response appear as secondary associations, but do not override the primary translation-focused theme.","confidence":"High","size":18,"edges":152,"triangles":800,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0009249","count":2}]},{"hash":"2002026748810105718","title":"Neurotransmitter Transport and Synaptic Signaling","description":"The top GO terms cluster around transport and uptake of neurotransmitters (taurine, serotonin, dopamine, glycine) and glycinergic synaptic transmission, plus dopamine catabolism, indicating a functional theme of synaptic signaling and neurotransmitter handling. A few development-related terms appear but are less representative.","confidence":"High","size":18,"edges":17,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0015734","count":4},{"id":"GO:0051610","count":3},{"id":"GO:0051583","count":3},{"id":"GO:0061537","count":3},{"id":"GO:0042420","count":3}]},{"hash":"2235047564510742579","title":"Ribosome biogenesis and translation","description":"The cluster centers on ribosome assembly and cytoplasmic translation (ribosome biogenesis, tRNA modification) with supporting growth processes (cell division, septum assembly) and energy production (ATP-linked respiration), indicating a cohesive translation machinery module.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042773","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0006400","count":2}]},{"hash":"1399898967969602565","title":"Mitotic control and DNA repair machinery","description":"The top GO terms point strongly to cell-cycle regulation and genome maintenance: G2/M transition, exit from mitosis, and chromosome segregation indicate mitotic control; SCF-dependent ubiquitin-proteasomal degradation and protein neddylation reflect regulated protein turnover during division; global genome nucleotide-excision repair highlights DNA repair; while viral process and interferon-beta response suggest related signaling, the core signal is mitosis progression and genome integrity maintenance. ","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0031146","count":18},{"id":"GO:0070911","count":18},{"id":"GO:0007059","count":18},{"id":"GO:0000086","count":18},{"id":"GO:0010458","count":18}]},{"hash":"311785561456191085","title":"Chromatin remodeling and transcription regulation","description":"This cluster is dominated by GO terms tied to chromatin dynamics: heterochromatin formation, transcription initiation-coupled chromatin remodeling, and DNA replication\u2013dependent chromatin assembly, plus negative regulation of transcription by RNA Pol II. Developmental terms like brain and gonad formation likely reflect context-specific expression, but the shared function appears to be chromatin-based control of transcription and chromosome structure.","confidence":"High","size":18,"edges":117,"triangles":442,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0051290","count":12},{"id":"GO:0000183","count":12},{"id":"GO:0045815","count":12},{"id":"GO:0006335","count":12},{"id":"GO:0000122","count":11}]},{"hash":"2042422889425678853","title":"Protein and polyamine acetylation","description":"This cluster is dominated by GO terms for various acetylation events\u2014peptidyl-lysine N6-acetylation, N-terminal propionylation, and acetylation of polyamines (putrescine, spermidine, spermine)\u2014along with related metabolic steps (melatonin biosynthesis, N-acetylglucosamine metabolism) and a chromatin-associated term. The shared theme is acetyltransferase activity and acetylation-based regulation, suggesting a cohesive module around acetylation processes and their metabolic connections. ","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":17},{"id":"GO:0018003","count":16},{"id":"GO:0009447","count":16},{"id":"GO:0032919","count":16},{"id":"GO:0045150","count":16}]},{"hash":"539133641579899978","title":"Neural development: adhesion and BMP signaling","description":"The cluster is dominated by GO terms tied to cell\u2013cell adhesion (both heterophilic and homophilic), positive regulation of synapse assembly, nervous system development, and BMP signaling. This points to proteins involved in neuronal adhesion, migration, and synapse formation during CNS development, with ossification and broader multicellular development appearing as broader morphogenetic roles rather than core themes.","confidence":"High","size":18,"edges":28,"triangles":2,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007157","count":10},{"id":"GO:0051965","count":10},{"id":"GO:0006958","count":9},{"id":"GO:0007156","count":9},{"id":"GO:0007399","count":9}]},{"hash":"842317742224930652","title":"Angiogenesis-Linked Developmental Transcription","description":"This cluster shows prominent GO terms for angiogenesis and multicellular organism development, along with DNA-templated transcription and its regulation, suggesting proteins involved in developmental signaling and gene expression control that supports vascular development. Some terms (mitochondrial assembly, ubiquitin-dependent protein catabolic process) are less directly connected, but the core enrichment centers on developmental angiogenesis and transcriptional regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0045766","count":2},{"id":"GO:0001525","count":2}]},{"hash":"866805433987084845","title":"AKT and ERK Signaling in Stress Responses","description":"These proteins show enrichment for PI3K/AKT and MAPK/ERK pathway terms (AKT activation and ERK cascade), indicating a core signaling module. The presence of GO terms for cellular responses to xenobiotics, cadmium, and nitric oxide, along with regulation of proliferation, axon extension, and bone mineralization, suggests the cluster centers on signaling pathways that mediate environmental and developmental stress responses affecting cell growth and neural development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043491","count":2},{"id":"GO:0032148","count":2},{"id":"GO:0070371","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0030517","count":2}]},{"hash":"106776522027114922","title":"Adaptive Immune Activation and Cytotoxic Signaling","description":"This cluster is dominated by GO terms related to adaptive immunity and cytotoxic function, including positive regulation of dendritic cell differentiation, ERK signaling in T cells, granzyme B production, CD8+ T cell proliferation, B cell receptor signaling, and general defense against bacteria. The combination points to proteins involved in T/B cell activation, antigen presentation, and cytotoxic responses, making this label representative.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001200","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0071663","count":3},{"id":"GO:2000566","count":3},{"id":"GO:0045663","count":3}]},{"hash":"2279884996265733096","title":"Synaptic vesicle trafficking and neurotransmitter release","description":"The top GO terms cluster around synaptic vesicle maturation, presynaptic dense core vesicle exocytosis, and neurotransmitter secretion, indicating a group of proteins involved in vesicle cycling and neuronal signaling. Additional terms like phosphatidylinositol-mediated signaling and endosome-to-lysosome transport support a vesicle trafficking theme, even though a few unrelated or obsolete terms may reflect annotation noise. Overall, the core function points to synaptic vesicle handling and neurotransmission.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0016188","count":4},{"id":"GO:0099525","count":4},{"id":"GO:0007269","count":4},{"id":"GO:0048015","count":4},{"id":"GO:0010796","count":4}]},{"hash":"889216215237257568","title":"Embryogenesis and Axis Formation","description":"The top GO terms point to vertebrate embryonic development and patterning, including somite axis specification, notochord differentiation, bone and lung development, and blood vessel maturation, along with regulation of key signaling pathways (BMP and activin). This convergence suggests a coordinated embryogenesis/organogenesis program rather than a single pathway, justifying a label focused on embryogenesis and axis formation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":4},{"id":"GO:0051497","count":4},{"id":"GO:0030514","count":3},{"id":"GO:0060034","count":3},{"id":"GO:0001955","count":3}]},{"hash":"2218417592568509901","title":"GTPase-regulated cytoskeletal remodeling","description":"The top GO terms converge on cytoskeletal dynamics and cell division: regulation of GTPase activity, podosome assembly, cleavage furrow formation, and cell morphogenesis. While a few terms relate to sporulation and organism development that are less connected, the dominant pattern points to actin-based remodeling and cytokinesis. Therefore this cluster best represents cytoskeletal remodeling driven by small GTPases.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0032258","count":3},{"id":"GO:0071800","count":3},{"id":"GO:0036089","count":3},{"id":"GO:1904888","count":3}]},{"hash":"1860656339353145534","title":"Ubiquitin-Dependent Proteolysis","description":"This cluster is enriched for ubiquitin-dependent protein catabolic processes, including autoubiquitination and K63-linked ubiquitination, pointing to a cohesive module of ubiquitin signaling and proteolysis; related terms about JNK regulation and ERAD further support a degradation- and regulation-centered function, despite some obsolete annotations and the absence of edges in this network.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051865","count":9},{"id":"GO:1903762","count":7},{"id":"GO:1901253","count":7},{"id":"GO:0046328","count":7}]},{"hash":"2208600054441458438","title":"GABAergic Neuronal Signaling","description":"This cluster is dominated by GO terms tied to gamma-aminobutyric acid signaling, neural transmission, and synaptic activity (e.g., GABA signaling, excitatory postsynaptic potential, and nerve impulse regulation), with supporting terms on ion transport and optic nerve development, suggesting a coherent theme of GABAergic neuronal communication and related neural functions.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007214","count":18},{"id":"GO:0060079","count":18},{"id":"GO:0001661","count":18},{"id":"GO:0007626","count":18},{"id":"GO:0035725","count":18}]},{"hash":"999200377092561325","title":"Lens development in camera-type eye","description":"This cluster is dominated by GO terms for lens and camera-type eye development (lens fiber cell differentiation, morphogenesis, and lens development in the eye), indicating proteins involved in lens formation and eye morphogenesis; other terms are less representative but provide context of transcriptional activity.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0043010","count":4},{"id":"GO:0070309","count":4},{"id":"GO:0002088","count":4},{"id":"GO:0070306","count":4}]},{"hash":"2060539149152975883","title":"Embryonic development and morphogenesis","description":"This cluster\u2019s top GO terms cluster around developmental processes\u2014cartilage morphogenesis, left-right pattern formation, placental/endocrine system development, and EMT-related heart cushion formation\u2014indicating a cohesive theme of embryogenesis and tissue/organ morphogenesis. A few terms about splicing and transcription regulation appear ancillary, but the prevalent signal is developmental patterning and morphogenesis.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060536","count":9},{"id":"GO:0003323","count":9},{"id":"GO:0060806","count":9},{"id":"GO:0060972","count":9},{"id":"GO:0060707","count":9}]},{"hash":"248244646295131674","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"This cluster is dominated by GO terms related to actin cytoskeleton organization, lamellipodium assembly, and regulation of Rho/Rac signaling, plus integrin signaling and cell migration, all pointing to cytoskeletal dynamics driving motility. Some terms like endothelial barrier establishment and spinal cord development are less central but can relate to tissue remodeling contexts; overall, the core theme is actin-driven movement and cytoskeletal regulation.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0030032","count":4},{"id":"GO:0030036","count":4},{"id":"GO:0090557","count":3},{"id":"GO:0007018","count":3}]},{"hash":"1844649999626613679","title":"Rho signaling and actin cytoskeleton remodeling","description":"The top GO terms cluster around Rho protein signal transduction, actin cytoskeleton organization, and lamellipodium assembly, all pointing to dynamic actin remodeling and cell motility driven by Rho GTPases, with supporting signals in synaptic plasticity and vesicle localization. This suggests a cohesive function in cytoskeletal dynamics rather than unrelated processes.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0051262","count":3},{"id":"GO:0007205","count":3},{"id":"GO:2000009","count":3},{"id":"GO:2001275","count":3}]},{"hash":"694328442401286640","title":"Developmental signaling and transcription regulation","description":"GO terms center on developmental processes (skin, skeletal system, male gonad development) and transcription/mRNA transport, with supporting signaling pathways (intracellular signal transduction, TORC1 signaling, GTPase regulation). This suggests the proteins cooperate to coordinate development via signaling and transcription control.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043588","count":5},{"id":"GO:0035556","count":4},{"id":"GO:0008584","count":4},{"id":"GO:0038202","count":4},{"id":"GO:0061408","count":4}]},{"hash":"1098391035328958931","title":"Unknown","description":"TheTop GO terms are highly diverse, including thermosensory behavior, tRNA processing, angiogenesis, transepithelial ammonium transport, amino acid transport, dendritic spine development, cell volume and chloride ion homeostasis, and nitric oxide production in inflammation. This lack of a single, coherent biological theme or shared pathway across the cluster suggests no clear unifying function, so a broad Unknown label is appropriate.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0040040","count":4},{"id":"GO:0008033","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0070634","count":3},{"id":"GO:0097640","count":3}]},{"hash":"2253040679447685429","title":"Sphingolipid Signaling and Lipid Metabolism","description":"The top terms cluster around sphingolipid metabolism (sphingosine and sphinganine-1-phosphate) and broad lipid processes (phosphatidylglycerol biosynthesis, phospholipid dephosphorylation) with regulatory sphingolipid signaling, indicating a lipid-centric functional theme for the group. Developmental terms appear less central, so the lipid signaling/metabolism focus best explains the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0044330","count":2},{"id":"GO:0006668","count":2},{"id":"GO:0006670","count":2},{"id":"GO:0015760","count":2}]},{"hash":"1249830263802391553","title":"Embryonic Morphogenesis and Skeletal Development","description":"The top GO terms cluster around embryogenesis and skeletal formation, including neural tube closure, embryonic digit and cranial skeleton morphogenesis, and bone development, indicating a developmental program focused on embryonic tissue patterning rather than metabolic processes. A few terms about transcription regulation and intracellular trafficking appear but are likely supportive to this developmental role.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0042733","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1608181854924226208","title":"RNA processing and ribosome biogenesis","description":"The cluster is dominated by RNA maturation activities (mRNA splicing, exon ligation, spliceosomal disassembly) and ribosome biogenesis pathways (cytosolic large subunit biogenesis, maturation of 5.8S and SSU rRNA, mitochondrial large subunit assembly), suggesting a coherent theme of RNA processing and ribosome assembly. A couple of outliers, including DNA replication and MDA-5 signaling, are present but do not outweigh the core RNA-processing/ ribosome-related signals.","confidence":"High","size":17,"edges":70,"triangles":133,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0042273","count":7},{"id":"GO:1902775","count":7},{"id":"GO:0039530","count":7},{"id":"GO:0000378","count":7}]},{"hash":"1978405734163140140","title":"Translation machinery and regulation","description":"This cluster is dominated by GO terms tied to protein synthesis\u2014initiation, elongation, termination, translation itself, and selenocysteine incorporation\u2014and by mRNA turnover linked to translation (deadenylation-dependent decay) plus positive regulation of cytoplasmic translation, indicating a cohesive translation-focused module. Some terms like glial proliferation and antibiotic response may reflect broader cellular contexts or annotation noise.","confidence":"High","size":17,"edges":132,"triangles":621,"max_degree":16,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0046677","count":5},{"id":"GO:0006415","count":5},{"id":"GO:0001514","count":4},{"id":"GO:0000288","count":4}]},{"hash":"405774338887050688","title":"RNA processing and post-transcriptional regulation","description":"This cluster centers on RNA-level control of gene expression: ncRNA-mediated silencing, regulation of splicing, mRNA stability and modification, and components involved in translation initiation (eIF4F assembly). Together these terms point to a cohesive post-transcriptional regulation module, with some development-related context (blastocyst formation) likely reflecting broader roles of RNA processing in development.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:1901407","count":7},{"id":"GO:0001825","count":7},{"id":"GO:0060211","count":6}]},{"hash":"1366222855895159388","title":"Cell Proliferation and Growth Signaling","description":"This cluster is enriched for mitotic cell cycle, multicellular growth, and cell population proliferation, pointing to core processes of cell division and growth regulation. Additional terms involving GTPase and serine/threonine kinase activity suggest signaling pathways that modulate proliferation, with hypoxia response reflecting stress-related regulation and skin development indicating tissue context. Overall, the dominant theme is proliferation and growth signaling linked to cell-cycle control.","confidence":"Medium","size":17,"edges":4,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0043588","count":8},{"id":"GO:0043547","count":7},{"id":"GO:0071902","count":7}]},{"hash":"1632535782187940731","title":"Proteostasis: Ubiquitin/SUMO Modification and ERAD","description":"This cluster centers on protein quality control and turnover, with emphasis on ubiquitin and SUMO modifications, deubiquitination, ER-associated degradation, and aggresome formation, plus translation and stress response to toxins, all pointing to proteostasis.","confidence":"High","size":17,"edges":126,"triangles":551,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":8},{"id":"GO:1904378","count":6},{"id":"GO:0030433","count":5},{"id":"GO:0010216","count":5},{"id":"GO:0016579","count":5}]},{"hash":"424618087572604499","title":"Unknown","description":"Top GO terms span diverse and largely unrelated themes (muscle and muscle fiber development; kidney morphogenesis; circadian rhythm; plant phototropism; immune signaling; ubiquitin-mediated proteolysis; cell cycle regulation), with no clear single functional core linking the proteins. This makes it hard to assign a specific, representative label for the cluster beyond Unknown.","confidence":"","size":17,"edges":18,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0072156","count":4},{"id":"GO:0007519","count":4},{"id":"GO:0045497","count":4},{"id":"GO:0032764","count":4},{"id":"GO:0042748","count":4}]},{"hash":"1799856010567589349","title":"Mitotic spindle and cell division machinery","description":"The top GO terms cluster around mitosis and spindle dynamics\u2014mitotic cell cycle, cell division, mitotic spindle assembly, and microtubule-based movement\u2014plus regulation of GTPase activity. Additional terms touch on transcription, growth, and developmental processes, which may reflect broader regulatory context. Overall, the set seems to represent components of the mitotic apparatus and its regulation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0051568","count":3}]},{"hash":"1378808545033328840","title":"MAPK-driven neuronal development and synaptic signaling","description":"The cluster is dominated by GO terms tied to MAPK pathway regulation (ERK/JNK), dendrite morphogenesis, axonogenesis regulation, learning, and excitatory synaptic transmission, indicating a cohesive role in activity-dependent neuronal development and synaptic plasticity. The inclusion of a T cell receptor signaling term likely reflects shared signaling modules rather than a primary immune function, reinforcing the neuronal emphasis on MAPK-regulated signaling and plasticity.","confidence":"High","size":17,"edges":127,"triangles":568,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050771","count":17},{"id":"GO:0060079","count":16},{"id":"GO:0090051","count":16},{"id":"GO:0070374","count":16},{"id":"GO:0000186","count":16}]},{"hash":"1021489281062315423","title":"RNA Processing and Transcription Regulation","description":"Based on the balance of GO terms, the proteins cluster around RNA processing (mRNA splicing via spliceosome, snoRNP assembly, snoRNA localization) and transcription control (chromatin remodeling, regulation of DNA-templated transcription), with ubiquitination potentially modulating these processes. Some terms related to sensory development and calcium transport appear incidental rather than defining the cluster. Overall, the dominant theme reflects RNA maturation and gene expression regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006338","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0031063","count":1}]},{"hash":"2041549853746934560","title":"Vesicle trafficking and secretory pathway","description":"This cluster is driven by GO terms tied to intracellular transport and membrane trafficking, including cytoplasm-to-vacuole targeting (Cvt pathway), mitochondrion transport along microtubules, and positive regulation of the constitutive secretory pathway, all pointing to vesicle movement and docking processes. The additional terms related to dendrite development, excitatory postsynaptic potential, heart contraction, and mast cell chemotaxis likely reflect tissue-specific roles of transport machinery rather than a different overarching function. Overall, the shared theme is vesicle trafficking and cytoskeleton-mediated transport.","confidence":"Medium","size":17,"edges":90,"triangles":257,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032258","count":17},{"id":"GO:0060079","count":17},{"id":"GO:0016358","count":17},{"id":"GO:0036035","count":17},{"id":"GO:0060047","count":17}]},{"hash":"1161171020455312003","title":"Centromeric chromatin assembly and transcription regulation","description":"The cluster is dominated by CENP-A containing chromatin assembly and chromosome condensation-related terms, plus negative regulation of transcription by RNA polymerase II, suggesting a cohesive theme of chromatin organization together with transcription control; the presence of a few developmental terms appears as noise rather than core function.","confidence":"High","size":17,"edges":111,"triangles":388,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0051290","count":14},{"id":"GO:0000122","count":14},{"id":"GO:0061641","count":12},{"id":"GO:0007338","count":12},{"id":"GO:2000973","count":12}]},{"hash":"2183544989259616441","title":"Developmental angiogenesis regulation","description":"The top GO terms mix broad multicellular development with explicit regulation of angiogenesis (positive VEGF signaling and negative angiogenesis), suggesting these proteins collectively modulate tissue growth and vascular signaling during development.","confidence":"High","size":17,"edges":5,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:1900748","count":6},{"id":"GO:0032331","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0034394","count":5}]},{"hash":"1692479296812989273","title":"Nuclear chromatin remodeling and actin dynamics","description":"The top terms cluster around nuclear processes (chromatin remodeling, homologous recombination repair, DNA-templated transcription, nuclear pore localization) and cytoskeletal regulation (Arp2/3-mediated actin nucleation, barbed-end capping), with additional development and signaling cues (TGF-beta response, TORC1 signaling, gonad and neuron development). This suggests a cohesive theme of coordinating genome regulation with cytoskeletal signaling during growth and development.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0000724","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0031081","count":2},{"id":"GO:0071560","count":2}]},{"hash":"208174264698494084","title":"Multi-tissue Development and Differentiation","description":"The cluster shows GO terms spanning neural development (cerebral cortex interneuron differentiation, spinal cord neuron differentiation, rhombomere development) as well as development of other organs (pancreas, thyroid, digestive tract) and epithelial maturation, suggesting a broad theme of embryonic/tissue differentiation across multiple systems; lipid biosynthesis (ceramide) may relate to membrane dynamics during development but does not define a single pathway for the cluster.","confidence":"Medium","size":17,"edges":32,"triangles":0,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046513","count":11},{"id":"GO:0007601","count":10},{"id":"GO:0002070","count":10},{"id":"GO:0030878","count":10},{"id":"GO:0021892","count":10}]},{"hash":"1909263021814110862","title":"FGF-MAPK Signaling in Vascular and Lung Mesenchyme","description":"The top terms cluster around regulation of angiogenesis, endothelial cell chemotaxis, and MAPK pathway regulation via FGF signaling, plus lung mesenchyme development, pointing to FGFR-MAPK\u2013driven vascular development in lung tissue. Additional terms about sodium transport and nerve impulse transmission suggest broader signaling roles but do not override the vascular\u2013lung development theme. ","confidence":"Medium","size":17,"edges":22,"triangles":0,"max_degree":14,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2000649","count":8},{"id":"GO:0001525","count":7},{"id":"GO:0019226","count":7},{"id":"GO:0000187","count":7},{"id":"GO:0043552","count":7}]},{"hash":"1206702759041415078","title":"Neural crest, craniofacial and brain development","description":"The GO terms point to embryonic development with emphasis on neural crest migration, craniofacial structures like the palate, and brain regions (midbrain, hypothalamus, pituitary), plus neuronal guidance and cartilage formation. This suggests a coherent theme of coordinated neural and craniofacial development during embryogenesis, with transcriptional regulation playing a regulatory role.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":9},{"id":"GO:0001755","count":6},{"id":"GO:0060021","count":6},{"id":"GO:0090009","count":6},{"id":"GO:0003323","count":5}]},{"hash":"2001995555884546643","title":"Unknown","description":"The top GO terms span cartilage development, neural/visual development, fertilization, vascular signaling, apoptosis, and transcription regulation, covering diverse tissues and processes with no single cohesive function. A specific, intuitive label is not supported by the common themes, so the cluster is best treated as Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051216","count":5},{"id":"GO:0000122","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0048010","count":2}]},{"hash":"1951273216609495405","title":"Dopamine receptor GPCR signaling with cAMP/PLC","description":"GO terms in this cluster emphasize dopamine receptor signaling via GPCRs, including adenylate cyclase-activated cAMP pathways and phospholipase C activation, along with phototransduction and heart development contexts. This points to a core theme of GPCR-mediated signaling involving cAMP and PLC, rather than a single specialized pathway. The association with cell proliferation and GTPase regulation further supports a broad GPCR signaling role.","confidence":"High","size":17,"edges":52,"triangles":69,"max_degree":13,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0043547","count":15},{"id":"GO:0010513","count":13},{"id":"GO:0007603","count":13},{"id":"GO:0071880","count":13},{"id":"GO:0060158","count":13}]},{"hash":"1802788668807307125","title":"Coagulation and fibrinolysis regulation","description":"This cluster is dominated by GO terms related to blood coagulation, fibrinolysis, and their regulation (including negative regulation of plasminogen activation and bradykinin catabolism), plus a link to angiotensin regulation and liver regeneration, which supports hepatic production of coagulation factors. A few terms on protein deglutamylation suggest regulatory post-translational modification, but the central theme clearly points to cardiovascular proteolytic control.","confidence":"Medium","size":17,"edges":31,"triangles":15,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0035611","count":5},{"id":"GO:0035609","count":5},{"id":"GO:0010757","count":5},{"id":"GO:0051918","count":5},{"id":"GO:0097421","count":5}]},{"hash":"56639121064677485","title":"Neural Development and Signaling","description":"The cluster shows strong representation of nervous system development terms\u2014axon guidance, synapse assembly, and ERK signaling regulation\u2014pointing to roles in neuronal development and connectivity; other terms (spermatid development, innate immune response) are present but less dominant, so the label emphasizes neural development and signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0043552","count":3}]},{"hash":"1221080115544479455","title":"Neural sensory perception and dopaminergic signaling","description":"Top terms show sensory modalities (pain, temperature, vision), dopaminergic synaptic transmission, cocaine response, and ERK-related signaling in the brain, plus prostaglandin stimuli. This suggests brain-centered sensory processing and reward-related signaling, making the label a fitting summary of the cluster.","confidence":"Medium","size":17,"edges":30,"triangles":1,"max_degree":8,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":13},{"id":"GO:0002024","count":12},{"id":"GO:0071502","count":12},{"id":"GO:0007601","count":8},{"id":"GO:0006468","count":8}]},{"hash":"631049620271125117","title":"Neural Perception and Dopaminergic Signaling","description":"The cluster is dominated by GO terms tied to sensory perception (pain, vision), dopaminergic synaptic transmission, and signal transduction (ERK cascade, phosphorylation). The presence of cocaine response and visual learning further suggests neural signaling and plasticity. While some terms (macrophage chemotaxis, prostaglandin response, heart development) are broader, the prevailing pattern points to neural perception and dopaminergic signaling as the core theme.","confidence":"High","size":17,"edges":100,"triangles":273,"max_degree":15,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":12},{"id":"GO:0007601","count":11},{"id":"GO:0070374","count":11},{"id":"GO:0048148","count":11},{"id":"GO:0010759","count":11}]},{"hash":"1450376643056397459","title":"Membrane Transport Proteins","description":"The GO terms show transmembrane transport for a variety of substrates (amino acids, sugars, ions, xenobiotics), indicating a cluster of transporter proteins with broad membrane transport activity rather than a single substrate.","confidence":"High","size":17,"edges":16,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0015824","count":2},{"id":"GO:0015751","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0015739","count":2}]},{"hash":"1452549848037673833","title":"Hormone and Growth Factor Signaling","description":"Top GO terms show insulin receptor signaling, growth hormone receptor signaling, and responses to prostaglandin E and VEGF, suggesting a cohesive theme around hormone/growth factor signaling. Some terms about visual perception and cerebellar cortex formation appear, indicating possible neural development roles or annotation noise, but the dominant pattern is receptor- and pathway-mediated signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0071380","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0007601","count":2}]},{"hash":"1720485933084216324","title":"Translation machinery and mRNA decay","description":"This cluster is dominated by translation-related terms (initiation, elongation, termination, and cytoplasmic translation) and mRNA decay (deadenylation-dependent), indicating a core role in protein synthesis and RNA turnover; a few terms like interferon response and neural sensory mentions may reflect contextual regulation or annotation noise rather than core function.","confidence":"Medium","size":17,"edges":38,"triangles":15,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0035455","count":5},{"id":"GO:0007605","count":5},{"id":"GO:0000288","count":4},{"id":"GO:0045901","count":4}]},{"hash":"1103652824659397197","title":"Planar cell polarity and morphogenesis","description":"This cluster shows a cohesive theme around planar cell polarity (PCP) and morphogenesis: terms referencing planar orientation in hair, PCP pathways in axon guidance, and lung branching morphogenesis all point to PCP-driven tissue organization. Additional terms related to cell adhesion (hemidesmosomes) support a broader morphogenetic context. Some entries (e.g., GPCR signaling, platelet aggregation) are less central, but the dominant signal is PCP/morphogenesis. ","confidence":"Medium","size":17,"edges":105,"triangles":455,"max_degree":14,"top_function":"wound healing","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0036515","count":6},{"id":"GO:0070527","count":6},{"id":"GO:0060488","count":6},{"id":"GO:0007213","count":6}]},{"hash":"341024240310624220","title":"Amino acid and chlorophyll biosynthesis","description":"These proteins cluster around biosynthetic processes, including protoporphyrinogen IX biosynthesis (a precursor to heme and chlorophyll), biotin biosynthesis, and multiple amino acid biosynthetic pathways (lysine, ornithine, proline, beta-alanine, alanine). This points to a cohesive theme of primary metabolism focused on synthesizing amino acids and tetrapyrrole pigments used in chlorophyll/heme, rather than signaling or degradation roles. The presence of an outlier term like \u201cbehavioral response to cocaine\u201d likely reflects annotation noise rather than a functional link. ","confidence":"Medium","size":17,"edges":27,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0019878","count":4},{"id":"GO:0019481","count":3},{"id":"GO:0055129","count":3}]},{"hash":"1406281178544944465","title":"Unknown","description":"The top GO terms are spread across diverse processes (platelet aggregation, CNS development, pneumocyte differentiation, inflammatory regulation, vacuolar acidification, calcium signaling, MAPK/JNK regulation, ion transport, and growth). There isn\u2019t a single cohesive function that ties these together, so a specific functional label isn\u2019t confidently supported.","confidence":"","size":17,"edges":17,"triangles":4,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":3},{"id":"GO:0060510","count":3},{"id":"GO:0002674","count":3},{"id":"GO:0007035","count":3},{"id":"GO:0007417","count":3}]},{"hash":"274138090669791219","title":"Mitochondrial stress and metabolism","description":"Proteins in this cluster are linked to mitochondrial processes and cellular energy stress: import of pyrimidine nucleotides and iron into mitochondria, thiosulfate transport, regulation of mitochondrial membrane permeability, and apoptotic mitochondrial changes; plus stress- and nutrient-related responses such as amino acid starvation, fatty acid response, adaptive thermogenesis, and glucose-triggered insulin regulation. The convergence on mitochondrial function and stress pathways supports a mitochondrial metabolism cluster.","confidence":"High","size":17,"edges":12,"triangles":0,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034198","count":5},{"id":"GO:0000303","count":5},{"id":"GO:0048250","count":5},{"id":"GO:0070542","count":5},{"id":"GO:0015709","count":5}]},{"hash":"1728179956665134526","title":"ER-Golgi Vesicle Transport","description":"This cluster is dominated by vesicle trafficking terms between the endoplasmic reticulum and Golgi (ER to Golgi and retrograde ER-Golgi transport), suggesting a core theme of secretory pathway transport. Other notable terms include mRNA transport, ribosomal subunit biogenesis, and TORC1 signaling, pointing to broader intracellular transport regulation and growth-related processes. While there are hints of cell cycle-related functions, the strongest common thread is vesicle-mediated intracellular transport within the secretory pathway.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0038202","count":4},{"id":"GO:0006890","count":4}]},{"hash":"1136983973164614581","title":"Purine nucleotide biosynthesis and related metabolism","description":"Based on the top GO terms, the cluster is dominated by nucleotide-related processes (GMP biosynthesis, GTP biosynthesis, and purine nucleobase metabolism) with a secondary link to gluconeogenesis, plus a frequent note on protein homotetramerization. Immune/neural terms appear but are less represented, so the core theme is nucleotide biosynthesis and associated metabolism.","confidence":"Medium","size":17,"edges":45,"triangles":81,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051289","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0006177","count":4},{"id":"GO:0006094","count":3},{"id":"GO:0006183","count":3}]},{"hash":"1061609416228002769","title":"TNF-NF-\u03baB signaling and ubiquitination","description":"This cluster shows strong representation of TNF-mediated signaling and NF-\u03baB activation (GO:0033209, GO:0007250), along with ubiquitin-related processes (ubiquitin-dependent protein catabolic process, protein autoubiquitination). The presence of V(D)J recombination also links to immune system function. Together, these terms suggest a module where inflammatory signaling is coordinated with ubiquitin-mediated regulation of protein turnover in immune responses. Some terms are obsolete, but the central theme remains TNF/NF-\u03baB signaling with ubiquitination.","confidence":"High","size":17,"edges":32,"triangles":3,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0033209","count":4},{"id":"GO:0070512","count":3},{"id":"GO:0042787","count":3},{"id":"GO:1903762","count":3},{"id":"GO:1901253","count":3}]},{"hash":"1430788218653469947","title":"Actin Cytoskeleton and Cell Migration","description":"The top terms point to actin filament organization and cell polarity, with a clear connection to endothelial cell chemotaxis and migratory processes, suggesting the proteins cluster around actin-driven motility and directional movement. While several terms are obsolete or regulatory (e.g., NF-kappaB sequestration, RNA polymerase II regulation), the dominant theme is cytoskeletal dynamics shaping migration, making this label a concise representation of the cluster\u2019s function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001028","count":1},{"id":"GO:0007015","count":1},{"id":"GO:0042989","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0007253","count":1}]},{"hash":"840391275980574163","title":"Transcriptional control of cell fate and differentiation","description":"The cluster is strongly centered on transcription by RNA polymerase II (GO:0006366 with 16 hits) and includes several development- and differentiation-related terms (e.g., exocrine pancreas development, brown fat cell differentiation, fat cell differentiation, erythrocyte differentiation, vascular wound healing). This suggests proteins acting in transcriptional regulation to guide lineage specification across tissues, linking gene expression programs to diverse differentiation outcomes. Some terms are obsolete, but the core signal remains transcriptional control of developmental differentiation.","confidence":"High","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":16},{"id":"GO:1990442","count":8},{"id":"GO:0060850","count":8},{"id":"GO:0006990","count":8},{"id":"GO:0035470","count":8}]},{"hash":"400871783252840970","title":"Neural development and differentiation","description":"The cluster\u2019s top GO terms cluster around neural lineage specification and neural differentiation, including cerebral cortex GABAergic interneuron differentiation, spinal cord motor neuron and oligodendrocyte fate specification, and subpallium neuron fate commitment, along with transcriptional regulation (RNA polymerase II\u2013mediated transcription) and regulation of synapse maturation. While there are a few less related terms (bronchiole development, endocrine pancreas development, MHC class II biosynthetic process), the dominant theme is genes involved in nervous-system development and neuronal differentiation, supported by broad transcriptional control. ","confidence":"Medium","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":13},{"id":"GO:0021892","count":8},{"id":"GO:0060435","count":8},{"id":"GO:0060163","count":8},{"id":"GO:0021520","count":8}]},{"hash":"2197019165164524722","title":"Regulated Signaling and Endocytic Trafficking","description":"The top GO terms cluster around positive regulation of major signaling pathways (ERK cascade and Wnt signaling) alongside vesicle trafficking processes (endocytosis, endosome-to-lysosome transport) and related GTPase activity, with additional developmental terms (hair follicle morphogenesis, substantia nigra development) suggesting roles in signaling-driven development. This points to proteins that modulate signaling output via endocytic trafficking and associated cellular processes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070374","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0031532","count":4},{"id":"GO:0032258","count":4},{"id":"GO:0006897","count":4}]},{"hash":"158050413620005610","title":"Immune cell adhesion and cytokine regulation","description":"The cluster is dominated by GO terms for cell adhesion (homophilic and heterophilic) and immune signaling/regulation (T cell costimulation, NK cell cytotoxicity regulation, and cytokine production such as IL-10 and IL-4), indicating a core theme of immune cell interactions and immunoregulation. A few developmental terms (skeletal system, lens morphogenesis, spermatid development) are present but do not override the primary adhesion/immunoregulatory signal.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007156","count":12},{"id":"GO:0007157","count":12},{"id":"GO:2001181","count":10},{"id":"GO:0001501","count":10},{"id":"GO:0031295","count":10}]},{"hash":"176147112568792725","title":"Actin-based motility and adhesion signaling","description":"The cluster centers on actin cytoskeleton dynamics and cell movement, evidenced by lamellipodium assembly, microspike and podosome assembly, Rac signaling, and integrin-mediated adhesion. Neutrophil chemotaxis and microglial migration terms reinforce the motility theme, with IGF receptor signaling potentially modulating these processes. Overall, the dominant pattern is actin remodeling underlying cellular migration and adhesion.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900275","count":4},{"id":"GO:1904140","count":3},{"id":"GO:0030593","count":3},{"id":"GO:0071803","count":3},{"id":"GO:0007229","count":3}]},{"hash":"1548307599863251064","title":"Endocytosis and Receptor Trafficking Regulation","description":"The top GO terms center on ubiquitin-dependent endocytosis and positive regulation of receptor internalization, suggesting vesicle trafficking and modulation of signaling at the cell surface as the core function. Related terms involving GTPase activity, phototransduction, and other signaling contexts imply broader regulatory roles where endocytosis shapes cellular responses; thus, the cluster is best described as membrane trafficking coupled to receptor signaling control.","confidence":"Medium","size":17,"edges":6,"triangles":0,"max_degree":4,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0070086","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0060613","count":5},{"id":"GO:0007601","count":4},{"id":"GO:0042742","count":4}]},{"hash":"1625615111375310462","title":"Embryonic Brain and Eye Morphogenesis","description":"This cluster is dominated by transcription-related GO terms (RNA polymerase II transcription and its positive regulation) and neural/eye developmental terms (brain segmentation, rhombomere 5 development, camera-type eye development, embryonic eye morphogenesis, pituitary gland development). The combination suggests a group of proteins coordinating early embryonic patterning and morphogenesis of neural and sensory organs through transcriptional control, with some additional broad developmental processes (lung morphogenesis) appearing as secondary associations.","confidence":"High","size":17,"edges":121,"triangles":482,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006366","count":10},{"id":"GO:0035284","count":9},{"id":"GO:0021571","count":9},{"id":"GO:0021983","count":7},{"id":"GO:0043010","count":6}]},{"hash":"1817648928671252551","title":"Innate Immune Response and Phagocytosis","description":"The top GO terms point to defense against bacteria, innate immune response, and phagocytosis recognition, suggesting the proteins mainly function in early immune signaling and pathogen uptake. Although there are also adhesion and neural development terms, these are likely secondary or related signaling contexts; the core theme is innate immunity and phagocytic activity.","confidence":"Medium","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0042742","count":9},{"id":"GO:0000187","count":9},{"id":"GO:0007156","count":8},{"id":"GO:0051965","count":8},{"id":"GO:0043931","count":8}]},{"hash":"1721868776376601396","title":"Neural development with cell adhesion and innate immunity","description":"This cluster is dominated by terms tied to nervous system development and synapse assembly, plus strong signals for cell-cell adhesion (homophilic/heterophilic) and components of the innate immune system (complement activation). The mix suggests a bundle of proteins involved in neural development and synaptic connectivity, with overlapping roles in adhesion and immune-related processes, rather than a single narrow pathway. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0051965","count":7},{"id":"GO:0007399","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0007156","count":6},{"id":"GO:0007157","count":6}]},{"hash":"456795437708312880","title":"Developmental Gene Regulation and Ubiquitination","description":"The top GO terms point to transcriptional control (DNA-templated transcription) and multiple developmental processes (multicellular organism growth, skin development, organism development, cell division), with a notable emphasis on protein ubiquitination and chromatin regulation (histone methylation). These together suggest a theme of regulating gene expression during development, with ubiquitin-mediated modification playing a key role, rather than a single specific pathway. The presence of diverse terms like innate immune response and DNA repair indicates broader cellular roles within this developmental context, supporting a general developmental regulation label rather than a highly specific function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0000724","count":3}]},{"hash":"1044903742112668746","title":"Host-pathogen interaction and autophagy","description":"The top GO terms cluster around host\u2013pathogen interactions and autophagy regulation, notably symbiont-mediated activation of host autophagy and suppression of ISG15 conjugation, along with viral RNA genome replication, indicating a theme of host defense and pathogen manipulation. Some outlier terms exist, but the dominant signal points to pathogen-host dynamics and autophagy-related processes. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0051725","count":1},{"id":"GO:0039520","count":1},{"id":"GO:0033128","count":1},{"id":"GO:1904815","count":1}]},{"hash":"1532661510220122985","title":"Ubiquitin-Dependent Innate Immune Signaling","description":"The cluster is characterized by strong enrichment for ubiquitin-related processes (ubiquitin-dependent protein catabolic process; K63- and K6-linked ubiquitination) together with innate immune response and defense against virus, and by components of NF-kappaB and TNF signaling. This points to a cohesive group of proteins that regulate immune signaling through ubiquitination, including antiviral defense and inflammatory pathways, with additional notes of histone turnover and autoubiquitination that fit within a broader regulatory context. Overall, the proteins appear to function as ubiquitin-mediated modulators of innate immunity and inflammatory signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0051607","count":7},{"id":"GO:0070534","count":5},{"id":"GO:0085020","count":5}]},{"hash":"426533502907657932","title":"Actin Patch\u2013Mediated Organelle Inheritance","description":"Most top GO terms point to actin cortex patch assembly/localization, actin filament bundle assembly, and inheritance of mitochondria and vacuoles, with cell polarity maintenance. This suggests a cluster of proteins coordinating cytoskeletal organization with organelle partitioning during cell processes, with a few chromatin-related terms appearing as secondary annotations.","confidence":"Medium","size":16,"edges":98,"triangles":336,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":7},{"id":"GO:0000147","count":7},{"id":"GO:0042766","count":7},{"id":"GO:0000011","count":7},{"id":"GO:0071963","count":7}]},{"hash":"1165831474009737776","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":118,"triangles":533,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070843","count":13},{"id":"GO:0090084","count":13},{"id":"GO:0071374","count":13},{"id":"GO:0051259","count":13},{"id":"GO:0006452","count":13}]},{"hash":"3311576045314593","title":"RNA processing and translation regulation","description":"The cluster's GO terms consistently point to post-transcriptional control: ncRNA-mediated gene silencing, regulation of mRNA tail shortening, mRNA stabilization and modification, spliceosome-mediated splicing, and initiation of translation via EIF4F complex assembly. Together these terms indicate a cohesive group centered on RNA maturation, stability, and translation control, especially under stress.","confidence":"High","size":16,"edges":95,"triangles":307,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":7},{"id":"GO:0060211","count":6},{"id":"GO:1905663","count":6},{"id":"GO:0097010","count":6},{"id":"GO:1903586","count":6}]},{"hash":"1794138645561206327","title":"Membrane transporters for vitamins, xenobiotics, and sugars","description":"This cluster is dominated by GO terms for transmembrane transport of vitamins, xenobiotics, and sugars (including D-glucose) as well as related ion transport, pointing to a group of membrane transporter proteins involved in import/export of small molecules and ions. The mix of transporter-related terms suggests a cohesive function in moving diverse nutrients and xenobiotic compounds across membranes, with a secondary hint at regulatory or cellular responses linked to nutrient availability.","confidence":"High","size":16,"edges":78,"triangles":205,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":15},{"id":"GO:0006855","count":15},{"id":"GO:0042908","count":13},{"id":"GO:0071805","count":12},{"id":"GO:0042891","count":12}]},{"hash":"1029394124586430183","title":"Unknown","description":"The top terms span diverse, context-specific processes (cardiac conduction and action potential regulation; microtubule dynamics; various viral and host interactions; T cell homeostasis; plant defense; and mRNA processing/translation). There is no single cohesive biological function tying all terms together, and the cluster has no observed edges, so no clear shared mechanism. ","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":3},{"id":"GO:0086091","count":2},{"id":"GO:0098911","count":2},{"id":"GO:0007026","count":2},{"id":"GO:0016032","count":2}]},{"hash":"999609800546065329","title":"Mitochondrial Metabolism and Stress Response","description":"The top GO terms cluster around mitochondrial functions: metabolic signaling (insulin, fatty acids), stress responses (oxidative stress, amino acid starvation), import of metabolites (iron, nucleotides), and mitochondrial membrane regulation linked to apoptosis, plus a note on mitochondrial genome maintenance, indicating a cohesive mitochondrial metabolism/stress theme.","confidence":"High","size":16,"edges":20,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":5},{"id":"GO:0000002","count":5},{"id":"GO:0034198","count":4},{"id":"GO:0000303","count":4},{"id":"GO:0048250","count":4}]},{"hash":"2248445057386551983","title":"Protein and Polyamine Acetylation","description":"The cluster is dominated by acetylation-related GO terms: peptidyl-lysine N6-acetylation, N-terminal protein amino acid propionylation, and acetylation of putrescine, spermidine, and spermine, plus related catabolic processes. This points to a cohesive theme of acetyltransferase activity modifying both proteins and polyamines, with chromatin-related context suggested by subtelomeric heterochromatin formation. Some terms like angiogenesis or melatonin biosynthesis appear peripheral to the core acetylation signal, but don\u2019t override the primary theme.","confidence":"High","size":16,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001525","count":9},{"id":"GO:0006348","count":9},{"id":"GO:0018003","count":7},{"id":"GO:0009447","count":7},{"id":"GO:0032919","count":7}]},{"hash":"1755060291082613546","title":"MAPK-activated neuronal signaling and dendrite morphogenesis","description":"The cluster centers on MAPK pathways (ERK and JNK cascades, with an obsolete MAPKK activation term) and neuronal function terms such as excitatory postsynaptic potential and dendrite morphogenesis, indicating a role in synaptic signaling and dendritic development. It also includes terms related to Wnt and ephrin receptor signaling and focal adhesion, suggesting a broader signaling hub that links neuronal signaling with adhesion and guidance processes. This combination points to a coherent theme of MAPK-regulated neuronal signaling and dendritic structure formation.","confidence":"High","size":16,"edges":82,"triangles":255,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000186","count":16},{"id":"GO:0060079","count":14},{"id":"GO:0070374","count":14},{"id":"GO:0046330","count":14},{"id":"GO:0048813","count":14}]},{"hash":"2165971900699695924","title":"Vesicle trafficking and secretory pathway regulation","description":"Based on the top GO terms, the cluster centers on membrane trafficking and protein handling: protein transmembrane transport, CVT pathway targeting, phospholipid homeostasis, and components of the secretory pathway, complemented by ubiquitination for protein turnover. The presence of dendrite development and heart contraction hints at the importance of vesicle dynamics in specialized tissues, but the dominant signal is intracellular transport and secretion regulation. Overall, these proteins likely function together in managing protein movement through secretory and vesicular pathways.","confidence":"Medium","size":16,"edges":14,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010628","count":12},{"id":"GO:0071806","count":12},{"id":"GO:0055091","count":12},{"id":"GO:0000060","count":12},{"id":"GO:0032258","count":11}]},{"hash":"1633785018603173076","title":"Neuro-muscular development and synapse formation","description":"This cluster centers on neural development (neurogenesis, CNS development, synapse organization) and muscle formation (myoblast fusion) with signaling (BMP) and cytoskeletal/ECM remodeling (Rho signaling, collagen fibril organization), suggesting coordinated morphogenesis across neural and muscular tissues rather than a single function.","confidence":"Medium","size":16,"edges":55,"triangles":64,"max_degree":14,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":8},{"id":"GO:0007520","count":7},{"id":"GO:0022008","count":7},{"id":"GO:0043065","count":6},{"id":"GO:0034351","count":6}]},{"hash":"236470792839434470","title":"Metabolism and Translation","description":"This cluster centers on core metabolic processes alongside protein production: translation, glycogen/alpha-glucan and fatty acid catabolism, and amino acid/PRPP biosynthesis, with an additional transcription term. The combination suggests a general metabolic/gene-expression theme, though a few terms (nylon catabolism, necroptosis) may reflect annotation noise or incidental associations. ","confidence":"Medium","size":16,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0005980","count":3},{"id":"GO:0070266","count":3},{"id":"GO:0006015","count":3},{"id":"GO:0030980","count":3}]},{"hash":"626166483849989627","title":"Neurovascular development and axon guidance","description":"This cluster shows a clear tilt toward nervous system connectivity (axon guidance, retinal/ganglion cell guidance, axon extension) alongside vascular signaling and coronary artery morphogenesis (VEGF signaling, platelet activation). The combination suggests coordination between neural wiring and blood vessel development, i.e., neurovascular development. A few terms on circadian rhythm and rhodopsin signaling appear peripheral but may reflect CNS/retinal signaling contexts. Overall, the dominant theme is neurons guiding connections in concert with vascular cues.","confidence":"Medium","size":16,"edges":52,"triangles":75,"max_degree":13,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0060982","count":11},{"id":"GO:0048842","count":11},{"id":"GO:0048010","count":9},{"id":"GO:1902336","count":9},{"id":"GO:0042748","count":9}]},{"hash":"612209475381845911","title":"Muscle and vascular morphogenesis","description":"This cluster is dominated by developmental and remodeling processes in muscle and vasculature: cardiac right atrium morphogenesis, skeletal muscle tissue regeneration, endothelial cell delamination, and cell migration, with supporting actin filament organization and ephrin signaling regulation. Some terms like response to cold or vitamin D reflect broader stress responses, but the strongest theme is tissue morphogenesis and remodeling in muscle and blood vessels.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":6},{"id":"GO:0009409","count":6},{"id":"GO:0051017","count":5},{"id":"GO:0097497","count":5},{"id":"GO:0035544","count":5}]},{"hash":"520579620056785595","title":"Embryonic Mesoderm and Heart Morphogenesis","description":"The GO terms converge on early development and mesoderm-derived tissues: primitive streak formation, BMP signaling in mesoderm fate, endocardial cushion development, and heart morphogenesis, with supporting roles in neural and stem cell development and transcriptional/miRNA regulation, pointing to a coherent embryonic-developmental program centered on mesoderm and heart formation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0000122","count":8},{"id":"GO:0050673","count":7},{"id":"GO:0030225","count":7},{"id":"GO:1902895","count":7},{"id":"GO:0090009","count":7}]},{"hash":"1992812864132152134","title":"Actin Dynamics and Membrane Protrusion Signaling","description":"This cluster is dominated by GO terms for actin filament polymerization, podosome and ruffle assembly, and Rac-mediated signaling, pointing to actin-driven membrane remodeling and protrusive structures. Additional terms for endocytosis, phagocytosis, and various receptor signaling pathways (T cell, ephrin) across cell types (immune, neuronal) suggest a shared theme of cytoskeletal remodeling linked to cell migration and membrane trafficking.","confidence":"High","size":16,"edges":6,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030838","count":5},{"id":"GO:0048813","count":5},{"id":"GO:0071803","count":5},{"id":"GO:0097178","count":5},{"id":"GO:0050852","count":5}]},{"hash":"2126239830882809073","title":"Hormone and vitamin metabolism","description":"This cluster centers on metabolic processes for vitamins (retinol/retinal and L-ascorbic acid) and hormones (androgen, testosterone) with related metabolic and homeostatic terms, suggesting a common theme of hormone- and vitamin-related metabolism. Confidence: Medium","confidence":"","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":15},{"id":"GO:0042572","count":15},{"id":"GO:0055114","count":13},{"id":"GO:0008209","count":13},{"id":"GO:0061370","count":13}]},{"hash":"1473002266612450839","title":"Potassium Transport and Membrane Potential in Muscle","description":"The GO terms cluster around potassium ion transmembrane transport, potassium homeostasis, stabilization of membrane potential, and cardiac muscle repolarization, suggesting a shared role in maintaining electrical excitability in muscle tissues. A mechanosensation term appears but is secondary to the ionic/electrical theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":9},{"id":"GO:0071805","count":9},{"id":"GO:0030007","count":9},{"id":"GO:0098914","count":9},{"id":"GO:0030322","count":9}]},{"hash":"1428041437753484741","title":"Cell wall and glycoconjugate biosynthesis","description":"The proteins are enriched for biosynthesis of cell wall components (peptidoglycan, LPS, lipid A, UDP-GlcNAc, GDP-mannose) and related processes (cell wall organization, morphogenesis, mannoprotein biosynthesis), suggesting a cohesive role in building/remodeling the cell envelope across cell types.","confidence":"High","size":16,"edges":111,"triangles":443,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000902","count":5},{"id":"GO:0009298","count":4},{"id":"GO:0008360","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0009252","count":4}]},{"hash":"1867491502619791145","title":"Dopaminergic Synaptic GPCR Signaling","description":"The cluster is dominated by terms for dopaminergic synaptic transmission, GPCR internalization, and ERK/MAPK signaling, plus behavioral responses to cocaine, pointing to neuronal GPCR-mediated signaling and plasticity involved in drug-related behaviors. Some terms about pain or vision likely reflect broader sensory roles in the same protein set, but the core theme remains dopaminergic synaptic signaling and related regulatory processes.","confidence":"High","size":16,"edges":14,"triangles":1,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0019233","count":16},{"id":"GO:0007601","count":15},{"id":"GO:0043547","count":15},{"id":"GO:0006468","count":15},{"id":"GO:0048148","count":15}]},{"hash":"1217765277689548340","title":"Membrane phospholipid biosynthesis","description":"The top terms are dominated by biosynthesis of phospholipids (PE, PS, PG) and related mediators like platelet activating factor, plus regulation of phosphatidylinositol biosynthesis, indicating a cohesive theme around membrane lipid production and signaling. Some entries (defense response, GABA signaling) are less central but do not outweigh the lipid-focused pattern.","confidence":"High","size":16,"edges":16,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006646","count":3},{"id":"GO:0006659","count":3},{"id":"GO:0006663","count":3},{"id":"GO:1905711","count":3},{"id":"GO:0010512","count":3}]},{"hash":"2206755063363497204","title":"Chromatin regulation and histone modification","description":"The cluster is enriched for chromatin- and transcription-related GO terms, including negative regulation of histone H3-K4 methylation, regulation of transcription by RNA Pol II, rDNA heterochromatin formation, and CENP-A containing chromatin assembly. These collectively point to a shared function in chromatin state maintenance, remodeling, and transcription control, with some broader or peripheral annotations. ","confidence":"High","size":16,"edges":95,"triangles":299,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0051572","count":7},{"id":"GO:0000122","count":6},{"id":"GO:0000183","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0032496","count":5}]},{"hash":"1932098594335688250","title":"Developmental morphogenesis and vascular remodeling","description":"The top GO terms span tissue morphogenesis (eye, endoderm, brown fat) and vascular development (endothelial proliferation, sprouting angiogenesis, VEGF signaling), plus adhesion, suggesting a cluster of proteins involved in developmental differentiation with a vascular remodeling emphasis rather than a single tissue-specific function.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0090331","count":2},{"id":"GO:0035987","count":2},{"id":"GO:0090051","count":2}]},{"hash":"1602475055100307835","title":"Lipid and Hormone Biosynthesis","description":"This cluster shows a strong representation of biosynthetic pathways for lipids and lipid-derived molecules (sphingolipid biosynthesis, fatty acid elongation, phylloquinone biosynthesis, tetrahydrobiopterin biosynthesis) and hormone-related biosynthesis/metabolism (estrogen biosynthesis, androgen catabolic process), suggesting a cohesive theme around production and turnover of lipid and steroid-related compounds. Some terms like lung development are likely context-specific or off-target, but the dominant signal supports this naming. ","confidence":"Medium","size":16,"edges":24,"triangles":5,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0030324","count":13},{"id":"GO:0042619","count":13},{"id":"GO:0055114","count":13},{"id":"GO:0006710","count":12},{"id":"GO:0042376","count":12}]},{"hash":"577767002258880794","title":"Cell adhesion and neural-lung morphogenesis","description":"The top GO terms emphasize adhesion (heterophilic cell-cell, integrin-mediated, and cell-matrix adhesion) alongside neural guidance (serotonergic and dopaminergic axon guidance) and signaling (G protein-coupled acetylcholine receptor). Several terms also relate to planar polarity and specific lung branching morphogenesis processes, suggesting a cluster of adhesion/signaling proteins coordinating tissue patterning and axon guidance during lung development. Overall, the theme points to adhesion-driven morphogenesis with neural guidance involvement in the lung. ","confidence":"Medium","size":16,"edges":35,"triangles":30,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007157","count":15},{"id":"GO:0033627","count":11},{"id":"GO:0007160","count":11},{"id":"GO:0036515","count":10},{"id":"GO:0060488","count":10}]},{"hash":"196206252272598112","title":"Ubiquitin-Proteasome\u2013Mediated Degradation","description":"The cluster is strongly enriched for ubiquitin-dependent proteolysis terms (ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal ubiquitin-dependent protein degradation, and polyubiquitination), indicating core involvement in targeted protein turnover. Additional terms point to regulation of DNA replication and mitotic checkpoints, suggesting a link between proteolysis and cell-cycle control, with some representation of stress responses to heavy metals. This combination centers the cluster on ubiquitin-proteasome\u2013driven proteostasis and its role in cell-cycle and DNA replication regulation.","confidence":"High","size":16,"edges":14,"triangles":2,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":13},{"id":"GO:0031146","count":10},{"id":"GO:0030433","count":9},{"id":"GO:0071276","count":9},{"id":"GO:1902916","count":9}]},{"hash":"249394561035150468","title":"Developmental signaling and morphogenesis","description":"The top GO terms point to developmental processes: Wnt signaling, eye morphogenesis, maternal axis specification, and pregnancy-related development, suggesting a core theme centered on embryonic development and tissue patterning. Some entries (complement activation, coagulation, collagen catabolism) are peripheral and reflect broader tissue remodeling or immune-related roles, but do not define the cluster\u2019s main function. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0001867","count":4},{"id":"GO:0006958","count":4},{"id":"GO:0043046","count":3},{"id":"GO:0007596","count":3}]},{"hash":"973640721350563154","title":"Neurodevelopmental and Transcriptional Regulation","description":"Top terms indicate neural development (peripheral nervous system neuron development, midbrain development, hypothalamus differentiation) and organismal development (primitive streak formation, muscle organ development), coupled with transcriptional regulation (negative regulation of transcription by RNA polymerase II, transcription by RNA polymerase II, regulation of DNA-templated transcription). This suggests proteins acting as regulators coordinating neurodevelopment with broader embryonic development. Therefore, the label 'Neurodevelopmental and Transcriptional Regulation' captures the main theme.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":8},{"id":"GO:0048935","count":6},{"id":"GO:0090009","count":6},{"id":"GO:0007275","count":5},{"id":"GO:0006355","count":5}]},{"hash":"823641594308930678","title":"Telomere-centered signaling and DNA damage response","description":"The Top Terms include multiple telomere-related processes (negative regulation of telomere maintenance via telomere lengthening, localization to telomeric chromosome regions, telomere-associated cohesion), along with a DNA-damage\u2013p53\u2013mediated apoptotic pathway, suggesting a core theme around telomere biology and genomic stress response. Supporting terms point to broader signaling contexts (Wnt, ephrin, GPCR signaling) that may modulate these processes, indicating a network of signaling linked to telomere maintenance and DNA damage response rather than a single, isolated function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010838","count":3},{"id":"GO:1901187","count":3},{"id":"GO:0007205","count":3},{"id":"GO:1904357","count":3},{"id":"GO:0070198","count":3}]},{"hash":"246140763786996016","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":2},{"id":"GO:0034394","count":2},{"id":"GO:0071347","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0070374","count":2}]},{"hash":"239676664810096184","title":"Endosomal trafficking and vesicle maturation","description":"These proteins are enriched for GO terms related to endosome transport (endosome to lysosome, early to late endosome), intralumenal vesicle formation, and intracellular/secretory vesicle maturation, with links to GTPase activity regulation that controls vesicle trafficking. This points to a coherent cluster of proteins involved in endosomal pathways and vesicle maturation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0031914","count":3},{"id":"GO:0051092","count":2},{"id":"GO:0000281","count":2},{"id":"GO:0008333","count":2}]},{"hash":"1970945534773786671","title":"Embryonic organ development","description":"The top GO terms cover development across multiple tissues and stages\u2014eye/visual perception, spinal cord and cortex neuron differentiation, and organogenesis for thyroid, pancreas, and digestive tract. This indicates a broad developmental theme rather than a single pathway, suggesting these proteins collectively participate in embryonic organogenesis and neurodevelopment. Given the diverse but development-centric terms, a concise label like Embryonic organ development captures the cluster\u2019s core function.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":16},{"id":"GO:0002070","count":16},{"id":"GO:0030878","count":16},{"id":"GO:0021892","count":16},{"id":"GO:0007501","count":16}]},{"hash":"2234244695103402168","title":"Calcium signaling and neural development","description":"This cluster is dominated by GO terms related to calcium release into the cytosol and broader signaling processes (protein phosphorylation, GTPase activity), with neural-context terms such as forebrain development and visual perception, suggesting a cohesive theme of calcium-mediated neural signaling and development across the included proteins.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051281","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0042755","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0007601","count":2}]},{"hash":"46339790564431055","title":"Unknown","description":"Top terms include mechanosensory detection and cellular response to mechanical stimulus, protein ubiquitination, differentiation programs (fat cells and follicular dendritic cells), hepatocyte apoptosis, vitamin D response, regulation of SA node action potential, and membrane protein localization. The collection spans diverse processes with no clear unifying function, so a concise, representative label cannot be inferred.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050966","count":7},{"id":"GO:0016567","count":7},{"id":"GO:0032088","count":7},{"id":"GO:0071260","count":7},{"id":"GO:0098907","count":7}]},{"hash":"89129224476866837","title":"Unknown","description":"The top GO terms span ubiquitination, immune response, neural development, germ cell apoptosis, and cell cycle checkpoints with no clear shared function; combined with zero edges, this cluster appears to be a heterogeneous collection rather than a cohesive functional module.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0016032","count":2},{"id":"GO:0031578","count":2},{"id":"GO:0002250","count":2}]},{"hash":"525311555717335550","title":"ECM Remodeling and Development","description":"The cluster shows a pattern of extracellular matrix\u2013related processes and organogenesis: collagen catabolic process, cartilage condensation/development, glomerular basement membrane development, and heart morphogenesis, along with negative regulation of endothelial differentiation and sprouting angiogenesis. These terms together suggest tissue remodeling and morphogenesis in ECM-rich contexts, with vascular and cardiac development as prominent themes; complement activation and coagulation terms may reflect remodeling responses rather than core functions. Confidence: Medium","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001867","count":5},{"id":"GO:0007596","count":4},{"id":"GO:0030574","count":4},{"id":"GO:0006958","count":4},{"id":"GO:0001502","count":4}]},{"hash":"853842151913964746","title":"Placental and embryonic organogenesis","description":"This cluster is strongly enriched for placental-related terms (trophoblast giant cell differentiation, embryonic placenta development, pancreatic endocrine development) and broader embryonic morphogenesis (cartilage morphogenesis, EMT in heart cushion formation, left/right patterning, endocrine development), with additional signals for angiogenesis and proteolysis that commonly accompany tissue remodeling during development. These converging themes indicate a set of proteins tied to placental and embryonic organ formation and patterning.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0060707","count":6},{"id":"GO:0035270","count":6},{"id":"GO:0060536","count":6},{"id":"GO:0060806","count":6},{"id":"GO:0003323","count":6}]},{"hash":"1558621984499498155","title":"Developmental Signaling and Morphogenesis","description":"This cluster centers on tissue development and morphogenesis across multiple systems (skeletal development, lens fiber and salivary gland morphogenesis, myelination, synapse organization) with hints of key signaling pathways (PI3K and ERK cascades) that regulate differentiation and connectivity. Despite some obsolete terms, the common thread is developmental signaling guiding tissue formation and maturation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014068","count":5},{"id":"GO:0001501","count":4},{"id":"GO:2000249","count":4},{"id":"GO:0060445","count":4},{"id":"GO:0050808","count":4}]},{"hash":"856587173631928873","title":"Nerve conduction and cell\u2013cell junctions","description":"The top GO terms emphasize paranodal junction assembly and transmission of nerve impulse, with several entries related to cell adhesion in nervous/heart conduction systems (AV node, bundle of His, maintenance of cell junctions). While immune processes appear, the dominant signal is neural/cardiac intercellular connectivity.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030913","count":9},{"id":"GO:0019226","count":8},{"id":"GO:2001181","count":7},{"id":"GO:0042742","count":7},{"id":"GO:0035855","count":7}]},{"hash":"1793951027518110729","title":"Developmental transcription and differentiation","description":"This cluster is dominated by GO terms for multicellular organism development and tissue differentiation (fat cell, skin, skeletal system) plus DNA-templated transcription, pointing to proteins involved in developmental gene regulation and lineage specification. Supporting terms reflect cytoskeletal remodeling and signaling (actin filament bundle assembly, GTPase activity) that drive differentiation. Although some terms pertain to heart conduction or neural signaling, these can represent broader developmental programs or shared pathways. Overall, it seems to group proteins coordinating transcriptional programs during development across tissues.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0043588","count":3}]},{"hash":"649213237334418938","title":"Telomere maintenance regulation and telomeric localization","description":"The top terms disproportionately concern telomere capping/maintenance (positive and negative regulation), and localization to the telomeric region, indicating a core theme of chromosome end protection and regulation. Additional terms like spindle assembly and ADP-ribosylation suggest related chromosome dynamics and protein modification, but the central cluster is telomere biology. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1904355","count":5},{"id":"GO:0032212","count":5},{"id":"GO:0016055","count":5},{"id":"GO:1904357","count":4},{"id":"GO:0070198","count":4}]},{"hash":"704604855588735848","title":"Organogenesis and Endothelial Morphogenesis (FGF/ERK)","description":"The terms cluster around developmental morphogenesis and organ formation, notably endothelial cell morphogenesis, organ induction, and branching morphogenesis (e.g., salivary gland) with signaling pathways involving FGF signaling and ERK/MAPK cascades. This suggests a cohesive theme of developmental morphogenesis regulated by FGF-ERK signaling, even though the protein network edges are not present.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0001886","count":3},{"id":"GO:2000546","count":3},{"id":"GO:0060665","count":3},{"id":"GO:0060445","count":3}]},{"hash":"1276431943293318393","title":"Tissue Development and Morphogenesis","description":"The top GO terms span neural development (axon extension, CNS development, synapse organization), vascular and bone-related morphogenesis (angiogenesis, endothelial morphogenesis, ossification), muscle contraction, and immune signaling (innate immune response, NF-kB regulation). This mix points to a broad developmental/morphogenesis theme across multiple tissues rather than a single, cohesive pathway, and the absence of direct interactions supports a cross-tissue developmental signature. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0048675","count":4},{"id":"GO:0007417","count":4},{"id":"GO:0050808","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0006936","count":4}]},{"hash":"1830513044872881064","title":"Neuronal development and cytoskeletal remodeling","description":"GO terms strongly point to neuron-specific morphogenesis (dendritic spine morphogenesis, neuron projection development) coupled with gene expression regulation (DNA-templated transcription, mRNA processing). Cytoskeletal dynamics and adhesion (actin cytoskeleton remodeling, sarcomere organization, substrate adhesion) support growth and spine formation, aligning with neuronal development. Some broader terms (glucose response, IL-2 production) are present but do not override the neuron-centric pattern.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060997","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0071333","count":2},{"id":"GO:0007155","count":2}]},{"hash":"532156930913567257","title":"Multi-tissue embryonic development","description":"The top GO terms span embryonic development and morphogenesis across multiple tissues (pancreas, mesoderm, palate, digestive tract, eye) plus related signaling and transcription regulation. This points to a broad developmental functions theme rather than a single pathway, so a general embryonic development label seems most representative, albeit with moderate confidence due to tissue diversity.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0003323","count":7},{"id":"GO:0007498","count":6},{"id":"GO:0060021","count":6},{"id":"GO:0048565","count":4},{"id":"GO:0070374","count":4}]},{"hash":"1982300968869875914","title":"RNA splicing and translation initiation cluster","description":"Top GO terms are dominated by mRNA splicing via spliceosome and translation initiation/ preinitiation complex formation, indicating a core theme of RNA processing and initiation of protein synthesis; secondary mentions of transcription and neural development likely reflect broader gene-expression programs rather than a single neural-specific function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000398","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0006351","count":5}]},{"hash":"1642282319523020176","title":"RNA processing and translation regulation","description":"This cluster centers on post-transcriptional control of gene expression: mRNA tail shortening, stability, modification, splicing, and regulation of translation initiation, with some ncRNA-mediated silencing, indicating a cohesive theme of RNA processing and translational control.","confidence":"High","size":15,"edges":44,"triangles":68,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0060211","count":8},{"id":"GO:1905663","count":8},{"id":"GO:0097010","count":8},{"id":"GO:1903586","count":8},{"id":"GO:0031047","count":8}]},{"hash":"2262408969300084052","title":"Innate immune signaling and regulation","description":"This cluster features GO terms centered on signaling pathways (EGFR signaling, JNK cascade regulation, IFN signaling, PI3K-related activity), innate immune response, and gene expression control (miRNA-mediated silencing, nuclear import). The common theme is signaling modulation in immune contexts, with some developmental and nuclear transport terms as peripheral associations.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0035278","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0030218","count":2}]},{"hash":"1705905429461046166","title":"Ribosome Biogenesis and Translation","description":"These proteins cluster around ribosome assembly and protein synthesis. The top GO terms highlight translation, ribosome biogenesis (including small and large subunit biogenesis), SSU-rRNA maturation, preinitiation complex formation, and regulation of translation initiation; with additional signals for mitochondrial and viral translation termination-reinitiation, indicating a core ribosome/translation machinery module.","confidence":"High","size":15,"edges":94,"triangles":367,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0042254","count":7},{"id":"GO:0042274","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0042273","count":4}]},{"hash":"2124052440511282460","title":"Mitotic Spindle and Cytokinesis","description":"The GO terms point to core cell division activities: spindle assembly, spindle pole duplication, cytokinesis, division site positioning, and the cell cycle. Collectively these proteins appear to coordinate chromosome segregation with physical cell division, i.e., mitosis and cytokinesis, with a possible ancillary link to translation regulation during division.","confidence":"High","size":15,"edges":95,"triangles":361,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051256","count":9},{"id":"GO:0051258","count":9},{"id":"GO:1903087","count":9},{"id":"GO:2000767","count":9},{"id":"GO:1905789","count":9}]},{"hash":"1635490739629930774","title":"Developmental transcriptional regulation","description":"This cluster shows enrichment for GO terms tied to controlling gene expression during development across multiple tissues\u2014bone (osteoblast differentiation), muscle, pancreas, heart valve development, and neural lineages\u2014alongside transcription by RNA polymerase II. The common theme is proteins involved in orchestrating differentiation and maturation through transcriptional control, rather than a single tissue-specific function.","confidence":"Medium","size":15,"edges":102,"triangles":419,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045668","count":12},{"id":"GO:0060766","count":12},{"id":"GO:0043433","count":10},{"id":"GO:0035914","count":10},{"id":"GO:0031018","count":10}]},{"hash":"2055391978086801188","title":"Intracellular transport and vesicle trafficking","description":"The top GO terms point to intracellular movement and targeting, including Cvt/autophagy targeting, mitochondrion transport along microtubules, and regulation of the secretory pathway, which together emphasize vesicle trafficking and organelle localization. Some terms relate to neuronal and cardiac development, but they can be viewed as broader contexts of cellular organization that rely on transport systems. Overall, the cluster appears enriched for intracellular trafficking and protein/organelle targeting functions.","confidence":"Medium","size":15,"edges":15,"triangles":4,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032258","count":15},{"id":"GO:0060079","count":15},{"id":"GO:0016358","count":15},{"id":"GO:0036035","count":15},{"id":"GO:0060047","count":15}]},{"hash":"2244175817442203113","title":"Developmental transcription regulators","description":"The cluster centers on transcriptional regulation by RNA polymerase II, enriched for both positive/negative transcription terms and several developmental processes (neural/neuronal development, primitive streak formation, pituitary development). This pattern suggests a group of factors that modulate transcription during development, particularly neuronal differentiation, with broader involvement in lineage differentiation.","confidence":"High","size":15,"edges":18,"triangles":3,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0021983","count":4},{"id":"GO:0030851","count":4},{"id":"GO:0045648","count":4},{"id":"GO:0008045","count":4}]},{"hash":"2250353601955862207","title":"Unknown","description":"The terms cover diverse processes from defense and development to organelle organization and stress responses, with no clear shared function linking all proteins. This lack of a cohesive theme makes a precise, informative label difficult, so I classify it as Unknown.","confidence":"","size":15,"edges":21,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042832","count":7},{"id":"GO:0006998","count":4},{"id":"GO:0044319","count":4},{"id":"GO:0001822","count":4},{"id":"GO:0006972","count":4}]},{"hash":"1965231299157415373","title":"Mitochondrial Energy Metabolism and Starvation Response","description":"This cluster centers on energy metabolism and nutrient status, with GO terms like mitochondrial translation, TCA cycle, fatty acid catabolism, and glycogen biosynthesis, plus a notable enrichment for response to starvation. These point to proteins involved in mitochondrial energy production and metabolic adaptation under low-nutrient conditions; a few outliers (nylon/antibiotic biosynthesis) may reflect broader enzymatic capabilities or annotation quirks rather than a cohesive alternative function.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":5},{"id":"GO:0019878","count":4},{"id":"GO:0009791","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0005978","count":3}]},{"hash":"188443721183532619","title":"Male Germ Cell Redox Regulation","description":"Strong enrichment for cellular oxidant detoxification, redox homeostasis, and ROS/ H2O2 catabolic processes, along with cytochrome complex assembly, points to a redox-centric function tied to mitochondrial activity in germ cells. The presence of GO terms related to male gonad development and regulation of male germ cell proliferation further supports a role in male germline redox regulation.","confidence":"Medium","size":15,"edges":99,"triangles":386,"max_degree":14,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0098869","count":10},{"id":"GO:0045454","count":9},{"id":"GO:2000255","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0030416","count":8}]},{"hash":"1007333193064023501","title":"Immune signaling and lymphoid homeostasis","description":"The cluster is dominated by immune-related GO terms (innate immune response, B cell homeostasis, spleen development, regulation of T cell proliferation) and protein ubiquitination. A single outlier term about synapse assembly is much less represented, so the overall theme fits immune system regulation and lymphoid development.","confidence":"High","size":15,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0010745","count":3},{"id":"GO:0046597","count":2},{"id":"GO:0016567","count":2}]},{"hash":"1383658959908163326","title":"Mesodermal Development and Vascular Growth Signaling","description":"The cluster\u2019s terms cluster around mesodermal development and growth factor\u2013driven signaling: skeletal system/metazoan mesoderm fate specification, VEGF/PDGF receptor\u2013mediated proliferation, MAPK/STAT signaling, and smooth muscle proliferation. Although there are a few outliers and obsolete terms, the dominant theme is signaling pathways guiding mesodermal development and vascular/smooth muscle growth.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001501","count":5},{"id":"GO:0000187","count":5},{"id":"GO:0048378","count":4},{"id":"GO:0038093","count":4},{"id":"GO:0038091","count":4}]},{"hash":"743347112792006150","title":"Integrin signaling and vesicle trafficking","description":"The cluster shows strong enrichment for integrin-mediated signaling, cell-matrix adhesion, actin filament bundling, exocytosis, and recycling, with platelet aggregation reinforcing adhesion/secretory processes. This points to a cohesive theme of adhesion-cytoskeleton coordination and vesicle trafficking rather than tissue-specific differentiation.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001046","count":13},{"id":"GO:2000691","count":13},{"id":"GO:0006887","count":13},{"id":"GO:0007160","count":13},{"id":"GO:0070527","count":13}]},{"hash":"1744928313313697902","title":"NOD2-MDP Innate Immunity and Cytokine Regulation","description":"The top GO terms point to detection of muramyl dipeptide and NOD2 signaling, combined with production/regulation of inflammatory cytokines (TNF, IL-6, IL-18) and chemokines, as well as ubiquitination and nuclear export, suggesting a cohesive theme of innate immune sensing driving cytokine responses.","confidence":"Medium","size":15,"edges":11,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032760","count":3},{"id":"GO:1905279","count":2},{"id":"GO:0032498","count":2},{"id":"GO:1904887","count":2},{"id":"GO:0016567","count":2}]},{"hash":"1993604729960462399","title":"Cardiovascular signaling and vascular development","description":"The cluster is dominated by terms related to heart development, vascular signaling, and vascular tone (G protein-coupled acetylcholine receptor signaling, VEGF response, vasoconstriction, heart development) along with key signaling modules (PI3K/AKT and Rho pathways) and sodium transport regulation, pointing to a cohesive cardiovascular/vascular signaling theme. Some terms (B cell affinity maturation, dendritic spine development regulation) are peripheral but do not overwhelm the main cardiovascular focus. Confidence: Medium","confidence":"","size":15,"edges":14,"triangles":0,"max_degree":14,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007213","count":9},{"id":"GO:0010765","count":9},{"id":"GO:0035924","count":8},{"id":"GO:0045907","count":8},{"id":"GO:0061000","count":8}]},{"hash":"408415947065520281","title":"Endocrine Signaling and ER Stress Regulation","description":"This cluster's GO terms converge on regulation of signaling pathways (insulin receptor, Fc receptor, cyclin-dependent kinase activity), control of translation during ER stress, and processes affecting calcium signaling, mitochondrial function, and cell migration. The inclusion of parathyroid gland development and smooth muscle/cell migration suggests an endocrine- and signaling-centric theme with stress-response integration. Overall, the proteins likely participate in coordinated regulation of signaling and stress responses in endocrine-related contexts.","confidence":"Medium","size":15,"edges":22,"triangles":0,"max_degree":6,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045737","count":11},{"id":"GO:0046626","count":10},{"id":"GO:0036493","count":9},{"id":"GO:0016477","count":9},{"id":"GO:0060368","count":9}]},{"hash":"1476551729039562530","title":"Steroid and Lipid Metabolism with Cofactor Biosynthesis","description":"The top GO terms point to lipid biosynthesis (sphingolipids, fatty acid elongation), steroid metabolism (androgen catabolic, estrogen biosynthetic), and cofactor biosynthesis (phylloquinone, tetrahydrobiopterin, polyhydroxybutyrate), with some catabolic processes as well. This coherence suggests a cluster centered on lipid- and steroid-related metabolism and cofactor biosynthesis rather than a single, narrow function.","confidence":"Medium","size":15,"edges":13,"triangles":3,"max_degree":6,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006710","count":6},{"id":"GO:0030324","count":6},{"id":"GO:0042376","count":6},{"id":"GO:0030148","count":6},{"id":"GO:0030497","count":6}]},{"hash":"2043722471864177692","title":"Embryonic organogenesis and morphogenesis","description":"This cluster is enriched for GO terms related to the development of multiple organs and tissues (pituitary, pancreas, digestive tract, eye, teeth) and processes like neural crest migration and organ morphogenesis, indicating a general embryonic development theme rather than a single function. The transcription-related terms likely reflect overarching gene-expression regulation during development, but the dominant signal points to organogenesis. ","confidence":"High","size":15,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":10},{"id":"GO:0021983","count":8},{"id":"GO:0090190","count":8},{"id":"GO:0001755","count":8},{"id":"GO:0048557","count":7}]},{"hash":"139330065945921592","title":"Actin Cytoskeleton Dynamics and Contractility","description":"This cluster is dominated by actin-related processes: polymerization, stress fiber regulation, and contractile ring assembly, all coordinated by GTPase signaling. The neural tube closure term points to morphogenesis driven by actin remodeling, while intracellular transport and signaling terms fit with actin-regulated trafficking and secretion contexts. Overall, the shared function centers on actin cytoskeleton remodeling and cell contractility.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0001843","count":3},{"id":"GO:0051497","count":3},{"id":"GO:0006886","count":3},{"id":"GO:0042989","count":2}]},{"hash":"2297847614172113567","title":"Chromatin silencing and transcriptional repression","description":"The cluster is dominated by GO terms related to negative regulation of transcription (by RNA Pol II and rRNA Pol I), histone modifications, and heterochromatin formation, including telomeric localization and dosage compensation. This points to proteins involved in establishing and maintaining repressive chromatin states and transcriptional silencing, rather than activation. An outlier term about keratinocyte differentiation is present but does not define the group. ","confidence":"High","size":15,"edges":47,"triangles":48,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":11},{"id":"GO:0033128","count":11},{"id":"GO:1904815","count":11},{"id":"GO:0051572","count":11},{"id":"GO:0007549","count":11}]},{"hash":"919775431234998053","title":"Golgi-ER and Endosomal Vesicle Trafficking","description":"These proteins show a clear pattern of involvement in vesicle formation and transport within the secretory pathway, including ER\u2013Golgi, Golgi\u2013plasma membrane, and Golgi\u2013ER retrograde trafficking, as well as multivesicular body/endosomal sorting. The dominant GO terms point to a cohesive module governing vesicle trafficking along the Golgi\u2013endosome axis; occasional cell cycle terms likely reflect broader cellular context rather than the core function.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902902","count":2},{"id":"GO:0010458","count":2},{"id":"GO:0071985","count":2},{"id":"GO:0036258","count":2},{"id":"GO:0051301","count":2}]},{"hash":"761247094350709000","title":"Ribosome Biogenesis and Growth Signaling","description":"Top terms indicate a core role in ribosome assembly and rRNA processing (endonucleolytic cleavage in ITS1; ribosome biogenesis), complemented by signaling and regulatory processes such as GTPase/kinase activity, Rap signaling, and ubiquitin ligase regulation, all of which can influence cell growth and division. This suggests a cluster that links ribosome production with growth and cell-cycle signaling pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0031954","count":3}]},{"hash":"1916189325533465313","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016260","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0009229","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0070329","count":2}]},{"hash":"167752109869537240","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":3},{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0007084","count":2},{"id":"GO:0051292","count":2}]},{"hash":"1310236138203154388","title":"NF-kappaB\u2013driven immune signaling","description":"This cluster centers on innate and adaptive immunity with strong representation of NF-kappaB signaling (canonical and positive regulation), TLR2 signaling, and lymphocyte activation pathways (B cell and T cell receptor signaling), indicating a coordinated immune activation program. The mixed terms like innate response, TLR2, NF-kB, and lymphocyte activation support a cohesive immune signaling theme rather than a single specialized process.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032094","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0007249","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0050871","count":2}]},{"hash":"1753747655694788388","title":"Craniofacial morphogenesis and ECM remodeling","description":"The top GO terms cluster around craniofacial development and tissue remodeling, including face morphogenesis, embryonic cranial skeleton morphogenesis, and craniofacial suture morphogenesis, with extracellular matrix disassembly supporting remodeling processes. A few immune-related terms appear but are less representative of the dominant theme. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":2},{"id":"GO:0045579","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0022617","count":2},{"id":"GO:0002639","count":2}]},{"hash":"641169456319701302","title":"Ephrin signaling and hematopoietic development","description":"This cluster is dominated by ephrin receptor signaling, plus a set of terms tied to cell adhesion, hematopoietic lineage development (megakaryocytes, osteoclasts, B cells), and related immune and neural differentiation processes. The combination suggests a theme around Eph-ephrin mediated signaling coordinating development and differentiation across hematopoietic and neural/immune lineages, with some involvement in cellular stress responses and immune regulation.","confidence":"Medium","size":15,"edges":42,"triangles":45,"max_degree":10,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0048013","count":15},{"id":"GO:0034446","count":15},{"id":"GO:0036493","count":14},{"id":"GO:0035855","count":14},{"id":"GO:1904140","count":14}]},{"hash":"244442075539928255","title":"Nuclear gene expression and genome maintenance","description":"This cluster centers on nuclear processes: DNA repair, DNA-templated transcription, mRNA processing, and translation initiation factor assembly, with supporting links to meiosis and regulation of signaling that influence gene expression. A few terms (e.g., neutrophil clearance) appear as noise or less connected, but the dominant theme ties to genome maintenance and how genes are expressed in the nucleus.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0045819","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0097350","count":2}]},{"hash":"790598241651475100","title":"Diverse solute transporter proteins","description":"The GO terms show multiple transmembrane transport activities across a range of substrates (sugars, ions, nitrate/nitrite, xenobiotics, etc.), suggesting a cluster of broad-substrate membrane transporters. A DNA-templated transcription term is present but not dominant, so the core theme is transport rather than transcription. Therefore, the label reflects the primary function of the cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0015751","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0015739","count":3}]},{"hash":"390570567063285334","title":"Embryonic development and tissue morphogenesis","description":"The top GO terms cluster around developmental processes\u2014placental and endocrine system development, left-right patterning, EMT in heart formation, cartilage morphogenesis, and collagen fibril organization\u2014indicating roles in organogenesis and extracellular matrix remodeling. Some terms (synapse assembly, complement activation) are less central but may reflect broader tissue interactions during development. Thus this label captures the core theme of development-driven morphogenesis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0003323","count":4},{"id":"GO:0060806","count":4},{"id":"GO:0060972","count":4},{"id":"GO:0060707","count":4},{"id":"GO:0003198","count":4}]},{"hash":"276388221901295077","title":"Podocyte Development and SMAD Signaling","description":"This cluster shows strong representation of podocyte development and podocyte migration terms, along with SMAD signaling and its regulation, suggesting a shared role in podocyte differentiation and TGF-beta/SMAD pathway activity. Nuclear transport-related terms are present but appear ancillary to the core podocyte/SMAD theme. Overall, the terms point to a coherent podocyte-centric signaling cluster.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0021957","count":2},{"id":"GO:1903206","count":1},{"id":"GO:0072015","count":1},{"id":"GO:0060391","count":1}]},{"hash":"1363761621445340929","title":"Chromatin regulation and transcription control","description":"This cluster centers on chromatin biology and transcription regulation, with terms related to negative regulation of RNA polymerase II transcription, histone modifications (K27 methylation, phosphorylation), and CENP-A\u2013containing chromatin assembly and chromosome condensation. A few terms refer to development (midbrain morphogenesis, fertilization, B-cell differentiation), but the dominant signal points to chromatin remodeling and transcription control.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0061086","count":3},{"id":"GO:0061641","count":2},{"id":"GO:0007338","count":2},{"id":"GO:2000973","count":2}]},{"hash":"2168662614476191687","title":"NF-kappaB/NFAT signaling and transcription regulation","description":"The GO terms center on regulation of NF-kappaB and NFAT signaling (canonical NF-kappaB, calcineurin-NFAT pathways) alongside nuclear import and transcription initiation steps (NLS-bearing protein import, RNA Pol II preinitiation complex assembly, DNA-templated transcription initiation), indicating a core role in transcriptional activation controlled by these pathways. Some terms also relate to angiogenesis and epithelial differentiation, which can be downstream contexts of NF signaling.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0051531","count":2},{"id":"GO:0043123","count":2}]},{"hash":"1242604182653072994","title":"Unknown","description":"The proteins map to a mix of developmental, nervous, immune, metabolic, and cardiovascular processes with no single dominant function among the top GO terms, so a cohesive label cannot be assigned.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":2},{"id":"GO:0050808","count":2},{"id":"GO:0035234","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0006013","count":2}]},{"hash":"1377436588744483886","title":"Nuclear RNA processing and splicing machinery","description":"The top terms overwhelmingly cluster around nuclear RNA processing and splicing (mRNA splicing via spliceosome, snRNP assembly, tRNA and rRNA maturation, RNA Pol II transcription termination, and nuclear import). There are additional chromatin-related terms (histone mRNA metabolism, pericentric heterochromatin formation) suggesting broader coordination with chromatin regulation, but the central theme is RNA processing/splicing in the nucleus.","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":10},{"id":"GO:0008033","count":8},{"id":"GO:0051170","count":8},{"id":"GO:0000290","count":8},{"id":"GO:0030490","count":8}]},{"hash":"302955414486816383","title":"Skeletal muscle actin filament and sarcomere assembly","description":"The cluster is dominated by GO terms for actin cytoskeleton organization and muscle structure, including actin filament bundle assembly, thin filament assembly, sarcomere organization, and skeletal muscle fiber development, pointing to a core role in muscle sarcomere formation and actin-based architecture. A few terms (e.g., histone acetylation and heterochromatin formation) appear unrelated and likely represent noise or shared components, while a term like platelet aggregation can reflect actin dynamics rather than muscle-specific function. Overall, the dominant signal supports a muscle structural assembly theme.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051666","count":11},{"id":"GO:0070527","count":11},{"id":"GO:0051017","count":11},{"id":"GO:0006348","count":11},{"id":"GO:0030240","count":11}]},{"hash":"2266453228460904019","title":"Arp2/3-driven actin nucleation and spine morphogenesis","description":"The cluster centers on actin cytoskeleton dynamics, with terms for actin nucleation, filament polymerization, Arp2/3-mediated nucleation, and actin filament-based movement, along with dendritic spine morphogenesis. This points to a cohesive theme of actin remodeling and spine structure, with secondary links to immune cell motility and membrane tubulation regulation. ","confidence":"High","size":14,"edges":40,"triangles":39,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045010","count":4},{"id":"GO:0030041","count":4},{"id":"GO:0006378","count":3},{"id":"GO:0032233","count":3},{"id":"GO:2000402","count":3}]},{"hash":"355845628251700320","title":"Translational initiation and reinitiation control","description":"This cluster is dominated by translation-related terms: initiation, preinitiation complex formation, translation, translation reinitiation, and IRES-dependent viral translation, indicating a shared role in translational regulation and ribosome assembly. A few terms relate to RNA processing or stress responses, but they are secondary to translation. DNA replication and SOS response appear only as minor associations. ","confidence":"High","size":14,"edges":35,"triangles":35,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0075525","count":3}]},{"hash":"1951424545871079221","title":"Nuclear transport and ribosome export","description":"The top GO terms concentrate on ribosomal subunit export from the nucleus, various nuclear import/export processes (including splicing factors and snRNPs), and nuclear transcription regulation, with additional hints of centrosome-related and intraflagellar transport. This points to a cohesive theme centered on nucleocytoplasmic trafficking and ribosome biogenesis, with ancillary roles in nuclear regulation and intracellular transport. Confidence: Medium","confidence":"","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0000056","count":7},{"id":"GO:0000055","count":7},{"id":"GO:0000060","count":7},{"id":"GO:0010824","count":6}]},{"hash":"1875783071647385417","title":"RNA processing and growth factor signaling","description":"The proteins show enrichment for RNA-related processes (translation, deadenylation-dependent decay, spliceosomal snRNP assembly) alongside signaling pathways (ERK1/2 cascade, cellular response to FGF stimulus, PMA response). This suggests a cluster of factors that link RNA metabolism with growth factor\u2013mediated signaling, rather than a single narrowly defined function. However, the connections are broad and diverse, so confidence is medium. ","confidence":"Medium","size":14,"edges":14,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000288","count":1},{"id":"GO:0003342","count":1},{"id":"GO:0000387","count":1},{"id":"GO:1904246","count":1}]},{"hash":"600534152187071006","title":"NF-kappaB and MAPK Signaling Regulators","description":"The top GO terms show strong enrichment for regulation of NF-kappaB signaling and ERK/MAPK cascades, along with related immune and calcium signaling and ubiquitination processes, indicating a coherent theme of signaling pathway regulation rather than a single structural function; while some terms touch development or hypoxia, the dominant signals point to transcription-factor\u2013driven kinase signaling control.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0010800","count":4},{"id":"GO:0043123","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0001666","count":3},{"id":"GO:0045086","count":3}]},{"hash":"1676351352335579786","title":"Autophagy and membrane trafficking regulation","description":"The cluster is centered on autophagy-related processes (positive regulation of macroautophagy) and endomembrane dynamics (exocytosis, endocytic recycling, plasma membrane tubulation), with some additional terms about protein complex stability. While a few terms relate to plant reproduction or DNA repair, the dominant theme points to regulation of autophagy and vesicle trafficking within the cell.","confidence":"Medium","size":14,"edges":70,"triangles":165,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0061635","count":3},{"id":"GO:0016239","count":3},{"id":"GO:0007131","count":1},{"id":"GO:0009555","count":1},{"id":"GO:0009553","count":1}]},{"hash":"1571597962001959530","title":"Tissue development and remodeling","description":"This cluster features several development-related terms: skeletal muscle tissue development, skeletal system development, and VEGF-induced cellular responses, along with cell migration and hyaluronan metabolism, all pointing to tissue morphogenesis and ECM remodeling. While some terms like visual perception and B cell receptor signaling are less obviously tied to development, the overall pattern centers on growth, differentiation, and remodeling of tissues. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0007601","count":8},{"id":"GO:0050853","count":8},{"id":"GO:0016477","count":8},{"id":"GO:0007519","count":8}]},{"hash":"922148932069149734","title":"Axonogenesis and myelination","description":"The top GO terms show strong signals for nervous system development, axon organization (paranode localization), myelination, neurogenesis, and nerve impulse transmission, plus VGSC clustering. This points to coordinated roles in forming and insulating axons and establishing functional neural circuits, including peripheral nervous system development. Therefore the label captures the cluster's focus on axon growth, organization, and myelination.","confidence":"High","size":14,"edges":90,"triangles":352,"max_degree":13,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007399","count":12},{"id":"GO:0050808","count":11},{"id":"GO:0042517","count":11},{"id":"GO:0002175","count":11},{"id":"GO:0042552","count":11}]},{"hash":"1644741571462977830","title":"Developmental Transcription Regulation and Stress Response","description":"Key terms center on DNA-templated transcription and its negative regulation, plus multiple development-related processes across distinct tissues (forebrain, mammary gland alveolus, Leydig cells, ovarian axis). The inclusion of endoplasmic reticulum unfolded protein response and p53-mediated apoptotic signaling suggests a broader regulatory network linking transcription control, development, and cellular stress responses. The glucosinolate metabolism term appears as an outlier, but overall the cluster is best described by developmental transcription regulation with stress response features.","confidence":"High","size":14,"edges":63,"triangles":129,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0030900","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0030968","count":5},{"id":"GO:0051301","count":5}]},{"hash":"1157760698526061196","title":"Embryonic FGF/MAPK Signaling and Translation Regulation","description":"GO terms point to ERK1/ERK2 cascade and cellular response to FGF, with mesendoderm and proepicardium development, suggesting a development-focused signaling module. Concurrently, mRNA deadenylation and negative regulation of cytoplasmic translation indicate post-transcriptional control of gene expression during these developmental processes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0000288","count":3},{"id":"GO:0003342","count":3},{"id":"GO:1904246","count":3},{"id":"GO:0070371","count":3},{"id":"GO:0044344","count":3}]},{"hash":"675182918100366012","title":"Iron Transport and Siderophore Import","description":"The top GO terms strongly point to iron metabolism: iron ion transport, detoxification and sequestration of iron, and specifically siderophore-iron import into the cell. This pattern suggests a cluster of proteins involved in iron acquisition and homeostasis, potentially bacterial, where siderophore-mediated uptake and iron handling are central. Some other terms appear as outliers, but the iron-focused signals dominate the cluster\u2019s theme.","confidence":"High","size":14,"edges":79,"triangles":286,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006880","count":13},{"id":"GO:0006950","count":13},{"id":"GO:1990461","count":13},{"id":"GO:0033214","count":13},{"id":"GO:0048147","count":13}]},{"hash":"447771194867896276","title":"GPCR-cAMP Signaling and Inflammation","description":"This cluster is dominated by GO terms related to G protein-coupled receptor signaling that modulates adenylate cyclase activity and cAMP production, including activating and inhibiting pathways, along with related peptide responses and inflammatory/defense processes. While some terms like electron transport chain and visual perception appear (likely outliers or multi-functional annotations), the recurring theme centers on GPCR-mediated signaling influencing inflammatory responses, suggesting a cohesive GPCR-cAMP/inflammation-related group.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":14},{"id":"GO:0045777","count":14},{"id":"GO:0010579","count":14},{"id":"GO:0007190","count":13},{"id":"GO:0007601","count":12}]},{"hash":"2026090846913138783","title":"Neural Crest Migration and Axon Guidance","description":"This cluster is dominated by neural development terms: ventral trunk neural crest cell migration, trigeminal nerve structural organization, axonal fasciculation, and sympathetic neuron projection guidance, with semaphorin-plexin signaling and related ERK/STAT signaling involved in these processes. A few immune-related terms appear (adaptive immune response, immunoglobulin production), but they are not as representative as the neural development terms, suggesting multifunctionality or annotation overlap. Overall, the theme is neural crest\u2013derived migration and axon pathfinding.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002250","count":3},{"id":"GO:0006910","count":3},{"id":"GO:0042511","count":3},{"id":"GO:0036486","count":3},{"id":"GO:1902287","count":3}]},{"hash":"1890169970391214453","title":"Adaptive Immune Signaling and Hematopoietic Development","description":"We labeled this cluster Adaptive Immune Signaling and Hematopoietic Development because the top GO terms concentrate on adaptive immunity (B cell affinity maturation, adaptive immune response, Fc-epsilon receptor signaling, T cell receptor signaling regulation, type I interferon signaling) and on hematopoietic lineage processes (megakaryocyte development), indicating a cohesive group of proteins involved in immune signaling and blood cell formation.","confidence":"High","size":14,"edges":45,"triangles":65,"max_degree":13,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0002344","count":12},{"id":"GO:0010765","count":11},{"id":"GO:0035023","count":11},{"id":"GO:0035855","count":9},{"id":"GO:0038095","count":9}]},{"hash":"168924773161197284","title":"Mitochondrial metabolism and stress response","description":"This cluster is dominated by GO terms tied to mitochondrial function and stress responses, including import of iron and pyrimidine nucleotides into mitochondria, regulation of membrane permeability and apoptotic changes, and responses to amino acid starvation, fatty acids, and oxidative stress, plus adaptive thermogenesis and glucose-linked insulin secretion regulation. Together these indicate a coherent theme around mitochondrial energy metabolism and stress signaling.","confidence":"High","size":14,"edges":11,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":7},{"id":"GO:0000303","count":6},{"id":"GO:0048250","count":6},{"id":"GO:0070542","count":6},{"id":"GO:0015709","count":6}]},{"hash":"470484189123464094","title":"Lens fiber morphogenesis and light-stress signaling","description":"This cluster centers on lens development (lens fiber morphogenesis) and a set of light- and stress-responsive processes (response to high light, UV-A, MAPK stress signaling), coupled with cytoskeletal dynamics (microtubule polymerization/depolymerization) and cellular growth regulation. The mix suggests a cohesive theme of lens cell development under photic stress and related signaling, with some supporting housekeeping processes like protein oligomerization regulation and amyloid fibril formation. Confidence: Medium","confidence":"Medium","size":14,"edges":88,"triangles":330,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0070309","count":11},{"id":"GO:0051403","count":11},{"id":"GO:0032355","count":11},{"id":"GO:0032463","count":11},{"id":"GO:0009644","count":11}]},{"hash":"598812283782993604","title":"Chondrocyte differentiation and proteoglycan biosynthesis","description":"The top GO terms include chondrocyte proliferation, chondrocyte differentiation, positive regulation of chondrocyte differentiation, and proteoglycan biosynthetic process, pointing to cartilage development. Translation/ribosome terms appear but are generic; the cartilage-related terms dominate, suggesting a focus on chondrogenesis and extracellular matrix production.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0007275","count":1},{"id":"GO:1903215","count":1},{"id":"GO:0045676","count":1}]},{"hash":"985046121132341156","title":"Lipid and steroid biosynthesis","description":"This cluster centers on lipid and steroid metabolism, with frequent terms for sphingolipid biosynthesis, fatty acid elongation, phylloquinone (vitamin K) catabolic/biosynthetic steps, and estrogen/androgen biosynthesis and catabolism. The inclusion of polyhydroxybutyrate biosynthetic process aligns as a lipid-like storage pathway, while one outlier term (lung development) is less related. Overall, the dominant theme is lipid and steroid biosynthesis/metabolism. ","confidence":"High","size":14,"edges":51,"triangles":85,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042619","count":13},{"id":"GO:0055114","count":13},{"id":"GO:0006710","count":12},{"id":"GO:0030324","count":12},{"id":"GO:0042376","count":12}]},{"hash":"628335604912259723","title":"Fatty acid metabolism and menaquinone biosynthesis","description":"The top GO terms point to fatty-acid metabolism (medium- and long-chain), fatty-acid import, and menaquinone biosynthesis, with supporting pathways including acetyl-CoA biosynthesis, pyruvate fermentation to acetate, and various catabolic routes. A siderophore biosynthetic term fits the microbial metabolic context, though seed coat development appears as an outlier annotation. Taken together, the cluster seems centered on microbial lipid metabolism and cofactor biosynthesis, with ancillary energy-yield pathways.","confidence":"Medium","size":14,"edges":51,"triangles":86,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":8},{"id":"GO:0036112","count":7},{"id":"GO:0010124","count":7},{"id":"GO:0019427","count":7},{"id":"GO:0001676","count":7}]},{"hash":"914158449351569308","title":"Vascular inflammation and lipoprotein clearance","description":"These terms collectively point to a vascular endothelium context where immune activation via complement pathways, lipoprotein transport/clearance, receptor-mediated endocytosis, and endothelial remodeling (proliferation and tight junction assembly) intersect; together they suggest a role in vascular inflammation linked to lipid handling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0006958","count":8},{"id":"GO:2001046","count":6},{"id":"GO:0051918","count":5},{"id":"GO:0001867","count":5},{"id":"GO:0006898","count":5}]},{"hash":"1459264617770381129","title":"Egg activation and pronucleus formation","description":"The top GO terms strongly point to fertilization-related nuclear events, with explicit mentions of egg activation and male pronucleus assembly. Supporting terms about chromatin remodeling and cytoskeletal organization fit the early zygotic and structural changes that follow fertilization. Some peripheral terms (estrogen response, autophagy regulation) do not contradict this core theme but are less central, so the label captures the dominant function while acknowledging some heterogeneity. ","confidence":"Medium","size":14,"edges":18,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045109","count":3},{"id":"GO:1902902","count":3},{"id":"GO:0035335","count":3},{"id":"GO:0030259","count":3},{"id":"GO:0045815","count":3}]},{"hash":"1617988107008756227","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The cluster is enriched for ubiquitin-dependent protein catabolic process and proteasome assembly, indicating core involvement in protein turnover via the ubiquitin-proteasome system. Other terms like Rho signaling and dendrite development may reflect broader regulatory roles, but the dominant theme is proteasome-mediated degradation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":3},{"id":"GO:0006511","count":3},{"id":"GO:0043248","count":3},{"id":"GO:1901224","count":2},{"id":"GO:0007266","count":2}]},{"hash":"6369512995700411","title":"Chromatin dynamics and proteostasis","description":"The top GO terms cluster around nucleosome assembly/disassembly and histone modification, coupled with ubiquitin-dependent protein degradation and aggresome assembly, pointing to chromatin remodeling linked to proteostasis. Some terms touch on microtubule localization and immune-related processes, but the dominant signal is chromatin dynamics with protein quality control.","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006337","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0098532","count":2},{"id":"GO:0032602","count":2}]},{"hash":"1280934721315656969","title":"Nuclear transcription and chromatin regulation","description":"The GO terms cluster around nuclear gene expression control: mRNA export, transcription elongation, and histone modification, with associated processes like nuclear membrane disassembly and G2/M cell cycle transition. Immune-response terms may reflect signaling impacts on transcription, but the core theme is nuclear regulation of transcription and cell-cycle control.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010793","count":4},{"id":"GO:0006378","count":3},{"id":"GO:0033127","count":3},{"id":"GO:0031065","count":3},{"id":"GO:0071222","count":3}]},{"hash":"1797894868376329655","title":"Developmental signaling and tissue differentiation","description":"The top GO terms span diverse developmental processes across multiple tissues (Sertoli cell development, cornea, prostatic bud elongation, radial glial scaffolds, cardiac fate), along with cellular responses to signaling (TGF-beta, heparin) and chromatin remodeling, suggesting a shared theme of development and differentiation rather than a single tissue-specific function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071560","count":5},{"id":"GO:0021943","count":5},{"id":"GO:0060009","count":5},{"id":"GO:0043044","count":5},{"id":"GO:0071504","count":5}]},{"hash":"1635658305731393020","title":"Negative Regulation of Signaling and Transport","description":"The terms point to multiple negative regulatory roles, including NF-kappaB and TNF signaling, HIF-1alpha signaling, and various transport/trafficking processes (endosome transport, protein localization to the cell surface). There are also diverse outcomes like barrier establishment, T cell death, brain development, and osteoclast differentiation, which together suggest a cluster of proteins that broadly dampen signaling and trafficking across contexts rather than a single, cohesive pathway. Confidence: Medium","confidence":"","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:1902306","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0033209","count":2},{"id":"GO:1902072","count":2}]},{"hash":"1935732536731137094","title":"Immune signaling and cell-cycle regulators","description":"The top GO terms point to modulation of key signaling pathways (ERK cascade, PI3K activity, NF-kappaB regulation) and immune processes (TH1 type response, IL-23 regulation, synaptic vesicle exocytosis), suggesting a cluster of proteins that broadly regulate signaling in immune and proliferative contexts. Some terms about mechanical stimulus response and mitotic spindle assembly imply additional roles in cell-cycle-related signaling, but the unifying thread is regulators of signaling pathways linked to immunity and cell growth.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070374","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0090307","count":4},{"id":"GO:0043124","count":4}]},{"hash":"1503920666931186620","title":"Rho GTPase signaling and cytoskeleton remodeling","description":"Dominated by Rho family GTPase\u2013mediated pathways that regulate actin dynamics (filopodium assembly, adhesion-dependent spreading) and cell migration; includes regulation of Rho signaling and GTPase activity, with connections to mitochondrial fission and, in neuronal contexts, GABAergic synaptic transmission, collectively pointing to coordinated cytoskeletal remodeling and cell movement.","confidence":"High","size":14,"edges":26,"triangles":6,"max_degree":7,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:1900026","count":10},{"id":"GO:0046847","count":10},{"id":"GO:0007264","count":9},{"id":"GO:0051932","count":9},{"id":"GO:0045792","count":9}]},{"hash":"97023219688124158","title":"Embryonic development and organ morphogenesis","description":"These proteins show enrichment for developmental and morphogenesis processes across several organs and tissues, including lens fiber differentiation, heart and pancreas morphogenesis, hindlimb morphogenesis, neuron migration, and general growth, as well as transcriptional regulation. The eye-related and limb/organ development terms suggest a role in developmental differentiation rather than a single pathway. An outlier term about defense response to Gram-positive bacteria is present but does not dominate the set. Overall, the label reflects a broad developmental/morphogenetic theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0050830","count":3},{"id":"GO:0070306","count":3},{"id":"GO:0001764","count":3},{"id":"GO:0014068","count":3}]},{"hash":"485098276643913465","title":"Axon guidance and nerve development","description":"The cluster is dominated by GO terms tied to neural development and axon pathfinding: branchiomotor neuron axon guidance, semaphorin-plexin signaling in axon guidance, trigeminal nerve structural organization, and myelination, along with cell-cell adhesion. Together these suggest a coherent theme of axon guidance and nerve maturation. A couple of terms (ossification in bone maturation, symbiont entry into host cell) are less connected and may reflect incidental annotations. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0021785","count":8},{"id":"GO:0007157","count":8},{"id":"GO:1902287","count":8},{"id":"GO:0043931","count":8},{"id":"GO:0000187","count":8}]},{"hash":"1089637276016122955","title":"Pyrimidine nucleotide salvage cluster","description":"The GO terms strongest signal in this cluster are CMP salvage, UMP salvage, CTP salvage and pyrimidine nucleobase metabolic process, indicating a core theme of pyrimidine nucleotide salvage/metabolism. Other terms (phosphorylation, glucose transport, myelin assembly, heart rate regulation) appear less connected to this theme, suggesting they may reflect peripheral or incidental associations. Confidence in this core label is Medium.","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0043407","count":2},{"id":"GO:1904659","count":2},{"id":"GO:0086091","count":2},{"id":"GO:0015937","count":1}]},{"hash":"778133647946571726","title":"Embryonic organogenesis","description":"The GO terms cluster around development of embryonic structures and organs, including craniofacial (roof of mouth) development, placental/trophoblast differentiation, cartilage morphogenesis, endocrine pancreas development, and broader endocrine system formation. A few terms about transcriptional regulation and RNA processing suggest supporting gene-expression control during development. Overall, the set points to a module of proteins involved in embryonic organogenesis rather than a single biochemical activity.","confidence":"Medium","size":14,"edges":19,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":12},{"id":"GO:0060707","count":9},{"id":"GO:0035270","count":9},{"id":"GO:0060536","count":9},{"id":"GO:0032298","count":9}]},{"hash":"2168925372272417004","title":"Spinal cord neuron differentiation","description":"Strong signals for spinal cord neuron development: motor neuron and interneuron differentiation, and ventral/medial spinal cord specification; other terms (roof of mouth, renal/gonad morphogenesis) appear less central, suggesting the core theme is spinal cord neuronal differentiation.","confidence":"High","size":14,"edges":14,"triangles":1,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:2001046","count":6},{"id":"GO:0021527","count":5},{"id":"GO:0035852","count":5},{"id":"GO:0021526","count":5},{"id":"GO:0072283","count":5}]},{"hash":"1454830230755741136","title":"Embryogenesis and organ morphogenesis","description":"The top GO terms cluster around broad developmental and morphogenetic processes across multiple tissues\u2014pancreatic development, placental development, left-right pattern formation, trophoblast differentiation, EMT in heart development, endocrine system development, cartilage and skeletal muscle morphogenesis, and regulatory transcription control. This suggests a cohesive theme of embryonic development and tissue morphogenesis rather than a single tissue or pathway, so the label reflects the common function of the proteins. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003323","count":5},{"id":"GO:0060806","count":5},{"id":"GO:0060972","count":5},{"id":"GO:0060707","count":5},{"id":"GO:0003198","count":5}]},{"hash":"608827616929695429","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by ubiquitin-related processes: protein ubiquitination and ubiquitin-dependent proteolysis (ERAD), suggesting main involvement in tagging substrates for degradation. Some terms also point to chromatin regulation via ubiquitin-related histone modifications and to immune signaling regulation (RIG-I, TNF) and V(D)J recombination, possibly reflecting ubiquitin ligase roles in these pathways. Overall, the common theme is ubiquitin-mediated regulation of protein turnover and signaling.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0030433","count":9},{"id":"GO:0039536","count":8},{"id":"GO:2000620","count":8},{"id":"GO:0085020","count":8}]},{"hash":"890355978612661883","title":"Eye development and vision proteins","description":"The GO terms show a clear emphasis on ocular biology: lens fiber cell differentiation, camera-type eye development, and visual perception, indicating proteins involved in eye formation and vision. Additional terms point to broader neural/sensory development (midbrain, left/right axis) and some regulatory processes, suggesting supportive roles in development and transcriptional control. Overall, the cluster is best described by eye development and vision functions.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0048839","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0043010","count":4}]},{"hash":"1408839190761179666","title":"Developmental morphogenesis and cytoskeletal remodeling","description":"The terms cluster around heart, muscle, and vascular development, with actin filament assembly and cell migration pointing to cytoskeletal remodeling during tissue morphogenesis; ephrin signaling aligns with developmental patterning. A couple of outliers (obsolete NF-kappaB regulation, SNARE assembly) are less connected but do not dominate.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0008584","count":3},{"id":"GO:0051017","count":2},{"id":"GO:0097497","count":2}]},{"hash":"695930906623188710","title":"Glycan processing and sialylation","description":"The GO terms are dominated by glycosylation and carbohydrate metabolism: N-glycan processing, oligosaccharide metabolism, glycosylceramide metabolism, and protein sialylation. This points to a cohesive theme of glycan biosynthesis/modification. A few terms about pollen germination or olfactory nerve formation seem tangential and may reflect annotation noise, but they don\u2019t negate the primary glycan-focused signal. Therefore, the cluster is best described as glycan processing and sialylation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007596","count":3},{"id":"GO:0051897","count":3},{"id":"GO:0018279","count":2},{"id":"GO:0006677","count":2},{"id":"GO:1990743","count":2}]},{"hash":"309464980189501524","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms tied to translation and ribosome assembly: translation (GO:0006412), cytoplasmic translation (GO:0002181), ribosome biogenesis (GO:0042254), and ribosomal subunit biogenesis (GO:0042273), along with translation initiation (GO:0006413) and rRNA processing (GO:0000448). These collectively point to a set of proteins involved in ribosome production and protein synthesis, with a few outliers indicating secondary stress-response associations. Confidence: High","confidence":"","size":13,"edges":54,"triangles":117,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0042273","count":2}]},{"hash":"1885216135859635124","title":"Actin dynamics and endocytosis regulators","description":"GO terms point to actin cytoskeleton remodeling (actin patch assembly, Arp2/3 regulation) and endocytosis control (clathrin-dependent endocytosis), with accompanying signaling roles (kinase activity and GTPase regulation), suggesting a cohesive theme of actin dynamics governing membrane trafficking.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000147","count":6},{"id":"GO:0006919","count":6},{"id":"GO:0034316","count":4},{"id":"GO:2000369","count":4},{"id":"GO:0043547","count":4}]},{"hash":"855462660082709249","title":"Mitotic Regulation and Ribosome Biogenesis","description":"The top terms point to critical cell cycle processes (mitotic cell cycle, spindle orientation), ribosome biogenesis, and ubiquitin- and kinase-mediated regulation, with links to actin cytoskeleton dynamics. This combination suggests a cohesive theme of coordinating cell growth, division, and protein quality control, even though skeletal development appears as a less central annotation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0001501","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0034316","count":5},{"id":"GO:0000447","count":4},{"id":"GO:0043547","count":4}]},{"hash":"1960600621209682124","title":"Protein homeostasis and vesicle trafficking","description":"Based on the top GO terms, the cluster centers on intracellular trafficking (ER-to-Golgi transport, Cvt pathway, constitutive secretory pathway) and protein turnover/quality control (regulation of protein stability, ubiquitination), with additional terms hinting at downstream developmental and physiological roles. This suggests a cohesive theme around maintaining protein homeostasis through trafficking and turnover.","confidence":"Medium","size":13,"edges":16,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031647","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0032258","count":6},{"id":"GO:0060079","count":6},{"id":"GO:0016358","count":6}]},{"hash":"815020902314915853","title":"Embryonic development and cytoskeletal adhesion","description":"This cluster centers on developmental processes (endodermal fate, oviduct development, embryonic cell cycle regulation) and on cytoskeletal and cell\u2013cell adhesion machinery (intermediate filament bundle assembly, adherens junctions, centriole regulation), with related signaling (Wnt) and GTPase regulation, suggesting a cohesive role in tissue organization during development.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0045110","count":12},{"id":"GO:0042144","count":12},{"id":"GO:0034333","count":12},{"id":"GO:0030997","count":12},{"id":"GO:0001711","count":12}]},{"hash":"1945204393296214129","title":"Organogenesis and Neural Development","description":"Based on the enriched GO terms, the proteins appear involved in development across multiple organs\u2014including brain regions (midbrain, forebrain, spinal cord), cochlea, heart, and pancreas\u2014pointing to a shared theme of organogenesis and neural development. The presence of apoptotic process terms suggests involvement in developmental cell turnover or regulation. Overall, the cluster seems to reflect broad developmental programs rather than a single tissue-specific function.","confidence":"Medium","size":13,"edges":22,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030901","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0021516","count":2},{"id":"GO:0031018","count":2},{"id":"GO:0003309","count":2}]},{"hash":"250647868697907985","title":"Developmental signaling and organ morphogenesis","description":"The proteins are enriched for developmental processes across nervous system development (including substantia nigra development) and multiple organ morphogenesis events (hair follicle, salivary gland, ossification, lung morphogenesis), with involvement of ERK signaling, Wnt signaling, and GTPase regulation. This suggests a cohesive role in coordinating growth and patterning during development via conserved signaling pathways.","confidence":"High","size":13,"edges":41,"triangles":81,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0001957","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0060501","count":4}]},{"hash":"1450527749495080188","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":49,"triangles":101,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0070843","count":2},{"id":"GO:0090084","count":2},{"id":"GO:0071374","count":2}]},{"hash":"1053860589102324013","title":"MAPK-PI3K Signaling in Development","description":"Developmental processes are emphasized by heart development, fat cell differentiation, and spermatid nucleus differentiation, while central signaling pathways (Ras, ERK, and PI3K/AKT) are repeatedly represented (positive ERK cascade, negative Ras regulation, PI3K/AKT signaling). This suggests a cohesive theme of signaling-driven differentiation and organ/tissue development, supported by associated cell cycle and cytoskeletal dynamics terms. Confidence reflects the clear linkage between differentiation and signaling terms.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0046580","count":4},{"id":"GO:0045444","count":4},{"id":"GO:0070374","count":3},{"id":"GO:0051225","count":3}]},{"hash":"1911237530792615056","title":"Endothelial growth factor signaling and transcription activation","description":"This cluster centers on VEGF receptor signaling, endothelial cell chemotaxis, and responses to EGF, with associated JUN and STAT serine phosphorylation, indicating a cohesive theme of growth factor\u2013driven signaling and transcriptional activation in endothelial contexts. Peripheral terms like glucose response or dsRNA response appear less central to the main pattern.","confidence":"High","size":13,"edges":52,"triangles":101,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071333","count":8},{"id":"GO:0043330","count":8},{"id":"GO:0006813","count":8},{"id":"GO:0007601","count":7},{"id":"GO:0048010","count":7}]},{"hash":"1580275667930982366","title":"Immune signaling and inflammatory response","description":"The cluster\u2019s top GO terms cluster around immune defense (defense response to bacterium, T cell chemotaxis, acute inflammatory response), inflammatory signaling, and GPCR-driven pathways (adenylate cyclase-inhibiting GPCR signaling). Protein phosphorylation and GTPase regulation also support signal transduction themes in immune responses. An outlier term for visual perception may reflect annotation noise rather than a shared function. Overall, the proteins appear tied to immune signaling and inflammatory regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007601","count":12},{"id":"GO:0042742","count":12},{"id":"GO:0043547","count":12},{"id":"GO:0007197","count":12},{"id":"GO:1901652","count":12}]},{"hash":"840235053350436795","title":"miRNA Silencing and Immune Signaling","description":"The GO terms center on miRNA pathways (miRNA metabolic process, miRNA-mediated gene silencing, and positive regulation of miRNA silencing) and immune modulation (TNF signaling, chemokine production, and host antiviral actions), suggesting proteins in this cluster coordinate post-transcriptional gene regulation with inflammatory and antiviral responses; additional terms related to ubiquitination and lipid remodeling may support cytoskeletal or membrane-related aspects of immune function.","confidence":"Medium","size":13,"edges":14,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0007014","count":2},{"id":"GO:1903886","count":2},{"id":"GO:0035278","count":2}]},{"hash":"1719315394531149775","title":"Mitochondrial metabolism and stress response","description":"The most represented GO terms all center on mitochondrial function\u2014oxidative stress response, regulation of mitochondrial membrane permeability, apoptotic mitochondrial changes, and import of nucleotides and metals into mitochondria\u2014along with energy-related processes like adaptive thermogenesis and responses to fatty acids or amino acid starvation. These collectively point to a cohesive theme of mitochondrial metabolism, transport, and stress signaling in this protein cluster.","confidence":"High","size":13,"edges":14,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":4},{"id":"GO:0000303","count":4},{"id":"GO:0048250","count":4},{"id":"GO:0070542","count":4},{"id":"GO:0015709","count":4}]},{"hash":"723971417879538109","title":"Chromatin organization and histone modification","description":"The top terms point to histone methylation (H3K4/K27), nucleosome assembly and positioning, heterochromatin organization, and chromatin localization to the nucleus, indicating a cohesive group involved in chromatin structure and epigenetic regulation within the nucleus. This cluster likely represents components of chromatin remodeling/epigenetic control machinery.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0080182","count":12},{"id":"GO:0098532","count":12},{"id":"GO:0016584","count":12},{"id":"GO:0006334","count":12},{"id":"GO:0097298","count":12}]},{"hash":"1894692570906434634","title":"Unknown","description":"The top GO terms span very different biological areas (cell junction assembly, receptor- and integrin-mediated signaling and internalization, viral attachment, immune development, lysosomal protein catabolism, LDL response, and visual perception), with no clear common function tying them together. This heterogeneity makes it hard to assign a coherent, specific label beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030913","count":4},{"id":"GO:0046813","count":4},{"id":"GO:2001046","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0090528","count":3}]},{"hash":"647426571122677295","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":4},{"id":"GO:0046085","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0006195","count":2},{"id":"GO:0002938","count":1}]},{"hash":"732895200320151189","title":"Unknown","description":"The top GO terms point to a mix of transcriptional regulation, development/differentiation, immune processes, germline RNA processing, and signaling (negative regulation of transcription, myoblast differentiation, IgA isotype switching, piRNA processing, Wnt signaling, synapse assembly, meiosis, and complement pathways). The absence of connectivity (edges/triangles) suggests no single cohesive function tying these proteins together, so a broad Unknown label is appropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0045662","count":4},{"id":"GO:0048298","count":4},{"id":"GO:0034587","count":3},{"id":"GO:0043046","count":3}]},{"hash":"475240932801104143","title":"Golgi\u2013vacuole trafficking and SNARE fusion","description":"This cluster centers on Golgi-to-vacuole transport, Golgi disassembly/ribbon formation, and SNARE complex assembly with vesicle fusion to vacuoles, plus exocytic insertion of neurotransmitter receptors and regulation of postsynaptic potentials. These terms collectively point to a cohesive module of vesicle trafficking and membrane fusion involving Golgi/vacuolar pathways and receptor trafficking at the synapse, with dephosphorylation indicating regulatory control. ","confidence":"High","size":13,"edges":17,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:2000463","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0032258","count":2},{"id":"GO:1903422","count":2},{"id":"GO:0006896","count":2}]},{"hash":"2015720636331014648","title":"Neuronal Synaptic Vesicle Priming and Signaling","description":"This cluster is driven by terms about synaptic vesicle priming/maturation and regulation of Rho/Ras signaling, suggesting a shared role in neuronal synaptic function and cytoskeletal signaling; other terms like RNA processing and DNA-related events appear ancillary.","confidence":"Medium","size":13,"edges":14,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0016082","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0032298","count":2},{"id":"GO:1903026","count":2}]},{"hash":"1742081225337019143","title":"Bacterial metabolism and detoxification","description":"The GO terms point to diverse bacterial metabolic activities (biosynthesis of biotin and antibiotics, nitrogen utilization, uracil catabolism, beta-ketoadipate degradation) together with detoxification and toxin response. This suggests a cluster capturing metabolic versatility and defense against toxic substances in bacteria, rather than a single focused pathway.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0019740","count":4},{"id":"GO:0006212","count":4},{"id":"GO:0098869","count":4}]},{"hash":"320063082611122392","title":"Embryonic development and organ differentiation","description":"The top GO terms point to development and differentiation across multiple organ systems (eye, thyroid, pancreas, digestive tract, spinal cord, hindbrain) and neural lineage specification (GABAergic interneuron differentiation), indicating proteins involved in broad developmental programs rather than a single tissue function. This cross-tissue developmental theme, including regional patterning like rhombomere development, supports a general embryogenesis/organogenesis role. Therefore, a label reflecting embryonic development and organ differentiation is appropriate.","confidence":"Medium","size":13,"edges":56,"triangles":140,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":13},{"id":"GO:0002070","count":13},{"id":"GO:0030878","count":13},{"id":"GO:0021892","count":13},{"id":"GO:0007501","count":13}]},{"hash":"1444318735939733737","title":"Embryonic morphogenesis and organogenesis","description":"The top GO terms cluster around tissue formation and organ development in embryos (palate, mesoderm, cartilage, hair follicle morphogenesis, placenta-related differentiation, endocrine system development), indicating a cohesive theme of embryonic morphogenesis; a couple of terms about transcriptional regulation are supplementary and reflect gene expression control during development.","confidence":"High","size":13,"edges":24,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060021","count":13},{"id":"GO:0007498","count":10},{"id":"GO:0031069","count":10},{"id":"GO:0060707","count":10},{"id":"GO:0035270","count":10}]},{"hash":"533974829599284225","title":"Neural development and neuron survival","description":"The proteins show a strong signal for neural development-related terms (brain development, cochlea morphogenesis, dendrite development, excitatory postsynaptic potential, glial cell proliferation, and negative regulation of neuron apoptotic process), suggesting a core role in neural differentiation and neuron maintenance. The presence of liver development, heart contraction, and osteoclast development terms may reflect broader developmental roles or pleiotropy, but the dominant theme centers on neural structure formation and function.","confidence":"Medium","size":13,"edges":18,"triangles":5,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0043524","count":4},{"id":"GO:0090103","count":4},{"id":"GO:0001889","count":4},{"id":"GO:0032258","count":2}]},{"hash":"1654606103525767896","title":"Immune receptor signaling and growth factor pathways","description":"The proteins here are enriched for immune signaling terms (B cell differentiation, T cell receptor signaling, follicular B cell differentiation) as well as growth factor receptor signaling (EGFR/IGF pathways) and GPCR-mediated signaling. This points to a shared theme of receptor-driven signal transduction across immune and growth-factor contexts, with IP3 biosynthesis supporting Ca2+-mediated signaling. Some terms like brain development or egg activation appear less directly connected but may reflect broader signaling roles. Overall, the cluster centers on receptor signaling modalities rather than a single specific pathway.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002337","count":2},{"id":"GO:0007213","count":2},{"id":"GO:0007343","count":2},{"id":"GO:1900122","count":2},{"id":"GO:0050852","count":2}]},{"hash":"242648247908625356","title":"GPI-anchor and sterol lipid biosynthesis","description":"The member GO terms point strongly to lipid metabolism: GPI anchor biosynthesis, ergosterol/sterol biosynthesis, fatty acid and ether lipid metabolism, and related sphingolipid processing. This pattern suggests proteins function in membrane lipid biosynthesis and assembly, making \"GPI-anchor and sterol lipid biosynthesis\" a concise, representative label.","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0032286","count":1},{"id":"GO:0080065","count":1},{"id":"GO:0046485","count":1},{"id":"GO:0006636","count":1}]},{"hash":"2274702306754223047","title":"Unknown","description":"The terms span telomere maintenance, signaling, differentiation, metabolism, and immune responses with no clear shared function across the proteins, so a cohesive label isn't evident.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:1904322","count":2},{"id":"GO:1905519","count":2},{"id":"GO:0060513","count":2},{"id":"GO:0051262","count":2}]},{"hash":"2124431146898891472","title":"RNA processing and post-transcriptional regulation","description":"The top GO terms cluster around mRNA maturation, splicing, stability, modification, and translation initiation, suggesting proteins engaged in post-transcriptional RNA metabolism and gene expression control via RNA-level regulation, including spliceosome activities and mRNA stabilization.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":9},{"id":"GO:0045292","count":8},{"id":"GO:0000245","count":6},{"id":"GO:0060211","count":6},{"id":"GO:1905663","count":6}]},{"hash":"1186886272811310600","title":"Skeletal muscle sarcomere and thin filament assembly","description":"The cluster is dominated by GO terms related to skeletal muscle architecture and contractile machinery, including thin filament assembly, sarcomere organization, and skeletal muscle fiber development, indicating proteins that contribute to muscle fiber structure and the contractile apparatus. Some other terms (e.g., chromatin-related processes and platelet aggregation) are present but appear peripheral to the central muscle structural theme.","confidence":"High","size":12,"edges":17,"triangles":7,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0051666","count":3},{"id":"GO:0070527","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0030240","count":3}]},{"hash":"185878524520716814","title":"Neuronal development and actin cytoskeleton","description":"Based on the strong presence of actin cytoskeleton-related terms (Arp2/3 complex\u2013mediated actin nucleation; actin cortical patch localization; establishment of cell polarity and cell shape) alongside brain development terms (brain development; substantia nigra development) and cytoskeletal involvement in platelet aggregation, the cluster seems to center on neuronal development coupled with actin remodeling. Although histone acetylation terms are listed (obsolete), they do not define the main theme. This makes a label tying neuronal development with actin dynamics the most representative. ","confidence":"Medium","size":12,"edges":52,"triangles":115,"max_degree":11,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043982","count":6},{"id":"GO:0043981","count":6},{"id":"GO:0034314","count":6},{"id":"GO:0007420","count":6},{"id":"GO:0010628","count":5}]},{"hash":"1023111435010428516","title":"RNA Processing and Translation Regulation","description":"The top GO terms cluster around RNA metabolism and post-transcriptional control, including regulatory ncRNA-mediated silencing, spliceosome-dependent mRNA splicing, formation of the translation preinitiation complex, and nonsense-mediated decay, with stress granule localization supporting cytoplasmic RNA management. A few DNA replication-related terms are present but do not define the primary theme of the cluster.","confidence":"Medium","size":12,"edges":34,"triangles":40,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:1903608","count":5},{"id":"GO:0001731","count":5},{"id":"GO:1901407","count":5}]},{"hash":"1426553428252532149","title":"Neurodevelopment and Synaptic Signaling","description":"The terms most prominent in this cluster point to brain development and synaptic function, including cerebral cortex development, hippocampus development, and long-term potentiation, indicating neural development and neuronal signaling roles. Additional terms cover transcription, signaling, and cellular stress responses, which can accompany neural development processes but are less central to the main theme. Overall, the neural development/synaptic plasticity theme is the strongest signal.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0021987","count":2}]},{"hash":"1153477191085339462","title":"Immune signaling and developmental regulation","description":"Top terms suggest a mix of innate immune pathway regulation (TLR signaling, IL-18 production, chemokine signaling) with developmental processes (Wnt signalosome assembly, otolith morphogenesis, lung connective tissue development) and endosomal trafficking, implying a broader role in regulating signaling during immunity and tissue development rather than a single pathway. Confidence: Medium","confidence":"","size":12,"edges":20,"triangles":12,"max_degree":11,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034123","count":3},{"id":"GO:1905279","count":3},{"id":"GO:0016525","count":3},{"id":"GO:0070100","count":3},{"id":"GO:0032474","count":3}]},{"hash":"842229869457063135","title":"Synaptic Transmission and Plasticity","description":"The cluster shows strong representation of neuronal synaptic function terms: excitatory postsynaptic potential, regulation of synaptic vesicle exocytosis and endocytosis, and regulation of long-term synaptic potentiation, pointing to a shared role in synaptic signaling and plasticity. The presence of additional development-related GO terms (e.g., substantia nigra development, ossification) suggests some members may participate in broader developmental processes, but the dominant signal centers on synaptic activity. ","confidence":"Medium","size":12,"edges":16,"triangles":7,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0035690","count":9},{"id":"GO:0021762","count":9},{"id":"GO:1900242","count":9}]},{"hash":"113493213723292159","title":"Post-transcriptional RNA processing and translation regulation","description":"The GO terms cluster around RNA processing and post-transcriptional control of gene expression, including ncRNA-mediated silencing, mRNA splicing regulation, translation initiation/reinitiation, and mRNA stability/poly(A) tail regulation, indicating a coherent theme of post-transcriptional regulation.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0002188","count":5},{"id":"GO:0001731","count":5},{"id":"GO:1901407","count":5}]},{"hash":"1346124045065760516","title":"Pol II transcription repression and chromatin regulation","description":"The top terms are dominated by negative regulation and termination of RNA polymerase II transcription, plus chromatin-associated processes (nucleosome density, histone acetylation). This points to a cluster enriched for transcriptional control and chromatin remodeling, with a few outlier terms (cobalamin biosynthesis, tRNA methylation) likely reflecting other cellular activities or annotation noise.","confidence":"Medium","size":12,"edges":34,"triangles":36,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0090398","count":5},{"id":"GO:0042766","count":5},{"id":"GO:0009236","count":4},{"id":"GO:0030488","count":4}]},{"hash":"2283263787851967474","title":"DNA replication, repair, and transcription cluster","description":"A few core themes stand out: DNA-templated transcription, DNA replication, and DNA repair (including double-strand break repair involved in meiotic recombination). These suggest a genome maintenance and transcription regulation module. The neuron development terms are present but secondary, potentially reflecting shared chromatin regulation roles or context-specific functions in neural cells. Overall, the cluster is best described by DNA maintenance and transcription control.","confidence":"Medium","size":12,"edges":35,"triangles":55,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0009636","count":4},{"id":"GO:0051260","count":4},{"id":"GO:1990918","count":4}]},{"hash":"1059333333277993001","title":"Innate immune signaling and ubiquitin-mediated pyroptosis","description":"The cluster is defined by innate immune defenses against viruses and bacteria, detection of muramyl dipeptide, and pyroptotic/apoptotic inflammatory signaling, with prominent protein ubiquitination and SCF proteasomal degradation, suggesting a module where ubiquitin-dependent regulation intersects innate immunity and inflammatory cell death.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0090307","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0051607","count":6},{"id":"GO:0016567","count":6},{"id":"GO:0045087","count":6}]},{"hash":"1523182346207013119","title":"Neuroimmune Development Signaling","description":"The cluster shows enrichment for nervous system development, angiogenesis, and multiple signaling pathways (prolactin signaling, T cell receptor signaling, TNF/NF-kB), suggesting a cohesive theme of developmental signaling that operates in neural-immune contexts. Additional terms on substrate adhesion and tyrosine autophosphorylation point to receptor-driven signaling, while proteostasis terms are less central. Overall, the proteins appear linked by roles in signaling during development with immune involvement.","confidence":"Medium","size":12,"edges":41,"triangles":59,"max_degree":10,"top_function":"autophagy","top_go_terms":[{"id":"GO:0007417","count":5},{"id":"GO:0038161","count":5},{"id":"GO:0034446","count":5},{"id":"GO:0001525","count":5},{"id":"GO:0051092","count":5}]},{"hash":"487594327652972151","title":"Cell cycle regulation and division","description":"The major GO terms center on cell cycle control, meiotic division, and chromosome segregation (female meiotic division, cell division, kinetochore localization), which together define a cell-cycle\u2013driven cluster. Additional terms related to transcriptional regulation and apoptosis fit into broader regulatory layers, while ribosome assembly and Wnt signaling modulation appear more peripheral. Overall, the proteins seem linked to cell cycle progression and division, justifying the label, even though the proteins are not tightly connected into a single complex in this dataset.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007143","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0043065","count":2}]},{"hash":"1789206749226580406","title":"Cell Adhesion and Tissue Remodeling","description":"This cluster is dominated by GO terms related to cell adhesion (heterophilic and general adhesion), wound healing, and multicellular development, indicating roles in tissue organization and repair. While there is a distant hint of host-symbiont interactions, the core signal is adhesion-driven cellular interactions and developmental/tibue remodeling processes, suggesting the proteins work together in maintaining or reorganizing tissue architecture. Confidence in this label is Medium.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0046718","count":4},{"id":"GO:0042511","count":4},{"id":"GO:0042552","count":4},{"id":"GO:0014068","count":4},{"id":"GO:2000391","count":4}]},{"hash":"214974410965983992","title":"Brain development and neurotransmission (GABAergic/dopaminergic)","description":"The top terms are dominated by nervous system development, brain development, midbrain dopaminergic neuron differentiation, and GABAergic synaptic transmission, with vesicle trafficking (COPII-coated) supporting neuronal secretion. A few terms like keratinization and ossification appear unrelated, suggesting some annotation noise, but the core signal points to neural development and neurotransmission.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0031424","count":4},{"id":"GO:0043931","count":4},{"id":"GO:0007399","count":4},{"id":"GO:0051932","count":4}]},{"hash":"2144449931819353469","title":"Multi-tissue developmental morphogenesis and adhesion","description":"The terms span bone ossification, nervous system development, heart valve formation, kidney tubule differentiation, and various cell adhesion processes (homophilic/heterophilic adhesion and integrin-mediated adhesion), as well as synapse assembly regulation. Together they point to broad developmental morphogenesis across multiple tissues guided by cell\u2013cell and cell\u2013matrix interactions, rather than a single specific pathway or tissue. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":6},{"id":"GO:0007157","count":6},{"id":"GO:0007399","count":6},{"id":"GO:0007156","count":5},{"id":"GO:0051965","count":5}]},{"hash":"86239385147136027","title":"Endocytosis and actin-driven vesicle trafficking","description":"The top GO terms point strongly to endocytosis, COPII vesicle loading, and actin cytoskeleton remodeling (barbed-end capping, actin cortical patches), all of which are linked through regulation by small GTPases and downstream signaling events (e.g., JUN phosphorylation). While there are additional signaling contexts (estrogen receptor signaling, TGF-beta response, ER stress\u2013related translation), the core theme centers on endocytic processes coordinated with actin dynamics and related signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0006897","count":3},{"id":"GO:0033146","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0050731","count":3}]},{"hash":"954962226829789031","title":"GPCR-Rho signaling and cell junction assembly","description":"The cluster is dominated by GO terms for G protein-coupled receptor signaling (GPCR pathway, forskolin response), regulation of GTPase activity, and Rho-mediated signal transduction, along with bicellular tight junction assembly. This points to a coherent theme where GPCR-driven signaling regulates cytoskeletal dynamics and cell-cell adhesion, with additional terms like melanocyte differentiation and blue light signaling providing contextual connections to pigment and photoreceptor-related pathways. Overall, the core theme is GPCR-mediated signaling coordinating cytoskeletal organization and junction formation.","confidence":"High","size":12,"edges":49,"triangles":105,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:1904322","count":8},{"id":"GO:0043547","count":8},{"id":"GO:0007266","count":8},{"id":"GO:0034379","count":8},{"id":"GO:0007213","count":8}]},{"hash":"748655118552757886","title":"GABAergic signaling and neuronal excitability","description":"This cluster centers on neural signaling, with terms for GABA signaling, postsynaptic potentials, and transmission of nerve impulses, plus ion transport channels (Na+/K+) that underlie action potentials. It also includes locomotory behavior and learning-related conditioning, consistent with neuronal circuits controlling movement and experience-dependent responses. A few terms point to neural development and rhythmic processes, but the dominant theme is neurotransmission and excitability.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007214","count":12},{"id":"GO:0060079","count":12},{"id":"GO:0001661","count":12},{"id":"GO:0007626","count":12},{"id":"GO:0035725","count":12}]},{"hash":"1491012935470997390","title":"Glycan Biosynthesis and Mammalian Tissue Remodeling","description":"Top GO terms show a strong emphasis on glycan biosynthesis (glycosphingolipids, keratan sulfate proteoglycans, protein glycosylation), indicating a glycosylation-centric function for the cluster. Several terms also describe mammalian tissue development and wound-healing processes (mammary gland development, angiogenesis in wound healing, epithelial proliferation), suggesting a role in tissue remodeling. Some items (infection structure formation, acrosome reaction regulation) are distant or context-specific annotations, but overall the cluster appears to represent glycosylation-related pathways linked to mammalian development and repair.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":5},{"id":"GO:0006688","count":4},{"id":"GO:0030879","count":3},{"id":"GO:0060054","count":3},{"id":"GO:0060055","count":3}]},{"hash":"387525310122947289","title":"Neuronal GPCR Signaling and Sensory Processing","description":"This cluster centers on GPCR signaling (adenylate cyclase-activating/inhibiting pathways), GTPase regulation, and dopaminergic synaptic transmission, with sensory-related terms such as visual perception. The dominant themes point to neuronal communication and sensory processing, though a few terms (e.g., electron transport) are less tightly linked.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0022900","count":7},{"id":"GO:0045777","count":7},{"id":"GO:0010579","count":7},{"id":"GO:0035025","count":6},{"id":"GO:0001963","count":5}]},{"hash":"1282578731223576936","title":"Innate Immune Signaling and Developmental Pathways","description":"This cluster centers on innate immune signaling (innate immune response and Fc receptor\u2013related signaling) and JUN/AP-1\u2013related phosphorylation, with additional links to classic developmental signaling (Wnt) and cellular responses to retinoic acid and nitric oxide, plus cell migration. The mix suggests proteins involved in immune signaling that also participate in broader developmental and signaling responses.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0007258","count":10},{"id":"GO:0016477","count":10},{"id":"GO:0002774","count":10},{"id":"GO:0010863","count":10},{"id":"GO:0045087","count":10}]},{"hash":"1804338280148283168","title":"Metal ion detox and mitochondrial respiratory assembly","description":"The cluster is enriched for metal ion homeostasis and detoxification (zinc and cadmium) and for mitochondrial respiratory chain/respirasome and complex IV assembly, with related regulation of cytochrome c release, suggesting a theme around metal handling linked to mitochondrial respiration. A few other terms (glucose and iron transport) are present but do not dominate the signal, so the core idea centers on metal detox/transport in concert with mitochondrial respiratory complex assembly.","confidence":"Medium","size":12,"edges":16,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006882","count":3},{"id":"GO:0010312","count":2},{"id":"GO:0070574","count":2},{"id":"GO:0097250","count":2},{"id":"GO:0033617","count":2}]},{"hash":"776160642707022688","title":"Cell cycle kinase signaling","description":"The cluster centers on terms related to cell cycle regulation and kinase activity, including regulation of the cell cycle, protein autophosphorylation, and positive regulation of serine/threonine kinase activity, which together suggest a set of signaling kinases controlling cell-cycle processes. Some items like glucose metabolism, mismatch repair, placenta development, and cocaine response appear but are likely peripheral or annotation noise relative to the dominant kinase/cell-cycle theme. High","confidence":"","size":12,"edges":15,"triangles":3,"max_degree":5,"top_function":"protein folding","top_go_terms":[{"id":"GO:0071157","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0043524","count":4},{"id":"GO:0001890","count":4},{"id":"GO:0032516","count":4}]},{"hash":"2213694052413740145","title":"Golgi-SNARE Mediated Synaptic Vesicle Trafficking","description":"This cluster centers on SNARE complex assembly and Golgi-related vesicle transport, including ER-to-Golgi, intra-Golgi, and Golgi-to-vacuole routes, plus exocytic insertion of neurotransmitter receptors and synaptic potentiation, indicating a cohesive function in vesicle trafficking at synapses.","confidence":"High","size":12,"edges":39,"triangles":58,"max_degree":8,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035493","count":8},{"id":"GO:0090161","count":8},{"id":"GO:0098967","count":8},{"id":"GO:0048280","count":8},{"id":"GO:0006888","count":8}]},{"hash":"920762980748808141","title":"Rho GTPase\u2013driven actin remodeling and cell migration","description":"The terms converge on Rho signal regulation, GTPase activity, actin filament organization/bundling, and cell migration, pointing to a cytoskeletal remodeling module governed by Rho-family GTPases. Additional terms suggest signaling cross-talk (e.g., JUN phosphorylation) and stress-related translation regulation, with some development/neuronal context (cranial skeletal development, synaptic vesicle processes). Overall, the cluster appears to center on cytoskeletal dynamics and motility driven by Rho signaling.","confidence":"Medium","size":12,"edges":14,"triangles":0,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0007258","count":4},{"id":"GO:0036493","count":4},{"id":"GO:0016191","count":4},{"id":"GO:0043547","count":4}]},{"hash":"718864105852065348","title":"Fatty acid and acetyl-CoA metabolism","description":"The top GO terms are dominated by fatty-acid metabolism (medium- and long-chain) and related CoA-linked processes, including long-chain fatty acid import and acetyl-CoA biosynthesis from acetate, plus supporting catabolic and biosynthetic activities (menaquinone and siderophore biosynthesis). This points to a cohesive theme of lipid/acetyl-CoA metabolism and related central-bacterial pathways, with a few outliers (e.g., seed coat development) likely reflecting annotation noise. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036112","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0019427","count":3},{"id":"GO:0001676","count":3}]},{"hash":"647011961503204106","title":"Embryonic organogenesis and signaling","description":"The top GO terms point to multiple aspects of embryonic development and organ formation: heart morphogenesis (right atrium and septum), foregut morphogenesis, neural boundary formation, and respiratory system development, along with regulatory processes like negative regulation of angiogenesis and growth factor signaling (FGF production) and thyroid hormone generation. This suggests a cluster of proteins involved in broad embryonic organogenesis and developmental signaling rather than a single, specific function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0006590","count":6},{"id":"GO:0090271","count":6},{"id":"GO:0097150","count":6},{"id":"GO:0021654","count":5},{"id":"GO:0034447","count":5}]},{"hash":"1403198907043333577","title":"Unknown","description":"The top GO terms are highly diverse (thalamus development, snoRNP assembly, male sex differentiation, glucocorticoid signaling, non-motile cilium assembly, mitotic cell cycle, histone methylation, cytokinin signaling, lead ion response, etc.), and there is no evident shared function or pathway linking the 12 proteins, especially with zero edges. This lack of a cohesive theme justifies an Unknown label.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0021794","count":4},{"id":"GO:0000492","count":3},{"id":"GO:0046661","count":3},{"id":"GO:2000324","count":3},{"id":"GO:1905515","count":3}]},{"hash":"564436517144175768","title":"Heart development and ECM remodeling","description":"The terms point to cardiac morphogenesis and extracellular matrix dynamics, including collagen fibril organization, heart trabecula formation, and epithelial-to-mesenchymal transition, with Notch signaling and ERK/MAPK involvement; plus vascular/inflammatory processes (platelet regulation, fibrinolysis, IL-1 response, complement) that often accompany heart tissue remodeling.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090331","count":5},{"id":"GO:0030199","count":5},{"id":"GO:0071347","count":4},{"id":"GO:0042730","count":4},{"id":"GO:0070374","count":4}]},{"hash":"1078355011759894162","title":"Nervous system development and axon guidance","description":"Most terms center on neural development and connectivity: myelination, synapse organization, nerve impulse transmission, and peripheral nervous system development, with axon guidance via Roundabout (Slit-Robo) signaling and chemotaxis of interneurons. Supporting signals include BMP pathway regulation and STAT tyrosine phosphorylation, while angiogenesis and myoblast differentiation reflect broader developmental processes. This combination suggests a cluster focused on nervous system development and axon pathfinding.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0042552","count":9},{"id":"GO:0050808","count":8},{"id":"GO:0030513","count":8},{"id":"GO:0019226","count":8},{"id":"GO:0007422","count":8}]},{"hash":"109865419607542222","title":"Vascular Innate Immunity and Lipoprotein Clearance","description":"This cluster mixes innate immune functions (complement activation, innate immune response) with lipid handling (lipoprotein transport/clearance, foam cell differentiation) and endothelial/ECM remodeling (endothelial proliferation, tight junctions, fibronectin organization), suggesting a coordinated vascular immune-lipid processing program affecting endothelial integrity.","confidence":"Medium","size":12,"edges":12,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":7},{"id":"GO:0045087","count":7},{"id":"GO:2001046","count":4},{"id":"GO:0006898","count":4},{"id":"GO:0010744","count":4}]},{"hash":"679390490643175040","title":"Translation Initiation and mRNA Stability","description":"The cluster is dominated by GO terms related to translation initiation and preinitiation complex assembly (translation reinitiation, EIF4F complex assembly) with additional links to mRNA stability and modification (poly(A) tail regulation, mRNA stabilization). This suggests a coherent group of proteins functioning in initiating translation and controlling mRNA fate after transcription.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0060211","count":4},{"id":"GO:1905663","count":4},{"id":"GO:0097010","count":4}]},{"hash":"1697523456559565289","title":"mRNA processing and translation regulation","description":"Based on the top GO terms, the cluster centers on post-transcriptional control: regulation of mRNA poly(A) tail shortening, mRNA stability and modification, splicing via the spliceosome, and regulation of translational initiation, along with translation initiation complex assembly and ncRNA-mediated gene silencing. This pattern points to a cohesive group of proteins involved in determining mRNA fate and the initiation of translation, rather than transcriptional regulation. High","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0060211","count":5},{"id":"GO:1905663","count":5},{"id":"GO:1903586","count":5},{"id":"GO:0097010","count":5},{"id":"GO:0031047","count":5}]},{"hash":"2035894366365908071","title":"DNA Repair and Genome Maintenance","description":"Top GO terms center on DNA repair (base-excision repair, DNA recombination) and cell-cycle regulation (G1/S transition), with additional stress-related terms like response to xenobiotic stimulus and redox homeostasis. Although some terms are obsolete or less related, the strongest shared theme is genome maintenance and DNA damage response, implying these proteins collectively participate in preserving genomic integrity and coordinating the cell cycle under stress.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":3},{"id":"GO:0006486","count":2},{"id":"GO:0006310","count":2},{"id":"GO:1900087","count":2},{"id":"GO:2000327","count":2}]},{"hash":"2061519132279095942","title":"Mechanosensation and apoptosis regulation","description":"This cluster shows strong signals for mechanical stimulus response and mechanosensing, alongside regulatory processes like ubiquitination, cell cycle, and epithelial polarity, with apoptosis noted in myeloid and hepatocyte contexts. The set appears to reflect a broad cellular stress/regulatory theme rather than a single pathway, centered on mechanosensory signals coupled with regulatory control. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0050966","count":3},{"id":"GO:0033028","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0090162","count":3}]},{"hash":"1055239218180207019","title":"Translational Regulation and Growth Signaling","description":"The cluster\u2019s top GO terms center on control of protein synthesis (regulation of translational initiation, mRNA transport) and growth-related signaling (TORC1 signaling, response to growth hormone), with additional guidance from GTPase activity regulation and phosphorylation status. Although some terms are obsolete, the dominant theme points to regulation of translation and growth signaling pathways. ","confidence":"Medium","size":11,"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:0043966","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0051028","count":2}]},{"hash":"73540778593089507","title":"Neural signaling and synapse formation","description":"The cluster is dominated by GO terms related to neural signaling, receptor clustering, Rho-mediated cytoskeletal changes, and synapse assembly, with behavioral regulation (grooming) and PI3K/AKT signaling. While there is also an immune-related response (lipopolysaccharide), the core theme centers on neuronal communication and synapse development.","confidence":"Medium","size":11,"edges":12,"triangles":1,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":8},{"id":"GO:0032496","count":8},{"id":"GO:0007275","count":8},{"id":"GO:2000821","count":6},{"id":"GO:0007266","count":6}]},{"hash":"1428176782704640263","title":"Neural development and myelination","description":"The cluster shows strong enrichment for nervous system\u2013related terms: CNS development, synapse organization, transmission of nerve impulse, and myelination, plus BMP signaling and collagen organization that support neural development and connectivity. A couple of peripheral terms (salivary gland boundary specification, endodermal differentiation) may reflect broader developmental roles, but the core theme is neural development and function.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0007432","count":10},{"id":"GO:0007417","count":10},{"id":"GO:0050808","count":10},{"id":"GO:0035987","count":10},{"id":"GO:0055072","count":10}]},{"hash":"632587466962589621","title":"Developmental signaling regulation","description":"The proteins appear enriched for GO terms involving regulation of signaling pathways linked to development and morphogenesis, notably BMP/TGF-\u03b2 signaling (SMAD-related), NF-\u03baB pathways, and MAPK signaling, plus responses to developmental cues. Additional terms on cell morphogenesis, nuclear protein export, and dephosphorylation suggest modulation of signaling outputs rather than core catalytic activity. Together this points to a cohesive function in regulating developmental signaling and morphological processes. ","confidence":"Medium","size":11,"edges":23,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0030514","count":2},{"id":"GO:0000173","count":2}]},{"hash":"46512481617494605","title":"Regulated neurotransmitter uptake and synaptic transmission","description":"This cluster is dominated by terms related to neurotransmitter handling and synaptic activity, including negative regulation of serotonin and norepinephrine uptake, positive regulation of neurotransmitter secretion, dopamine biosynthesis, and excitatory postsynaptic potential, along with behavioral links to locomotion. Peripheral terms about mitochondrial regulation and apoptotic protease activity are less central, so the label emphasizes neuronal signaling and neurotransmitter dynamics.","confidence":"Medium","size":11,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043154","count":4},{"id":"GO:0051612","count":3},{"id":"GO:0051622","count":3},{"id":"GO:0001956","count":3},{"id":"GO:1903285","count":3}]},{"hash":"1966451338644650486","title":"Unknown","description":"Top terms are spread across immune regulation, epithelial development, neural support, and general signaling, with no clear unifying function tying the proteins together. This lack of a cohesive theme leads to labeling as Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014009","count":2},{"id":"GO:0045662","count":2},{"id":"GO:0034145","count":2},{"id":"GO:0061153","count":2},{"id":"GO:0048298","count":2}]},{"hash":"1576475885272257849","title":"Immune signaling and hematopoietic development","description":"These proteins show strong ties to immune regulation (negative regulation of TLR4 signaling, Fc receptor signaling regulation, interferon production) and hematopoietic lineage processes (megakaryocyte and osteoclast development, erythrocyte differentiation), suggesting a shared role in coordinating immune responses with blood cell development.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1904140","count":11},{"id":"GO:0035855","count":11},{"id":"GO:0034144","count":11},{"id":"GO:0036035","count":11},{"id":"GO:1902715","count":11}]},{"hash":"2152261740450931423","title":"Neural signaling and locomotion","description":"This cluster is dominated by GO terms for GABA signaling, postsynaptic potentials, and transmission of nerve impulses, along with locomotory behavior, ion transport, and skeletal muscle contraction, plus optic nerve morphogenesis and reproductive rhythm regulation. These collectively point to neural signaling guiding movement and neuromuscular function, with some involvement in neural development. Therefore, the label neural signaling and locomotion is a concise, representative theme for this cluster.","confidence":"High","size":11,"edges":34,"triangles":48,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007214","count":10},{"id":"GO:0060079","count":10},{"id":"GO:0001661","count":10},{"id":"GO:0007626","count":10},{"id":"GO:0035725","count":10}]},{"hash":"786685844219120240","title":"Centriole dynamics and endosomal trafficking","description":"This cluster centers on centriole/centrosome-related processes (centriole elongation, cell division, DNA replication) and vesicle trafficking and turnover pathways (late endosomal microautophagy, intralumenal vesicle formation, Golgi retention, proteasomal degradation), suggesting a cohesive theme of coordinating centrosome dynamics with intracellular cargo processing and protein quality control.","confidence":"Medium","size":11,"edges":12,"triangles":0,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0070389","count":5},{"id":"GO:0051260","count":4},{"id":"GO:1903724","count":4},{"id":"GO:0061738","count":4}]},{"hash":"451922942828844000","title":"Heart and Brain Morphogenesis","description":"The dominant terms describe morphogenesis and development in heart (outflow tract morphogenesis) and brain (cerebellar development), plus vascular remodeling (endothelial delamination). Other terms relate to cell\u2013matrix adhesion and ion signaling that support tissue maturation and functional differentiation, including cardiac electrophysiology (His bundle action potential) and cGMP signaling. This combination suggests a theme of heart and brain development and structural organization.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097497","count":7},{"id":"GO:0071321","count":7},{"id":"GO:0086048","count":7},{"id":"GO:0051262","count":7},{"id":"GO:0050976","count":7}]},{"hash":"2089252907199271951","title":"Chromatin regulation and transcription control","description":"The GO terms cluster around epigenetic control of gene expression (histone methylation, heterochromatin formation, histone modification) and transcriptional regulation (RNA polymerase II regulation), with additional links to cell cycle coordination (sister chromatid cohesion) and hormonal signaling (estradiol response). This suggests a coherent theme of chromatin state control driving transcription and related cellular responses, despite some terms being obsolete. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061086","count":1},{"id":"GO:0070481","count":1},{"id":"GO:0030466","count":1},{"id":"GO:0045618","count":1},{"id":"GO:0071392","count":1}]},{"hash":"2190380500960377574","title":"Isoprenoid/Terpenoid Biosynthesis","description":"The terms point to terpenoid/isoprenoid biosynthesis (FPP, GGPP, GPP, monoterpene, cholesterol and quinone biosynthesis) as the dominant theme, with a few general processes like ATP-driven proton motive force and transport that are not defining for the cluster.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0051290","count":1},{"id":"GO:0006695","count":1},{"id":"GO:1901663","count":1}]},{"hash":"1634709281787336576","title":"Chromatin remodeling and genome maintenance","description":"These terms cluster around chromatin dynamics and genome integrity: heterochromatin formation, transcription initiation-coupled chromatin remodeling, DNA replication\u2013dependent chromatin assembly, telomere capping, and nonhomologous end-joining repair. The inclusion of regulatory ncRNA-mediated gene silencing and beta-catenin-TCF complex assembly suggests transcription regulation within a chromatin context. Overall, the proteins appear to coordinate chromatin structure with transcription and DNA repair, i.e., chromatin remodeling linked to genome maintenance.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0051290","count":9},{"id":"GO:0000183","count":9},{"id":"GO:0045815","count":9},{"id":"GO:0006335","count":9},{"id":"GO:0016233","count":7}]},{"hash":"1999372789535269309","title":"Unknown","description":"The top GO terms are highly heterogeneous (muscle and neural differentiation, plant phloem development, cytoskeleton and tight junction processes, hormone signaling, platelets), with no single coherent biological theme linking all terms. This suggests the cluster lacks a unifying function and may reflect annotation noise or broad, mixed functions.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:2000691","count":3},{"id":"GO:0070527","count":3},{"id":"GO:2000324","count":3},{"id":"GO:0051017","count":3}]},{"hash":"1327776009593050585","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0097171","count":1},{"id":"GO:0045226","count":1},{"id":"GO:0033358","count":1},{"id":"GO:0033481","count":1}]},{"hash":"2200647385028428339","title":"Embryonic and neural development","description":"The top GO terms cluster around developmental processes across multiple organs (embryogenesis, heart, face, and vagina development) and neural elements (axonogenesis and paranode localization), with retinoic acid response and transcriptional regulation supporting developmental signaling. Immune-related terms (TLR9 signaling, LPS response) appear less central, suggesting the core theme is developmental biology rather than immunity.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071300","count":4},{"id":"GO:0071222","count":4},{"id":"GO:0021952","count":4},{"id":"GO:0060068","count":4},{"id":"GO:0007507","count":4}]},{"hash":"627484956132500165","title":"Wnt signaling and inflammatory ECM remodeling","description":"The GO terms point to a combination of Wnt signaling, inflammatory responses (complement activation, leukocyte migration), and extracellular matrix remodeling (ECM disassembly, plasminogen activation, cell-matrix adhesion). This suggests a cluster of proteins involved in signaling cross-talk related to development and immunity, with active ECM remodeling. Confidence: Medium","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":5},{"id":"GO:0032496","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0001867","count":3},{"id":"GO:0032078","count":3}]},{"hash":"2050186448151806181","title":"Lipid catabolism and vesicle trafficking","description":"This cluster is dominated by GO terms related to lipid and glycosphingolipid breakdown (lipid catabolic, triglyceride catabolic, ganglioside catabolic, LDL remodeling) and an ER-to-Golgi vesicle transport step, suggesting a functional theme of lipid turnover coordinated with secretory pathway trafficking. Some terms are obsolete or organism-specific, but the overarching pattern points to lipid metabolism coupled with vesicle transport. ","confidence":"Medium","size":11,"edges":15,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0006689","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0016042","count":2}]},{"hash":"2082905797438081685","title":"Signaling and growth regulation","description":"The top GO terms point to signaling and regulatory control of development and proliferation (synapse organization, angiogenesis, MAPK-related signaling, and negative regulation of cell proliferation). Although some terms are divergent (root cap development, vacuolar transport, stress responses), the strongest shared theme is cellular communication guiding growth and developmental processes, suggesting a cluster centered on signaling pathways that govern growth and development. Confidence: Medium","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0050808","count":2},{"id":"GO:0035234","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0000187","count":2},{"id":"GO:0008285","count":2}]},{"hash":"533062364657838303","title":"Embryonic organogenesis and patterning","description":"The top GO terms focus on morphogenesis and developmental patterning of various organs (cartilage, pancreas, heart endocardial cushions) and axis formation (left-right), indicating an embryonic organogenesis theme; some terms relate to gene expression and RNA processing but these appear supportive to developmental processes.","confidence":"Medium","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0060536","count":10},{"id":"GO:1903026","count":10},{"id":"GO:0003323","count":10},{"id":"GO:0000055","count":10},{"id":"GO:0000398","count":10}]},{"hash":"1318906266897283585","title":"Developmental transcription and organogenesis regulators","description":"The cluster centers on transcriptional control and chromatin remodeling (DNA-templated transcription, transcription regulation, chromatin remodeling) with GO terms spanning diverse developmental processes (endodermal fate, atrial septum morphogenesis, skeletal muscle differentiation, lacrimal gland development, ureteric bud branching, megakaryocyte differentiation). This points to a set of proteins involved in regulating gene expression during embryonic development and organ formation.","confidence":"Medium","size":11,"edges":20,"triangles":13,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0003290","count":6},{"id":"GO:0035914","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0045654","count":6}]},{"hash":"543187395034941989","title":"Rho GTPase\u2013driven cytoskeleton remodeling and migration","description":"The proteins in this cluster strongly align with actin cytoskeleton organization, lamellipodium assembly, and cell migration, all linked to Rho and small GTPase signaling, suggesting a core role in cytoskeletal remodeling that enables cell movement. The presence of related terms in immune cell differentiation and heart development may reflect broader developmental and migratory roles of cytoskeletal dynamics; overall the theme is GTPase-regulated cytoskeleton changes driving motility.","confidence":"High","size":11,"edges":11,"triangles":0,"max_degree":5,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007507","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0030032","count":5},{"id":"GO:0030036","count":5}]},{"hash":"474438125183537938","title":"Exocytosis and vesicle trafficking","description":"The top GO terms cluster around exocytosis, vesicle tethering, Golgi to plasma membrane transport, exocyst assembly/localization, and SNARE regulation, indicating proteins that function in vesicle trafficking and membrane fusion. Additional terms related to lamellipodium assembly and neutrophil chemotaxis reflect cytoskeletal remodeling and migratory processes that rely on vesicle delivery to the plasma membrane. The myelination term is less central but does not outweigh the dominant exocytic machinery signal. Overall, the cluster appears to represent components of the vesicle trafficking and exocytosis apparatus.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006887","count":2},{"id":"GO:0090522","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0030593","count":2},{"id":"GO:0007266","count":2}]},{"hash":"1022917931890335986","title":"Rho-driven cytoskeleton and cell junction organization","description":"The top GO terms emphasize Rho signaling, actin cytoskeleton organization, and localization to adherens and tight junctions, indicating a common role in cytoskeletal dynamics that support cell\u2013cell adhesion. Additional terms involving endocytosis, centrosome localization, and barrier establishment fit within broader trafficking and junction-maintenance processes, reinforcing a coherent theme of coordinating cytoskeleton with junction assembly.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":3},{"id":"GO:0070830","count":3},{"id":"GO:1903760","count":3},{"id":"GO:2000821","count":3},{"id":"GO:0051660","count":3}]},{"hash":"166017957585170262","title":"Musculoskeletal and cardiovascular development","description":"The top GO terms cluster around development and morphogenesis of muscle-and-bone\u2013related tissues and cardiac structures: skeletal system development, aortic valve morphogenesis, and myocardial precursor cell differentiation, with supporting signal for myoblast differentiation and neuromuscular junction assembly. While other terms (insulin response, fatty acid response, complement activation, hair cycle) are present, the dominant signal is developmental processes in musculoskeletal and cardiovascular systems.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":3},{"id":"GO:0030194","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0003256","count":2},{"id":"GO:0001867","count":2}]},{"hash":"2106434490477068293","title":"Nuclear import and NPC assembly","description":"The top GO terms center on nucleocytoplasmic trafficking: import of NLS-bearing and ribosomal proteins into the nucleus, and nuclear pore complex assembly, which together point to a shared role in nuclear transport and NPC biogenesis. While other terms touch on related regulatory or cell-cycle processes, the dominant pattern is proteins involved in transporting cargo into the nucleus and assembling the nuclear pore complex. Confidence: High","confidence":"","size":10,"edges":14,"triangles":0,"max_degree":4,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007080","count":8},{"id":"GO:0048364","count":7},{"id":"GO:0043547","count":5},{"id":"GO:0042176","count":5},{"id":"GO:0006607","count":5}]},{"hash":"1567825507309663410","title":"Gene Expression Regulation","description":"The Top Terms span transcription (DNA-templated transcription, splicing, polyadenylation) as well as translation control (initiation, reinitiation, preinitiation complex, viral translation) plus TORC1 signaling and mRNA decay. This suggests a broad theme of gene expression regulation from transcription through RNA processing to translation, rather than a single specific process.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0075522","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0045292","count":3}]},{"hash":"192586490129223116","title":"Lipid metabolism and energy storage under stress","description":"This cluster centers on lipid- and energy-related processes (polyhydroxybutyrate biosynthesis, cholesterol metabolism, lipid transport, ketone body and amino acid catabolism) and starvation response, indicating metabolic remodeling during nutrient limitation. Sporulation and certain development terms appear as less central signals, but do not override the dominant lipid/metabolic theme.","confidence":"Medium","size":10,"edges":43,"triangles":105,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060612","count":7},{"id":"GO:0030435","count":7},{"id":"GO:0042619","count":7},{"id":"GO:0008203","count":7},{"id":"GO:0007420","count":7}]},{"hash":"788275215930385725","title":"SRP-dependent membrane targeting and ER stress","description":"This cluster is dominated by GO terms for SRP-dependent cotranslational and post-translational targeting of proteins to the membrane and translocation, plus a cellular response to unfolded protein, pointing to a core theme of protein trafficking to membranes and ER stress. Remaining terms appear more peripheral to this central theme. ","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1900035","count":10},{"id":"GO:0006880","count":10},{"id":"GO:0070880","count":10},{"id":"GO:0031204","count":10},{"id":"GO:0006616","count":10}]},{"hash":"2223721185087498023","title":"Nuclear DNA replication and transcription regulation","description":"This cluster is dominated by nuclear processes: DNA replication, its regulation, the centrosome cycle, transcription regulation by RNA polymerase II, and mRNA splicing. These core nuclear functions suggest a group of proteins involved in DNA replication and gene expression control, with additional terms pointing to developmental contexts such as Wnt signaling, keratinocyte differentiation, and cranial skeleton morphogenesis, indicating roles in development and differentiation as well. ","confidence":"Medium","size":10,"edges":8,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0010571","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0045944","count":5},{"id":"GO:0007098","count":5}]},{"hash":"1900478312984553677","title":"Unknown","description":"The listed GO terms span stress response, inflammation, gonad development, muscle differentiation, DNA damage\u2013induced apoptosis, cell cycle regulation, and RNA processing including snoRNA-guided pseudouridylation and telomerase RNA localization; they do not converge on a single coherent function or pathway. This heterogeneity suggests no single characteristic function defines the cluster, so I label it Unknown.","confidence":"","size":10,"edges":12,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071502","count":1},{"id":"GO:0048147","count":1},{"id":"GO:0002526","count":1},{"id":"GO:2000194","count":1},{"id":"GO:0008584","count":1}]},{"hash":"545691692313285117","title":"Actin-dependent transport and cytoskeletal dynamics","description":"This cluster is strongly enriched for GO terms related to actin cytoskeleton organization and actin-based transport, including actin filament bundle distribution, vesicle transport along actin, and positive regulation of actin nucleation, as well as processes like pigment granule (melanosome) transport and cell migration. These consistently point to a cohesive theme centered on actin-driven vesicle movement and cytoskeletal remodeling, with some peripheral links to membrane targeting and junction assembly. Confidence: High","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007118","count":10},{"id":"GO:2000810","count":8},{"id":"GO:0090314","count":8},{"id":"GO:0006930","count":7},{"id":"GO:0051904","count":7}]},{"hash":"103798741426921524","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0097171","count":3},{"id":"GO:0033574","count":3},{"id":"GO:0071318","count":3},{"id":"GO:0032361","count":3}]},{"hash":"834381304392548657","title":"ER-Golgi trafficking and ubiquitination in development","description":"The top GO terms point to COPII vesicle budding and retrograde Golgi-to-ER transport, along with protein polyubiquitination and ubiquitin-dependent ERAD, suggesting a core role in ER-Golgi trafficking and protein quality control. At the same time, developmental and proliferation terms (skeletal system development, multicellular growth, mitotic cell cycle, cell population proliferation) indicate involvement in growth and cell division during organismal development. Together, these signals imply a cluster centered on secretory/ER quality-control pathways as they relate to development. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0001501","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0035264","count":4}]},{"hash":"288672528803485763","title":"Unknown","description":"The terms span diverse processes (immune signaling, development, cytoskeleton organization, cell junction assembly, and other cellular functions) with no clear shared theme. Thus a single cohesive label is not evident for this cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050853","count":3},{"id":"GO:0007015","count":2},{"id":"GO:1904888","count":2},{"id":"GO:0070830","count":2},{"id":"GO:1903760","count":2}]},{"hash":"998224143434981734","title":"Proteolysis-ECM Remodeling in Development","description":"The cluster is dominated by proteolysis and ECM-related terms (ubiquitin-dependent protein catabolic process, proteasome assembly, regulation of metallopeptidase activity) alongside cell adhesion and chondrocyte morphogenesis, suggesting protein turnover with extracellular matrix remodeling during development. Some terms (stamen formation, chlorophyll biosynthesis, dendrite regeneration, T cell activation) appear as outliers or cross-kingdom annotations, but the core signal is proteolysis- and ECM-focused development.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048455","count":7},{"id":"GO:0006511","count":7},{"id":"GO:0015995","count":7},{"id":"GO:0043248","count":7},{"id":"GO:1901202","count":6}]},{"hash":"2062697570476474495","title":"Neural signaling and development","description":"Based on the GO terms, the cluster is enriched for neural signaling and development processes: ephrin receptor signaling regulation, Wnt signaling, and receptor localization to synapses affecting synaptic plasticity, along with corticospinal tract morphogenesis. Post-translational modification processes like ubiquitination and poly-ADP-ribosylation likely modulate these signaling events. Although there are a few telomere-related terms, the dominant theme centers on neuronal signaling and development, so this label best captures the cluster\u2019s function.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901187","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0007205","count":3},{"id":"GO:1904357","count":3},{"id":"GO:0070198","count":3}]},{"hash":"1649991836301899044","title":"Neural development and signaling regulation","description":"The Top Terms show a strong emphasis on neural development and signaling, including neuron migration, neuronal signal transduction, response to cocaine, and regulation of amyloid-beta, with accompanying modulation of pathways like PI3K/AKT and Rho that influence neural differentiation and cytoskeletal dynamics. Some terms also touch on broader differentiation and morphogenesis (EMT, osteoblast differentiation), but the neural-related terms appear most representative of the cluster\u2019s function.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":3},{"id":"GO:0034113","count":2},{"id":"GO:2001223","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0023041","count":2}]},{"hash":"1408630708246742820","title":"Oxidative stress response and redox metabolism","description":"This cluster centers on oxidative stress and redox biology: several GO terms describe response to hydrogen peroxide, removal of superoxide radicals, glutathione metabolism, and oxidation-reduction processes. Autophagy aligns with cellular responses to oxidative stress, and a broader \u201cresponse to toxic substance\u201d fits redox-related defense. A couple of terms touch on vascular processes, but the dominant theme is redox/homeostatic defense.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008217","count":3},{"id":"GO:0042542","count":3},{"id":"GO:0019430","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0055114","count":2}]},{"hash":"641619241503910762","title":"Glycolysis and carbohydrate metabolism","description":"The GO terms show a strong emphasis on glycolysis, fructose-6-phosphate metabolism, glycogen catabolism, and carbohydrate phosphorylation, indicating a cluster centered on central sugar metabolism. While there are secondary biosynthetic terms (menaquinone, chlorophyll, antibiotic biosynthesis), the carbohydrate metabolism terms dominate, supporting a glycolysis-centric interpretation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0005980","count":3},{"id":"GO:0061621","count":3},{"id":"GO:0006002","count":3}]},{"hash":"632318168443244311","title":"Cellular stress signaling and tissue remodeling","description":"The cluster centers on mitochondrial stress responses (positive regulation of mtDNA replication, membrane potential, stress-induced fusion) and signaling pathways (PKC signaling, SREBP pathway), while also including lipid metabolism, immune signaling (IL-2 production), secretion, and extracellular matrix remodeling with cadherin-mediated adhesion. This pattern suggests a broad stress- or remodeling-related signaling program that integrates energy metabolism, signaling, and extracellular environment changes rather than a single narrow function.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0090297","count":10},{"id":"GO:0010918","count":10},{"id":"GO:0022617","count":10},{"id":"GO:0045541","count":10},{"id":"GO:0070528","count":10}]},{"hash":"976523937378923375","title":"Epidermal barrier and innate immune signaling","description":"This cluster centers on epidermis development, wound response, cytokine production, and innate immune activity (complement), with supporting lipid-related terms (cholesterol homeostasis, fatty acid response) that are critical to skin barrier function. Although an outlier term for visual perception appears, the dominant pattern reflects skin barrier integrity and immune defense.","confidence":"High","size":10,"edges":11,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0070542","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006957","count":2},{"id":"GO:0048385","count":2}]},{"hash":"1760876028705577070","title":"B cell activation with phagocytosis and innate immunity","description":"The cluster shows enrichment for B cell\u2013related signaling and activation (B cell receptor signaling, positive regulation of B cell activation), along with phagocytosis (recognition and engulfment) and innate immune response, plus complement activation. This points to a module centered on adaptive immune activation with phagocytic/innate components, supported by cytoskeletal regulation (Rho signaling). Some terms like heart development may reflect broader protein roles rather than core function of the cluster.","confidence":"High","size":10,"edges":10,"triangles":0,"max_degree":6,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0010765","count":7},{"id":"GO:0006958","count":6},{"id":"GO:0006910","count":6},{"id":"GO:0006911","count":6},{"id":"GO:0050853","count":6}]},{"hash":"1844902310620000518","title":"Neuronal development and survival signaling","description":"The most represented terms point to neuronal development and signaling: dendrite development, substantia nigra development, ephrin receptor signaling, ERK cascade regulation, and neuron apoptotic regulation. These suggest a theme of neuronal differentiation, connectivity, and cell survival, even though a couple terms (ribosome biogenesis, hair follicle morphogenesis) are less central. Overall, the cluster appears to reflect neuronal growth and signaling pathways more than other processes.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0016358","count":2},{"id":"GO:0031069","count":2},{"id":"GO:0043652","count":2},{"id":"GO:0021762","count":2}]},{"hash":"838207077242122407","title":"Immune signaling and development regulators","description":"The cluster includes GO terms tied to innate immune signaling (cellular response to fungal origin, regulation of TLR4 signaling, STAT phosphorylation) and to differentiation/development of various lineages (megakaryocytes, B cells, osteoclasts, Bergmann glial cells). This combination suggests a broad regulatory role affecting both signaling pathways and cell differentiation rather than a single specific function.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0071226","count":8},{"id":"GO:0036493","count":5},{"id":"GO:0035855","count":5},{"id":"GO:1904140","count":5},{"id":"GO:0001922","count":5}]},{"hash":"1214081632691431013","title":"Neuronal Mitochondrial Dynamics and Vesicle Recycling","description":"Most terms describe neuronal vesicle cycling (endocytic recycling, synaptic vesicle budding) together with mitochondrial dynamics (mitochondrial fission, mitophagy, cytochrome c release, mitochondrion localization) and calcium signaling (voltage-gated calcium channel activity). This points to a cohesive function in neuronal energy management and synaptic vesicle trafficking, justifying the chosen label. ","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0032456","count":7},{"id":"GO:0016185","count":7},{"id":"GO:0048662","count":7},{"id":"GO:0034643","count":7},{"id":"GO:1901387","count":7}]},{"hash":"1188849750387800685","title":"Mitochondrial Import and Neuronal Signaling","description":"The cluster is enriched for mitochondrial-centric processes (protein import into the mitochondrial matrix, calcium import into mitochondria, mitophagy regulation, ROS regulation) alongside neuron-specific activities (neuron-neuron synaptic transmission, fear behavior). This suggests a cohesive role in mitochondrial maintenance within neurons, linking energy/ion homeostasis and quality control to neuronal signaling and behavior, with additional hints of ciliogenesis-related regulation. Overall, these proteins likely coordinate mitochondrial function and neuronal signaling, possibly affecting neuron function and plasticity.","confidence":"High","size":10,"edges":12,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":4},{"id":"GO:2000378","count":4},{"id":"GO:0001662","count":4},{"id":"GO:0031101","count":3},{"id":"GO:0036444","count":3}]},{"hash":"149557720646871464","title":"Lipid Biosynthesis and Membrane Remodeling","description":"The top GO terms are dominated by lipid metabolism and membrane lipid synthesis/remodeling, including CDP-diacylglycerol biosynthesis, phosphatidylcholine remodeling, triglyceride and ether lipid biosynthesis, and related energy-linked processes like mitochondrial ATP synthesis. While there are a couple of developmental and immune-related terms, the strongest, recurrent signal is lipid production and membrane assembly, which unifies the cluster.","confidence":"Medium","size":10,"edges":8,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016024","count":5},{"id":"GO:0006663","count":4},{"id":"GO:0070236","count":4},{"id":"GO:0036151","count":4},{"id":"GO:0021587","count":4}]},{"hash":"2217468011325427443","title":"Dendrite and Synapse Development","description":"Reasoning: The top GO terms point to neural morphology and connectivity, notably dendrite development and synapse organization, with Rho signaling supporting cytoskeletal changes essential for neurite outgrowth and synaptic formation. Some terms touch unrelated processes (tight junctions, centrosome localization, ion transport), but the predominant theme is neuronal development and synaptic assembly.","confidence":"Medium","size":10,"edges":41,"triangles":92,"max_degree":9,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0007266","count":6},{"id":"GO:0016358","count":6},{"id":"GO:0070830","count":6},{"id":"GO:1903760","count":6},{"id":"GO:2000821","count":6}]},{"hash":"1041060648860198446","title":"Centromeric Chromatin Assembly and Remodeling","description":"The top GO terms strongly point to chromatin dynamics and centromere maintenance\u2014transcription-coupled remodeling, replication-dependent chromatin assembly, CENP-A\u2013containing chromatin assembly, and heterochromatin formation\u2014suggesting proteins in this cluster are focused on chromatin organization and centromere function. A few outliers (plasmid partitioning, plasminogen activation) are present but do not define the core theme.","confidence":"Medium","size":10,"edges":35,"triangles":63,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045815","count":10},{"id":"GO:0006335","count":10},{"id":"GO:0051290","count":10},{"id":"GO:0000183","count":10},{"id":"GO:0061641","count":9}]},{"hash":"724738642746538472","title":"Unknown","description":"The top GO terms are diverse (male differentiation, unfolded protein response, interferon signaling, glucocorticoid signaling, morphine response) and several are obsolete, providing no coherent unifying function for the cluster. Confidence is None.","confidence":"","size":10,"edges":14,"triangles":0,"max_degree":7,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0046661","count":5},{"id":"GO:1903070","count":5},{"id":"GO:2000324","count":5},{"id":"GO:0006986","count":5},{"id":"GO:1903646","count":5}]},{"hash":"1153574829605353737","title":"GPCR/Wnt/Ephrin Signaling and Telomere Regulation","description":"These proteins are enriched for GPCR signaling (GO:0007205), Wnt signaling (GO:0016055), and ephrin receptor signaling (GO:1901187), along with related processes like cell migration and telomere/chromosome localization and maintenance. This points to a theme of diverse cell signaling pathways with a telomere regulation component.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0016477","count":4},{"id":"GO:1901187","count":4},{"id":"GO:1904357","count":4},{"id":"GO:0070198","count":4}]},{"hash":"311297976073426564","title":"Pancreas Development Transcription Regulators","description":"The dominant signals are transcription-related GO terms (DNA-templated transcription; regulation of transcription by RNA polymerase II), suggesting a cluster of transcription factors or regulators. The presence of pancreas development terms (pancreas morphogenesis; exocrine pancreas development) points to involvement in pancreatic formation, while terms like myeloid dendritic cell differentiation and response to lipopolysaccharide hint at broader regulatory roles in immune signaling. Taken together, these proteins likely function as transcriptional regulators with developmental and immune-associated roles, rather than enzymatic proteins.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0061113","count":4},{"id":"GO:0035264","count":4},{"id":"GO:0031017","count":3}]},{"hash":"106592731377726655","title":"Rac/Ras-GTPase\u2013driven Lamellipodium and Filopodium Formation","description":"The top GO terms cluster around actin cytoskeleton remodeling, including lamellipodium and filopodium assembly, substrate adhesion-dependent spreading, and small GTPase signaling (Rac and Ras) which together drive cell migration. While a few terms touch on lymphocyte differentiation (NK T cells, B cell maturation), the dominant theme is cytoskeletal dynamics enabling movement and adhesion. This supports labeling as Rac/Ras-regulated migration-related remodeling.","confidence":"Medium","size":10,"edges":11,"triangles":2,"max_degree":9,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0016477","count":7},{"id":"GO:0030032","count":7},{"id":"GO:0035020","count":7},{"id":"GO:0098761","count":7},{"id":"GO:1900026","count":7}]},{"hash":"1573266599771141201","title":"TLR-Mediated Innate Immune Regulation","description":"The cluster is dominated by GO terms for innate immune response and Toll-like receptor signaling, including positive regulation of TLR pathways, regulation of chemokine signaling, and IL-18 production, which together point to modulators of innate immunity. The other terms (bone/uterus development, otolith morphogenesis, angiogenesis) likely reflect broader multifunctionality or process cross-talk, but do not override the central immune signaling theme. Confidence: High","confidence":"","size":10,"edges":9,"triangles":0,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":8},{"id":"GO:0060348","count":8},{"id":"GO:0060065","count":5},{"id":"GO:0034123","count":5},{"id":"GO:0016525","count":5}]},{"hash":"1231439718294696046","title":"DNA Replication and Cell Cycle Regulators","description":"Although there are signaling-related terms (VEGF signaling, EGFR response, JUN and STAT phosphorylation, endothelial chemotaxis), the dominant terms are DNA-templated transcription, DNA replication, DNA repair, and the mitotic cell cycle. This suggests the proteins cluster around nuclear DNA maintenance and cell division processes, with signaling annotations likely reflecting multifunctionality rather than the cluster\u2019s core theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0006281","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0007601","count":9}]},{"hash":"246236750156946450","title":"Embryonic Development and Organ Differentiation","description":"The top GO terms largely pertain to developmental processes and lineage specification (cartilage morphogenesis, left-right pattern formation, placental and trophoblast differentiation, EMT in heart development, endocrine system development, and pancreatic cell development), suggesting a cluster of proteins involved in embryogenesis and organogenesis. Some terms touch on transcriptional regulation and RNA processing, which can underpin developmental gene expression, but the overarching theme is embryonic development and differentiation.","confidence":"High","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0032298","count":8},{"id":"GO:0060536","count":8},{"id":"GO:1903026","count":8},{"id":"GO:0003323","count":8},{"id":"GO:0000398","count":8}]},{"hash":"457004596342584185","title":"ER calcium signaling and COPII transport","description":"This cluster centers on calcium handling in the ER (store-operated calcium entry regulation, calcium ion transport, intracellular calcium homeostasis) together with ER-to-Golgi trafficking (COPII-coated vesicle budding, protein localization to the ER). Those terms together imply a module linking calcium signaling with secretory pathway transport. A few host-virus interaction terms appear but are isolated, not forming a coherent theme for the cluster. Overall, the ER calcium signaling and COPII transport combination best explains the set.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001256","count":1},{"id":"GO:0006816","count":1},{"id":"GO:0006874","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0060304","count":1}]},{"hash":"1224981874881568907","title":"Neural signaling and muscle contraction","description":"This cluster centers on ion transport and neurotransmitter signaling that underpin neural excitability and subsequent muscle activity. The presence of sodium/potassium transport, nerve impulse transmission, acetylcholine and GABA pathways, and associations with startle response and skeletal muscle contraction/growth point to a cohesive module of neural control of muscle function. Some terms like optic nerve morphogenesis and ovulation-cycle rhythm may reflect broader neural regulation or pleiotropy rather than a single tight function. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0003009","count":1},{"id":"GO:0060112","count":1},{"id":"GO:0051970","count":1}]},{"hash":"1472507109446560815","title":"Cardiovascular development and smooth muscle dynamics","description":"The terms cluster around heart/vascular development (vasculogenesis, neural crest contributions to cardio, ductus arteriosus closure), regulation of smooth muscle contraction, and cytoskeletal processes (stress fibers, Rho signaling), indicating a theme of cardiovascular morphogenesis and smooth muscle function. Some outliers exist, but the core theme is cardiovascular development.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001755","count":2},{"id":"GO:0001570","count":1},{"id":"GO:0045987","count":1},{"id":"GO:0043388","count":1},{"id":"GO:0007266","count":1}]},{"hash":"1581594972243261800","title":"Neurodevelopmental transcription regulation","description":"This cluster is driven by terms tied to regulation of transcription and neural development, such as regulation of DNA-templated transcription, cerebral cortex development, neuroblast proliferation, and retrograde axonal transport. While there are a few outliers (TLR4 signaling and muscle development), the dominant pattern points to transcriptional control during neural development, suggesting the proteins work together in neurodevelopmental regulation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0035660","count":6},{"id":"GO:0007527","count":6},{"id":"GO:0021987","count":2},{"id":"GO:0045599","count":1}]},{"hash":"1811352613542419682","title":"Translation initiation and preinitiation complex assembly","description":"The top GO terms are centered on initiation of translation and assembly of initiation machinery (IRES-dependent initiation, translation reinitiation, preinitiation complex formation, and eIF4F complex assembly), indicating proteins involved in starting and regulating translation. Some accompanying terms about mRNA tail regulation and ncRNA-mediated silencing hint broader RNA regulatory context, but the core signal is translation initiation. ","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0075522","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0075525","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0001731","count":4}]},{"hash":"1455884729524562870","title":"Broad signaling and proliferation cues","description":"These GO terms cover a range of stimulus-responsive processes (VEGF, PTH, IL-7 signaling), GPCR signaling modulation, cell migration, DNA replication, and cell cycle regulation, along with hyaluronan metabolism. The cluster doesn\u2019t point to a single cohesive pathway but rather to general cellular responsiveness to extracellular cues and growth-related activities. Thus this label captures the broad functional theme without overcommitting to any one pathway.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0030212","count":3},{"id":"GO:0035924","count":3},{"id":"GO:0071374","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1640667175073772638","title":"mRNA processing and stability regulation","description":"The proteins in this cluster are enriched for mRNA maturation and post-transcriptional regulation, with top terms spanning splicing, polyadenylation, poly(A) tail regulation, mRNA stability and modification, and even translation initiation complex assembly. This suggests a cohesive role in RNA processing and stability control, linking RNA maturation to translation readiness.","confidence":"High","size":9,"edges":29,"triangles":44,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":8},{"id":"GO:0006378","count":8},{"id":"GO:0060211","count":7},{"id":"GO:1905663","count":7},{"id":"GO:0097010","count":7}]},{"hash":"790939630229991075","title":"Vertebrate development and stress signaling","description":"This cluster centers on vertebrate developmental processes such as skeletal system development, neural tube closure, and overall multicellular organism development, with strong involvement in transcriptional regulation and cell-cycle control. The accompanying terms reflect cellular stress responses, including ER stress\u2013induced apoptosis, metal ion responses (cadmium), and growth changes under metabolic stress, plus an immune defense component. The combination suggests a cohesive theme of developmental programs intertwined with stress signaling and gene regulation.","confidence":"Medium","size":9,"edges":14,"triangles":7,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001501","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0050830","count":9},{"id":"GO:0001843","count":9},{"id":"GO:0006349","count":9}]},{"hash":"14343501251138352","title":"MAPK signaling in synaptic development","description":"The top terms point to neuronal signaling and synaptic function (excitatory postsynaptic potential, dendrite morphogenesis) with strong emphasis on MAPK pathways (ERK, JNK, MAPKK) and related regulatory processes; additional terms for Wnt and ephrin signaling suggest broader cell signaling integration, but the core theme is MAPK-regulated synaptic signaling and dendritic development.","confidence":"Medium","size":9,"edges":5,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":8},{"id":"GO:0070374","count":8},{"id":"GO:0000186","count":8},{"id":"GO:0046330","count":8},{"id":"GO:0048813","count":8}]},{"hash":"317547916010471258","title":"Embryonic organ morphogenesis and eye development","description":"The proteins' GO terms cluster around embryonic development and organ formation, especially eye morphogenesis, left-right patterning, and in utero development. While a few immune-related terms appear, the dominant signal is developmental morphogenesis across multiple organs, making a single theme of embryonic organogenesis appropriate.","confidence":"High","size":9,"edges":28,"triangles":42,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060972","count":5},{"id":"GO:0006366","count":4},{"id":"GO:0043010","count":4},{"id":"GO:0048294","count":4},{"id":"GO:0060441","count":4}]},{"hash":"1748574483271978599","title":"Mitotic Cell Cycle Regulation","description":"The proteins cluster around core mitotic processes: DNA-templated transcription, G1/S and G2/M transitions, spindle pole separation, and histone H3-S10 phosphorylation, all hallmark features of mitotic cell-cycle control. Some GO terms relate to proliferation in specific tissues or signaling pathways, but the dominant theme is regulation of mitosis and transcription during cell division, making this an appropriate, concise label.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0000320","count":9},{"id":"GO:0046626","count":9},{"id":"GO:0010696","count":9},{"id":"GO:0000082","count":9}]},{"hash":"69933698889315053","title":"MAPK and PI3K/AKT Immune Signaling","description":"The dominant terms point to MAPK cascades (ERK, JNK) and PI3K/AKT signaling, including LPS-mediated signaling, all indicating innate immune and inflammatory signaling pathways. While a few terms are outliers (e.g., lymph node development), the core theme across multiple terms is signaling that coordinates immune responses. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043491","count":3},{"id":"GO:0031663","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0070371","count":2},{"id":"GO:0051897","count":2}]},{"hash":"649030423901286071","title":"Innate Immune Signaling and Cytoskeletal Remodeling","description":"The top terms point to cytoskeletal dynamics (actin filament network formation; mitotic spindle assembly) alongside innate immune pathways (NOD2 muramyl dipeptide detection; TLR10 signaling) and cytokine regulation (IL-6, IL-18, chemokines), with regulatory roles in ubiquitination and nuclear export. This suggests a module where cytoskeletal remodeling intersects with signaling and trafficking in immune responses, rather than a single isolated function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051639","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0032498","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0046827","count":4}]},{"hash":"1466309184123574187","title":"Developmental morphogenesis and cell migration","description":"In this cluster, several GO terms point to developmental processes such as oviduct development, cranial skeletal system development, and mesenchymal proliferation in lung development, along with cell movement and calcium-dependent cell\u2013cell adhesion. While there are also broader cellular processes (DNA replication regulation, DNA damage response, proton transport, GTPase activity), the strongest signal centers on tissue morphogenesis and remodeling driven by cell migration and adhesion, justifying this label.","confidence":"Medium","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0015991","count":5},{"id":"GO:0043547","count":3},{"id":"GO:0060066","count":3},{"id":"GO:0007143","count":3},{"id":"GO:1904888","count":3}]},{"hash":"261841875555516866","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050427","count":3},{"id":"GO:0007417","count":3},{"id":"GO:0045765","count":3},{"id":"GO:0006898","count":2},{"id":"GO:0030505","count":2}]},{"hash":"200146758124627463","title":"Brain development and MAPK signaling","description":"The top terms show brain development and sensory perception of touch, and prominent positive regulation of ERK1/ERK2 and JNK cascades, which points to neural development and signal transduction. Supporting terms related to cytoskeletal remodeling (stress fiber assembly), ubiquitination, and COPII vesicle budding suggest neuronal growth and trafficking processes that underpin brain development. While ribosome biogenesis and GTPase regulation are general cellular functions, the neural development and MAPK signaling themes are the most representative for this cluster.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0043149","count":5},{"id":"GO:0033138","count":5},{"id":"GO:0016567","count":5}]},{"hash":"507831535197740905","title":"Integrin adhesion and Rho/Ras signaling","description":"Top GO terms cluster around extracellular matrix interactions and cytoskeletal signaling (hyaluronan metabolic process; integrin-mediated signaling; regulation of Rho and Ras signaling; heterotypic cell\u2013cell adhesion). These point to adhesion-dependent signaling pathways coordinated by integrins and small GTPases. A few terms (stamen formation, chlorophyll biosynthesis, obsolete ADP-ribosylation) appear noise or cross-species. The absence of edges suggests the proteins co-occur due to shared annotation rather than direct interaction, reinforcing a theme of adhesion and signaling rather than a single pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030212","count":4},{"id":"GO:0007229","count":4},{"id":"GO:0035023","count":4},{"id":"GO:0046580","count":4},{"id":"GO:0048455","count":3}]},{"hash":"1302993333921565597","title":"Neural development and synapse formation","description":"The cluster shows strong enrichment for neural development and connectivity processes: positive regulation of synapse assembly, interneuron migration (chemorepulsion), corpus callosum development, and myelination, along with cell\u2013cell adhesion and RTK signaling. ECM-related collagen fibril organization and skeletal system development suggest accompanying connective tissue remodeling during neural network formation. This combination supports a cohesive theme of neural development and synaptic organization.","confidence":"High","size":9,"edges":14,"triangles":11,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0051965","count":6},{"id":"GO:0048661","count":5},{"id":"GO:0001501","count":5},{"id":"GO:0030199","count":5},{"id":"GO:0042552","count":5}]},{"hash":"1237751376606439161","title":"ER Stress Response and Protein Homeostasis","description":"The terms cluster around unfolded protein response and ER stress, including regulation of translation initiation in response to ER stress, protein folding/chaperone activity, and ER-associated degradation, all pointing to a proteostasis theme. Additional terms touch on cell cycle and ciliary/photoreceptor localization, suggesting some peripheral roles, but the core signal is ER stress\u2013driven proteostasis. Confidence: Medium.","confidence":"","size":9,"edges":22,"triangles":22,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046661","count":3},{"id":"GO:0045842","count":3},{"id":"GO:1903070","count":3},{"id":"GO:2000324","count":3},{"id":"GO:0006986","count":3}]},{"hash":"802141691978251699","title":"Immune Defense and Signaling","description":"The most represented GO terms are defense response to virus, adaptive immune response, innate immune response, and B cell homeostasis, indicating a core immune function. Some terms about GPCR signaling and cardiac processes may reflect multifunctional proteins or annotation noise, but the dominant signal clusters around immune defense and host response.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":3},{"id":"GO:0002250","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0046597","count":2},{"id":"GO:0001782","count":2}]},{"hash":"206496804059178357","title":"Phosphorylation-regulated signaling pathways","description":"This cluster is enriched for GO terms related to phosphorylation of serine/threonine residues and regulation of kinase activity, with connections to signaling pathways such as Wnt and activin/TGF-\u03b2 (SMAD) signaling. While a couple terms are less directly tied to signaling (e.g., transcription by RNA polymerase III, phosphatidylcholine biosynthesis), the dominant theme is kinase-driven signal transduction and pathway regulation. Confidence: Medium.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018107","count":2},{"id":"GO:0016055","count":1},{"id":"GO:0033574","count":1},{"id":"GO:0033211","count":1},{"id":"GO:0010862","count":1}]},{"hash":"580259558332160640","title":"Iron transport and detoxification","description":"The cluster centers on iron handling, with multiple terms for iron ion transport, siderophore-iron import, and detoxification of iron ions, all connected to a general stress response. This pattern points to a cohesive iron homeostasis module, despite a few unrelated terms present in the set.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006880","count":9},{"id":"GO:0006950","count":9},{"id":"GO:1990461","count":9},{"id":"GO:0033214","count":9},{"id":"GO:0048147","count":9}]},{"hash":"811122980004815082","title":"TGF-beta/BMP Signaling Regulation","description":"Based on the GO terms, the cluster centers on regulation of TGF-beta signaling through SMAD complex assembly, BMP pathway modulation, and related cellular responses; this suggests a cohesive theme of signaling control rather than isolated functions. Some terms related to dephosphorylation and nuclear export further support modulation and trafficking of signaling components, although a few items appear unrelated and may reflect noise.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010991","count":3},{"id":"GO:0080005","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0042006","count":3}]},{"hash":"343509891557332403","title":"Proteoglycan Biosynthesis and Cartilage ECM","description":"These proteins are enriched for proteoglycan metabolism terms (dermatan/heparan/chondroitin sulfate pathways) and cartilage-related processes (chondrocyte development, ECM remodeling including angiogenesis in wound healing). The cluster seems to center on synthesis/modification of extracellular matrix proteoglycans, particularly those in cartilage and connective tissue; an outlier is maltose transport, which does not align with the main theme.","confidence":"High","size":9,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0060055","count":2},{"id":"GO:0002063","count":2},{"id":"GO:0033037","count":2},{"id":"GO:0030202","count":2},{"id":"GO:0030208","count":2}]},{"hash":"634943666263127661","title":"Multicellular development and growth","description":"The Top Terms show strong representation of developmental processes across tissues: brain development, male gonad development, osteoblast differentiation, single fertilization, and general multicellular organism growth. Additional terms for translation, ribosome biogenesis, and rRNA maturation reflect basic cellular machinery that often accompanies diverse gene sets, but the dominant pattern centers on developmental biology and organogenesis across different tissues.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0007338","count":2},{"id":"GO:0008584","count":2}]},{"hash":"880334213691896655","title":"Mitochondrial transcription, translation, and respiration","description":"The GO terms cluster around mitochondrial gene expression and energy metabolism: mitochondrial DNA metabolic process, DNA-templated transcription, mitochondrial translation, and tRNA aminoacylation (alanyl-, histidyl-, and related tRNAs) as part of mitochondrial protein synthesis, together with the respiratory electron transport chain. Some terms are obsolete or variably specific, but the dominant signal points to mitochondrion-based gene expression driving respiration.","confidence":"High","size":9,"edges":26,"triangles":39,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1901006","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001701","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0070143","count":1}]},{"hash":"1692223891507682057","title":"Mitochondrial Oxidative Phosphorylation and Protein Import","description":"These proteins converge on mitochondrial energy production and biogenesis: electron transport, proton translocation, oxidative phosphorylation, and assembly of respiratory chain complexes, with supporting roles in importing proteins into the mitochondrial matrix and inserting them into the inner membrane. This consistent set of mitochondrial respiration and import-related terms supports a cohesive label for the cluster.","confidence":"High","size":9,"edges":23,"triangles":28,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":3},{"id":"GO:0006122","count":3},{"id":"GO:0009060","count":2},{"id":"GO:0006119","count":1},{"id":"GO:0019646","count":1}]},{"hash":"41317021475117522","title":"Unknown","description":"The GO terms span plant-specific processes (phloem development, anthocyanin biosynthesis) and animal processes (platelet aggregation, cardiac myoblast differentiation, spinal cord neuron differentiation), plus general stress responses, with no unifying function. The cluster has no edges, offering no evidence of a shared pathway, so a cohesive label cannot be assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0001666","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0009718","count":3},{"id":"GO:2000691","count":3}]},{"hash":"197302699143705993","title":"Embryonic organogenesis and amino acid metabolism","description":"The ensemble of GO terms centers on embryonic development across multiple organs (forelimb, heart, pancreas, eye), indicating a developmental program. Intertwined with this, several terms involve biosynthesis or catabolism of amino acids and related compounds (glycine betaine, proline, GABA, putrescine), suggesting metabolic processes that support developing tissues. The cluster thus appears to group proteins linked to embryonic tissue formation with associated metabolic activity.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0019285","count":9},{"id":"GO:0035115","count":9},{"id":"GO:0055129","count":9},{"id":"GO:0048738","count":9},{"id":"GO:1901023","count":9}]},{"hash":"495445132201349331","title":"Developmental signaling and morphogenesis","description":"These proteins cluster around developmental processes and signaling: brain development, male gonad and spermatid development, neuron migration, and branching morphogenesis. The inclusion of transcriptional regulation and Rho signaling terms suggests roles in cell differentiation and cytoskeletal rearrangements central to morphogenesis. A few immune-related terms appear, but they do not define the core theme here; overall, the group seems focused on developmental regulation and organogenesis.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0007338","count":5},{"id":"GO:0008584","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0050830","count":4}]},{"hash":"2068127297005123076","title":"Central carbon metabolism and redox balance","description":"The top GO terms point strongly to core metabolic pathways: pyruvate and malate metabolism, L-malate catabolic and broader NADP metabolic regulation, plus poly-hydroxybutyrate biosynthesis, all of which indicate enzymes involved in central carbon metabolism and redox balance. Although some terms are obsolete, the dominant theme is energy metabolism and redox cofactor regulation, suggesting these proteins function together in central metabolic processes rather than a specific, isolated pathway. ","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042619","count":4},{"id":"GO:1902031","count":3},{"id":"GO:0006090","count":3},{"id":"GO:0006108","count":3}]},{"hash":"2138112348460685187","title":"Mitochondrial lipid and steroid biosynthesis","description":"This cluster\u2019s strongest signals are lipid biosynthesis (fatty acid elongation, very long-chain FA biosynthesis, sphingolipid biosynthesis) and mitochondrial-related processes (regulation of mitochondrial translation, complex IV assembly), with additional representation for steroidogenesis (testosterone biosynthesis) and androgen catabolism. Together, these point to a theme of mitochondrial involvement in lipid metabolism and steroid biosynthesis, outweighing the more minor, noise-like terms. ","confidence":"Medium","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030497","count":2},{"id":"GO:0061370","count":2},{"id":"GO:0042761","count":2},{"id":"GO:0070130","count":2},{"id":"GO:0033617","count":2}]},{"hash":"392893641553400145","title":"Glycerolipid and phospholipid biosynthesis","description":"The top GO terms are centered on lipid creation and remodeling\u2014platelet activating factor biosynthesis, phosphatidylcholine acyl-chain remodeling, triglyceride and ether lipid biosynthesis, and CDP-diacylglycerol biosynthesis\u2014pointing to a cohesive theme of glycerolipid/phospholipid metabolism and membrane lipid synthesis. Some developmental terms appear, but they are less directly tied to the core lipid biosynthesis signal. Confidence: Medium","confidence":"","size":9,"edges":17,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006663","count":7},{"id":"GO:0070236","count":7},{"id":"GO:0036151","count":7},{"id":"GO:0021587","count":7},{"id":"GO:0002071","count":7}]},{"hash":"605469138453763359","title":"Neuronal neurotransmission and feeding regulation","description":"The top GO terms cluster around neurotransmitter handling and signaling (serotonin and dopamine uptake, glycine secretion, dopamine catabolic process) and a behavioral aspect (positive regulation of feeding behavior), suggesting a set of proteins involved in neural signaling and modulation of feeding. The presence of a ciliary motility regulation term and a neuroprotective/oxidative stress-related term adds some breadth, but the core theme appears to be neural communication and feeding control rather than a structural or metabolic pathway. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009791","count":2},{"id":"GO:2000253","count":1},{"id":"GO:0060296","count":1},{"id":"GO:0018095","count":1},{"id":"GO:0051610","count":1}]},{"hash":"1974626628669264994","title":"Ubiquitin-dependent mitotic cell cycle regulation","description":"The cluster is dominated by GO terms tying mitosis to ubiquitin-mediated control: mitotic cell cycle and G2/M transition, SCF-dependent ubiquitin tagging for proteasomal degradation, and K11-linked ubiquitination, along with neddylation. This points to a cohesive theme of regulating cell division via the ubiquitin-proteasome system, with additional notes on chromatin-related regulation.","confidence":"High","size":9,"edges":33,"triangles":65,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001701","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0031146","count":9},{"id":"GO:0000086","count":9},{"id":"GO:0070979","count":9}]},{"hash":"2143124184373163386","title":"Cell signaling and cytoskeletal dynamics","description":"This cluster centers on signaling pathways (ERK cascade, GPCR-related signaling, B cell receptor signaling) and regulators of the cytoskeleton and ECM (Rho signaling, cell migration, collagen organization), suggesting proteins that coordinate signal transduction with cytoskeletal remodeling and adhesion. The diverse terms still coalesce around how cells sense, transmit, and respond to cues to move and reorganize their structure. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":4},{"id":"GO:0016477","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0021707","count":3}]},{"hash":"1945454417756121560","title":"Calcium-regulated muscle contraction and sarcomere organization","description":"This cluster centers on sarcomere organization and regulation of calcium release channels, affecting cardiac and skeletal muscle contraction via calcium signaling. The presence of terms like regulation of ryanodine-sensitive calcium-release channel activity and regulation of calcium release for muscle contraction suggests a core function in excitation-contraction coupling, with additional hints from ER retention and redox/homeostasis that support protein handling in muscle cells. Overall, a coherent theme around muscle contraction control through calcium signaling. ","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":2},{"id":"GO:0051258","count":2},{"id":"GO:2001238","count":2},{"id":"GO:0010649","count":2},{"id":"GO:0060315","count":2}]},{"hash":"576328940726397856","title":"Innate and adaptive immune activation","description":"This cluster is dominated by immune-related processes: complement activation, phagocytosis (recognition and engulfment), B cell receptor signaling and B cell activation, innate immune response, T cell costimulation, and NK cell cytotoxicity, with additional regulation of interleukin-10 production. Together these terms point to coordinated activation and communication across innate and adaptive immune components, as well as phagocytic activity, justifying the name.","confidence":"High","size":9,"edges":32,"triangles":60,"max_degree":8,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0006958","count":8},{"id":"GO:0006910","count":8},{"id":"GO:0006911","count":8},{"id":"GO:0050853","count":8},{"id":"GO:0045087","count":8}]},{"hash":"1909092095963318199","title":"Insect cuticle development and molting","description":"The strongest signals are chitin-based cuticle-related terms (chitin catabolic process, chitin-based cuticle development, ecdysis) alongside related developmental terms, suggesting these proteins cluster around insect exoskeleton formation and molting. Other terms (cartilage/lung development, NF-kappaB signaling, IL-6 response) appear as less dominant associations, which may reflect annotation cross-talk or broader regulatory connections but do not override the clear cuticle/molting theme.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051216","count":2},{"id":"GO:0006032","count":2},{"id":"GO:0070741","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0000272","count":2}]},{"hash":"162927622509788347","title":"Xenobiotic and lipid metabolism","description":"Based on the top GO terms, the proteins appear enriched for xenobiotic processing (dibenzo-p-dioxin catabolic process; insecticide metabolic process) as well as lipid and steroid-related metabolism (cholesterol catabolic process; aldosterone biosynthetic process; oxylipin biosynthetic process). This suggests a functional theme around detoxification and lipid/hormone metabolism rather than a single isolated pathway, so the label reflects both xenobiotic handling and lipid/steroid metabolism.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019341","count":7},{"id":"GO:0002677","count":7},{"id":"GO:0010193","count":7},{"id":"GO:1900087","count":7},{"id":"GO:0017143","count":7}]},{"hash":"409442584862495016","title":"Unknown","description":"The top GO terms are mixed across sensory perception, lipid metabolism, skin and adipocyte differentiation, mitochondrial inheritance, and even obsolete or fungal-specific processes, giving no single cohesive function for the cluster. Therefore a meaningful, confident label cannot be determined.","confidence":"","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0070542","count":1},{"id":"GO:0033561","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0050872","count":1}]},{"hash":"153049710974853956","title":"Cross-tissue Developmental Regulation","description":"The top GO terms span neural development (serotonergic neuron axon guidance, synaptic vesicle clustering) and organogenesis (nephron development, mitral valve formation, lung branching morphogenesis, melanogenesis), suggesting a broad theme of developmental regulation across tissues rather than a single, cohesive pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048023","count":9},{"id":"GO:0032912","count":9},{"id":"GO:0036515","count":9},{"id":"GO:2000807","count":9},{"id":"GO:0060488","count":9}]},{"hash":"1147798421639021788","title":"Unknown","description":"The GO terms span metabolism, chromatin regulation, host-symbiont interactions, differentiation, and viral processes with no obvious unifying function. Given the lack of a shared pathway or cohesive signal (no edges), there isn\u2019t a clear label beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042355","count":2},{"id":"GO:0051725","count":2},{"id":"GO:0039520","count":2},{"id":"GO:0033128","count":2},{"id":"GO:1904815","count":2}]},{"hash":"1362619163398901631","title":"Cellular Stress Response and DNA Replication Control","description":"The top GO terms point to several stress and signaling responses (glucocorticoid pathway regulation, xenobiotic response, lead ion detection, calcium signaling) together with core genome maintenance activities (DNA replication, intra-S checkpoint signaling, transcription termination by exosome). This suggests a theme of how cells sense stress and coordinate transcription- and replication-related processes, rather than a single, narrow function. ","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000324","count":8},{"id":"GO:0060079","count":8},{"id":"GO:0006260","count":8},{"id":"GO:1905213","count":8},{"id":"GO:0001915","count":8}]},{"hash":"1432031043047226156","title":"Drosophila Oogenesis and Cytoskeletal Regulation","description":"The top GO terms cluster around oocyte development in the Drosophila germarium (egg chamber formation, oocyte fate determination, oocyte differentiation) and cytoskeletal remodeling signals (GTPase activity, Arp2/3-mediated actin nucleation, cleavage furrow ingression). This suggests a cohesive theme of oogenesis linked with cytoskeletal dynamics and nutrient signaling (TORC1, amino acid response), tying together development and cytoskeletal control during egg formation. Some terms are ancillary, but the dominant pattern supports this interpretation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0034316","count":3},{"id":"GO:1904263","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0034198","count":2}]},{"hash":"1457127116055259364","title":"Unknown","description":"The set includes terms from translation, spliceosome-mediated RNA processing, CENP-A chromatin assembly, fertilization, B cell differentiation, plasmid partitioning, plasminogen activation, and midbrain morphogenesis. The terms do not point to a single coherent pathway or process, but rather a mix of nuclear gene expression, chromatin dynamics, development, and signaling, suggesting the cluster is not functionally cohesive.","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000245","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0061641","count":1},{"id":"GO:0007338","count":1}]},{"hash":"566920758731295979","title":"Ribosome biogenesis and mitotic regulation","description":"A set of terms centers on ribosome biogenesis and rRNA processing (GO:0042254, GO:0000447), with accompanying mitotic processes (GO:0000278, GO:0000132) and cell-cycle\u2013related regulatory activities (GO:0071902, GO:1904668). This suggests a concerted role in ribosome production linked to cell division control. Some outlier terms exist, but the core pattern aligns with nucleolar ribosome assembly and mitosis regulation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0007568","count":6},{"id":"GO:0000447","count":5},{"id":"GO:0071902","count":5},{"id":"GO:0042254","count":5}]},{"hash":"19678518090241196","title":"TCA and glyoxylate metabolism","description":"The top GO terms are dominated by central carbon metabolism: tricarboxylic acid cycle, isocitrate metabolic process, and the glyoxylate cycle, with accompanying mentions of menaquinone biosynthesis and oxidative stress response. This pattern strongly suggests a cluster centered on energy metabolism and respiration, with some ancillary regulatory or stress-related signals. Obsolete biosynthetic terms appear as noise rather than core themes. Confidence: High","confidence":"","size":8,"edges":25,"triangles":39,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0006537","count":2}]},{"hash":"324872564992276145","title":"Rho/Ras signaling and vesicle priming","description":"The cluster is enriched for regulation of Rho and Ras signaling, along with phosphoinositide/PI3K-related processes (IP3 biosynthesis, phospholipid catabolic process) and vesicle-associated events (synaptic vesicle priming, acrosome reaction). This pattern points to a theme of modulating small GTPase signaling and phosphoinositide pathways that coordinate vesicle trafficking and exocytosis, even as immune signaling (B cell receptor activation) is also represented. Overall, a cohesive label is that these proteins influence GTPase-mediated signaling intertwined with vesicle priming/fusion.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":7},{"id":"GO:0046580","count":7},{"id":"GO:0038028","count":6},{"id":"GO:0060313","count":6},{"id":"GO:0050861","count":6}]},{"hash":"969616725345711416","title":"Neural development and cell cycle regulation","description":"The cluster combines neural development terms (brain development, spinal cord development) with core cell cycle and mitosis terms (mitotic cell cycle, cell division, APC-dependent catabolic process), plus growth-signaling (TORC1) and phosphorylation regulation, suggesting a module coordinating neural development with cell proliferation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:2001162","count":5},{"id":"GO:0035264","count":5},{"id":"GO:0031145","count":5},{"id":"GO:0021510","count":5}]},{"hash":"845613707714296069","title":"Cytoplasmic Translation Cluster","description":"The top GO terms are dominated by translation, especially cytoplasmic translation, indicating these proteins primarily relate to protein synthesis machinery. The remaining terms pertain to diverse metabolic and antibiotic-related processes, which are less cohesive, so the primary theme is translation.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":2},{"id":"GO:0042372","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0017000","count":1}]},{"hash":"1098207488448733763","title":"Cell Cycle and Centrosome Regulation","description":"The top GO terms center on DNA replication, centrosome cycle, and nuclear cell cycle regulation, with supporting terms for microtubule localization, ubiquitination, and apoptosis. These collectively point to coordinated control of cell division and centrosome/microtubule dynamics, with some developmental and signaling overlaps that are often linked to cell cycle regulators. Thus the cluster likely represents proteins involved in cell cycle control and centrosome maintenance, rather than a single signaling pathway. ","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0007098","count":2},{"id":"GO:0010571","count":2},{"id":"GO:0048701","count":2}]},{"hash":"1801327322245547667","title":"Integrin-mediated adhesion and ECM remodeling","description":"The top GO terms cluster around cell-ECM adhesion (integrin-mediated and calcium-independent adhesion), cell-cell adhesion, ECM organization/remodeling (collagen fibril organization, hyaluronan metabolism, metallopeptidase activity), and processes related to cell migration and extravasation, with a note on coagulation. This suggests proteins that coordinate adhesion to the extracellular matrix and remodeling of the ECM to enable movement through tissues.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007161","count":4},{"id":"GO:0035987","count":4},{"id":"GO:0007229","count":4},{"id":"GO:0034113","count":3},{"id":"GO:1905050","count":3}]},{"hash":"981475208470778022","title":"Nucleotide and amino acid metabolism with calcium signaling","description":"Most terms point to metabolism of nucleotides (nucleotide metabolic process, ribonucleoside monophosphate catabolic process, adenosine metabolic process) and amino acids (L-serine biosynthetic process), with an additional term for intracellular calcium ion homeostasis. There are also broad metabolic pathway terms (stilbene catabolic process, epoxygenase P450 pathway) that support a general metabolic/signal context rather than a single cohesive function. This suggests a cluster tied to basic metabolic processes with a calcium signaling component, hence the label.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006874","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0033574","count":2},{"id":"GO:0097755","count":2},{"id":"GO:0019509","count":2}]},{"hash":"431518384002767539","title":"Unknown","description":"The GO terms show a scattered mix of amino acid biosynthesis (lysine, histidine, tyrosine), cobalamin biosynthesis, sphingomyelin biosynthesis, fatty acid transport/homeostasis, Notch signaling, and salicylic acid\u2013mediated defense, with no single, cohesive function tying the proteins together. This suggests either annotation noise or multi-functional proteins rather than a focused biological cluster.","confidence":"","size":8,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":4},{"id":"GO:0007219","count":3},{"id":"GO:0009862","count":2},{"id":"GO:0006686","count":2},{"id":"GO:0000105","count":2}]},{"hash":"877887328077677619","title":"Unknown","description":"The top terms include immune signaling, DNA replication regulation, transcriptional control, splicing, mechanosensory behavior, and germ cell development, with no single shared function clearly tying all eight proteins together; thus there isn\u2019t a coherent theme for a label.","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1901223","count":2},{"id":"GO:0032298","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0007638","count":1},{"id":"GO:0000398","count":1}]},{"hash":"1744902896364203745","title":"Ubiquitin-Proteasome Pathway Components","description":"This cluster is dominated by ubiquitination-related terms (protein ubiquitination, polyubiquitination, autoubiquitination, K63-linked ubiquitination) and proteasomal/ERAD degradation processes (SCF-dependent proteasomal ubiquitin-dependent protein catabolic process), indicating a set of proteins involved in tagging substrates for degradation and turnover, with downstream links to apoptosis regulation and transcriptional control.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0000209","count":4},{"id":"GO:0051865","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0043066","count":3}]},{"hash":"298064393358186633","title":"Inner ear development and ion transport signaling","description":"Reasoning: The top terms show a coherent emphasis on inner ear development and broader multicellular development, paired with ion transport across membranes (sodium/potassium) and signaling pathways involving cAMP/cGMP and guanylyl cyclase. This suggests a functional theme around auditory system development with ion homeostasis and related signaling, despite a few outliers like aerotaxis. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006349","count":8},{"id":"GO:0048839","count":8},{"id":"GO:0007275","count":8},{"id":"GO:0019233","count":8},{"id":"GO:0098719","count":7}]},{"hash":"212839155034961382","title":"Nuclear export and centrosome/kinetochore regulation","description":"This cluster highlights nucleocytoplasmic transport (ribosomal subunit and mRNA export), transcriptional regulation, and components related to centrosome duplication and kinetochore localization, with links to ciliary transport. The convergence on nuclear-cytoplasmic transport and cell cycle/mitotic structures suggests a cohesive role in coordinating gene expression with cell division machinery.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010824","count":4},{"id":"GO:0042493","count":4},{"id":"GO:0000056","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0042176","count":4}]},{"hash":"556733042213234270","title":"Diverse Biosynthetic Processes","description":"The top GO terms are mainly biosynthetic processes (serine, GMP, histidine, glycolipid, lipopolysaccharide biosynthesis), suggesting the proteins cluster around biosynthetic activities. A few bone-related terms appear, which may reflect annotation spillover or multi-species data, but the overall signal centers on biosynthesis. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":3},{"id":"GO:0009247","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0001958","count":2},{"id":"GO:0019509","count":2}]},{"hash":"1814885546127581351","title":"Glycosylation and proteoglycan biosynthesis","description":"These proteins show enrichment for GO terms tied to carbohydrate processing and glycosylation, including protein N-linked glycosylation and biosynthesis of proteoglycans (chondroitin sulfate, heparan sulfate) as well as related glycan assembly (glucuronoxylan, plant-type secondary cell wall biosynthesis). The dominant theme is glycosylation and extracellular matrix/cell-wall carbohydrate synthesis, with a few broader development or proliferation terms as less-supported noise. Overall, a cohesive label is \u201cGlycosylation and proteoglycan biosynthesis.\u201d","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":3},{"id":"GO:0006487","count":3},{"id":"GO:0050650","count":2},{"id":"GO:0009834","count":2},{"id":"GO:0015012","count":2}]},{"hash":"246424247517862274","title":"Sterol and lipid biosynthesis","description":"The terms are heavily weighted toward lipid and sterol metabolism (ergosterol and cholesterol biosynthesis, fatty acid and ether lipid pathways, sphingolipid metabolism), plus a note on myelin maintenance which is lipid-rich. This suggests the cluster comprises proteins involved in sterol and lipid biosynthesis rather than a single signaling or immune function. A few terms like B cell chemotaxis may reflect broader multifunctionality or annotation overlap, but the dominant theme is lipid/sterol metabolism.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":2},{"id":"GO:0080065","count":2},{"id":"GO:0046485","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006675","count":2}]},{"hash":"1779520975461130951","title":"Transmembrane Transporters","description":"The GO terms are dominated by various transmembrane transport activities (chloride, oxalate, aspartate, fructose, bicarbonate) and regulation of membrane potential, indicating a group enriched for proteins that move ions and small molecules across membranes. While a few terms (sporulation, sperm capacitation, auditory perception, transcription regulation) are present, they are less representative. Overall, the core theme is membrane transport, supporting this label.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042391","count":2},{"id":"GO:1902476","count":2},{"id":"GO:0019532","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0089712","count":2}]},{"hash":"1626023260965589760","title":"Innate immune defense proteins","description":"The top GO terms are dominated by innate immunity and defense: defense responses to protozoan and Gram-negative bacteria, cellular response to interferon-beta, and innate immune response, suggesting these proteins function in innate defense. While there are a few terms related to translation and ribosome biogenesis, they are less representative of the cluster\u2019s main theme. Therefore, the core label best captures the common function suggested by the strongest terms.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042832","count":4},{"id":"GO:0050829","count":4},{"id":"GO:0035458","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0051260","count":4}]},{"hash":"445293441610787849","title":"Ubiquitin-SUMO Proteostasis and Mitophagy","description":"This cluster is dominated by protein quality-control processes: sumoylation and ubiquitination, ERAD, aggresome assembly, mitophagy, and autophagy regulation. Together these terms point to a module focused on tagging and degrading misfolded proteins and damaged mitochondria, i.e., proteostasis with mitochondrial quality control. A stray rRNA maturation term is likely noise.","confidence":"High","size":8,"edges":12,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:1901097","count":3}]},{"hash":"92865595220088577","title":"Unknown","description":"The GO terms are very heterogeneous, including embryonic development and angiogenesis on one hand and multiple metabolic processes (adenosine/adenine catabolism, fatty acid and carbohydrate biosynthesis) on the other, plus plant-specific and bacterial pathways, giving no clear, shared function for the cluster. ","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001701","count":2},{"id":"GO:0045766","count":2},{"id":"GO:0006154","count":2},{"id":"GO:0050850","count":2},{"id":"GO:0009234","count":2}]},{"hash":"815829324148675602","title":"Membrane receptor signaling and cell adhesion","description":"The top terms cluster around signaling at the cell surface (receptor-mediated tyrosine phosphorylation, ephrin and B cell receptor signaling) and processes tied to cell\u2013cell contacts (tight junction assembly, substrate adhesion-dependent spreading, transcytosis). While some terms relate to transport or proliferation, the common thread is membrane signaling and adhesion functions. ","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045056","count":3},{"id":"GO:0070830","count":3},{"id":"GO:0050861","count":3},{"id":"GO:0070574","count":2},{"id":"GO:0050731","count":2}]},{"hash":"1554069920653065489","title":"Modulators of Immune and Developmental Signaling","description":"The GO terms point to regulation of diverse signaling pathways, especially immune-related signaling (TLR, chemokine, IL-18 production, estrogen receptor signaling) and developmental processes (Wnt signaling, otolith morphogenesis, angiogenesis), plus related regulatory roles in endosome-to-Golgi transport. The common theme is broad modulation of signaling cascades rather than a single pathway, with both positive and negative regulatory roles. Medium","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0034123","count":3},{"id":"GO:1905279","count":3},{"id":"GO:0016525","count":3},{"id":"GO:0070100","count":3}]},{"hash":"899535744545213220","title":"Neddylation and Ubiquitination in Chromatin Regulation","description":"This cluster centers on post-translational modification pathways that regulate chromatin state, notably protein neddylation and ubiquitin signaling, which influence histone modification and chromatin maintenance. The presence of terms like neddylation, ubiquitin chain polymerization, and histone modification regulation (even with obsolete annotations) points to a cohesive theme of chromatin regulation linked to development and cell cycle processes.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0001701","count":8},{"id":"GO:0045116","count":8},{"id":"GO:0006344","count":8},{"id":"GO:0035458","count":8},{"id":"GO:0051569","count":8}]},{"hash":"1074883550664620364","title":"Development and morphogenesis","description":"This cluster's GO terms largely point to developmental processes and tissue morphogenesis across diverse contexts (muscle, neural, hair, cartilage, phloem), with actin cytoskeleton organization as a common underpinning. Although some terms are more specialized (e.g., platelet aggregation), the dominant theme is differentiation and morphogenesis across multiple tissues.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:2000691","count":7},{"id":"GO:0070527","count":7},{"id":"GO:2000324","count":7},{"id":"GO:0051017","count":7},{"id":"GO:0021527","count":7}]},{"hash":"1402333695113208878","title":"Unknown","description":"The GO terms are highly diverse, including lens development, atrial septum development, male sex differentiation, blood pressure regulation, morphine response, and ER stress\u2013related translation initiation, with only a couple pointing to ER stress. There is no clear, cohesive function or pathway uniting the cluster, so a single, meaningful label cannot be confidently assigned.","confidence":"","size":8,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0003085","count":2},{"id":"GO:0002088","count":2},{"id":"GO:0043278","count":1},{"id":"GO:0046661","count":1},{"id":"GO:0045842","count":1}]},{"hash":"1194008740238373229","title":"Cardiac and neuronal ion-channel signaling","description":"The GO terms converge on membrane potential regulation, ion-channel activity (notably calcium channels), and electrical signaling in heart and nervous system (including GABA signaling, atrial action potential, and cardiac conduction). Phosphorylation is a common regulatory theme. Some entries touch on development or epithelial integrity, but the core theme is excitability and ion-channel\u2013driven signaling.","confidence":"Medium","size":8,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:1903286","count":2},{"id":"GO:0007214","count":2},{"id":"GO:0055113","count":2},{"id":"GO:0090557","count":2}]},{"hash":"1571388788269225770","title":"Negative regulation of signaling pathways","description":"This cluster is dominated by GO terms describing dampening or inhibition of signaling across multiple systems: IL-6 signaling and production, prolactin signaling, p38 MAPK cascade, and TLR9 signaling. Other terms mention modulation of vascular permeability and neuronal membrane depolarization, as well as glial and hematopoietic development contexts, suggesting the proteins function as broad regulators that restrain signaling activity across cell types. Despite a few outliers (e.g., a positive regulation term and megakaryocyte development), the unifying theme is negative regulation of signaling.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035855","count":3},{"id":"GO:0070104","count":3},{"id":"GO:0060020","count":3},{"id":"GO:0043116","count":3},{"id":"GO:0048671","count":3}]},{"hash":"262401206384713075","title":"Multitissue cell differentiation","description":"These GO terms point to differentiation programs across multiple tissues (club cells, enterocytes, type II pneumocytes, cardiac tissue, erythrocytes, endocrine secretion). The common theme is developmental or differentiation processes affecting diverse cell types, rather than a single pathway or function. ","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0060486","count":8},{"id":"GO:1903703","count":8},{"id":"GO:1900461","count":8},{"id":"GO:0060510","count":8},{"id":"GO:0061026","count":8}]},{"hash":"363035900308924345","title":"Developmental Gene Regulation and Germline Processes","description":"The cluster is characterized by transcriptional regulation (negative regulation of transcription by RNA polymerase II and DNA-templated transcription) alongside germline/gamete-associated activity (piRNA processing, DNA methylation in gamete generation), plus development-related terms such as brain development, male meiotic division, somatic stem cell maintenance, and growth signaling (TGF-beta). This pattern points to a cohesive theme of developmental regulation and germline/somatic stem cell biology, with a few terms (e.g., immune response) likely representing broader or incidental connections. Confidence in this theme is moderate.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0034587","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0035019","count":3}]},{"hash":"2006560346434588793","title":"Lectin- and Fc receptor\u2013mediated innate immune activation","description":"This cluster is dominated by GO terms for lectin pathway complement activation, C-type lectin receptor signaling, Fc-gamma receptor signaling, leukocyte tethering/rolling, and phagocytosis recognition, highlighting innate immune activation, opsonization, and leukocyte recruitment. Platelet activation and adhesion molecule production further support an inflammatory signaling context; a single development term (cartilage condensation) appears ancillary. Overall, the group centers on immune signaling and inflammatory processes.","confidence":"High","size":8,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010572","count":4},{"id":"GO:0008285","count":3},{"id":"GO:0001867","count":3},{"id":"GO:0002223","count":3},{"id":"GO:0090238","count":3}]},{"hash":"2226204811195510915","title":"Genome stability and nuclear processes","description":"Top GO terms cluster around DNA damage response, centrosome duplication, meiotic division, nucleolar localization, and translation regulation under stress, suggesting a theme of nuclear processes and genome maintenance. Some terms (e.g., bone resorption, mechanical stimulus) are less consistent, but the dominant signal points to nuclear/cell cycle regulation and genome stability.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0044130","count":2},{"id":"GO:0045780","count":2},{"id":"GO:0007338","count":1},{"id":"GO:0045836","count":1}]},{"hash":"322551797596229114","title":"Developmental chromatin regulation and transcription","description":"This cluster centers on nuclear processes: chromatin assembly and localization to chromatin, and negative regulation of transcription by RNA Pol II, alongside several development-related terms (vitellogenesis, fertilization, gonad and brain development). This suggests a shared theme of chromatin- and transcription-level control during development, with a few terms appearing as peripheral or artifact. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0007296","count":5},{"id":"GO:0007338","count":4},{"id":"GO:0008584","count":4},{"id":"GO:0007420","count":4}]},{"hash":"455630342964474836","title":"NF-kappaB-driven Innate Immune Activation","description":"This cluster centers on innate immune signaling, with GO terms for activation of NF-kappaB-inducing kinase activity and innate immune/defense responses to virus, indicating a core theme of NF-kB\u2013mediated antiviral signaling. Some translation regulation and ribosome-related terms appear, likely reflecting secondary or stress-related roles in antiviral responses, but the dominant pattern supports NF-kB-driven innate immunity.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007250","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:1902775","count":1}]},{"hash":"1964115384923704515","title":"NF-\u03baB\u2013driven immune signaling and cytokine production","description":"Most terms point to immune activation and inflammatory signaling: T cell receptor signaling, TLR4 signaling, canonical NF-kappaB pathway, immunoglobulin production, IL-1/IL-8 related regulation, and JNK cascade. The brain development term appears as an outlier and may reflect annotation overlap rather than a core feature. Overall, the cluster reflects NF-\u03baB\u2013mediated immune responses and cytokine production.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050852","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0001783","count":3},{"id":"GO:0007249","count":3},{"id":"GO:0002377","count":3}]},{"hash":"1952245828006884948","title":"Embryonic development and morphogenesis","description":"This cluster's top GO terms cluster around developmental processes and tissue morphogenesis, including left-right patterning, placenta-related differentiation, EMT in heart formation, cartilage morphogenesis, and endocrine system development, with additional terms on pancreatic cell development and transcription/splicing that may reflect proliferative developmental regulation. The common theme is embryonic tissue differentiation and morphogenesis, so this label captures the main function of the cluster.","confidence":"High","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032298","count":7},{"id":"GO:0060536","count":7},{"id":"GO:1903026","count":7},{"id":"GO:0003323","count":7},{"id":"GO:0000398","count":7}]},{"hash":"816673815376087071","title":"Embryonic Development and Tissue Morphogenesis","description":"The top GO terms are dominated by developmental and morphogenesis processes across multiple tissues, including roof of mouth development, cartilage morphogenesis, endocrine system development, pancreatic cell development, and endocardial cushion EMT. While there are also general gene expression regulators (RNA Pol II regulation, mRNA splicing) and nuclear export terms, the prevailing theme points to proteins involved in embryonic tissue formation and morphogenesis, making the label representative of the cluster\u2019s shared function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001046","count":6},{"id":"GO:0060021","count":6},{"id":"GO:0060536","count":6},{"id":"GO:1903026","count":6},{"id":"GO:0003323","count":6}]},{"hash":"538992222152813017","title":"Integrin-mediated adhesion and cytoskeletal signaling","description":"The top GO terms center on cell-surface localization, cell-matrix adhesion, and integrin signaling, plus actin-based cytoskeletal dynamics (actin contraction, membrane rafts). This points to proteins that function at the plasma membrane to mediate adhesion to the extracellular matrix and transmit signals to the cytoskeleton, governing adhesion, spreading, and possibly migration. While there are also terms related to osteoclast development and embryo implantation, these can be understood in the context of adhesion and matrix interactions. Overall, the cohesive theme is membrane-associated adhesion and cytoskeletal signaling.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001205","count":3},{"id":"GO:0034394","count":3},{"id":"GO:0007566","count":3},{"id":"GO:0010226","count":3},{"id":"GO:0007160","count":3}]},{"hash":"717096925821552757","title":"Microtubule-based mitosis and spindle dynamics","description":"The proteins in this cluster repeatedly relate to microtubules and mitotic processes: spindle pole separation, plus-end transport and sliding along microtubules, maintenance of microtubule polarity, nuclear migration, cytokinesis, and related chromosome events. While some terms span different organisms (yeast mating, plant cytokinesis, flagellar microtubules), the unifying theme is microtubule-driven mitotic/meiosis-related dynamics.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":7},{"id":"GO:0000073","count":7},{"id":"GO:0072383","count":7},{"id":"GO:0031535","count":7},{"id":"GO:0000743","count":7}]},{"hash":"299385865864738654","title":"Spliceosome Assembly and RNA Processing","description":"The top GO terms cluster around spliceosomal complex assembly, mRNA splicing via spliceosome, snRNP assembly, and related RNA maturation steps (tRNA processing, rRNA maturation, and transcription termination), indicating a nucleus-focused RNA processing/splicing module. While a couple terms (ABA response, heterochromatin formation) are peripheral, they do not contradict the dominant RNA-processing theme. This cluster is best described as proteins involved in spliceosome function and broader RNA processing.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000245","count":7},{"id":"GO:0045292","count":6},{"id":"GO:0008033","count":6},{"id":"GO:0051170","count":6},{"id":"GO:0000290","count":6}]},{"hash":"1036040887646422937","title":"Unknown","description":"The top GO terms cover a wide, unrelated mix of biosynthetic processes (histidine, tyrosine, lysine, cobalamin; sphingomyelin), transport (fatty acids), and signaling pathways (Notch, cAMP, glucocorticoid, salicylic acid\u2013mediated defense). This lack of a cohesive, shared function among the proteins suggests there isn\u2019t a single clear theme tying the cluster together.","confidence":"","size":7,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051591","count":4},{"id":"GO:0051384","count":4},{"id":"GO:0009862","count":4},{"id":"GO:0006686","count":4},{"id":"GO:0000105","count":4}]},{"hash":"1203760781516075260","title":"Endothelial growth factor signaling and cell growth regulation","description":"This cluster centers on growth factor signaling pathways (VEGF receptor signaling, EGF response) and associated phosphorylation events (JUN, STAT), linked to endothelial cell chemotaxis and regulation of cell growth, with a note of mitotic checkpoint signaling, indicating cell-cycle control. Although there are terms related to neuronal processes (visual perception, postsynaptic potential), the predominant theme is endothelial signal transduction and growth regulation, which supports the label.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":7},{"id":"GO:0048010","count":7},{"id":"GO:0007258","count":7},{"id":"GO:2001028","count":7},{"id":"GO:0070849","count":7}]},{"hash":"398383781440266710","title":"Unknown","description":"The cluster mixes signals related to neuronal function (excitatory postsynaptic potential, Schwann cell development, response to cocaine) with cell cycle and DNA replication processes (DNA replication, G1/S transition, mitotic and meiotic cycles, kinetochore localization). There is no single unifying theme tying these terms together, so a concise, representative label cannot be determined.","confidence":"","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060079","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0034501","count":4},{"id":"GO:0042220","count":4},{"id":"GO:0014044","count":4}]},{"hash":"1041308528719223662","title":"Neural synaptic signaling and development regulation","description":"The cluster centers on synaptic signaling and plasticity (AMPA receptor activity, ephrin signaling, learning) together with neural development processes (Wnt/PCP, astrocyte differentiation, differentiation signals), indicating a cohesive theme around neuronal communication and development regulation.","confidence":"High","size":7,"edges":10,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1901187","count":3},{"id":"GO:1900383","count":3},{"id":"GO:0035264","count":3},{"id":"GO:0035026","count":2},{"id":"GO:0007258","count":2}]},{"hash":"518965166526834899","title":"Organogenesis and Tissue Differentiation","description":"The GO terms are all about development and differentiation across multiple tissues and organs (eye, brain, pancreas, digestive tract, thyroid, spinal cord, rhombomeres). Although there isn\u2019t a single pathway, the common theme is embryonic organogenesis and tissue specification, so this label best captures the cluster\u2019s function.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0002070","count":3},{"id":"GO:0030878","count":3},{"id":"GO:0021892","count":3},{"id":"GO:0007501","count":3}]},{"hash":"590158603828386833","title":"Mitotic Regulation and Histone Methylation","description":"The cluster\u2019s main terms cluster around mitosis and chromatin state: mitotic cell cycle, APC/C-dependent catabolic process, and K11-linked ubiquitination point to cell-cycle control, while several histone methylation terms (H3-K79, K4, K27) indicate chromatin modification. DNA-templated transcription and growth terms fit with the broader regulation during cell division. This combination suggests proteins involved in coordinating mitosis with chromatin regulation rather than a single narrow function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:2001162","count":4},{"id":"GO:0051568","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0035264","count":4}]},{"hash":"21935646940607906","title":"Nervous system development and signaling regulation","description":"The top GO terms are dominated by nervous system development (notably substantia nigra development) and signaling pathways (ERK, Wnt) that regulate neural differentiation and gene expression; other terms reflect broader developmental processes, but the core theme ties to neural development and its signaling modulation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":5},{"id":"GO:0070374","count":5},{"id":"GO:0010628","count":5},{"id":"GO:0060501","count":5},{"id":"GO:0090263","count":5}]},{"hash":"1167809982936368194","title":"Developmental Signaling and Chromatin Dynamics","description":"The GO terms cluster around broad developmental processes (brain, gonad, bone) and include chromatin assembly (CENP-A) plus regulatory signaling and RNA modification activities, suggesting a general theme of developmental regulation with chromatin and signaling components rather than a single pathway.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0031954","count":2}]},{"hash":"1196446391607901312","title":"Mitophagy and Cellular Quality Control","description":"This cluster centers on autophagy and mitochondrial turnover, with multiple terms for mitophagy, regulation of autophagosome maturation, and regulation of mitochondrial fusion, plus aggresome assembly and protein sumoylation indicating broader proteostasis and stress responses. Some terms (rRNA maturation, spindle pole body duplication, nucleotide-excision repair) are less directly related, but the dominant theme ties to mitochondrial quality control and cellular proteostasis.","confidence":"Medium","size":7,"edges":18,"triangles":23,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":5},{"id":"GO:1901097","count":3},{"id":"GO:0010637","count":3},{"id":"GO:0000423","count":3},{"id":"GO:1902283","count":3}]},{"hash":"754742355965604931","title":"Developmental Signaling and Tissue Remodeling","description":"The highlighted GO terms point to developmental processes and cell behavior, including luteinization (ovarian differentiation), positive regulation of Hippo signaling (growth control), and fibroblast migration (tissue remodeling). Skeletal system development ties to organismal structure formation. A few terms for ribosome biogenesis and ubiquitin ligase regulation reflect general cellular regulation that supports development. Overall, the cluster centers on signaling and movement during tissue development, with some broader cellular processes present.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001553","count":2},{"id":"GO:0035332","count":2},{"id":"GO:0010761","count":2},{"id":"GO:0000447","count":1},{"id":"GO:0043547","count":1}]},{"hash":"777119274384071295","title":"Neural calcium signaling and synaptic activity","description":"The top GO terms cluster around neural signaling and calcium dynamics: visual perception, excitatory postsynaptic potential, and regulation of voltage-gated and store-operated calcium channels, with astrocyte activation also represented. Together these point to calcium-dependent synaptic activity in neural cells. Some terms like karyogamy and mitotic cycle appear as outliers, but the dominant theme supports a neural calcium signaling function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0048143","count":3},{"id":"GO:0038163","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071902","count":3}]},{"hash":"92302054197590164","title":"Unknown","description":"The top GO terms span several distinct themes, including nuclear organization (tRNA gene clustering, maintenance of rDNA, heterochromatin formation), vesicle trafficking (anterograde/retrograde transport, lysosome targeting), and varied developmental/immune processes (microsporogenesis, gravitropism, antigen processing). There isn\u2019t a single unifying function or pathway linking these proteins, so a cohesive label isn\u2019t justifiable.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070058","count":2},{"id":"GO:0043007","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0048007","count":2},{"id":"GO:0009556","count":2}]},{"hash":"2136012446348068862","title":"Innate and adaptive immune signaling and antigen presentation","description":"These proteins show enrichment for innate immune sensing (stimulatory C-type lectin receptor signaling), NF-kappaB signaling, and T cell receptor signaling, along with antigen processing and presentation via MHC class I. The convergence of innate sensing, adaptive signaling, and antigen presentation suggests a role in coordinating immune responses rather than a single stress or developmental pathway. Some terms related to stress or other pathways may be incidental. ","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0002223","count":4},{"id":"GO:0010972","count":4},{"id":"GO:0061418","count":4},{"id":"GO:0009651","count":4},{"id":"GO:0060071","count":4}]},{"hash":"502566780530468023","title":"MVB-Dependent Endosomal-Vacuolar Sorting","description":"The top GO terms cluster around multivesicular body (MVB) sorting, endosome maturation/transport, and delivery to the vacuole, including ubiquitin-dependent pathways. Terms referring to the MVB pathway and endosome-to-vacuole traffic strongly imply a vesicular trafficking/degradation module, with ancillary signals like autophagy regulation and mitotic exit playing secondary roles. This name captures the core shared function of the cluster.","confidence":"High","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:1902902","count":3},{"id":"GO:0090611","count":3},{"id":"GO:1902188","count":3},{"id":"GO:0010458","count":3}]},{"hash":"950352731015718953","title":"Ribosome Biogenesis and Cell Cycle Machinery","description":"The top GO terms cluster around ribosome biogenesis, translation, and rRNA maturation, with supporting signals from cell cycle and mitosis (mitotic spindle assembly, cell division). This suggests a cohesive module dedicated to ribosome assembly and protein synthesis linked to cell cycle progression; a couple of terms about fertilization/conjugation may reflect broader fusion-related pathways but do not dominate the theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007338","count":2}]},{"hash":"1239654467704381250","title":"Ribosome Biogenesis and SRP-Mediated Translation","description":"This cluster centers on translation and ribosome assembly, with terms for translation, initiation, termination, and maturation of 5.8S/SSU/LSU rRNA, plus SRP-dependent cotranslational targeting to membranes. The presence of mRNA quality control (non-stop decay) reinforces a broader theme of translation fidelity and ribosome function, despite one outlier term on lymph gland hemopoiesis. Overall, the proteins appear to participate in ribosome biogenesis and co-translational membrane targeting.","confidence":"High","size":7,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006413","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1}]},{"hash":"2104208335254759081","title":"Cell cycle and intracellular trafficking","description":"The terms converge on cell cycle and division, with supporting themes of vesicle trafficking and cytoskeletal dynamics (microtubule depolymerization, pinocytosis, Golgi retention). Autophagy and apoptotic processes also appear, suggesting coordinated remodeling during proliferation or stress. Overall, the cluster seems to reflect a module linking cell cycle progression to intracellular transport and membrane trafficking.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0048013","count":2},{"id":"GO:0045071","count":2}]},{"hash":"1367231701372287578","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":2},{"id":"GO:0039520","count":1},{"id":"GO:0002127","count":1},{"id":"GO:0042256","count":1},{"id":"GO:0000453","count":1}]},{"hash":"1310852882901633567","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009812","count":3},{"id":"GO:0030573","count":3},{"id":"GO:0050427","count":3},{"id":"GO:0006711","count":3},{"id":"GO:0006068","count":3}]},{"hash":"1615814509848773497","title":"Mesodermal and organ morphogenesis","description":"The top GO terms cluster around developmental morphogenesis across tissues derived from the mesoderm and related organ formation (hair follicle morphogenesis, cartilage morphogenesis, mesoderm development, endocrine system development, and heart-associated EMT in endocardial cushion formation). While some terms reflect general cellular processes (RNA splicing/export, DNA replication regulation), the dominant theme is tissue and organ morphogenesis during development, particularly mesodermal derivatives. ","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0031069","count":6},{"id":"GO:0060536","count":6},{"id":"GO:1903026","count":6},{"id":"GO:0003323","count":6},{"id":"GO:0007498","count":6}]},{"hash":"317384530386317285","title":"Immune signaling (innate and adaptive)","description":"The proteins map predominantly to immune responses, including innate antiviral defense, adaptive immunity, and signaling pathways such as Toll-like receptor signaling and NF-kappaB regulation, with IL-18 production also represented. A couple of terms related to unrelated processes (sarcomere organization and otolith morphogenesis) likely reflect background noise. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0051092","count":2},{"id":"GO:0007026","count":2},{"id":"GO:0046007","count":2}]},{"hash":"1845508441571977754","title":"Mitochondrial respiration and oxidative phosphorylation","description":"The cluster is dominated by GO terms related to mitochondrial electron transport and oxidative phosphorylation (oxidative phosphorylation, aerobic respiration, mitochondrial electron transport chain, electron transport coupled proton transport, aerobic electron transport chain), indicating a core function in energy production within mitochondria; some biosynthetic terms are present but secondary.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":2},{"id":"GO:0006119","count":1},{"id":"GO:0019411","count":1},{"id":"GO:0006123","count":1},{"id":"GO:0015990","count":1}]},{"hash":"1616425787952422837","title":"Lymphoid Immunity and NF-kappaB Signaling","description":"The top GO terms cluster around lymphoid biology and NF-kappaB\u2013related signaling: lymph node development, B and T cell homeostasis, regulation of immunoglobulin production, innate immune response, and activation of NF-kappaB pathways. These together point to proteins coordinating adaptive immune regulation and NF-kB\u2013driven transcription, with vitamin D response potentially modulating this activity. Despite some obsolete terms, the shared theme is clear immune signaling in lymphoid contexts.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048535","count":5},{"id":"GO:0051092","count":5},{"id":"GO:0000185","count":4},{"id":"GO:0007250","count":4},{"id":"GO:0001782","count":4}]},{"hash":"1804160378260812070","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2001240","count":2},{"id":"GO:0034394","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0097202","count":2},{"id":"GO:0035725","count":2}]},{"hash":"255254333913244819","title":"Golgi\u2013Endosome Vesicle Trafficking","description":"The terms cluster around intracellular membrane traffic involving the Golgi and endosomal pathways, including intralumenal vesicle formation, protein retention in the Golgi, and various endosome\u2013lysosome/Golgi transport steps, which together point to vesicle formation and trafficking as the main theme. A few terms (splicing, ECM disassembly, podosome assembly, cleavage furrow formation) seem less directly related and may reflect annotation noise or secondary roles.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070676","count":2},{"id":"GO:0045053","count":2},{"id":"GO:0000398","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0008333","count":1}]},{"hash":"157875556198094828","title":"Unknown","description":"The GO terms are heterogeneous, spanning immune responses (LPS, interferon, defense to Gram-positive bacteria), cell growth/division, transcription regulation, and even heart-related development (pericardium morphogenesis, cardiac conduction). There isn\u2019t a single coherent functional theme connecting these terms, so a unique high-level label isn\u2019t justifiable.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0035457","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0031639","count":2}]},{"hash":"104462673899621115","title":"Developmental receptor signaling networks","description":"These proteins cluster around receptor- and kinase-mediated signaling pathways (IGF receptor signaling, PKC signaling, GPCR-related pathways, cGMP responses) and developmental processes (vitellogenesis, radial glial cell differentiation). The common theme is receptor-driven signaling that governs developmental processes across tissues, justifying a label like Developmental receptor signaling networks. Some terms are context-specific or historical, but the overall pattern is signaling-driven development.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048009","count":3},{"id":"GO:0035021","count":2},{"id":"GO:0007296","count":2},{"id":"GO:0038168","count":1},{"id":"GO:0090557","count":1}]},{"hash":"707759485308040150","title":"Neural development and synaptic connectivity","description":"The cluster\u2019s top GO terms cluster around neural development, including synapse assembly, nervous system development, axonal fasciculation, and myelination, plus adhesion functions that underlie neuron\u2013neuron and neuron\u2013glia interactions. Some bone/ear morphogenesis terms appear as broader developmental roles but do not override the neural connectivity theme. Overall, the proteins seem tied to forming and myelinating neural networks, so this label represents the core function of the cluster.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051965","count":5},{"id":"GO:0007156","count":4},{"id":"GO:0043931","count":4},{"id":"GO:0007157","count":4},{"id":"GO:0007399","count":4}]},{"hash":"1887496495849508308","title":"Chromatin Organization and Remodeling","description":"These proteins show strong associations with centromeric and chromatin-related processes (CENP-A chromatin assembly, transcription-coupled chromatin remodeling, and regulation of chromosome condensation), indicating a chromatin-dynamics core. The presence of developmental terms (midbrain morphogenesis, male gonad development) and other outliers suggests broader roles, but the dominant theme centers on chromatin architecture and remodeling.","confidence":"Medium","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":7},{"id":"GO:0007338","count":7},{"id":"GO:2000973","count":7},{"id":"GO:0030543","count":7},{"id":"GO:0031639","count":7}]},{"hash":"1535792272446690955","title":"Osteoclastogenesis and cytokine-driven myeloid differentiation","description":"The cluster is dominated by osteoclast-related terms (osteoclast proliferation and multinuclear osteoclast differentiation) and by myeloid lineage differentiation (monocyte and dendritic cell differentiation), with cytokine signaling cues (interleukin-4, TNF) and estrogen response. A protein transport term is present but secondary, suggesting a theme centered on bone-resorbing osteoclast biology and cytokine-influenced immune differentiation.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0090290","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0035045","count":1},{"id":"GO:0071391","count":1}]},{"hash":"2132799855515969206","title":"Immune Activation and Signaling","description":"Based on the top GO terms, this cluster centers on immune system functions: complement activation (classical pathway), phagocytosis (recognition and engulfment), B cell signaling and activation, innate immune response, T cell costimulation, NK cell\u2013mediated cytotoxicity, and regulation of IL-10. The outlier term spermatid development is likely unrelated noise. Overall, the proteins seem to participate in leukocyte activation and communication in both innate and adaptive immunity.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006958","count":5},{"id":"GO:0006910","count":5},{"id":"GO:0006911","count":5},{"id":"GO:0050853","count":5},{"id":"GO:0045087","count":5}]},{"hash":"341447404636583715","title":"RNA cap and protein methyltransferases","description":"The cluster is driven by RNA methylation terms (RNA guanine-N7 methylation and mRNA capping) and multiple protein methylation terms (N-terminal methylation, arginine methylation), indicating a group of methyltransferase enzymes acting on RNA and proteins. Some brain development and growth terms may reflect broader expression or secondary roles, but the core signal is methyltransferase activity.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0018013","count":1},{"id":"GO:0019919","count":1},{"id":"GO:0018012","count":1}]},{"hash":"765095939904688462","title":"RNA Processing and Genome Maintenance","description":"The top GO terms cluster around nuclear RNA processing (spliceosome dynamics, TRAMP tRNA surveillance, nonsense-mediated decay) and genome maintenance (DNA replication, nucleotide-excision repair, UV protection). While endocytosis and brain-derived neurotrophic factor response appear, the dominant signal is RNA maturation/quality control paired with DNA repair and genome integrity processes, justifying the name. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000388","count":3},{"id":"GO:1990416","count":3},{"id":"GO:0006897","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0009650","count":2}]},{"hash":"2168268570697715788","title":"Nuclear DNA replication and RNA processing","description":"Top GO terms indicate core nuclear activities: DNA replication, DNA damage tolerance, chromatin-related processes and nucleosome maintenance (some entries marked obsolete), ribosome large subunit biogenesis, rRNA processing, and components of mRNA splicing regulation. The mix points to a cluster of proteins involved in genome maintenance and RNA maturation/splicing within the nucleus, rather than a single pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0070870","count":6},{"id":"GO:0071038","count":6},{"id":"GO:0042273","count":6},{"id":"GO:0060303","count":6}]},{"hash":"1117555093722030746","title":"Translation initiation and mRNA processing","description":"The dominant GO terms indicate a focus on the ribosome and initiation of translation, including translation, translational initiation, ribosomal large subunit assembly, and eIF4F complex assembly. The additional terms point to RNA regulatory processes such as mRNA stability in stress, mRNA modification, and ncRNA-mediated gene silencing, suggesting a cohesive group of translation machinery with linked post-transcriptional regulation. Overall, this cluster appears to encompass translation machinery plus RNA processing/regulation functions.","confidence":"High","size":6,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006413","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0060211","count":1},{"id":"GO:1905663","count":1}]},{"hash":"1248931270636463530","title":"Muscle calcium handling and excitability","description":"The top GO terms cluster around calcium signaling and ion transport linked to skeletal muscle function\u2014calcium transport into the endoplasmic reticulum, release of sequestered Ca2+ by Golgi, stabilization of membrane potential, and skeletal muscle relaxation\u2014along with a testosterone response indicative of muscle physiology. Together, these suggest proteins involved in calcium handling and excitability in muscle cells, with some related metabolic regulation signals.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090076","count":3},{"id":"GO:0033574","count":3},{"id":"GO:1903515","count":3},{"id":"GO:0099132","count":3},{"id":"GO:0097755","count":3}]},{"hash":"1141680939093333298","title":"Immune signaling and antigen presentation regulators","description":"The cluster includes terms tied to innate/adaptive immune signaling (stimulatory C-type lectin receptor signaling; non-canonical NF-kappaB signaling) and antigen processing and presentation via MHC class I, plus deubiquitination as a regulatory layer. While there are also general regulatory processes (splicing, hypoxia response, etc.), the strongest coherent theme is immune signaling and antigen presentation regulation.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010950","count":5},{"id":"GO:0000398","count":3},{"id":"GO:0002223","count":3},{"id":"GO:0010972","count":3},{"id":"GO:0061418","count":3}]},{"hash":"1036886203870290460","title":"GPCR-cAMP Signaling","description":"These terms cluster around GPCR signaling that activates adenylyl cyclase and increases cAMP, covering responses to forskolin, glucagon, adrenergic/adenosine receptors, and light-related signaling; together they define GPCR-cAMP signaling activity.","confidence":"High","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:1904322","count":5},{"id":"GO:0071361","count":5},{"id":"GO:0071880","count":5},{"id":"GO:0007190","count":5},{"id":"GO:0071377","count":5}]},{"hash":"1981061870063664978","title":"Endocytosis and vesicle trafficking regulation","description":"These proteins co-occur with GO terms centered on receptor-mediated endocytosis and vesicle sorting (including the multivesicular body pathway) and relate to regulation of EGFR signaling and APP processing, suggesting a shared function in endocytic trafficking. Some terms are obsolete, but the core theme points to endocytosis and vesicle trafficking regulation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015032","count":4},{"id":"GO:0071985","count":4},{"id":"GO:0060453","count":4},{"id":"GO:0045742","count":4},{"id":"GO:0048261","count":4}]},{"hash":"1469849429367131102","title":"Immune and Endothelial Signal Transduction","description":"The Top Terms cluster around responses to immune stimuli (lipopolysaccharide, GM-CSF), adaptive signaling (T cell receptor signaling), growth factor\u2013mediated pathways (VEGF receptor signaling, EGF response), and downstream transcriptional regulation (JUN phosphorylation, STAT phosphorylation). Together these indicate a shared theme of extracellular cues activating intracellular signaling that drives transcription in immune and vascular/endothelial contexts.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071222","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0097011","count":4},{"id":"GO:0007601","count":3}]},{"hash":"124006042199237462","title":"Mitotic progression and ER-Golgi vesicle trafficking","description":"These proteins show enrichment for mitotic processes (mitotic cell cycle, cell division, mitotic spindle assembly) as well as components of early secretory pathway trafficking (retrograde Golgi-to-ER transport, COPII-coated vesicle budding). The co-occurrence suggests a function tying cell division to vesicle trafficking during mitosis.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0035264","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0090114","count":4}]},{"hash":"1902127394614381527","title":"ER stress response and protein quality control","description":"The cluster is driven by GO terms centered on endoplasmic reticulum (ER) stress, unfolded protein response, and protein quality control (translation initiation upregulation during ER stress, unfolded protein response, and ER-associated degradation/chaperone-assisted refolding). These themes suggest a cohesive function in managing misfolded proteins and maintaining ER homeostasis, despite a few unrelated terms that may reflect broad annotations.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0036494","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0046661","count":2}]},{"hash":"24837818217254886","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0007601","count":5},{"id":"GO:0042068","count":5},{"id":"GO:0007117","count":5},{"id":"GO:0000278","count":5}]},{"hash":"107480467508331271","title":"Ribosome Biogenesis and Translation","description":"The top terms cluster around ribosomal subunit assembly (large and small), translation, and nucleolar localization, pointing to a shared role in ribosome production and protein synthesis. Stress-related regulation of translation (eIF2\u03b1 phosphorylation) and related signaling further support a cohesive theme of translation control during cellular stress.","confidence":"High","size":6,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0051092","count":2},{"id":"GO:0045836","count":2}]},{"hash":"1919765010266671345","title":"TGF-\u03b2/BMP signaling in endocrine development","description":"Proteins here repeatedly show negative regulation of SMAD/TGF-\u03b2/BMP signaling and are linked to developmental and endocrine processes, including gonad and thyroid development, luteinizing hormone secretion, and cellular responses to hormones. This suggests a theme of controlling growth and organ development through TGF-\u03b2/BMP pathways in an endocrine context.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010991","count":2},{"id":"GO:0030514","count":2},{"id":"GO:0030512","count":2},{"id":"GO:0048589","count":2},{"id":"GO:0032275","count":2}]},{"hash":"864754446207921059","title":"Neuromuscular development and movement","description":"The top GO terms point to motor neuron differentiation, neuromuscular processes, glutamate reuptake, and Schwann cell regulation, suggesting a cluster centered on neuromuscular development and nerve\u2013muscle signaling, with supporting structural/metabolic context from collagen and ceramide biosynthesis.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046513","count":2},{"id":"GO:0021523","count":2},{"id":"GO:0002238","count":2},{"id":"GO:0032964","count":2},{"id":"GO:0050884","count":2}]},{"hash":"1009773648456478273","title":"Growth factor signaling and endothelial responses","description":"The terms cluster around VEGF/EGF signaling, downstream phosphorylation events (JUN, STAT), and endothelial cell chemotaxis, pointing to a shared theme of signal transduction and endothelial response; a translation term and a few outliers are present but do not define the main function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007601","count":1},{"id":"GO:0048010","count":1},{"id":"GO:0007258","count":1},{"id":"GO:2001028","count":1}]},{"hash":"1381200535273781734","title":"Iron homeostasis and stress response","description":"The cluster\u2019s top GO terms are dominated by iron metabolism: iron transport, detoxification of iron ion, and intracellular sequestration of iron, plus siderophore-iron import, all pointing to iron homeostasis. A few terms touch on stress response and basic metabolism, but the iron-related terms provide a coherent theme for the proteins in this cluster. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006880","count":1},{"id":"GO:0006950","count":1},{"id":"GO:1990461","count":1},{"id":"GO:0033214","count":1},{"id":"GO:0048147","count":1}]},{"hash":"1688118693694637223","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are translation, translational termination, and ribosomal large subunit assembly, plus mitochondrial translation, pointing to ribosome formation and protein synthesis. A few secondary terms reference stress and cell-cycle regulation but do not override the primary ribosome/translation theme.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006415","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0032986","count":1}]},{"hash":"32726208167573299","title":"Plant Meiosis and Chromosome Organization","description":"The cluster features meiotic chromosome condensation, synaptonemal complex assembly, and meiotic chromosome separation, plus plant-associated processes like microsporogenesis, amyloplast organization, and gravitropism, along with chromatin maintenance terms. Together these suggest a common theme of meiosis-driven chromosome dynamics and chromatin remodeling in plants.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070058","count":2},{"id":"GO:0043007","count":2},{"id":"GO:0009556","count":2},{"id":"GO:0009959","count":2},{"id":"GO:0030466","count":2}]},{"hash":"569875834142127125","title":"Growth Factor Signaling and Immune Cell Migration","description":"The GO terms cluster around responses to growth factor stimuli (PDGF, TGF-beta) and ERK signaling, alongside immune-related processes (neutrophil chemotaxis, macrophage CSF stimulus) and developmental morphogenesis (retinoic acid response, branching). This suggests a theme of signaling pathways that govern both immune cell movement and tissue remodeling during development, supporting a label focused on growth factor\u2013driven signaling and immune cell migration.","confidence":"Medium","size":6,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071226","count":5},{"id":"GO:0014911","count":4},{"id":"GO:0036006","count":4},{"id":"GO:0070374","count":4},{"id":"GO:0060444","count":4}]},{"hash":"1802674483594287638","title":"Embryonic organ development","description":"The majority of top GO terms point to morphogenesis and development of various organs (forelimb, eye, pancreas, heart, endothelium), suggesting the cluster centers on embryonic organ development. Some metabolic terms appear, but they seem secondary to the overarching developmental theme, supporting a label focused on embryonic organogenesis.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0019285","count":6},{"id":"GO:0035115","count":6},{"id":"GO:0055129","count":6},{"id":"GO:0048738","count":6},{"id":"GO:1901023","count":6}]},{"hash":"1605682773621070895","title":"Developmental Regulation & Chromatin Assembly","description":"The top GO terms cluster around developmental processes (fertilization, male gonad development, brain development, regulation of B cell differentiation) and chromatin-related regulation (CENP-A chromatin assembly and transcriptional regulation). This suggests a theme of developmentally tied gene regulation with chromatin involvement, though a few terms (plasmid partitioning, photomorphogenesis) are less related outliers.","confidence":"Medium","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":4},{"id":"GO:0008584","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0061641","count":3}]},{"hash":"1057309223377424361","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":2},{"id":"GO:0019243","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0006364","count":2}]},{"hash":"513505551443482659","title":"Plant phenylpropanoid and lignan biosynthesis","description":"The top GO terms cluster around phenylpropanoid metabolism and lignan biosynthesis (pinoresinol and lariciresinol) with related anthocyanin biosynthesis, indicating these proteins participate in plant secondary metabolism producing lignans and phenylpropanoids. Some terms appear obsolete or ancillary, but the strongest signals point to a plant-specific biosynthetic program rather than general cellular processes. This makes \"Plant phenylpropanoid and lignan biosynthesis\" a concise, representative label for the cluster.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:1902123","count":2},{"id":"GO:1902129","count":2},{"id":"GO:0019835","count":2},{"id":"GO:1902125","count":2}]},{"hash":"881277288387540898","title":"Mitochondrial proteostasis and calcium regulation","description":"The top terms cluster around mitochondrial function (complex IV assembly and mitochondrial calcium handling) and ubiquitin-proteasome\u2013mediated protein turnover, pointing to a module focused on mitochondrial proteostasis and calcium signaling. Negative regulation of RIG-I signaling and developmental terms (hippocampus, cochlea) are ancillary, possibly reflecting shared ubiquitin-related pathways or broader tissue contexts. Overall, the group seems centered on maintaining mitochondrial function via proteostasis and calcium regulation, with some divergent signals. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0032436","count":2},{"id":"GO:0039536","count":2},{"id":"GO:0021766","count":2}]},{"hash":"685067932094357959","title":"Embryonic and placental development","description":"The terms cluster around early development, especially placental/trophoblast differentiation, embryonic placenta development, mesoderm formation, and related morphogenetic processes (left-right patterning, endocardial cushion-related EMT, palate development). Although a few terms are more specific to endocrine or vitamin D processes, the dominant theme is embryogenesis with placental and mesodermal morphogenesis. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060707","count":5},{"id":"GO:0035270","count":5},{"id":"GO:0060536","count":5},{"id":"GO:0060806","count":5},{"id":"GO:0003323","count":5}]},{"hash":"703256097154602250","title":"Embryonic chromatin regulation and ubiquitination","description":"The cluster\u2019s top GO terms cluster around embryonic development, histone modification and chromatin maintenance, and ubiquitin/neddylation processes (including protein polyubiquitination and free ubiquitin chains), along with mitotic cell cycle activity. This suggests proteins that regulate chromatin state through ubiquitin-like modifiers during embryogenesis and cell division.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0001701","count":6},{"id":"GO:0045116","count":6},{"id":"GO:0006344","count":6},{"id":"GO:0035458","count":6},{"id":"GO:0051569","count":6}]},{"hash":"2270123124357955530","title":"Developmental Signaling and Telomere Regulation","description":"The top GO terms point to developmental processes such as lens fiber morphogenesis and prostatic bud formation, alongside various signaling pathways (Wnt, ephrin receptor signaling, and receptor-localized synaptic plasticity). Some terms also touch on chromatin/telomere regulation (telomere maintenance regulation, telomeric localization), suggesting a cluster of proteins involved in development-linked signaling with ancillary roles in genome/chromosome regulation. Overall, the set centers on developmental signaling with a subtle emphasis on chromosomal maintenance, rather than a single, cohesive pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070309","count":3},{"id":"GO:0060513","count":2},{"id":"GO:1901187","count":2},{"id":"GO:0007205","count":2},{"id":"GO:1904357","count":2}]},{"hash":"473481851808368704","title":"Neural lipid homeostasis and neuroinflammation","description":"This cluster includes GO terms for cholesterol homeostasis, astrocyte activation, visual perception (retina), and immune-related responses (lipopolysaccharide response, Fc receptor signaling) along with apoptosis-related phosphatidylserine exposure and mitophagy regulation. Taken together, these suggest a brain/retina\u2013related program centered on lipid regulation and neuroinflammatory/ cell-clearance processes, rather than a single canonical pathway. Confidence: Medium","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":2},{"id":"GO:0042632","count":1},{"id":"GO:0001300","count":1},{"id":"GO:0071222","count":1},{"id":"GO:0060368","count":1}]},{"hash":"2141351935735506425","title":"Rho-Driven Actin Remodeling and Migration","description":"The top GO terms cluster around actin cytoskeleton dynamics (actin filament organization, actin bundle assembly) and regulation by Rho GTPases (Rho signaling, positive regulation of GTPase activity), with associated processes like cell migration and tight junction assembly. This points to a core function in actin cytoskeleton remodeling governing motility and junctional organization, with some secondary links to membrane trafficking and stress-related translation regulation. Overall, the cluster seems centered on cytoskeleton-driven migration and adhesion dynamics.","confidence":"High","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0036493","count":3},{"id":"GO:0016191","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007015","count":3},{"id":"GO:0051017","count":3}]},{"hash":"1634458801861641004","title":"Unknown","description":"The top terms are very diverse, including keratinocyte differentiation, Rho signaling, insulin response, bone development, CENP-A chromatin assembly, fertilization, B cell differentiation, plasmid partitioning, plasminogen activation, and histone phosphorylation. This mix spans developmental biology, signaling, chromatin regulation, and plasmid biology, with no clear shared function tying all six proteins. A single cohesive label cannot be determined.","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045618","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0032869","count":3},{"id":"GO:0060348","count":3},{"id":"GO:0061641","count":2}]},{"hash":"1817392939108121837","title":"Developmental Diversity","description":"The terms point to development across multiple lineages (megakaryocyte, mesoderm, neuron projection, proboscis) and signaling (Wnt), with supporting general processes such as mRNA export and protein localization, suggesting a loosely connected developmental/signaling cluster rather than a single pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035855","count":2},{"id":"GO:0031175","count":2},{"id":"GO:0051497","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0016055","count":1}]},{"hash":"1062142616855803699","title":"Embryonic organogenesis and neural development","description":"The top GO terms point to diverse developmental processes across multiple organs (nephron development, mitral valve formation, lung branching morphogenesis, endothelial lumen formation), along with neural development elements such as serotonergic neuron axon guidance and synaptic vesicle clustering. This spread suggests proteins involved in broad developmental regulation rather than a single pathway, so a general label for embryonic development is appropriate.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048023","count":1},{"id":"GO:0032912","count":1},{"id":"GO:0036515","count":1},{"id":"GO:2000807","count":1},{"id":"GO:0060488","count":1}]},{"hash":"1807713057014326739","title":"Golgi vesicle trafficking and SNARE assembly","description":"These terms center on vesicle transport and membrane fusion tied to the Golgi apparatus (ER-to-Golgi transport, intra-Golgi transport, Golgi ribbon formation, COPI coating) and SNARE complex assembly, plus exocytic insertion of receptors at the postsynaptic membrane and related synaptic plasticity. The shared thread is Golgi- and SNARE-mediated vesicle trafficking and membrane fusion, with neuronal receptor trafficking as a specific example.","confidence":"High","size":6,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0090161","count":3},{"id":"GO:0035493","count":2},{"id":"GO:0098967","count":2},{"id":"GO:0048280","count":2}]},{"hash":"1979782086478670941","title":"Mitotic progression and cell division","description":"This cluster is dominated by mitosis- and cell-cycle-related GO terms (mitotic cell cycle, cell division, and positive regulation of mitotic metaphase/anaphase transition), suggesting proteins function in mitotic progression and chromosome segregation. The inclusion of related terms like intracellular mitochondrial distribution and protein complex assembly supports coordinated mitotic events, though a few terms appear peripheral (e.g., certain differentiation or signaling terms). Overall, the core theme is mitosis/cell-cycle regulation.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051291","count":5},{"id":"GO:0048312","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0046661","count":4}]},{"hash":"1729163365163550328","title":"RNA maturation and miRNA regulation","description":"The top GO terms cluster around RNA processing: snRNA modification, snRNA capping, miRNA metabolic process, and regulation of pre-miRNA processing. While a few terms touch on chromatin binding, cell cycle, and development, the strongest commonality is RNA maturation and regulation of small RNA pathways.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040031","count":1},{"id":"GO:1990273","count":1},{"id":"GO:0035562","count":1},{"id":"GO:0010586","count":1},{"id":"GO:1900087","count":1}]},{"hash":"1357534859746302445","title":"Neuronal axon growth and synapse formation","description":"The terms cluster around neural development and wiring: axon growth, fasciculation, collateral sprouting, and regeneration-related extension; myelination and synapse assembly point to maturation and connectivity, while mechanoreceptor differentiation and otolith morphogenesis reflect sensory-neuron lineage development and sensory structure formation. Despite a couple of obsolete GO entries, the core theme is neuronal differentiation and axon-guided circuit assembly.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000187","count":3},{"id":"GO:0048672","count":3},{"id":"GO:0042490","count":3},{"id":"GO:0032474","count":3},{"id":"GO:0007413","count":3}]},{"hash":"2101726134558700892","title":"Neural morphogenesis and signaling regulation","description":"The cluster centers on neural development and signaling, including regulation of nerve branching, dopamine receptor signaling, and cytoskeletal remodeling (filopodium assembly, cell spreading), alongside related trafficking and signaling cascades (endosome-to-Golgi transport, CAMKK-AMPK). Some terms (manganese response, Th1 immune response, kidney size) are less directly connected but reflect broader regulatory signaling roles.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071287","count":3},{"id":"GO:2000172","count":3},{"id":"GO:0035564","count":3},{"id":"GO:0060161","count":3},{"id":"GO:1905289","count":3}]},{"hash":"1556073865802656077","title":"Cytoskeletal Regulation and Cell Adhesion in Mesodermal Tissues","description":"The cluster centers on structural and signaling themes: sarcomere organization (muscle), Rho-mediated cytoskeletal dynamics, and cell\u2013cell junction maintenance, with supporting terms for vascular wound healing, megakaryocyte development, and Sertoli cell barrier formation. These reflect cytoskeletal regulation and intercellular adhesion in mesoderm-derived tissues, often during remodeling and immune-modulated contexts, indicating a cohesive functional theme across muscle, vascular, and hematopoietic settings.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0045214","count":3},{"id":"GO:0035023","count":3},{"id":"GO:1900042","count":3},{"id":"GO:0007155","count":3},{"id":"GO:2001181","count":2}]},{"hash":"1195842794736088209","title":"Mitotic Cycle and Nuclear RNA Processing","description":"The cluster is dominated by mitotic cell cycle and division terms, with DNA-templated transcription and snoRNP assembly indicating nuclear RNA processing; additional terms for oxidative stress, defense response to virus, and mitochondrial protein import appear but are less central, suggesting a focus on cell-cycle control coupled with nuclear RNA processing rather than a single broader function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0006351","count":2}]},{"hash":"2292815911783374130","title":"Craniofacial morphogenesis: lens and hair-cell differentiation","description":"This cluster shows strong signals for lens fiber cell morphogenesis and differentiation as well as neuromast hair cell differentiation, with supporting terms related to cartilage condensation, integrin-mediated adhesion, and apical constriction, all pointing to craniofacial organ development involving lens and sensory hair cells.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070309","count":2},{"id":"GO:0001502","count":2},{"id":"GO:0048903","count":2},{"id":"GO:0070306","count":2},{"id":"GO:0033628","count":2}]},{"hash":"1817643919856222016","title":"Glycan processing and olfactory development","description":"The dominant GO terms cluster around N-linked glycosylation and glycosphingolipid metabolism (N-glycan processing, glycosylceramide metabolism, sialylation, ganglioside biosynthesis, N-acetylneuraminate metabolism) and connect to olfactory system development (olfactory nerve formation, olfactory placode morphogenesis), suggesting a cohesive theme of glycan modification in neural/olfactory Development.","confidence":"Medium","size":6,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:0006677","count":2},{"id":"GO:1990743","count":2},{"id":"GO:0009846","count":2},{"id":"GO:0021628","count":2}]},{"hash":"1880970281553937503","title":"Pain and Temperature Sensing with Chemokine Regulation","description":"Based on the GO terms, the cluster centers on nociceptive and thermoceptive processes (thermal and mechanical pain detection, cold response, capsazepine-related signaling) and on regulation of chemokine production. This points to a coherent theme of sensory/pain signaling intertwined with inflammatory chemokine signaling, with a broader immune context suggested by T cell homeostasis and endothelial changes. The combination is plausible but includes some outliers, so the label is reasonably representative but not exclusively tied to a single pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":3},{"id":"GO:0097497","count":3},{"id":"GO:0050955","count":3},{"id":"GO:2000340","count":3},{"id":"GO:1903444","count":3}]},{"hash":"1559875380687187446","title":"Nuclear RNA Processing and Transcription Termination","description":"This cluster centers on nuclear RNA processing and transcription-related activities, including mRNA splicing, tRNA and rRNA maturation, spliceosome assembly, and mRNA decapping, all consistent with nuclear RNA metabolism. The presence of nuclear import and transcription termination terms supports a shared nuclear localization and regulation. A few terms related to chromatin processes and hormone response are present but do not override the core RNA-processing theme.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":5},{"id":"GO:0008033","count":5},{"id":"GO:0051170","count":5},{"id":"GO:0000290","count":5},{"id":"GO:0030490","count":5}]},{"hash":"1178218627181152262","title":"Nuclear RNA processing and splicing","description":"Top GO terms cluster around RNA maturation in the nucleus: tRNA processing, mRNA splicing via the spliceosome, snRNP assembly, rRNA maturation, and nuclear mRNA decapping, plus transcription termination and nuclear import. This combination indicates a cohesive role in nuclear RNA processing and splicing, with chromatin-related terms likely reflecting linked transcription and histone mRNA regulation rather than a separate process.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":5},{"id":"GO:0045292","count":4},{"id":"GO:0051170","count":4},{"id":"GO:0000290","count":4},{"id":"GO:0030490","count":4}]},{"hash":"867630417590903835","title":"RNA Granule Assembly and Synaptic Regulation","description":"The proteins show enrichment for P-body and stress granule assembly and regulation of cytoplasmic mRNA processing bodies, indicating RNA granule dynamics. In addition, there are GO terms related to neuronal synaptic plasticity (long-term potentiation regulation, synapse structural plasticity), suggesting a neuronal context for RNA regulation at synapses. There are some outlier terms (TCA cycle, rDNA maintenance), but the dominant signal points to RNA granule\u2013mediated post-transcriptional regulation in neurons. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0000288","count":1},{"id":"GO:0043007","count":1},{"id":"GO:0042051","count":1},{"id":"GO:0045671","count":1}]},{"hash":"2270405128631026078","title":"Unknown","description":"This cluster's GO terms span very diverse processes: negative regulation of autophagosome maturation, placenta and anther morphogenesis, thymocyte migration regulation, spindle assembly, and various chromatin modification terms (some obsolete). There is no evident common function or pathway tying these proteins together, and several terms seem unrelated, making it unclear what unifies the cluster. Consequently, I cannot assign a coherent, specific label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901097","count":1},{"id":"GO:0060669","count":1},{"id":"GO:0098532","count":1},{"id":"GO:0032602","count":1},{"id":"GO:2000410","count":1}]},{"hash":"904346058533722372","title":"Endocytic Trafficking and Receptor Signaling Regulation","description":"This cluster is dominated by GO terms for receptor-mediated endocytosis regulation, multivesicular body sorting, and modulation of EGFR signaling, with supporting involvement of actin dynamics via Arp2/3. Although a couple of terms are less directly connected (and some are obsolete), the core theme centers on endocytic trafficking and its impact on signaling pathways. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034316","count":4},{"id":"GO:0015032","count":2},{"id":"GO:0071985","count":2},{"id":"GO:0060453","count":2},{"id":"GO:0045742","count":2}]},{"hash":"2020648124452698108","title":"Centromeric chromatin assembly and remodeling","description":"The top GO terms are dominated by chromatin-related processes: CENP-A\u2013containing chromatin assembly, silent mating-type cassette heterochromatin formation, chromosome condensation regulation, histone phosphorylation regulation, and transcription-initiation\u2013coupled chromatin remodeling, with plasmid partitioning tying to genome maintenance. Together these indicate a cluster focused on chromatin organization, centromere maintenance, and remodeling. A few outlier terms exist but do not override the core theme.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030466","count":4},{"id":"GO:0061641","count":3},{"id":"GO:0007338","count":3},{"id":"GO:2000973","count":3},{"id":"GO:0030543","count":3}]},{"hash":"929759956784387891","title":"Cellular stress and innate immune response","description":"The dominant GO terms point to responses to lipopolysaccharide, xenobiotics, hypoxia, and apoptotic processes, with complement activation, suggesting a cluster tied to cellular stress and innate immune signaling. Some outlier terms (visual perception, fatty acid processes) may reflect broader regulatory roles or annotation noise.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0007601","count":2},{"id":"GO:0070542","count":2},{"id":"GO:0051345","count":2}]},{"hash":"1028957298518041876","title":"Developmental signaling and protein oligomerization","description":"Based on the top GO terms, the proteins cluster around developmental processes (skin development, multicellular organism development) and protein interactions/assembly (heterotrimerization, homooligomerization) with some signaling context (NF-kappaB, interferon regulation). The combination suggests a group involved in developmental signaling pathways and formation of protein complexes, despite some terms being obsolete. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0070208","count":2},{"id":"GO:0051260","count":2}]},{"hash":"857041154621981612","title":"Cell migration and morphogenesis","description":"The top GO terms cluster around cell movement and tissue shaping: sprouting angiogenesis and smooth muscle cell migration point to migratory processes; calcium-independent cell\u2013matrix adhesion and receptor clustering hint at coordinated signaling and adhesion dynamics essential for migration. Morphogenesis terms (pericardium, prostate gland epithelium) reinforce a theme of development-associated tissue remodeling. Together these suggest a label capturing migration, adhesion, and morphogenesis as the cluster's core function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043113","count":4},{"id":"GO:0002042","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0014909","count":3},{"id":"GO:0045429","count":3}]},{"hash":"1611231080172986603","title":"DNA replication and recombination repair","description":"This cluster is dominated by GO terms tied to DNA replication, meiotic recombination, and recombinational repair (e.g., DNA replication, meiotic recombinase assembly, joint molecule formation, and recombinational repair). There are also hints of DNA damage response (camptothecin) and replication stress, suggesting a genome maintenance function, with a few peripheral signals like glucoside response and phosphorylation regulation accompanying the core theme.","confidence":"High","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0051106","count":3},{"id":"GO:1904631","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0001932","count":3}]},{"hash":"1883642658301165737","title":"CoQ and tocopherol biosynthesis regulation","description":"Top GO terms point to regulation of ubiquinone biosynthetic process and regulation of tocopherol cyclase activity, alongside lipid and redox homeostasis, suggesting a mitochondrial lipid metabolism module involved in antioxidant cofactor production. While a few neural-related terms appear, the dominant theme across the cluster is CoQ and vitamin E biosynthesis regulation and related redox/lipid balance.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0055088","count":2},{"id":"GO:1901006","count":2}]},{"hash":"1085323905220162227","title":"Mitotic Regulation and Protein Dephosphorylation","description":"Because the top GO terms are dominated by protein dephosphorylation and cell cycle, with an explicit mitotic term (positive regulation of mitotic sister chromatid biorientation), the cluster likely represents regulation of mitosis through dephosphorylation. Other terms are more incidental (development, apoptotic regulation) and do not define a single broader function beyond cell-cycle control.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0001701","count":1},{"id":"GO:0031031","count":1},{"id":"GO:0016191","count":1}]},{"hash":"2286453062084624781","title":"Embryonic neural and cardiac development","description":"The GO terms show strong signals for neural development (neuron migration, axon extension, visual perception) and cardiac development (heart development, pulmonary myocardium development, organ induction), plus related morphogenesis like cranial skeleton and inner ear formation. This suggests a cohesive set of proteins involved in early embryonic patterning of nervous and cardiovascular tissues, with broader developmental roles.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0001764","count":3},{"id":"GO:0048675","count":3},{"id":"GO:0021759","count":3},{"id":"GO:0048839","count":3}]},{"hash":"729913956099078497","title":"Ubiquitin-Mediated Transcription Regulation","description":"The cluster\u2019s top terms revolve around protein ubiquitination and deubiquitination, including regulatory processes of transcription by RNA polymerase II, suggesting a coherent theme of ubiquitin-dependent control of gene expression. A few terms (chloroplast mRNA modification, atrial septum development) appear as outliers, but the dominant signal points to ubiquitin-related transcriptional regulation.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035518","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0003283","count":3},{"id":"GO:0071947","count":3},{"id":"GO:1904404","count":3}]},{"hash":"1015095648773168702","title":"Unknown","description":"The top GO terms are very diverse, spanning gene expression regulation, tissue cell number homeostasis, lipid homeostasis, interferon production, autophagy targeting, neuronal development, osteoclast and heart-related processes, and protein ubiquitination. There is no single clear function or pathway linking all five proteins, so a specific, confident label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010628","count":3},{"id":"GO:0048873","count":3},{"id":"GO:0055091","count":3},{"id":"GO:0032729","count":3},{"id":"GO:0032258","count":2}]},{"hash":"1493019901299053814","title":"Golgi trafficking and neuronal plasticity","description":"This cluster shows a cohesive theme around Golgi apparatus dynamics (Golgi reassembly, establishment of Golgi localization) and neuronal function (regulation of synaptic plasticity, hippocampus development, membrane depolarization during action potential), suggesting a link between intracellular trafficking/organization and synaptic regulation. Some keratinocyte-related terms appear but are less central to the main signal, which is neuronal Golgi-associated trafficking impacting plasticity. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048167","count":4},{"id":"GO:0090168","count":4},{"id":"GO:0051683","count":4},{"id":"GO:0010839","count":4},{"id":"GO:1902309","count":4}]},{"hash":"588539294321772655","title":"Mechanosensation and cell-adhesion proteins","description":"The top GO terms point to mechanical sensing (touch) and thermoception, plus calcium-dependent cell-matrix adhesion and protein oligomerization, suggesting a core role for structural/scaffold proteins that sense or transmit mechanical signals and mediate adhesion. Developmental and electrophysiological terms appear as secondary roles, but the strongest signal is mechanosensation and adhesion.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0097497","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0086048","count":2},{"id":"GO:0051262","count":2}]},{"hash":"2292595171573616789","title":"Unknown","description":"The GO terms are diverse and only loosely related, with potassium ion transport and membrane depolarization suggesting excitability, alongside terms about fibroblast migration, B cell homeostasis, endothelial delamination, and various signaling and development processes. There are no edges connecting the proteins, and the terms do not cohere into a single clear function, so there isn\u2019t a reliable, concise label to capture the cluster\u2019s theme. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006813","count":4},{"id":"GO:0010762","count":3},{"id":"GO:0001922","count":3},{"id":"GO:0097497","count":3},{"id":"GO:0097338","count":3}]},{"hash":"940317865849545130","title":"Ion transport and metal ion homeostasis","description":"Top GO terms point to transport of monoatomic cations and movement of Ca2+ into the endoplasmic reticulum, as well as zinc ion homeostasis and manganese ion response. This pattern suggests a cluster of proteins involved in ion transport and metal ion regulation across membranes. Some terms (phosphorylation, testosterone response, glycoside response) appear less related and may reflect broader signaling contexts or annotation noise.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0090076","count":1},{"id":"GO:0071287","count":1},{"id":"GO:0033574","count":1},{"id":"GO:1903515","count":1}]},{"hash":"1734269013353019271","title":"Brain lipid transport & vascular signaling","description":"This cluster centers on lipids and brain vasculature: terms for lipid transport across the blood-brain barrier, lipid catabolism, and clearance of lipoprotein particles, plus endothelial proliferation. There are also neuron-related terms (postsynaptic membrane organization, synaptic plasticity) suggesting a link between lipid metabolism and brain signaling. Although some terms (ufmylation, estrogen signaling) are less directly tied, the dominant pattern points to lipid handling in the brain vasculature and its influence on synaptic function, justifying a label focused on brain lipid transport and vascular signaling.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1990592","count":2},{"id":"GO:0033146","count":2},{"id":"GO:1903002","count":1},{"id":"GO:1900272","count":1},{"id":"GO:0034447","count":1}]},{"hash":"269926458275063262","title":"Unknown","description":"There is no single coherent function linking these GO terms across organisms; terms include mesonephros development, regulation of renin-angiotensin and aldosterone, MHC II antigen processing, antibacterial peptide production, systemic acquired resistance, proteolysis, and even plant xylan catabolism, indicating diverse and unrelated roles rather than a common pathway.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0001823","count":4},{"id":"GO:0042985","count":4},{"id":"GO:0002803","count":4},{"id":"GO:0019886","count":4},{"id":"GO:0002016","count":4}]},{"hash":"1096563958979382588","title":"RNA Processing and Post-transcriptional Regulation","description":"This cluster centers on RNA maturation and post-transcriptional control, with terms for translation, tRNA processing, and, notably, various forms of gene silencing and mRNA cleavage regulation. While a few terms touch neural development and immune responses, the strongest shared signal is RNA processing and post-transcriptional gene regulation, justifying a name focused on RNA processing/silencing. ","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0008033","count":2},{"id":"GO:1900369","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0021618","count":2}]},{"hash":"1479438338884102175","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030260","count":1},{"id":"GO:0071031","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0010587","count":1}]},{"hash":"427962540936978506","title":"Nucleotide metabolism and RNA modification","description":"These proteins show GO terms centered on nucleotide handling (adenosine metabolic process, purine nucleotide catabolic process) and RNA processing/modification (tRNA modification, tRNA methylation), with additional signals from phosphorylation events. The dominant theme is nucleotide turnover and RNA modification, though a few singleton biosynthetic or stress-response terms are present, making the link less global but still coherent.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046085","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0006195","count":2},{"id":"GO:0006400","count":1}]},{"hash":"582454646551514490","title":"Unknown","description":"The terms span developmental processes (fertilization, brain and gonad development), chromatin organization/remodeling (CENP-A assembly, heterochromatin formation, histone phosphorylation regulation), and other disparate functions (transcription regulation, plasmid partitioning, plasminogen activation), with no clear unifying theme among the cluster proteins.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":3},{"id":"GO:0008584","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0000183","count":3}]},{"hash":"1639145013107600122","title":"Unknown","description":"The top GO terms span very different processes (anthocyanin and antibiotic biosynthesis, poly-hydroxybutyrate biosynthesis, various hydroxylation and demethylation events, RITS complex localization, and even spermatid nucleus elongation), with several terms marked obsolete. There is no clear, cohesive functional theme tying these five proteins together, so a single interpretable label cannot be confidently assigned.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0018395","count":2}]},{"hash":"1883239299088317455","title":"Neuronal Axon Guidance and Planar Polarity","description":"The top GO terms point to axon guidance for serotonergic and dopaminergic neurons, along with several planar polarity and cell adhesion-related terms. These together suggest a module coordinating guidance of neural processes with planar cell polarity and related tissue organization, with a few morphogenesis terms that fit within the planar polarity context.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036515","count":3},{"id":"GO:0060488","count":3},{"id":"GO:0090251","count":3},{"id":"GO:0007156","count":3},{"id":"GO:0060490","count":3}]},{"hash":"46787568481509476","title":"Mesodermal and cardiac development","description":"Top terms are dominated by mesoderm formation and heart-related morphogenesis (gastrulation, mesodermal fate, paraxial mesoderm, pericardium, mitral valve) with broader differentiation programs (type II pneumocytes, club cells). This points to a cluster of proteins involved in mesodermal organogenesis and cardiac development.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001702","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0001710","count":3},{"id":"GO:0060039","count":3},{"id":"GO:1905305","count":3}]},{"hash":"2046540354054800271","title":"Anthocyanin and flavonoid biosynthesis","description":"The strongest signals are GO:0009718 (anthocyanin-containing compound biosynthetic process) and GO:0033485 (cyanidin 3-O-glucoside biosynthetic process), which together imply flavonoid/anthocyanin production. Other terms reference related glycosylation and carbohydrate metabolism but do not override the central flavonoid biosynthesis theme. ","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":3},{"id":"GO:0005975","count":2},{"id":"GO:0052696","count":2},{"id":"GO:0030259","count":2},{"id":"GO:0006488","count":2}]},{"hash":"451197414874414745","title":"Chromatin assembly and remodeling","description":"The proteins cluster around chromatin-related processes (CENP-A chromatin assembly, transcription initiation-coupled chromatin remodeling, and regulation of chromosome condensation), indicating a chromatin dynamics theme; a few terms about development and plasmid partitioning appear as outliers.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":3},{"id":"GO:0007338","count":3},{"id":"GO:2000973","count":3},{"id":"GO:0030543","count":3},{"id":"GO:0031639","count":3}]},{"hash":"950681113615345500","title":"Amino Acid and One-Carbon Metabolism","description":"These proteins are linked to a set of GO terms centered on amino acid biosynthesis and catabolism (serine, alanine, methionine), the shikimate pathway for aromatic amino acid production, and one-carbon metabolic processes. Additional terms touch formate catabolism and related redox processes, suggesting a broader metabolic cluster focused on amino acid metabolism and one-carbon unit flux rather than a single specific pathway. This makes \"Amino Acid and One-Carbon Metabolism\" a concise, representative label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":1},{"id":"GO:0042183","count":1},{"id":"GO:0006564","count":1},{"id":"GO:0009854","count":1},{"id":"GO:0019632","count":1}]},{"hash":"1527399762237845214","title":"Ubiquitin-Dependent Protein Turnover","description":"Predominant GO terms are ubiquitin-related: ubiquitin-dependent protein catabolic process and protein ubiquitination dominate the Top Terms, with additional signals from K6-linked ubiquitination and histone catabolic process, pointing to a core function in ubiquitin-proteasome\u2013mediated protein turnover. Some outlier terms (X chromosome inactivation, V(D)J recombination, TNF signaling) may reflect broader regulatory roles of ubiquitination, but the central theme is ubiquitin-dependent degradation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0060816","count":1},{"id":"GO:0085020","count":1},{"id":"GO:0036205","count":1}]},{"hash":"588131363606036005","title":"Ubiquitin-Dependent Protein Turnover and Methylation Modifiers","description":"This cluster is driven by GO terms for ubiquitin-dependent protein catabolic process and autoubiquitination, pointing to roles in ubiquitin-proteasome\u2013mediated protein turnover. The presence of peptidyl-lysine dimethylation and rRNA methylation terms suggests involvement in methylation-based post-translational modifications. Other terms are more disparate (RIG-I signaling, telomere maintenance, amyloid-beta clearance, ductus arteriosus closure), but the strongest shared theme centers on ubiquitin-mediated degradation and methylation-related modification processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0032208","count":1}]},{"hash":"233184221269022096","title":"Nucleotide metabolism and DNA maintenance","description":"This cluster shows strong enrichment for nucleotide metabolic processes: AMP salvage, ADP biosynthetic and nucleoside monophosphate phosphorylation pathways, and ITP metabolism, with an additional DNA repair term, suggesting a core link to nucleotide availability and genome maintenance. Some other terms (brain/liver development, viral process) may reflect multifunctional proteins or annotation noise rather than a cohesive theme, but the dominant signal is nucleotide metabolism with a DNA repair connection.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0044209","count":4},{"id":"GO:0016032","count":3},{"id":"GO:0015937","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0046939","count":3}]},{"hash":"423377817075684589","title":"Chromatin dynamics and centromere assembly","description":"This cluster's GO terms center on chromatin organization, including CENP-A containing chromatin assembly, chromatin remodeling during transcription initiation, and regulation of chromosome condensation. While other terms touch on development and plasmid partitioning, the strongest common thread is chromatin dynamics governing genome packaging and centromere function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035264","count":2},{"id":"GO:0061641","count":1},{"id":"GO:0007338","count":1},{"id":"GO:2000973","count":1},{"id":"GO:0030543","count":1}]},{"hash":"508619655207471429","title":"Chromatin assembly and transcription regulation","description":"The dominant GO terms point to chromatin-related processes and transcription control, including negative regulation of transcription by RNA polymerase II, histone H3 acetylation, and CENP-A-containing chromatin assembly, as well as chromosome condensation regulation. While a few terms (e.g., midbrain morphogenesis, fertilization) seem less connected, the overall theme centers on chromatin structure and transcriptional regulation.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0043966","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0007338","count":2},{"id":"GO:2000973","count":2}]},{"hash":"637983392702733055","title":"TNF/NF-\u03baB signaling with ubiquitination","description":"The top GO terms point to positive regulation of TNF-mediated signaling, activation of NF-kappaB-inducing kinase, and I-kappaB phosphorylation, all central to TNF-driven NF-\u03baB activation. Additional terms for innate immune response and various ubiquitination types (K63, K6-linked) suggest a module coordinated by ubiquitin signaling that modulates NF-\u03baB and inflammatory responses. Together these terms indicate a cluster of proteins involved in TNF/NF-\u03baB signaling and ubiquitin-mediated regulation of innate immunity.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090073","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0007250","count":4},{"id":"GO:1903721","count":4},{"id":"GO:0033209","count":4}]},{"hash":"1722278887004175980","title":"Purine nucleotide salvage and metabolism","description":"Top GO terms are dominated by purine nucleotide metabolism: PRPP biosynthesis, IMP and GMP salvage, guanine salvage, GMP catabolism, and regulation of purine metabolism. This suggests a cluster centered on maintaining purine nucleotide pools through salvage and associated biosynthesis. Some terms like cytolysis, lymphocyte proliferation, striatum development, and lactation likely reflect multifunctional annotations or cross-terms rather than a single cohesive function.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006015","count":4},{"id":"GO:0046038","count":3},{"id":"GO:0032264","count":3},{"id":"GO:0019835","count":3},{"id":"GO:0046651","count":3}]},{"hash":"166961520764662147","title":"Isoprenoid and sterol biosynthesis","description":"The GO terms show several terpenoid/isoprenoid biosynthesis processes (farnesyl diphosphate, geranyl/geranylgeranyl diphosphate, monoterpene) and cholesterol biosynthesis, pointing to a common theme of terpenoid/sterol production. A couple other terms (protein transport, heterotetramerization) are less central to this theme.","confidence":"High","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015015","count":2},{"id":"GO:0030206","count":2},{"id":"GO:0051290","count":1},{"id":"GO:0006695","count":1},{"id":"GO:1901663","count":1}]},{"hash":"2013976963003827834","title":"Neural development and synaptic regulation","description":"We name this cluster Neural development and synaptic regulation because the top GO terms prominently point to neural development and synaptic processes, including serotonergic neuron axon guidance and regulation of synaptic vesicle clustering. While there are also broader developmental terms (valve formation, nephron development, lung morphogenesis), the strongest signals tie to neural patterning and synaptic organization, suggesting these proteins collectively contribute to neural development and synaptic function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048023","count":5},{"id":"GO:0032912","count":5},{"id":"GO:0036515","count":5},{"id":"GO:2000807","count":5},{"id":"GO:0060488","count":5}]},{"hash":"1761972168863949924","title":"Actin dynamics in muscle and NMJ","description":"This cluster centers on actin cytoskeleton remodeling and contractile activity: multiple terms relate to actin nucleation, actin filament assembly, and actomyosin-driven contraction in skeletal muscle, as well as subsynaptic reticulum organization and NMJ-related synaptic regulation. While a few terms are peripheral or obsolete, the dominant signal is actin-mediated muscle contraction and neuromuscular junction organization.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045010","count":1},{"id":"GO:0003009","count":1},{"id":"GO:1902404","count":1},{"id":"GO:0032233","count":1},{"id":"GO:0045886","count":1}]},{"hash":"895627687861551099","title":"Unknown","description":"The GO terms span mitochondrial dynamics (fusion, cristae formation), neural and glial functions (visual perception, excitatory postsynaptic potential, astrocyte activation), and various signaling pathways (VEGF, thrombopoietin, kinase activity) with no clear common function tying all five proteins together. Because there is no coherent theme, a generic Unknown label is most appropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030948","count":2},{"id":"GO:0008053","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0048143","count":1}]},{"hash":"2294050943697369823","title":"Ribosome biogenesis and rRNA processing","description":"The top GO terms are dominated by ribosome biogenesis (GO:0042254) and endonucleolytic ITS1 cleavage separating rRNAs, indicating a core function in ribosome production and rRNA processing. Other terms point to broader regulatory roles (e.g., cell cycle, kinase activity), which may reflect pleiotropy or annotation noise, but the strongest, most consistent signal centers on ribosome assembly and rRNA maturation.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0046784","count":2}]},{"hash":"955955288458440575","title":"Actin remodeling and Rho GTPase signaling","description":"These terms cluster around actin cytoskeleton dynamics (microspike assembly, actin crosslinking) and regulation of small GTPases (Rho, Ras), linking actin remodeling to signaling that controls cell shape and polarity, including dendritic spine morphogenesis. The proteins likely cofunction in reorganizing actin while modulating GTPase activity, justifying this label.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0030035","count":2},{"id":"GO:0060997","count":2}]},{"hash":"1637319016440111156","title":"Embryonic organ morphogenesis","description":"Many top GO terms point to morphogenesis and organ development during embryogenesis across diverse tissues (ureteric bud branching, bile duct and digestive tract development, neural crest migration, oligodendrocyte differentiation, endocrine pancreas development). While there are some regulatory/immune terms, the dominant theme is embryonic organ development and tissue morphogenesis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090190","count":2},{"id":"GO:0035622","count":2},{"id":"GO:0001755","count":2},{"id":"GO:0048709","count":2},{"id":"GO:0048557","count":2}]},{"hash":"1193592120625895526","title":"Ubiquitination and microtubule regulation in host-virus interactions","description":"The terms cluster around ubiquitin signaling (K63-linked ubiquitination and NF-kappaB regulation), responses to viral infection (entry and suppression of release, inflammasome regulation), and cytoskeletal control (microtubule localization/depolymerization and aggresome assembly). Despite one placental morphogenesis term, the dominant pattern is host antiviral processes tied to ubiquitination and microtubule dynamics, justifying a label focused on host-virus interplay and protein quality control.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0060669","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0070534","count":4},{"id":"GO:0007026","count":4},{"id":"GO:0046598","count":4}]},{"hash":"2038573503514668545","title":"Hair follicle development and keratinization","description":"Top GO terms are dominated by hair follicle morphogenesis and keratinization, both hallmarks of epidermal/keratinocyte biology. The presence of actin filament bundle assembly and cellular responses to mechanical stimulus supports a skin/cytoskeletal theme, while ubiquitination is a general regulatory process common in keratinocytes. A few terms (B cell affinity maturation, dendrite development, Cvt pathway) are less consistent with this theme and may reflect annotation noise or broad shared processes. Overall, the cluster appears to reflect epidermal differentiation and keratinization with supporting cytoskeletal dynamics.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031069","count":3},{"id":"GO:0031424","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0035690","count":3}]},{"hash":"536133799113570097","title":"RNA and protein methylation","description":"This cluster is dominated by GO terms involving methylation of RNA (rRNA guanine-N7 methylation) and various protein methylation events (N-terminal methylation, arginine methylation, histone methylation). These recurring methyltransferase activities suggest the proteins function mainly as methyltransferases or in methylation-modification pathways, with other terms like biosynthesis or signaling likely incidental. Therefore, the label reflects the shared function of methylation across nucleic acids and proteins.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070555","count":2},{"id":"GO:0009234","count":1},{"id":"GO:0036068","count":1},{"id":"GO:0018013","count":1},{"id":"GO:0070476","count":1}]},{"hash":"2098419432015331404","title":"Chromatin assembly and centromere maintenance","description":"The cluster\u2019s top GO terms center on chromatin dynamics, including replication-coupled chromatin assembly, CENP-A\u2013containing chromatin assembly, and transcription-related chromatin remodeling, pointing to a role in assembling and maintaining chromatin structure, especially at centromeres. While other terms touch on broader processes like spermatogenesis and fertilization, the dominant theme is chromatin organization and centromere maintenance during replication.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051290","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0045815","count":3},{"id":"GO:0006335","count":3},{"id":"GO:0007283","count":3}]},{"hash":"1323998464332340167","title":"Symbiont-driven host immune modulation","description":"Based on the GO terms, several entries clearly point to symbiont effects on host immunity (symbiont-mediated suppression of host adaptive immune response, MHC II antigen processing/presentation, regulation of tolerance, and perturbation of ubiquitin-related processes). Although there are some plant cell wall biosynthesis terms in the set, the dominant theme is immune modulation by symbiotic interactions, which justifies a label focused on host immune processes in the context of symbiosis.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0039504","count":1},{"id":"GO:0002495","count":1},{"id":"GO:1900490","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0002643","count":1}]},{"hash":"1394456267782890251","title":"Diverse signaling pathways","description":"The GO terms span multiple receptor-mediated signaling cascades and phosphorylation events (T cell receptor signaling, response to LPS and GM-CSF, EGF/VEGF signaling, JUN and STAT phosphorylation, endothelial chemotaxis). This breadth suggests the proteins are involved in a variety of signaling processes rather than a single cohesive pathway, so a broad label like \u201cDiverse signaling pathways\u201d best captures the cluster. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0050852","count":4},{"id":"GO:0071222","count":4},{"id":"GO:0097011","count":4},{"id":"GO:0007601","count":3},{"id":"GO:0048010","count":3}]},{"hash":"112057819375624092","title":"Lipid metabolism with circadian and immune regulation","description":"The GO terms cluster around lipid metabolism: foam cell differentiation regulation, cholesterol efflux, fatty acid oxidation, and phosphatidic acid biosynthesis, pointing to metabolic control. There are also circadian-related terms (circadian temperature homeostasis, circadian regulation of gene expression) and immune signaling terms (IL-17 production, TLR4 signaling regulation, estrogen receptor signaling), suggesting links between metabolism, circadian rhythms, and immune pathways. Taken together, this cluster appears to reflect lipid metabolic regulation with broader circadian and immune connections.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010745","count":5},{"id":"GO:0010875","count":5},{"id":"GO:0046321","count":5},{"id":"GO:0001701","count":4},{"id":"GO:0060086","count":4}]},{"hash":"643390299115335909","title":"Extracellular matrix remodeling","description":"This cluster\u2019s terms cluster around proteolytic remodeling of the extracellular matrix and related tissue restructuring: collagen catabolic process, basement membrane disassembly, and bone resorption point to ECM degradation; decidualization and macrophage apoptotic processes reflect tissue remodeling contexts. The combination suggests proteins involved in ECM modification rather than a single tissue-specific function.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060448","count":1},{"id":"GO:0051603","count":1},{"id":"GO:0045453","count":1},{"id":"GO:0046697","count":1},{"id":"GO:0034769","count":1}]},{"hash":"2072919351058467776","title":"Ciliary Assembly and Development","description":"The top GO terms converge on cilium assembly and broad developmental processes across tissues (lens, neurons, spinal cord, skeletal system, multicellular development). This suggests a theme where ciliary functions interface with tissue morphogenesis, rather than a single narrowly defined pathway. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060271","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0001501","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0070306","count":2}]},{"hash":"640640937948818660","title":"Neural and endocrine development","description":"This cluster groups proteins enriched for neural development (neuron migration, serotonergic axon guidance, motor learning) and endocrine development (endocrine pancreas development, somatotropin-secreting cell development, thyroid hormone generation). The most frequent GO terms point to embryonic neuroendocrine formation and maturation, with in utero embryonic development reinforcing this theme. A few terms (osteoblast development, certain organ morphogenesis terms) reflect broader developmental roles but do not override the core neuroendocrine focus.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0001764","count":5},{"id":"GO:0007338","count":5},{"id":"GO:0060133","count":5},{"id":"GO:0031018","count":5},{"id":"GO:0002076","count":5}]},{"hash":"746877961966843751","title":"Neurovascular signaling and plasticity","description":"The terms show both neural functions (long-term potentiation, memory, vision, astrocyte activation) and vascular/cardiovascular processes (angiogenesis, endothelial migration, heart-rate regulation), plus signaling pathways like GTPase activity and thrombopoietin signaling. This suggests a neurovascular signaling and plasticity theme, where proteins participate in coordinated neural activity and vascular responses.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0002027","count":3},{"id":"GO:0010595","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0007614","count":3}]},{"hash":"1915556398428414329","title":"Unknown","description":"The GO terms are very diverse, spanning bone mineralization, ECM remodeling, immune phagocytosis, hormone response, reproductive development, and metabolism, with no dominant shared process. Because there is no clear unifying function among these proteins, a specific, representative label cannot be confidently assigned.","confidence":"","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030502","count":1},{"id":"GO:0009636","count":1},{"id":"GO:0050766","count":1},{"id":"GO:0060548","count":1},{"id":"GO:0010716","count":1}]},{"hash":"1640640664898226449","title":"Corticosteroid Secretion and Stress Response","description":"The GO terms cluster around positive regulation of corticotropin, corticosterone, and cortisol secretion, as well as responses to corticosterone and stress-related behaviors (startle, locomotion). This points to a shared role in HPA-axis signaling and stress/arousal pathways, with supporting cAMP biosynthesis. A lung development term is likely incidental given the small cluster size.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051461","count":1},{"id":"GO:2000854","count":1},{"id":"GO:0051464","count":1},{"id":"GO:0001964","count":1},{"id":"GO:0030324","count":1}]},{"hash":"80743063988079079","title":"Immune Response and Host Cell Interaction","description":"Based on GO terms such as positive regulation of T cell mediated immune response to tumor cell, response to ATP, response to cocaine, and translocation of peptides or proteins into host cell cytoplasm, the proteins appear linked to immune signaling and manipulation of host cells. Although several terms are obsolete, the recurring theme centers on immune-related activity and host interaction, justifying this label as a concise, representative description of the cluster.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071866","count":4},{"id":"GO:0014823","count":4},{"id":"GO:0052212","count":4},{"id":"GO:0051086","count":4},{"id":"GO:0002842","count":4}]},{"hash":"1056621318535615191","title":"Vesicle trafficking and cytoskeleton remodeling","description":"This cluster centers on vesicle trafficking and actin-driven remodeling, with terms like endosome-to-lysosome and endosome-to-Golgi transport, Cvt/vacuolar targeting, podosome assembly, and cleavage furrow formation pointing to coordinated vesicular transport and cytoskeletal dynamics. Translation appears as a minor or incidental term rather than a core shared function. Overall, the dominant theme is vesicle trafficking coupled with cytoskeletal organization.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0022617","count":1},{"id":"GO:0008333","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0032258","count":1}]},{"hash":"654000744030619476","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000447","count":1},{"id":"GO:0000461","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0042254","count":1}]},{"hash":"671484754172049409","title":"Potassium and Calcium Ion Transport","description":"The GO terms cluster around transport and homeostasis of monoatomic cations, especially potassium and calcium, including membrane potential stabilization, potassium import/export, and calcium movement to the ER, indicating a cohesive role in ion flux across membranes and muscle excitability.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030322","count":3},{"id":"GO:0030007","count":3},{"id":"GO:0097623","count":3},{"id":"GO:1990573","count":3},{"id":"GO:0090076","count":2}]},{"hash":"523109780184664387","title":"Angiogenic and growth signaling","description":"The GO terms point to VEGF receptor signaling, endothelial cell chemotaxis, and responses to growth factors (EGF), with downstream phosphorylation events (JUN, STAT) and regulation of cell growth, suggesting a theme of signaling pathways that drive endothelial behavior and proliferation. A few terms (visual perception, EPSP) seem unrelated noise, and the cluster is small with minimal edges, giving only moderate confidence in a tight cohesive function. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":1},{"id":"GO:0048010","count":1},{"id":"GO:0007258","count":1},{"id":"GO:2001028","count":1},{"id":"GO:0070849","count":1}]},{"hash":"320984566879505706","title":"Embryogenesis and organ morphogenesis","description":"The top GO terms are dominated by developmental and morphogenetic processes across embryo and placenta (in utero development, left-right patterning, cartilage morphogenesis, trophoblast differentiation, EMT in heart), suggesting a broad theme of embryonic development and organ formation; there isn\u2019t a single tight pathway, but a general developmental theme across tissues.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006689","count":1},{"id":"GO:0051692","count":1},{"id":"GO:0003323","count":1},{"id":"GO:0060806","count":1},{"id":"GO:0060972","count":1}]},{"hash":"2190740217991717262","title":"Ubiquitin-Mediated Regulation of Apoptosis and Signaling","description":"Several top GO terms converge on ubiquitin biology (ubiquitin-dependent protein catabolic process, protein ubiquitination, K63-linked ubiquitination, autoubiquitination) and apoptotic processes, with additional terms pointing to the regulation of signaling cascades (JNK, ERK) and Wnt signaling. This pattern suggests a cluster of proteins involved in ubiquitin-dependent control of apoptosis and major signaling pathways, potentially influencing development (placenta morphogenesis). ","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0046328","count":3},{"id":"GO:0060669","count":3}]},{"hash":"104436134109622832","title":"T cell activation and cell migration","description":"This cluster features GO terms tied to adaptive immune activation (T cell receptor\u2013MHC\u2013mediated activation) alongside processes involved in cell movement and signaling (cell migration, PI3K/AKT signaling, GPCR signaling, ARF regulation) and hyaluronan metabolism, suggesting a theme of immune cell activation coupled with trafficking through extracellular matrix. The mix hints at a cohesive, but not narrowly defined, immune signaling and migration role, rather than a single, highly specific pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0002291","count":4},{"id":"GO:0030212","count":4},{"id":"GO:0043491","count":3},{"id":"GO:1904140","count":3},{"id":"GO:1904261","count":3}]},{"hash":"1146787875347840049","title":"Unknown","description":"There are no GO terms and no edges among the four proteins, so there is no identifiable shared function to label; this cluster cannot be confidently assigned a function.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"416229632979851591","title":"Ribosome Biogenesis and Nucleolar Organization","description":"Based on the GO terms, the strongest signals are ribosome biogenesis and nucleolus organization, suggesting involvement in nucleolar ribosome assembly. While there is also a signal for protein kinase activation and several transporter terms, the dominant theme across the cluster appears to be ribosome-related nucleolar processes, making this the most representative label for the group.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0007000","count":1},{"id":"GO:0015751","count":1},{"id":"GO:1900754","count":1}]},{"hash":"1673138070113831062","title":"BMP/TGF-\u03b2 Signaling Regulation","description":"The top GO terms center on negative regulation of BMP signaling, SMAD complex regulation, and TGF-\u03b2\u2013related responses, suggesting these proteins collectively modulate BMP/TGF-\u03b2 signaling; a few seemingly unrelated terms may reflect annotation noise in a small cluster.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010991","count":3},{"id":"GO:0080005","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0000173","count":3},{"id":"GO:0042006","count":3}]},{"hash":"401267319524300405","title":"Unknown","description":"The GO terms point to diverse processes (mitosis, NF-kappaB signaling, vision, astrocyte activation, and various signaling activities) with no clear shared function across the proteins, so a coherent, specific label isn\u2019t evident.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0007601","count":1},{"id":"GO:0048143","count":1},{"id":"GO:0038163","count":1}]},{"hash":"158087714866100586","title":"Ribosome biogenesis","description":"The dominant terms are about rRNA processing and ribosome assembly (endonucleolytic ITS1 cleavage and ribosome biogenesis), suggesting these proteins function together in ribosome production. A few unrelated terms (mitotic/spindle and development) appear but are not central to the cluster\u2019s core theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0001501","count":1}]},{"hash":"1150681122846145754","title":"Unknown","description":"The top GO terms span diverse processes (mesoderm/muscle development, synapse organization, endocytosis, mitophagy, GTPase regulation, and yeast mating projection growth), with no single unifying function across the four proteins and no edges connecting them. This suggests no coherent shared role to name more specifically.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0061734","count":2},{"id":"GO:0031384","count":2},{"id":"GO:0016203","count":2},{"id":"GO:0000117","count":2}]},{"hash":"1973231137257540719","title":"Endothelial VEGF signaling and chemotaxis","description":"The top GO terms cluster around VEGF receptor signaling, positive regulation of endothelial cell chemotaxis, and responses to growth factors (EGF), as well as downstream signaling events (JUN/STAT phosphorylation) and cell growth regulation. This points to a cohesive theme of endothelial cell signaling, migration, and growth control in response to vascular and growth cues, despite a couple of outlier terms likely due to multifunctional proteins or annotation noise.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0048010","count":4},{"id":"GO:0007258","count":4},{"id":"GO:2001028","count":4},{"id":"GO:0070849","count":4}]},{"hash":"775912289808849820","title":"Growth signaling and nutrient transport","description":"This cluster combines GO terms for activation of protein kinase activity and ribosome biogenesis, suggesting roles in growth signaling and protein synthesis. The presence of multiple transport-related terms (glucose, nitrite, xenobiotic, vitamin transmembrane transport) and stress/nutrient-response terms (cellular response to glucose starvation) points to metabolic adaptation and nutrient handling in cells, possibly in epithelial contexts. Together, these themes fit a label centered on growth signaling coupled with nutrient transport and metabolism.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0052106","count":1},{"id":"GO:0060731","count":1},{"id":"GO:1904728","count":1}]},{"hash":"1445027740619196728","title":"Developmental transcription and ribosome biogenesis","description":"The frequent GO terms include DNA-templated transcription and multicellular organism development, plus ribosome biogenesis, suggesting proteins involved in gene expression during development and basic cell growth. While some terms are obsolete, the core themes point to transcriptional activity in development and ribosome assembly.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0007275","count":2}]},{"hash":"894967172515119902","title":"Mitotic spindle assembly and mitosis","description":"The strongest signals are mitotic processes\u2014mitotic spindle assembly, mitotic cell cycle, and spindle orientation\u2014pointing to cell division machinery as the core theme. Other terms (ribosome biogenesis, ubiquitin ligase activity) appear secondary and may reflect broader cellular regulation during division. Overall, the cluster is best described by mitotic spindle assembly and mitosis functions.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0000447","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2274000364854118256","title":"Metabolic pathways and membrane transport","description":"The top GO terms point to diverse metabolic activities (quinone biosynthesis, antibiotic biosynthesis, multiple catabolic pathways, fatty acid beta-oxidation, and valine catabolism) along with membrane-related processes (proton transmembrane transport and mitochondrial protein import), suggesting a cluster centered on metabolism and transport rather than a single function. The CNS development term appears as potential noise rather than a unifying theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0006635","count":1}]},{"hash":"232413030269758446","title":"Chromosome replication and centromeric chromatin assembly","description":"The proteins cluster around nuclear processes: cell division, DNA replication, CENP-A-containing chromatin assembly, and mRNA export from the nucleus, indicating a role in chromosome maintenance and cell-cycle progression. Some terms for cytosolic processes like SNARE complex disassembly and aggresome assembly are likely incidental noise.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006406","count":4},{"id":"GO:1903007","count":3},{"id":"GO:0061641","count":3},{"id":"GO:0035494","count":3}]},{"hash":"86561537818181581","title":"Unknown","description":"These terms cover endothelial/vascular development, heart morphogenesis, brain development, and sensory signaling, plus adhesion and ion homeostasis. There is no single shared function tying all proteins in this cluster, so a cohesive, specific label cannot be assigned.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097497","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0086048","count":3},{"id":"GO:0051262","count":3},{"id":"GO:0050976","count":3}]},{"hash":"1668201615617613647","title":"Mitochondrial respiration and ATP synthesis","description":"The top GO terms point to mitochondrial electron transport chain assembly and activity (respiratory chain complex IV assembly, cytochrome-c oxidase activity) and proton-motive-force-driven ATP production, with copper homeostasis supporting COX function. While a few terms touch vacuolar functions and ion transport, the dominant theme is mitochondrial respiration and energy generation, so this label captures the core cluster function.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033132","count":2},{"id":"GO:0008535","count":2},{"id":"GO:1904960","count":2},{"id":"GO:0006878","count":1},{"id":"GO:0042777","count":1}]},{"hash":"634152197362758412","title":"Neural development and axonogenesis","description":"The top GO terms are dominated by neural-related processes: visual perception, excitatory postsynaptic potential, axonogenesis, neural crest development, and synaptic/signaling activities. While there are a few outliers (cell cycle, plant hormone signaling, and morphogenesis aspects), the common thread across the terms is neural development and connectivity. Therefore, a label focusing on neural development and axon formation fits best.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0014032","count":2}]},{"hash":"1050582272342743886","title":"Chondrocyte and tendon development (ECM)","description":"The cluster's top GO terms cluster around cartilage and tendon formation (cartilage condensation, growth plate chondrocyte development, tendon development) and ECM-related processes (integrin biosynthetic process). While a few terms pertain to immune complement pathways or endocrine regulation, the dominant theme is cartilage/tendon development and extracellular matrix remodeling, so the label reflects the main function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0001867","count":3},{"id":"GO:2000860","count":3},{"id":"GO:0030853","count":3},{"id":"GO:0006958","count":3},{"id":"GO:0035989","count":3}]},{"hash":"1167682962330472424","title":"Hypoxia-driven angiogenesis and chemotaxis signaling","description":"This cluster centers on hypoxia response, promotion of angiogenesis and chemotaxis (monocytes and endothelial cells), and activation of PI3K/ERK signaling pathways. The combination of endothelial proliferation, chemotactic guidance, and pro-growth kinase signaling under hypoxic conditions points to a coordinated angiogenic and chemotactic response, making this label representative of the cluster\u2019s function.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0050930","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0045766","count":2},{"id":"GO:0051897","count":2},{"id":"GO:0061098","count":2}]},{"hash":"1640832555300426800","title":"GPCR-Mediated Cardiac Signaling and Contraction Regulation","description":"The top GO terms cluster around GPCR signaling pathways (tachykinin and acetylcholine receptors), GPCR desensitization and internalization, and cardiac muscle contraction including its negative regulation by signaling. This suggests a cohesive theme of GPCR-driven control of heart muscle function, with another term (visual perception) likely incidental noise.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007217","count":2},{"id":"GO:0007213","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0003108","count":2},{"id":"GO:0002029","count":2}]},{"hash":"1803018329323250891","title":"Innate antiviral signaling and ubiquitin regulation","description":"This cluster centers on innate immune defense and antiviral responses, tied together by ubiquitin-dependent processes (ubiquitination and proteasomal catabolism) and NF-kappaB/TNF signaling. The presence of terms related to aggresome assembly and microtubule localization suggests a role in the trafficking and regulation of signaling complexes via ubiquitin pathways, reinforcing a cohesive theme of ubiquitin-regulated innate immune signaling.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0000185","count":2},{"id":"GO:0070842","count":2}]},{"hash":"1934833681526378438","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms for ribosomal large subunit assembly, preribosome maturation, ribosomal biogenesis, and translation, suggesting proteins involved in ribosome production and protein synthesis. The few mitosis or retina-related terms appear peripheral and do not change the core interpretation of ribosome-related function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0010458","count":1},{"id":"GO:0031290","count":1}]},{"hash":"1945095054810626334","title":"Hormone and lipid metabolism","description":"The terms point to a metabolic theme: hormone turnover (androgen catabolic; estrogen biosynthetic), lipid metabolism (sphingolipid biosynthesis; fatty acid elongation), and vitamin/cofactor biosynthesis (phylloquinone catabolic; tetrahydrobiopterin biosynthetic). Some terms like lung development and sporulation are less directly tied but may reflect broader GO annotations. Overall, the cluster seems to group metabolic processes rather than a single signaling or structural role.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006710","count":4},{"id":"GO:0030435","count":4},{"id":"GO:0030324","count":4},{"id":"GO:0042376","count":4},{"id":"GO:0030148","count":4}]},{"hash":"2288946100403936538","title":"Glycosylation and carbohydrate metabolism","description":"The term set is dominated by carbohydrate metabolic and glycosylation-related GO terms (e.g., dolichol-linked oligosaccharide biosynthetic process, glucuronidation, lipid glycosylation), with several flavonoid-related biosynthesis terms that often involve sugar modifications. This points to a cohesive theme around glycan assembly and sugar metabolism, even though a few terms are more divergent, and the small, edge-less cluster may reflect broad annotations across species.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":2},{"id":"GO:0052696","count":2},{"id":"GO:0030259","count":2},{"id":"GO:0006488","count":2},{"id":"GO:0006711","count":2}]},{"hash":"247171768513918520","title":"Immune signaling and leukocyte trafficking","description":"The cluster\u2019s GO terms cluster around immune and inflammatory processes: IL-10 production regulation, defense against bacteria, cytokine production in immune responses, monocyte extravasation, and endothelial chemotaxis. These point to modulation of immune signaling and movement of leukocytes through vessels. Some terms on cell adhesion and hematopoietic development (megakaryocyte development) fit within vascular-immune contexts, supporting a cohesive hematopoietic/immune theme. Therefore the label reflects the cluster\u2019s core function.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2001181","count":1},{"id":"GO:0042742","count":1},{"id":"GO:0035855","count":1},{"id":"GO:0048378","count":1},{"id":"GO:0045217","count":1}]},{"hash":"175161320046437370","title":"Central Carbon Metabolism and Lipid Biosynthesis","description":"These four proteins appear linked to core energy metabolism, including glycolysis, pyruvate decarboxylation to acetyl-CoA, the TCA cycle (2-oxoglutarate), malonyl-CoA biosynthesis, and long-chain fatty acid biosynthesis, with a note of a metabolic shift response (e.g., sucrose starvation). The common thread is central carbon metabolism funneling into lipid biosynthesis, suggesting a cohesive metabolic cluster rather than disparate processes.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033512","count":1},{"id":"GO:0006096","count":1},{"id":"GO:0000002","count":1},{"id":"GO:0006213","count":1},{"id":"GO:2001295","count":1}]},{"hash":"346295116086333134","title":"TGF-beta signaling in development","description":"This cluster\u2019s top terms are dominated by TGF-beta pathway components (SMAD complex assembly; TGF-beta receptor signaling) along with developmental processes (cartilage development; lung development). Additional terms include NF-kappaB activation and apoptotic processes, which align with signaling-driven cell fate decisions during tissue remodeling. A few terms related to chitin and ecdysis hint at insect-specific remodeling, but the core theme centers on TGF-beta\u2013mediated development and related signaling. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051216","count":3},{"id":"GO:0007183","count":2},{"id":"GO:0007179","count":2},{"id":"GO:0006032","count":2},{"id":"GO:0070741","count":2}]},{"hash":"1131510149124793901","title":"Innate Immune NF-kappaB Signaling","description":"The GO terms point strongly to innate immune response and NF-kappaB pathway activation, including activation of NF-kappaB-inducing kinase and TNF-mediated signaling, with a theme around non-canonical NF-kappaB signaling. While a couple of terms touch on protein organization (aggresome/microtubule localization), the dominant signal is NF-kappaB\u2013driven innate immune signaling, justifying a cohesive label.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0000185","count":3},{"id":"GO:0070842","count":3},{"id":"GO:0035372","count":3},{"id":"GO:0090073","count":3},{"id":"GO:1901224","count":3}]},{"hash":"823360530685230510","title":"Regulators of TCR and Fc receptor signaling","description":"The GO terms center on immune signal transduction and its regulation, including T cell receptor signaling, Fc-epsilon receptor signaling, negative regulation of TLR4 signaling, and modulation of NF-\u03baB/JNK pathways, along with protein ubiquitination; this points to a coherent role as immune receptor signaling regulators, with some peripheral neuronal/microglial terms that are less central.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0038095","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0010976","count":3}]},{"hash":"1003236280681029694","title":"Unknown","description":"The Top Terms show a highly diverse set of processes (X chromosome inactivation, amino acid starvation response, placenta morphogenesis, T cell proliferation, ubiquitination signaling, and several obsolete/regulatory terms), with no clear shared function or pathway linking the proteins. This heterogeneity makes it unlikely that a single coherent biological theme defines the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060816","count":1},{"id":"GO:0034198","count":1},{"id":"GO:0060669","count":1},{"id":"GO:0042098","count":1},{"id":"GO:0070534","count":1}]},{"hash":"1870438058490490326","title":"Synapse Assembly and Proteostasis","description":"The top GO term points to neuronal synapse assembly, and accompanying terms like ubiquitin-dependent proteolysis, aggresome assembly, and microtubule localization suggest a shared role in protein quality control and transport relevant to synaptic formation and maintenance; a few immune signaling terms appear but do not define the core theme. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0060386","count":4},{"id":"GO:0048536","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0000185","count":3},{"id":"GO:0032479","count":3}]},{"hash":"1767277346276486040","title":"DNA replication and chromosome maintenance","description":"The cluster\u2019s GO terms cluster around DNA replication (DNA-templated replication, DNA topology changes), chromosome maintenance (telomere maintenance via telomerase, rDNA maintenance), recombination, and sister chromatid separation, suggesting a cohesive role in preserving and duplicating chromosomal integrity during cell division.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030263","count":1},{"id":"GO:0000712","count":1},{"id":"GO:0051304","count":1},{"id":"GO:0043007","count":1},{"id":"GO:0006310","count":1}]},{"hash":"1887284203505432811","title":"Ubiquitin-Dependent Protein Turnover","description":"The cluster is dominated by ubiquitin-related processes: ubiquitin-dependent protein catabolic process and positive regulation of protein polyubiquitination, pointing to proteostasis via ubiquitination. Additional terms hint at links to circadian rhythm and regulation of DNA-templated DNA replication initiation, suggesting connections to cell-cycle control, while microtubule polymerization aligns with cytoskeletal dynamics that interact with turnover mechanisms. Some GO terms are obsolete, so the signal should be interpreted cautiously. Overall, the common theme appears to be protein turnover and regulation via ubiquitination in the context of cell-cycle and cytoskeletal processes.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006516","count":3},{"id":"GO:0070544","count":3},{"id":"GO:0030174","count":3},{"id":"GO:0042752","count":3},{"id":"GO:1902916","count":3}]},{"hash":"748443062858954779","title":"Synapse formation and dendritic spine morphogenesis","description":"This cluster is dominated by neuronal synaptic development and cytoskeletal remodeling terms: synapse assembly, dendritic spine morphogenesis, and regulation of glutamatergic transmission, along with actin cytoskeleton organization and lamellipodium dynamics, all pointing to synapse formation and spine maturation. Behavioral terms like vocalization and grooming regulation suggest circuit-level output linked to these synaptic processes. There is one outlier term (megakaryocyte development) that is not core to the neuronal theme, likely incidental. ","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035855","count":3},{"id":"GO:2000821","count":3},{"id":"GO:0007416","count":3},{"id":"GO:0030032","count":3},{"id":"GO:0030036","count":3}]},{"hash":"130650324807581090","title":"Nervous system development and signaling","description":"These proteins show a strong enrichment for GO terms tied to neural development and brain function, including cerebellum development, dendrite development, startle response, and excitatory postsynaptic potential, indicating a shared role in nervous system development and synaptic signaling. While some terms touch on embryonic development or chromatin processes, the dominant pattern is neural development and neural activity. This makes \"Nervous system development and signaling\" an informative, specific label for the cluster.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002087","count":2},{"id":"GO:0001701","count":1},{"id":"GO:0051151","count":1},{"id":"GO:0048132","count":1},{"id":"GO:0001964","count":1}]},{"hash":"1828292283341484354","title":"Nucleotide Metabolism and Xenobiotic Response","description":"The top terms cluster around nucleotide and nucleoside metabolism (adenosine, guanosine, ribonucleoside monophosphate catabolism, and general nucleotide metabolic processes), with an additional signal of cellular response to xenobiotic stimulus. The presence of several unrelated terms (glucose metabolism, GPI anchor biosynthesis, plant cell wall biogenesis, feeding behavior) suggests a broad, mixed set, but the strongest coherent theme is nucleotide/nucleoside turnover, giving a plausible, albeit imperfect, functional label for this cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0009117","count":1},{"id":"GO:0046085","count":1},{"id":"GO:1901069","count":1},{"id":"GO:0009158","count":1}]},{"hash":"1294278683531073232","title":"Ribosome biogenesis and RNA methylation","description":"The cluster is dominated by GO terms related to ribosome assembly and rRNA/tRNA processing and methylation (e.g., ribosome biogenesis, maturation of LSU rRNA, cytosolic ribosome assembly, rRNA base methylation, tRNA wobble cytosine methylation), and translation-related processes (including mitochondrial translation). A few terms (regulation of transcription, UV response, ERAD) are less connected but present at lower frequencies. Overall, the prominent theme is ribosome biogenesis and RNA modification/translation, justifying a label centered on ribosome production and RNA methylation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0002127","count":1},{"id":"GO:0042256","count":1}]},{"hash":"902082792576536797","title":"Rab GTPases: Prenylation and Vesicle Trafficking","description":"Top GO terms center on Rab protein signal transduction, activation of GTPase activity, protein transport, and protein geranylgeranylation. The combination of GTPase activation and geranylgeranylation (a key prenylation step) is characteristic of Rab family proteins that regulate vesicle trafficking and membrane targeting. Though a couple of terms refer to pigment cell differentiation and swim bladder development (likely tissue-specific contexts), the shared signal is Rab-dependent membrane trafficking and post-translational modification.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0048798","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0050935","count":1},{"id":"GO:0018344","count":1}]},{"hash":"1087679176452352142","title":"Metanephric kidney development","description":"The proteins show enrichment for GO terms tied to kidney organogenesis and metanephric tubule morphogenesis (distal/proximal tubule development, mesonephric/duct formation, kidney development). Although a few terms touch other tissues, the dominant pattern is kidney tubule morphogenesis, justifying this label.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072287","count":4},{"id":"GO:0072237","count":4},{"id":"GO:0036303","count":4},{"id":"GO:0007156","count":3},{"id":"GO:0072177","count":2}]},{"hash":"2052610144245315153","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045010","count":1},{"id":"GO:0035320","count":1},{"id":"GO:0061164","count":1},{"id":"GO:0030866","count":1},{"id":"GO:0035372","count":1}]},{"hash":"2157937879113681536","title":"Embryonic neural development and circadian transcription","description":"The top GO terms center on in utero embryonic development, neuron maturation, and DNA-templated transcription, with additional emphasis on circadian regulation of gene expression and circadian temperature homeostasis. This suggests a cluster of proteins involved in early neural development whose transcriptional programs are modulated by circadian timing. While some terms touch on signaling pathways, the dominant theme appears to be developmental neurogenesis governed by circadian transcriptional control.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001701","count":3},{"id":"GO:0042551","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0060086","count":2},{"id":"GO:1905695","count":2}]},{"hash":"103916899150462503","title":"Embryonic development and hematopoiesis","description":"The GO terms center on developmental processes, especially embryogenesis and cardiovascular/blood formation (primitive streak formation, endocardial cushion development, megakaryocyte and hematopoietic stem cell proliferation) and transcriptional regulation during development. Some terms appear tangential (e.g., vitellogenesis, obsolete BMP signaling), but the dominant signal is embryonic development with links to heart and blood lineages, implying a developmental-regulatory cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0007296","count":4},{"id":"GO:0090009","count":3},{"id":"GO:0035855","count":3},{"id":"GO:0003197","count":3}]},{"hash":"413788095281758107","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070843","count":2},{"id":"GO:0090084","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0051259","count":2},{"id":"GO:0006452","count":2}]},{"hash":"1175975120991993002","title":"Bacterial cell wall glycosylation and teichoic acid biosynthesis","description":"GO terms center on cell wall biosynthesis and glycosylation (cellulose biosynthetic process, teichoic acid biosynthesis, O-linked glycosylation, UDP-glucose metabolism, cell wall organization), implying these proteins participate in building and modifying the bacterial cell envelope, especially glycopolymers like teichoic acids.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030244","count":2},{"id":"GO:0018243","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0019350","count":2},{"id":"GO:0002378","count":2}]},{"hash":"1240419490822467930","title":"Lectin-mediated innate immunity and phagocytosis","description":"This cluster is dominated by terms related to innate immune signaling and phagocytic processes: lectin-pathway complement activation, C-type lectin receptor signaling, Fc-gamma receptor signaling, phagocytosis recognition, leukocyte adhesion, and lipid mediator (arachidonate) release. While there are a few developmental terms (nephron/cartilage), the core theme ties to innate immune recognition and phagocytic activity.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072218","count":4},{"id":"GO:0001867","count":3},{"id":"GO:0002223","count":3},{"id":"GO:0090238","count":3},{"id":"GO:0001502","count":3}]},{"hash":"1191497820054834180","title":"Embryonic Development and Circadian Regulation","description":"The GO terms center on developmental processes (heart development, in utero embryonic development) and circadian control (circadian temperature homeostasis, circadian regulation of gene expression), with additional hormonal and immune signaling links (estrogen receptor signaling, IL-17 production, TLR4 signaling). This suggests a theme of developmental processes coordinated by circadian and signaling pathways, though the presence of diverse immune/hormonal terms makes the connection broad rather than a single, tight function.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0001701","count":3},{"id":"GO:0060086","count":3},{"id":"GO:1905695","count":3},{"id":"GO:0030520","count":3}]},{"hash":"1505436136990235719","title":"Signaling and Endocytosis Regulators","description":"Top terms converge on signaling cascades (ERK, Wnt), post-translational regulation (ubiquitination), and membrane trafficking (endocytosis), with developmental processes like osteoclast development and growth also represented. This points to a cohesive theme of how signaling is modulated via ubiquitination and endocytosis to influence development.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060079","count":4},{"id":"GO:0036035","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0043652","count":4}]},{"hash":"1018678798927611155","title":"ECM remodeling and matrix turnover","description":"This cluster is anchored by GO terms highlighting extracellular matrix (ECM) breakdown and remodeling, such as collagen catabolic process, basement membrane disassembly, and bone resorption. Additional terms (lung branching development, decidualization, macrophage apoptosis) point to remodeling and turnover in developmental, reproductive, and immune contexts. Together, the dominant theme is ECM remodeling and tissue turnover across contexts.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060448","count":1},{"id":"GO:0051603","count":1},{"id":"GO:0045453","count":1},{"id":"GO:0046697","count":1},{"id":"GO:0034769","count":1}]},{"hash":"2191591251592493258","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045719","count":3},{"id":"GO:0006935","count":3},{"id":"GO:0006898","count":2},{"id":"GO:0030505","count":2},{"id":"GO:0035860","count":2}]},{"hash":"576391280130826627","title":"Glycoprotein modification","description":"The terms point mainly to glycoprotein handling and post-translational modification (N-linked glycosylation, glycoprotein catabolic process, and general PTMs), with S-layer organization suggesting surface-associated glycoproteins. Some terms appear as noise (visual perception, blood pressure regulation) or obsolete annotations, but the dominant theme is glycoprotein processing and modification. Confidence: Medium.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:0006516","count":2},{"id":"GO:0043687","count":2},{"id":"GO:0045232","count":2},{"id":"GO:0043686","count":2}]},{"hash":"421105044048541000","title":"Multisystem Development and Differentiation","description":"These proteins are linked to development and differentiation across multiple tissues, including nervous system, endocrine organs, immune cells, and digestive tract, indicating a broad developmental role rather than a single pathway.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0007636","count":4},{"id":"GO:0030520","count":4},{"id":"GO:0002335","count":4},{"id":"GO:0002070","count":4}]},{"hash":"2208477629264941151","title":"Golgi-vesicle trafficking and SNARE exocytosis","description":"This cluster centers on vesicle transport and fusion events tied to the Golgi apparatus, including SNARE complex assembly, vesicle fusion with Golgi, and retrograde Golgi-to-ER transport, plus exocytic delivery of receptors and mucus secretion. These GO terms collectively point to a coordinated secretory pathway, especially at the Golgi and during exocytosis.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":1},{"id":"GO:0034197","count":1},{"id":"GO:0090316","count":1},{"id":"GO:0035493","count":1},{"id":"GO:0043134","count":1}]},{"hash":"1831300002236438453","title":"Unknown","description":"The top GO terms are diverse and include immune response, host-cell interactions, and several obsolete entries, offering no single cohesive function for the cluster. This suggests mapping noise rather than a shared, specific pathway among the proteins.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071866","count":3},{"id":"GO:0014823","count":3},{"id":"GO:0052212","count":3},{"id":"GO:0051086","count":3},{"id":"GO:0002842","count":3}]},{"hash":"2295153678116354638","title":"DNA Replication and Cell Cycle","description":"The top GO terms cluster around core nuclear processes: DNA replication, mitotic cell cycle, DNA-templated transcription, and DNA repair, indicating a group of proteins involved in DNA metabolism and cell-cycle progression. Other terms like VEGF signaling and EGFR response appear but are secondary; overall the theme is DNA replication and cell cycle control.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0007601","count":2}]},{"hash":"1132961482980056832","title":"Nucleic acid metabolism and RNA quality control","description":"This cluster's terms cluster around DNA replication, DNA damage response (UV protection), transcription initiation, ribosome biogenesis, and RNA surveillance/decay (TRAMP, NMD), indicating a nuclear program coordinating genome maintenance with RNA processing and expression.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0009650","count":2},{"id":"GO:0070870","count":2},{"id":"GO:0033683","count":2},{"id":"GO:0071038","count":2}]},{"hash":"1764174351720438228","title":"Nuclear transport and protein oligomerization","description":"The top GO terms strongly cluster around movement of molecules across the nucleus (nuclear pore organization, NLS-bearing protein import, tRNA export) and assembly of protein complexes (heterooligomerization, heterotrimerization, homooligomerization), with some regulation of nuclear import. A few terms about virus transport and glucose transport appear peripheral, but the core theme is nuclear transport and protein complex formation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051290","count":3},{"id":"GO:0010827","count":3},{"id":"GO:0075733","count":3},{"id":"GO:0070208","count":3},{"id":"GO:0051260","count":3}]},{"hash":"1572099747958818832","title":"Ribosome Biogenesis and Translation","description":"The GO terms are dominated by ribosome-related processes: maturation of SSU-rRNA, small subunit biogenesis/assembly, ribosome biogenesis, and translation, indicating a coherent module of proteins involved in ribosome production and protein synthesis.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042274","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0030490","count":3},{"id":"GO:0006407","count":3},{"id":"GO:1900153","count":3}]},{"hash":"71133372376101541","title":"Unknown","description":"The GO terms span very different metabolic and cellular processes (quinone biosynthesis, antibiotic biosynthesis, various catabolic paths, lipid oxidation, protein transport, and signaling responses) with no clear shared function across the cluster. Because of this lack of a unifying theme, there isn't a sensible specific label beyond Unknown.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0006635","count":1}]},{"hash":"2070097593351352318","title":"Tissue Development and Differentiation","description":"The GO terms point to developmental and differentiation processes across multiple tissues (thyroid gland development, digestive tract development, mesodermal fate specification, spinal cord and cortical neuron differentiation, epithelial maturation, etc.), with a few sensory and endocrine-related terms. This suggests a broad theme of development and maturation rather than a single focused function, justifying a tissue-development/differentiation label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0007636","count":3},{"id":"GO:0030520","count":3},{"id":"GO:0002335","count":3},{"id":"GO:0002070","count":3}]},{"hash":"1437604700371601075","title":"Angiogenesis and Endothelial Signaling","description":"The GO terms center on endothelial cell signaling and growth: VEGF receptor signaling, EGF response, JUN and STAT phosphorylation, and regulation of endothelial chemotaxis and cell growth. Although a couple of terms pertain to neural processes (visual perception, excitatory postsynaptic potential), the strongest signals are about angiogenesis-related pathways, suggesting the cluster represents endothelial signaling/growth rather than neural signaling.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0048010","count":2},{"id":"GO:0007258","count":2},{"id":"GO:2001028","count":2},{"id":"GO:0070849","count":2}]},{"hash":"2240723455421435292","title":"Unknown","description":"The terms span chromatin maintenance, transcription regulation, cell cycle, development, stress responses, and protein quality control, with no unifying function, so a specific label cannot be assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009861","count":2},{"id":"GO:0006344","count":2},{"id":"GO:0061198","count":2},{"id":"GO:1902894","count":2},{"id":"GO:0006348","count":2}]},{"hash":"317151596180767714","title":"Unknown","description":"The GO terms are highly diverse (glycan processing, visual perception, astrocyte activation, signaling, yeast budding polarity, GTPase/cytoskeleton regulation, synaptic activity), with no clear, common function tying all members together. This appears to be a non-cohesive set or noisy annotations, so an Unknown label with no confidence is appropriate.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006491","count":2},{"id":"GO:0007601","count":1},{"id":"GO:0048143","count":1},{"id":"GO:0038163","count":1},{"id":"GO:0007120","count":1}]},{"hash":"237377450920005940","title":"Ubiquitination/deubiquitination and transcription regulation","description":"The top GO terms show strong signals for ubiquitin-related processes (protein ubiquitination and deubiquitination: GO:0016567, GO:0071947, GO:1990168) and for transcription regulation (GO:0000122) with a related note on cell cycle regulation (GO:0071157). A few heart development and chloroplast mRNA modification terms are present but less represented, suggesting annotation noise rather than a coherent additional theme. Therefore, the most cohesive interpretation is a cluster centered on ubiquitin-mediated protein modification and transcriptional regulation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003283","count":2},{"id":"GO:0071947","count":2},{"id":"GO:1904404","count":2},{"id":"GO:0071157","count":2},{"id":"GO:1900871","count":2}]},{"hash":"1374970944976556197","title":"VEGF/EGF signaling in endothelial cells","description":"The GO terms point to VEGF receptor signaling, endothelial cell chemotaxis, and responses to EGF, along with downstream phosphorylation events (JUN, STAT) and regulation of cell growth, which together suggest a cluster centered on endothelial growth factor signaling and cell migration. Some terms (e.g., visual perception, neuronal excitatory potential) seem outliers, possibly annotation noise, but the core theme is endothelial signaling and growth regulation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":1},{"id":"GO:0048010","count":1},{"id":"GO:0007258","count":1},{"id":"GO:2001028","count":1},{"id":"GO:0070849","count":1}]},{"hash":"610017237094310287","title":"Chromatin regulation and transcription control","description":"This cluster centers on chromatin state and transcriptional regulation, as indicated by GO terms for DNA-templated transcription, heterochromatin maintenance/forming, and negative regulation of transcription (miRNA) and hormone signaling; the cohesive theme is epigenetic control of gene expression, with some peripheral or multi-functional annotations likely reflecting cross-talk or annotation noise.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0009861","count":2},{"id":"GO:0006344","count":2},{"id":"GO:0061198","count":2},{"id":"GO:1902894","count":2}]},{"hash":"776879766686354358","title":"Autophagy and mitophagy regulation","description":"The core terms show negative regulation of autophagosome maturation, negative regulation of mitochondrial fusion, mitophagy, and aggresome assembly, indicating autophagy/protein quality control as the cluster\u2019s main theme; a few other terms are broader cellular processes, but do not override the dominant autophagy/mitophagy signature.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901097","count":3},{"id":"GO:0010637","count":3},{"id":"GO:0000423","count":3},{"id":"GO:0086004","count":3},{"id":"GO:1902283","count":3}]},{"hash":"7109780883893677","title":"Ciliogenesis and microtubule dynamics","description":"The top GO terms point strongly to cilium assembly and intraflagellar transport, plus microtubule- and centrosome-related processes (spindle orientation, nuclear migration, microtubule anchoring). Germline development terms (spermatid elongation, oogenesis) and neurogenesis suggest related cytoskeletal roles in development, while an outlier immune term appears less connected. Overall, the cluster seems centered on ciliogenesis and microtubule-based cellular organization.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0044458","count":2},{"id":"GO:0022008","count":2},{"id":"GO:0019886","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0007290","count":2}]},{"hash":"1370218455874129548","title":"Skeletal muscle development and sarcomere organization","description":"The GO terms strongly cluster around skeletal muscle development, skeletal muscle fiber development, and sarcomere organization, indicating a muscle-formation/structure theme. A few terms are unrelated (flower development, kidney morphogenesis), but they are rare, so the overall signal supports labeling this cluster as skeletal muscle-related.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072156","count":1},{"id":"GO:0007519","count":1},{"id":"GO:0009911","count":1},{"id":"GO:0042752","count":1},{"id":"GO:0042787","count":1}]},{"hash":"1696660301697731262","title":"Endocytosis and vesicle trafficking regulation","description":"The top GO terms cluster around endocytosis, receptor-mediated endocytosis, and vesicle sorting (multivesicular body sorting, regulation of endocytosis), with some links to related signaling (EGF receptor) and amyloid-beta formation, suggesting the proteins function in endocytic trafficking and its regulation rather than a single metabolic activity.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006919","count":3},{"id":"GO:0000147","count":3},{"id":"GO:0015032","count":2},{"id":"GO:0071985","count":2},{"id":"GO:0060453","count":2}]},{"hash":"872314015800017413","title":"Endothelial VEGF signaling and growth regulation","description":"The most represented terms point to endothelial cell signaling and growth control: VEGF receptor signaling, endothelial chemotaxis, responses to epidermal growth factor, and serine phosphorylation of transcription factors (JUN, STAT). Together these suggest a theme of signaling pathways governing endothelial cell behavior and growth rather than a single molecular function. Some terms (visual perception, mitotic spindle checkpoint) appear tangential or annotation noise.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0048010","count":3},{"id":"GO:0007258","count":3},{"id":"GO:2001028","count":3},{"id":"GO:0070849","count":3}]},{"hash":"1833267616203399461","title":"Bacterial quinone biosynthesis","description":"This cluster prominently features quinone biosynthesis, with GO terms for phylloquinone and menaquinone biosynthetic processes, pointing to bacterial vitamin K\u2013type quinone production. Additional terms cover antibiotic biosynthesis and various catabolic pathways (phenylacetate, fatty acids, valine), suggesting a broader bacterial metabolic context, but the strongest signal remains quinone biosynthesis.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":3},{"id":"GO:0009234","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0010124","count":3},{"id":"GO:0006635","count":3}]},{"hash":"1419918103521681773","title":"Mucosal T Cell Regulation and Interferon Signaling","description":"The enriched GO terms point to immune regulation in mucosal tissues, especially T cell activity, negative regulation of T cell proliferation and IL-2 production, mucosal immune responses, and tissue homeostasis. While there are also signals related to angiogenesis and PI3K/AKT signaling, the dominant theme is regulation of T cell responses and interferon-related activity in mucosa.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032689","count":3},{"id":"GO:0042130","count":2},{"id":"GO:0001808","count":2},{"id":"GO:0042110","count":2},{"id":"GO:0045766","count":2}]},{"hash":"1681186770196613954","title":"Angiogenic Growth Factor Signaling","description":"The GO terms point to growth factor\u2013driven signaling pathways (VEGF receptor signaling, EGF response) with downstream transcription factor activation (JUN phosphorylation, STAT phosphorylation), plus endothelial cell\u2013specific processes like chemotaxis. Together they indicate a functional theme of angiogenic signaling and endothelial proliferation/movement, with some peripheral neuronal-related terms likely representing broader signaling roles.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0048010","count":3},{"id":"GO:0007258","count":3},{"id":"GO:2001028","count":3},{"id":"GO:0070849","count":3}]},{"hash":"639763810946801546","title":"Interferon-driven antiviral and immune activation","description":"This cluster is strongly enriched for type I interferon signaling, cellular responses to dsRNA, and activation of innate (NK cell) and adaptive (B cell) immune processes, indicating a coordinated antiviral immune response with modulation of cytokine pathways.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042742","count":2},{"id":"GO:0002312","count":2},{"id":"GO:0060337","count":2},{"id":"GO:0035458","count":2},{"id":"GO:0071359","count":2}]},{"hash":"1277959413105729739","title":"Unknown","description":"The top GO terms span diverse processes (GTPase regulation, mitophagy, muscle attachment, mesoderm development, synapse organization, and cell migration) across different organisms, with no clear unifying function tying all proteins together. Therefore a coherent, specific label cannot be assigned. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":1},{"id":"GO:0061734","count":1},{"id":"GO:0016203","count":1},{"id":"GO:0031384","count":1},{"id":"GO:0000117","count":1}]},{"hash":"1891062063603757080","title":"Unknown","description":"The terms span diverse processes (signal transduction, vascular and cardiac development, cerebellar development, sensory perception, and calcium-dependent adhesion) with no clear single theme tying the three proteins together, so a cohesive functional label cannot be justified. ","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0097497","count":2},{"id":"GO:0071321","count":2},{"id":"GO:0086048","count":2},{"id":"GO:0051262","count":2}]},{"hash":"2087251262477905924","title":"Unknown","description":"The GO terms include DNA replication and mitotic checkpoints, transcription termination, and multiple stress/ signaling responses (glucocorticoid signaling, xenobiotic response, calcium sensing) as well as a neuronal activity term, with no single coherent function linking all three proteins. Therefore a clear, representative label cannot be inferred.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:2000324","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1905213","count":3},{"id":"GO:0001915","count":3}]},{"hash":"363274274414998727","title":"Immune signaling and inflammation","description":"The terms show a pattern focused on defense against bacteria, inflammatory responses including acute inflammation and T cell chemotaxis, and signaling processes (GPCR signaling, GTPase regulation, and phosphorylation). While a few terms pertain to other processes, the dominant theme is immune signaling and inflammatory responses. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":1},{"id":"GO:0042742","count":1},{"id":"GO:0043547","count":1},{"id":"GO:0007197","count":1},{"id":"GO:1901652","count":1}]},{"hash":"1912879118517567246","title":"Immune signaling and chemotaxis","description":"The prominent GO terms center on immune processes and cell movement, including B cell chemotaxis across high endothelial venules, positive regulation of immunoglobulin production, chronic inflammatory response, induction of positive chemotaxis, and signaling pathways like PI3K/AKT and VEGF receptor signaling. These together suggest a module of immune activation and chemotaxis. A couple of terms (myoblast fusion, locomotory behavior) are less related, so while there is a plausible immune/migration theme, the signal is not perfect; hence a Medium confidence label. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901741","count":2},{"id":"GO:0045071","count":2},{"id":"GO:0008344","count":2},{"id":"GO:0035769","count":1},{"id":"GO:0048010","count":1}]},{"hash":"2034994439206218694","title":"One-carbon metabolism and nucleotide synthesis","description":"This cluster shows strong representation of one-carbon metabolic processes (one-carbon metabolic process; tetrahydrofolate biosynthesis; tetrahydrobiopterin biosynthesis) and nucleotide production (thymidine biosynthetic process). These GO terms together suggest a shared role in supplying one-carbon units and cofactors for nucleotide biosynthesis, with a possible link to NOS regulation via BH4, while other terms like axon regeneration or drug response might be less central or incidental to this core metabolic theme. Confidence reflects the clear core of metabolism-related terms despite some noise.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051000","count":2},{"id":"GO:0031103","count":2},{"id":"GO:0046654","count":2},{"id":"GO:0046105","count":2},{"id":"GO:0000083","count":2}]},{"hash":"2135588180574463871","title":"Leukocyte adhesion and migration signaling","description":"The cluster centers on immune cell trafficking with integrin-mediated adhesion and signaling, as shown by terms for leukocyte migration, monocyte activation, and integrin signaling; a few terms (myelination, bone resorption) appear as noise but do not define the core function.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002523","count":2},{"id":"GO:0033631","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0007229","count":2},{"id":"GO:0007338","count":1}]},{"hash":"1069018695219766557","title":"Developmental Differentiation Across Tissues","description":"The top GO terms cluster around development and differentiation across multiple tissues, notably neural (neuronal differentiation, synapse maturation), cardiac/muscular morphogenesis (heart valve, cardiac septum, muscle tissue morphogenesis), and regulatory processes (circadian regulation of gene expression). This suggests a broad role in developmental regulation rather than a single, specific pathway, so a label emphasizing cross-tissue development is appropriate, given the small protein set.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090128","count":3},{"id":"GO:0010374","count":3},{"id":"GO:2000793","count":3},{"id":"GO:0048715","count":3},{"id":"GO:0021892","count":3}]},{"hash":"1882131992553401139","title":"Unknown","description":"The top GO terms span diverse, seemingly unrelated processes (oxidation-reduction, blood vessel remodeling, cell-surface localization, heat response, transcription regulation, neuronal proliferation, sporulation, and various metabolic pathways) with no clear shared function or pathway tying the proteins together. There are no edges among members, and the terms appear from different organisms/contexts, so a specific, representative label cannot be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0001974","count":2},{"id":"GO:0034394","count":2},{"id":"GO:0034605","count":2},{"id":"GO:0045944","count":2}]},{"hash":"1886421209948811930","title":"Diverse catabolic processes","description":"The top GO terms span multiple, unrelated catabolic pathways (aldonic acid, N-acetylneuraminate, trans-4-hydroxy-L-proline, D-glucarate, ureide, purine nucleobase) and include proteolysis/peptide catabolism, with no shared pathway or interaction evident (no edges or triangles). This suggests a cluster of proteins involved in various degradation processes rather than a single cohesive function. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":2},{"id":"GO:0019877","count":2},{"id":"GO:0046176","count":1},{"id":"GO:0019262","count":1},{"id":"GO:0019470","count":1}]},{"hash":"944077311364643330","title":"Developmental Regulation and Differentiation","description":"The top GO terms point to broad developmental roles across tissues (fertilization, gonad, brain, eye, epithelial maturation) and include transcriptional regulation, suggesting these proteins are involved in development and gene expression control rather than a single pathway. Occasional cytoskeletal organization hints at morphogenesis and differentiation processes as well.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0007601","count":1}]},{"hash":"1010025255504429189","title":"Organogenesis and Neural Development","description":"The GO terms cluster around developmental processes across multiple organs (lung morphogenesis, inner ear development, heart cushion formation, ossification) and neural development (neural stem cells, axon guidance, synapse assembly, B cell differentiation within a developmental context). This points to a broad embryonic morphogenesis theme rather than a single pathway, so the label Organogenesis and Neural Development fits best.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007157","count":2},{"id":"GO:0060489","count":2},{"id":"GO:0002315","count":2},{"id":"GO:0097150","count":2},{"id":"GO:0048839","count":2}]},{"hash":"541287748506891651","title":"Embryonic development and chromatin regulation","description":"The GO terms repeatedly point to embryogenesis and pattern formation (adaxial/abaxial patterning, ventral cord development, gastrulation, in utero embryonic development), suggesting a developmental role. The concurrent signals for chromatin modification and ubiquitin-dependent proteolysis imply epigenetic control and protein turnover as part of this developmental regulation, supporting a cohesive theme of development-linked chromatin remodeling and proteostasis.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000011","count":3},{"id":"GO:0007419","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0039536","count":3},{"id":"GO:0001702","count":3}]},{"hash":"1853889151199073250","title":"Molybdenum cofactor biosynthesis and sulfur metabolism","description":"The GO terms converge on cofactors and sulfur-containing compound biosynthesis (MoCo assembly, cysteine/hydrogen sulfide, methionine pathways, glutathione, FAD), indicating a cohesive role in molybdenum cofactor biosynthesis and broader sulfur metabolism.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019344","count":1},{"id":"GO:0009086","count":1},{"id":"GO:0019379","count":1},{"id":"GO:0032324","count":1},{"id":"GO:0018315","count":1}]},{"hash":"813070798163931047","title":"Diverse small-molecule catabolism","description":"This cluster\u2019s top GO terms are dominated by various catabolic processes affecting small molecules (aldonic/uronic acids, sialic acid, glucarate, proline, inosine synthesis), suggesting a broad metabolic theme rather than a single specific pathway. Some immune-regulation terms appear among the terms, likely annotation noise rather than a core function of the cluster, so the label reflects general metabolism rather than immune function. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046176","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0019262","count":1},{"id":"GO:0019470","count":1},{"id":"GO:0019877","count":1}]},{"hash":"1459421712457164300","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is enriched for ubiquitin-dependent protein catabolic process and protein polyubiquitination, pointing to proteostasis via the ubiquitin-proteasome system as the core function. The presence of a p38MAPK cascade term suggests possible cross-talk with stress signaling, but ubiquitin-mediated degradation appears to be the primary theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0038066","count":2},{"id":"GO:0016336","count":1},{"id":"GO:0071287","count":1}]},{"hash":"157001103233571153","title":"SCF/Ubiquitin Proteolysis in Cell Cycle Regulation","description":"The top GO terms point to SCF-dependent ubiquitin-proteasome\u2013mediated protein degradation, coupled with neddylation, and key cell-cycle events (G2/M transition, mitotic exit, chromosome segregation). This suggests a core theme of ubiquitin ligase activity driving cell-cycle progression, with neddylation linking to SCF complex activation; while antiviral/interferon-related terms may reflect broader interfaces with DNA damage response and immune signaling, the central thread is proteolysis controlling mitosis. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0010458","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0007059","count":3}]},{"hash":"102353405977870997","title":"Unknown","description":"The top terms are extremely diverse, spanning ubiquitin-dependent proteolysis, skeletal muscle and organ morphogenesis, circadian rhythm and sleep, plant development and phototropism, plus immune cell differentiation. With no clear shared function or pathway across the few proteins, there is no coherent theme to assign a specific label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0007519","count":2},{"id":"GO:0072156","count":2},{"id":"GO:0045497","count":2},{"id":"GO:0032764","count":2}]},{"hash":"706369120121410495","title":"ERAD and Ubiquitin-Proteasome Degradation","description":"The top GO terms point to ubiquitin-dependent protein catabolic processes, polyubiquitination, and ERAD, with links to ER-stress\u2013induced apoptotic signaling and JNK regulation, suggesting a cohesive theme of ubiquitin-mediated quality control in the ER and related stress responses.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0070059","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0060816","count":2}]},{"hash":"1589216398363556112","title":"Lipid Biosynthesis and Membrane Lipid Metabolism","description":"The top GO terms converge on lipid biosynthesis and lipid-related membrane processes (unsaturated fatty acid biosynthesis, ergosterol/sphingolipid metabolism, fatty acid response, sebaceous gland differentiation, and even myelin maintenance), suggesting the cluster reflects lipid metabolism and membrane lipid homeostasis across contexts. Some terms (nitrate assimilation, mitochondrion inheritance) are less directly tied, but do not override the lipid-focused theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":3},{"id":"GO:0032443","count":3},{"id":"GO:0006636","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0006675","count":3}]},{"hash":"304543174417241594","title":"Unknown","description":"The GO terms are highly diverse (neural myelin maintenance, various lipid and sphingolipid biosynthesis processes, nitric oxide and nitrate metabolism, mitochondrial inheritance, and muscle-related regulation), showing no single shared function or pathway for this cluster. With zero edges and no cohesive theme, Unknown best fits as a label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032286","count":3},{"id":"GO:0032443","count":3},{"id":"GO:0006636","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0006675","count":3}]},{"hash":"25447760153572212","title":"Developmental signaling and differentiation","description":"The GO terms point to broad developmental regulation and differentiation across multiple lineages (neurons, muscle, endothelium, germline) and associated signaling pathways (IGF, TGF-beta), as well as processes like cell polarity and axon extension, suggesting the cluster reflects general developmental signaling rather than a single specific function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048023","count":2},{"id":"GO:0032912","count":2},{"id":"GO:0098730","count":2},{"id":"GO:1902354","count":2},{"id":"GO:0071681","count":2}]},{"hash":"378278198952486127","title":"Unknown","description":"The terms span plant and animal development, immune signaling, ECM remodeling, adhesion, proteolysis, and chlorophyll biosynthesis, with no single shared theme; the zero edges/triangles imply little direct interaction, so no cohesive function can be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901202","count":3},{"id":"GO:0048455","count":3},{"id":"GO:0034113","count":3},{"id":"GO:0003429","count":3},{"id":"GO:0006511","count":3}]},{"hash":"1805553324948799667","title":"Glycosphingolipid transport","description":"These proteins show GO terms dominated by glycosphingolipid metabolism and lipid transport, especially ceramide and glycolipid trafficking between the ER and Golgi, with related glycolipid transport. Although a few other transport terms appear, the recurring theme is lipid trafficking rather than enzymatic activity, supporting a label focused on glycosphingolipid transport.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006687","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0009751","count":1},{"id":"GO:0072488","count":1},{"id":"GO:0015695","count":1}]},{"hash":"2205542949295276976","title":"Intracellular transport and protein processing","description":"These GO terms cluster around intracellular cargo movement (cytoplasm to vacuole targeting, mitochondrion transport along microtubules) and protein handling (ubiquitination, regulation of the secretory pathway), pointing to a theme of trafficking and processing inside the cell. The additional developmental and physiological terms probably reflect broader tissue-specific roles, but the core signal is intracellular transport and protein management.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0016358","count":2},{"id":"GO:0036035","count":2},{"id":"GO:0060047","count":2}]},{"hash":"1297257731131623152","title":"Immune signaling and cell migration","description":"These GO terms cluster around immune signaling and cell movement. Several terms point to immune regulation, including NF-kappaB-related transcription, TLR4 signaling, and STAT phosphorylation, as well as B cell homeostasis. Other terms relate to cytoskeletal remodeling and migration, such as actin filament organization and regulation of fibroblast and microglial migration. Some terms touch on lineage differentiation (glial and megakaryocyte contexts), which can intersect immune/hematopoietic roles. Overall, the common thread appears to be signaling pathways in immune contexts coupled with cytoskeletal changes that drive cell movement, though the links are broad and not tightly specific.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0036493","count":1},{"id":"GO:0035855","count":1},{"id":"GO:1904140","count":1},{"id":"GO:0010762","count":1}]},{"hash":"170746151311244560","title":"Immune signaling and host-virus interactions","description":"The GO terms point to immune signaling (T cell proliferation, NF-kappaB-related activity, ubiquitination) and antiviral host responses (viral entry modulation, host suppression of viral release, aggresome involvement). Development-related term (placenta morphogenesis) suggests a broader signaling context but does not dominate; overall the cluster is best described by immune signaling and host-virus interaction themes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042098","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0000185","count":2}]},{"hash":"732765678870428111","title":"NF-kB\u2013driven immune signaling","description":"The top GO terms point to immune regulation and NF-kappaB pathway activity (including positive regulation of NF-kappaB transcription factor activity and modulation of TLR4 signaling), plus B cell homeostasis and microglial migration regulation, all of which flag a shared theme of inflammatory and innate/adaptive immune signaling. Additional terms related to STAT phosphorylation and osteoclast/bone-related development can align with NF-kB\u2019s broader roles in signaling cross-talk between immunity and other tissues. Thus the cluster is best described as NF-kB\u2013driven immune signaling.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":3},{"id":"GO:0036493","count":2},{"id":"GO:0035855","count":2},{"id":"GO:1904140","count":2},{"id":"GO:0001922","count":2}]},{"hash":"318727062719365065","title":"Interferon signaling and cytoskeletal remodeling","description":"The top GO terms cluster around type II interferon signaling and negative regulation of interferon production, plus JUN phosphorylation, actin filament bundle assembly, GTPase activity, and ubiquitination. This points to a theme of immune signaling coordinated with cytoskeletal remodeling and transcriptional regulation rather than a single straightforward process.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060333","count":1},{"id":"GO:0045358","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0045355","count":1},{"id":"GO:1902524","count":1}]},{"hash":"147174645354065363","title":"Lectin and Fc receptor\u2013mediated immune signaling","description":"The top GO terms point to innate immune recognition and signaling: lectin pathway complement activation, stimulatory C-type lectin receptor signaling, Fc-gamma receptor signaling, phagocytosis recognition, and leukocyte adhesion. These collectively suggest a coherent theme of lectin- and Fc-receptor\u2013driven immune responses and cell-cell interactions, with a possible mix of unrelated developmental terms annotation noise. Overall, the cluster is best described by immune signaling via lectin and Fc receptors.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001867","count":3},{"id":"GO:0002223","count":3},{"id":"GO:0090238","count":3},{"id":"GO:0001502","count":3},{"id":"GO:0006910","count":3}]},{"hash":"1821895072146839909","title":"Actin Cytoskeleton Organization and Filopodium Assembly","description":"The cluster is best characterized by GO terms centered on actin dynamics, including actin filament bundle assembly, cytoskeleton organization, and positive regulation of filopodium assembly, with some negative regulation of actin filament binding. This points to a coherent theme of actin cytoskeleton remodeling and protrusion formation, despite a few metabolic/catabolic annotations appearing in the list.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0019381","count":2},{"id":"GO:1904530","count":2},{"id":"GO:0019556","count":2}]},{"hash":"1376173168631926962","title":"Ubiquitin-Proteasome Regulation","description":"The top GO terms are centered on ubiquitin-dependent proteolysis, including SCF-dependent ubiquitination and proteasomal degradation, as well as polyubiquitination, indicating a cohesive theme of protein turnover by the ubiquitin-proteasome system. Additional terms touch on cytoskeletal dynamics (microvillus assembly) and signaling (Rho pathway), which can be modulated by ubiquitination, plus stress-related processes like oxidative stress-induced apoptotic signaling and autophagy regulation. Overall, the dominant signal points to ubiquitin-mediated protein degradation and turnover as the cluster\u2019s core function.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030033","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0031146","count":1},{"id":"GO:1902916","count":1},{"id":"GO:1903378","count":1}]},{"hash":"704651387535749372","title":"Embryonic Development and Hematopoiesis Regulators","description":"The terms cluster around early embryogenesis (primitive streak formation) and blood/immune lineage development (megakaryocyte and hematopoietic stem cell proliferation, NK cell proliferation, endocardial cushion development, epithelial proliferation), with additional notes on transcriptional regulation. This points to a cohesive theme of developmental programs and hematopoiesis rather than a single, narrow pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0090009","count":2},{"id":"GO:0035855","count":2},{"id":"GO:0003197","count":2},{"id":"GO:0001787","count":2}]},{"hash":"1252474111012466241","title":"Diverse Transmembrane Transporters","description":"The GO terms are all about transmembrane transport across membranes for a variety of substrates (arabinose, nitrate/nitrite, galactose, sialic acid, phosphate, potassium, xenobiotics, etc.). This suggests the proteins act as membrane transporters with broad substrate specificity rather than a single pathway component. The shared function across substrates supports a transporter-annotation cluster.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015751","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0015757","count":3}]},{"hash":"113549646002927478","title":"Organ Development and Tissue Organization","description":"The terms repeatedly point to development and organization across several tissues (brain, inner ear, liver) and to related sensory and locomotor functions, as well as junction formation and endothelial barrier establishment, indicating a cluster tied to broad organogenesis rather than a single function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007626","count":2},{"id":"GO:0045216","count":2},{"id":"GO:0048839","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0001889","count":2}]},{"hash":"1260976387439690301","title":"Unknown","description":"Top terms span chromatin assembly, DNA replication, ribosome biogenesis, SNARE/aggresome processes, and energy metabolism, with no single shared function among the proteins. No coherent theme emerges, so the cluster is labeled Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903007","count":1},{"id":"GO:0061641","count":1},{"id":"GO:1990048","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0035494","count":1}]},{"hash":"1029923021112282570","title":"Ubiquitination-Driven NF-kappaB Signaling","description":"The top GO terms cluster around ubiquitin modification and turnover (K63- and K6-linked ubiquitination, ubiquitin-dependent protein catabolic process, autoubiquitination) and regulatory steps in NF-kappaB signaling (I-kappaB phosphorylation, TNF-mediated signaling), suggesting a cohesive theme of ubiquitin-mediated control of NF-kB pathway activity, with some related terms touching chromatin and immune gene regulation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0085020","count":2},{"id":"GO:0036205","count":2},{"id":"GO:0090073","count":2}]},{"hash":"268315991571425121","title":"Negative regulation of adaptive type 2 immune responses","description":"The top GO terms cluster around dampening adaptive immune functions and Th2-type activity, including negative regulation of T cell proliferation, suppression of IL-4 and isotype switching (IgE/IgG), and general negative regulation of inflammatory and type 2 immune responses, with a minor signal about protein ubiquitination. This suggests the proteins act to downregulate humoral and cellular immune activation, particularly type 2 responses.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048294","count":1},{"id":"GO:0042130","count":1},{"id":"GO:0032713","count":1},{"id":"GO:0045619","count":1},{"id":"GO:0030001","count":1}]},{"hash":"1580099283062309850","title":"Mesodermal Tissue Morphogenesis","description":"The cluster is dominated by GO terms for morphogenesis and development (hair follicle, cartilage, mesoderm, endocardial EMT, endocrine/pancreatic development), indicating a cohesive role in formation and differentiation of mesoderm-derived tissues; the other terms likely reflect background cellular processes rather than core function.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031069","count":3},{"id":"GO:0060536","count":3},{"id":"GO:1903026","count":3},{"id":"GO:0003323","count":3},{"id":"GO:0007498","count":3}]},{"hash":"751377832278533537","title":"ER stress response and protein homeostasis","description":"The listed terms include response to unfolded protein, positive regulation of translation initiation in response to ER stress, and ER-associated protein catabolic processes, which together point to cellular protein quality control under ER stress (UPR). While a few terms touch on other processes like centrosome biology and development, the strongest and most recurrent theme is ER stress and protein homeostasis. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043278","count":1},{"id":"GO:0046661","count":1},{"id":"GO:0045842","count":1},{"id":"GO:1903070","count":1},{"id":"GO:2000324","count":1}]}]