[{"hash":"108568789500707407","title":"Neuronal development and synaptic signaling","description":"The cluster\u2019s top GO terms center on brain development, regulation of synaptic vesicle exocytosis, and glutamatergic synaptic transmission, with additional links to Rho/GTPase signaling and cytoskeletal regulation, all suggesting roles in neuronal differentiation and synaptic function. Some terms (myoblast fusion, abscisic acid signaling) are less directly related and may reflect broader developmental contexts or cross-species annotations, but the dominant theme is neuronal development and synaptic regulation.","confidence":"High","size":29,"edges":224,"triangles":1316,"max_degree":21,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043065","count":7},{"id":"GO:0007420","count":7},{"id":"GO:2000300","count":7},{"id":"GO:0035023","count":7},{"id":"GO:0043087","count":7}]},{"hash":"1107663175228293763","title":"Cerebellar development and metabolic regulation","description":"This cluster is enriched for DNA-templated transcription and multiple development-related terms (cerebellar cortex development, multicellular organism development, myotube differentiation) plus angiogenesis and glucose metabolism, suggesting a cohesive program of neural/muscle development intertwined with metabolic signaling and vascularization (including Wnt pathway modulation). Confidence: Medium","confidence":"","size":29,"edges":46,"triangles":33,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006349","count":6},{"id":"GO:0021695","count":6},{"id":"GO:0001403","count":6},{"id":"GO:0051436","count":6}]},{"hash":"1045822110057032823","title":"Mitochondrial inner-membrane protein import and assembly","description":"The cluster's top GO terms cluster around mitochondrial processes: inserting proteins into the inner membrane and assembling respiratory chain complexes I and III, indicating a cohesive theme of mitochondrial protein import/assembly. Additional terms related to protein processing and quality-control\u2013associated degradation/autophagy support organelle maintenance, though other terms are less mitochondrial-specific; overall, the mitochondria-focused terms predominate.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0032981","count":3},{"id":"GO:0045053","count":3},{"id":"GO:0034551","count":2}]},{"hash":"78487960650631562","title":"Cardiovascular Oxidative Stress and NO Transport","description":"This cluster's top GO terms cluster around redox responses (response to hydrogen peroxide; hydrogen peroxide catabolic process) and cardiovascular-related processes (heart development; blood coagulation; nitric oxide transport and biosynthesis; oxygen transport). There are additional unrelated terms (endocytosis, hepatic stellate activation), but the dominant pattern points to cardiovascular redox signaling and vascular function, justifying the label.","confidence":"Medium","size":29,"edges":79,"triangles":121,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0006898","count":4},{"id":"GO:0006626","count":3},{"id":"GO:2000490","count":3}]},{"hash":"1854993909454787340","title":"Membrane Transport of Ions, Lipids, and Drugs","description":"The cluster\u2019s top GO terms cluster around membrane-associated transport, including cobalt ion transport, glycine betaine transport, phospholipid translocation, lipoprotein transport, fatty acid import into peroxisomes, and oligopeptide export from mitochondria, suggesting a cohesive theme of membrane and nutrient/drug transport. Some terms (antibiotic response, doxorubicin transport, and MHC class I antigen processing) may reflect xenobiotic handling or annotation noise, but the dominant signal points to transport-related functions across membranes and related pathways.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":6},{"id":"GO:0045332","count":5},{"id":"GO:0090374","count":4},{"id":"GO:0072089","count":4},{"id":"GO:1900753","count":4}]},{"hash":"53292972817429812","title":"Membrane Transport and Antigen Processing","description":"This cluster is dominated by GO terms for membrane transport (oligopeptide export from mitochondrion, cobalt ion transport, glycine betaine transport, ceramide translocation, long-chain fatty acid import into peroxisome, lipoprotein transport) and a related immune function (antigen processing and presentation via MHC class I). The mix suggests a general theme of substrate trafficking and peptide handling across organelles, with a few outliers like stem cell proliferation or antibiotic response that may be less connected.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":7},{"id":"GO:0090374","count":5},{"id":"GO:0072089","count":5},{"id":"GO:1900753","count":5},{"id":"GO:0019885","count":5}]},{"hash":"1520432201980472560","title":"Splicing and mRNA surveillance","description":"The cluster is dominated by terms tied to RNA processing, especially splicing (U2-type prespliceosome assembly) and mRNA quality control via nonsense-mediated decay, with supportive signals from transcription-related steps (RNA Pol II promoter clearance). A few redox-related terms appear but seem ancillary. This points to a cohesive role in splicing and mRNA surveillance.","confidence":"High","size":29,"edges":166,"triangles":483,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":5},{"id":"GO:0032508","count":3},{"id":"GO:0030416","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0055114","count":2}]},{"hash":"88605531116334427","title":"Muscle development and growth regulation","description":"The terms cluster around muscle biology and growth control: myoblast fusion, regulation of cardiac muscle cell proliferation, hippo signaling, and responses related to muscle activity, alongside broader development and cell-cycle processes. This suggests a group of proteins coordinating muscle differentiation and organ growth during development.","confidence":"Medium","size":29,"edges":27,"triangles":13,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0007601","count":8},{"id":"GO:0060044","count":8},{"id":"GO:0014850","count":8},{"id":"GO:0007275","count":8}]},{"hash":"510518661817324871","title":"Proteolytic Processing and Peptide Maturation","description":"This cluster centers on proteolysis-related processes: autoprocessing, maturation of angiotensin, amyloid-beta metabolism, digestion, membrane protein proteolysis, and regulation of APP biosynthesis. These collectively point to proteolytic modification and maturation of peptide hormones and membrane/secreted proteins, making this label representative of the group's function.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016540","count":3},{"id":"GO:0002003","count":3},{"id":"GO:0050435","count":3},{"id":"GO:0007586","count":3},{"id":"GO:0036151","count":2}]},{"hash":"1941658074166225517","title":"Mitochondrial lipid biosynthesis and remodeling","description":"This cluster features strong enrichment for lipid biosynthesis and remodeling (triglyceride, cardiolipin, phosphatidylcholine, ether lipids, CDP-diacylglycerol) and mitochondrial ATP synthesis coupling electron transport, indicating a module for mitochondrial membrane lipid production that supports energy metabolism. IL-2 production appears but does not define the main theme.","confidence":"High","size":29,"edges":214,"triangles":811,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":11},{"id":"GO:0010143","count":9},{"id":"GO:0035965","count":9},{"id":"GO:0006663","count":9},{"id":"GO:0008611","count":9}]},{"hash":"1016203689309978272","title":"Unknown","description":"This cluster contains a mix of functions: DNA-templated transcription, nucleotide metabolism (pentose phosphate shunt and uridine biosynthesis), vesicle transport (ER to Golgi), protein interactions/oligomerization, dephosphorylation, and even brain development. The wide range of processes provides no clear, single unifying function, so a cohesive label cannot be confidently assigned.","confidence":"","size":29,"edges":28,"triangles":3,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006098","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0061087","count":4},{"id":"GO:0070262","count":3}]},{"hash":"1758273646371886179","title":"Neural development and dendritic spine morphogenesis","description":"This cluster is dominated by GO terms tied to neural development and synapse-structuring, notably brain development and dendritic spine morphogenesis, with support from multicellular development and transcriptional regulation during development. Although there are a few broader or non-neural terms (e.g., ossification, lipid signaling), the strongest signals point to neural development and synapse formation as the core theme. Confidence: Medium","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0043087","count":2}]},{"hash":"556355263355933333","title":"Cardiac conduction and heart development","description":"The top GO terms are dominated by heart-related processes\u2014SA node and Purkinje signaling, outflow tract morphogenesis, and regulation of cardiac hypertrophy\u2014pointing to a shared role in cardiac development and electrical conduction. While a few terms touch on general cellular processes (nuclear import, mRNA transport), the strongest theme across the cluster is cardiac structure and function, justifying a label focused on heart development and conduction.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903244","count":5},{"id":"GO:0006607","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0007602","count":4}]},{"hash":"1500319056796905305","title":"Unknown","description":"The top GO terms are highly diverse and span metal stress response (cadmium), innate immune signaling, virus defense regulation, photosynthesis, cell-cycle transitions, and development. With only one edge and several obsolete terms, plus proteins re-added by ReCIPE, there isn\u2019t a coherent shared function to name a specific cluster; it likely reflects noisy or artifact clustering.","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071276","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0050689","count":3},{"id":"GO:0006478","count":3},{"id":"GO:0043278","count":3}]},{"hash":"1343951822905855128","title":"Developmental Epigenetic Regulation and Ubiquitination","description":"The cluster\u2019s GO terms point to developmental processes (brain and lens development) alongside core epigenetic regulation (imprinting, histone methylation) and post-translational control via ubiquitin pathways (K11-linked ubiquitination, ubiquitin-dependent proteolysis) plus signaling and ribosome-related processes. This suggests a cohesive theme of development governed by epigenetic marks and protein turnover, with supplementary roles in cell division and stress response. Confidence: Medium","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0006349","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0061087","count":4},{"id":"GO:0071902","count":4}]},{"hash":"672424836457025122","title":"ER Stress, Protein Folding, and Redox Homeostasis","description":"The cluster is dominated by GO terms related to the endoplasmic reticulum (ER) stress response, including protein folding in the ER, chaperone-assisted refolding, and the unfolded protein response, plus translation initiation in response to ER stress. Redox-related terms (cellular oxidant detoxification and response to hydrogen peroxide) suggest concurrent management of oxidative stress linked to ER function. Together, these indicate a cohesive role in ER-associated protein folding and stress mitigation, with redox balance as a supporting aspect. Some unrelated terms (e.g., cytokinin signaling, morphine response) may reflect broader stress signaling cross-talk but do not override the core ER-focused theme.","confidence":"High","size":29,"edges":128,"triangles":268,"max_degree":22,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0045454","count":14},{"id":"GO:0006986","count":12},{"id":"GO:0070389","count":11},{"id":"GO:0036494","count":11},{"id":"GO:0034975","count":11}]},{"hash":"336495339776663043","title":"Gene Regulation and Chromatin Modification","description":"The top GO terms cluster around DNA-templated transcription and its regulation, plus histone methylation marks (H3K4 and H3K27), suggesting these proteins are primarily involved in transcription control and epigenetic regulation. Some heart development and receptor recycling terms appear as secondary annotations, but these are less central to the core theme. Overall, the cluster seems best described by transcriptional regulation and chromatin modification.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0098532","count":2}]},{"hash":"1250761649439977541","title":"Carbon-source-regulated transcription","description":"This cluster is dominated by DNA-templated transcription and transcriptional regulation from RNA polymerase II promoter in response to carbon sources, including nonfermentable carbon sources and oleic acid, suggesting a nutrient-responsive transcription regulatory module. While some metabolic biosynthesis terms appear (maltose, aflatoxin, amino acid biosynthesis), the overarching theme is transcriptional control in response to carbon/nutrient signals; the lack of network edges supports grouping by shared function rather than direct interactions.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0000023","count":3},{"id":"GO:0035969","count":2},{"id":"GO:1904741","count":2},{"id":"GO:0061429","count":2}]},{"hash":"1569086047073423565","title":"Unknown","description":"This cluster mixes diverse GO terms\u2014from sodium ion transport to histone modification, ubiquitin recycling, and mRNA processing, plus behavioral responses like ethanol exposure and righting reflex\u2014without a unifying function. The network is sparse (Edges: 1, Triangles: 0, Max Degree: 1) and several terms are obsolete, making a cohesive biological theme unlikely. Therefore, there is no clear, interpretable cluster function to name.","confidence":"","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":2},{"id":"GO:0035616","count":1},{"id":"GO:0035192","count":1},{"id":"GO:0010995","count":1},{"id":"GO:0000289","count":1}]},{"hash":"949686390697842220","title":"Proteostasis and ubiquitin-mediated degradation","description":"The strongest signals are ubiquitin-related processes (K11-linked ubiquitination, ER-associated ubiquitin-dependent protein catabolic process) and the unfolded protein response, pointing to protein quality control and degradation pathways. While some terms touch on cell cycle or development, the dominant theme across terms is proteostasis via ubiquitin-mediated proteolysis.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0007091","count":12},{"id":"GO:1903071","count":12},{"id":"GO:0051348","count":12},{"id":"GO:0070979","count":12},{"id":"GO:0006986","count":12}]},{"hash":"398767269207624844","title":"Neuronal vesicle trafficking and cell division","description":"Top GO terms indicate brain development, synaptic vesicle exocytosis regulation, ER-Golgi and Golgi-ER transport, and mitotic spindle assembly/cell division, along with GTPase activity regulation. The common thread appears to be vesicle trafficking and cytoskeletal dynamics, with relevance to neural development and cell division, suggesting a cluster of proteins involved in neuronal vesicle transport and related cytoskeletal processes.","confidence":"Medium","size":29,"edges":64,"triangles":7,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:2000300","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0090307","count":5},{"id":"GO:0006888","count":5}]},{"hash":"1916079898758753365","title":"Cranial neural crest development and migration","description":"The top GO terms cluster around cranial development, neural crest\u2013derived structures (cranial ganglia, cranial skeleton), dorsal-identity patterning, and Wnt signaling, all characteristic of migratory cranial neural crest cells. Frequent cell migration and GTPase regulation support crest cell motility, with NLS-bearing protein import reflecting transcriptional control. A single outlier term (Cvt vesicle assembly) may be noise.","confidence":"Medium","size":29,"edges":63,"triangles":39,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0016477","count":9},{"id":"GO:0061550","count":8},{"id":"GO:0044336","count":8}]},{"hash":"426683762070529383","title":"Cerebellar development and signaling regulation","description":"The most represented terms point to cerebellar cortex formation, Bergmann glial differentiation, and regulation of axon regeneration, indicating neural development in the cerebellum. Supporting terms involve signaling pathway regulation (insulin receptor signaling, ERK cascade) and cell-cycle control (CDK activity), suggesting coordinated developmental signaling. An immune signaling term (T cell receptor signaling) may reflect shared signaling components rather than a primary function. Overall, the cluster centers on cerebellar development with signaling regulation.","confidence":"Medium","size":29,"edges":174,"triangles":721,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008285","count":22},{"id":"GO:0050852","count":22},{"id":"GO:0048679","count":21},{"id":"GO:0008286","count":21},{"id":"GO:0060020","count":21}]},{"hash":"1060212100999476470","title":"DNA-Templated Transcription Regulators","description":"The top GO terms center on DNA-templated transcription and transcription regulation (GO:0006351; GO:0000122; GO:0043388; GO:0045087), plus positive regulation of DNA binding. This points to proteins that bind DNA and modulate transcription, i.e., transcription factors or regulators. While some terms touch on innate immunity and differentiation, the primary signal is transcriptional control. ","confidence":"Medium","size":29,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0055114","count":5},{"id":"GO:0090090","count":3},{"id":"GO:0097350","count":3},{"id":"GO:0045087","count":3}]},{"hash":"2233085430358891942","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":396,"triangles":3406,"max_degree":28,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":29},{"id":"GO:1905869","count":29},{"id":"GO:0035330","count":29},{"id":"GO:0042068","count":29},{"id":"GO:0006547","count":29}]},{"hash":"2050144652164684534","title":"Oxidative Stress Response and Redox Homeostasis","description":"This cluster centers on redox biology, with GO terms for oxidation-reduction processes, cell redox homeostasis, and cellular response to oxidative stress. Additional links to endoplasmic reticulum stress and redox-regulated activities (e.g., deglutathionylation) support a cohesive theme of managing oxidative stress; transcription-related terms suggest broader regulatory connections, while a viral process term is less central. Confidence: Medium","confidence":"","size":29,"edges":11,"triangles":0,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0045454","count":4},{"id":"GO:0016032","count":4},{"id":"GO:0006662","count":4}]},{"hash":"1470439353449819945","title":"Telomere Maintenance Regulation","description":"The top GO terms are dominated by telomere-related processes (maintenance, capping, telomerase regulation, and telomeric DNA binding), with some ADP-ribosylation (PARP) annotations and a peripheral spindle assembly term, suggesting a broader chromatin/mitotic context but a clear telomere maintenance theme overall.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":9},{"id":"GO:0032212","count":6},{"id":"GO:1904355","count":6},{"id":"GO:0070213","count":6},{"id":"GO:0051225","count":6}]},{"hash":"1107080693655624207","title":"Ubiquitin-dependent innate immune signaling","description":"This cluster centers on ubiquitination processes (protein ubiquitination, ubiquitin-dependent catabolism, autoubiquitination) alongside innate immune functions (defense against virus, innate immune response) and signaling pathways (NOD2 signaling, JNK regulation), suggesting a module of ubiquitin-regulated immune signaling components influencing NF-kB/MAPK pathways.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0016567","count":6},{"id":"GO:0032088","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":5}]},{"hash":"333162230419434144","title":"Mitotic DNA replication initiation machinery","description":"The cluster's GO terms are dominated by DNA replication, mitotic DNA replication, initiation, and GINS complex assembly, pointing to a cohesive replication machinery during mitosis. A couple of non-replication terms (Wnt signaling, cell adhesion) appear but are much less represented and do not define the cluster.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0000727","count":1},{"id":"GO:1902977","count":1}]},{"hash":"2280846838305936812","title":"Unknown","description":"The top GO terms span viral processes, host cell entry, protein oligomerization (homotetramer and heterooligomer), ubiquitin recycling, and mitochondrial respiration. This mix lacks a single unified function or pathway, so there isn't a coherent label beyond Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0032461","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0010992","count":2}]},{"hash":"1901930102357932117","title":"Cell wall remodeling and sporulation","description":"The cluster\u2019s top GO terms center on cell wall dynamics (organization, macromolecule catabolic processes, peptidoglycan biosynthesis), plus chitin-related responses and sporulation. Together these point to processes involving remodeling of the cell envelope and formation of spores, making a label focused on cell wall remodeling and spore formation appropriate. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0030435","count":2},{"id":"GO:1902083","count":2}]},{"hash":"1569781941174708328","title":"Microtubule Transport & Neural Development","description":"Top GO terms cluster around cytoskeleton dynamics and intracellular transport along microtubules (e.g., regulation of GTPase activity, intracellular and microtubule-based transport), with themes of neuron projection morphogenesis and nervous system development. This points to a cohesive module of microtubule-mediated transport and cytoskeleton organization linked to neural development, justifying the label. ","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0075521","count":1},{"id":"GO:0019060","count":1},{"id":"GO:0007286","count":1}]},{"hash":"2167510759545093921","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0035234","count":3},{"id":"GO:0006508","count":3},{"id":"GO:1904924","count":3},{"id":"GO:0030163","count":3},{"id":"GO:0035023","count":2}]},{"hash":"1136368219523090702","title":"RNA Pol II Transcription Regulation & Cell Cycle","description":"The proteins in this cluster are enriched for GO terms related to DNA-templated transcription and regulation by RNA polymerase II, including both positive and negative regulation. A couple of terms point to cell division/mitotic cell cycle, suggesting the cluster comprises transcription regulators that may influence the cell cycle. Overall, the dominant theme is transcriptional regulation by RNA Pol II with some cell-cycle connections.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0000122","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1902499","count":2}]},{"hash":"1967689496377078337","title":"Mitotic spindle regulation and chromatid segregation","description":"GO terms in the cluster center on mitosis: spindle-kinetochore attachments, regulation of sister chromatid biorientation, mitotic checkpoints, and septation/cytokinesis signaling. A minority of terms touch transcription regulation or stress response, but the primary signal is mitotic control and chromosome segregation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0044878","count":1},{"id":"GO:1990598","count":1},{"id":"GO:1902425","count":1},{"id":"GO:0031572","count":1}]},{"hash":"1793488824303719120","title":"Developmental signaling and cytoskeletal dynamics","description":"This cluster centers on broad developmental processes across multiple tissues (spinal cord, hair follicle, placenta, embryonic development) with accompanying signaling and transcription activity (e.g., TGF-beta stimulus, DNA-templated transcription). In addition, cytoskeletal-related terms (microtubule severing, spindle orientation) point to cellular organization essential for development. The mixture of development-associated terms with signaling and cytoskeletal functions suggests a general developmental program rather than a single tissue-specific function.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:0048820","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0071560","count":2}]},{"hash":"387223742467543942","title":"Cardiometabolic Hormone Signaling","description":"This cluster is best described by cardiometabolic regulation: several terms point to heart-related signaling (cardiac muscle hypertrophy, cardiac muscle cell action potential) and hormonal/metabolic processes (aldosterone biosynthesis, diet-induced thermogenesis), suggesting integration of hormonal signals with cardiovascular function. Other terms (skin and multicellular development, pain perception, protein oligomerization, GPCR signaling) are broader or less central to this core theme, but do not override the main cardiometabolic motif.","confidence":"Medium","size":28,"edges":33,"triangles":22,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":9},{"id":"GO:0043588","count":8},{"id":"GO:0019233","count":8},{"id":"GO:0051260","count":8},{"id":"GO:1903244","count":7}]},{"hash":"1375346093328764808","title":"Oxidative Stress Response and Redox Homeostasis","description":"The cluster is dominated by GO terms tied to redox balance and oxidative defense, including cellular redox homeostasis, cellular oxidant detoxification, cellular response to oxidative stress, and protein deglutathionylation. These repeatedly point to antioxidant mechanisms and redox regulation as the central theme. Some other terms (methylamine metabolism, deoxyribonucleotide biosynthesis, calcium-release channel regulation, and neural crest-related heart development) are more peripheral to this core theme, but do not overwhelm the redox signal. Confidence is High.","confidence":"","size":28,"edges":47,"triangles":18,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0030416","count":3},{"id":"GO:0022417","count":3},{"id":"GO:0060315","count":3}]},{"hash":"86541348027873203","title":"Cell cycle and DNA replication","description":"The cluster shows strong representation for DNA replication, meiotic cell cycle, and kinetochore localization, along with growth-related regulation of cell size, which together point to core cell division machinery. There are a few outlier terms (e.g., response to cocaine, placenta development) that likely reflect broader or non-specific annotations, but the dominant theme across the top terms is cell cycle progression and DNA replication.","confidence":"Medium","size":28,"edges":33,"triangles":6,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":13},{"id":"GO:0006260","count":12},{"id":"GO:0006006","count":12},{"id":"GO:0001890","count":12},{"id":"GO:0006935","count":12}]},{"hash":"398860948849928638","title":"Synaptic signaling and cardiac muscle regulation","description":"The terms cluster around neuronal signaling and synaptic plasticity (long-term potentiation, regulation of synaptic vesicle exocytosis, calcium transport) and cardiac muscle function (contraction, hypertrophy in response to stress), with transcriptional regulation and hypoxia responses reflecting stress adaptation.","confidence":"Medium","size":28,"edges":13,"triangles":2,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0070588","count":3},{"id":"GO:0045944","count":3},{"id":"GO:2001015","count":3}]},{"hash":"1692880702696968563","title":"Ribosome Biogenesis and rRNA Processing","description":"This cluster is enriched for rRNA maturation (SSU/LSU/5.8S) and ribosomal large subunit biogenesis, with supporting signals from DNA replication and transcription-coupled repair terms. The dominant theme is ribosome assembly and RNA maturation, suggesting a core role in ribosome production, while developmental terms may reflect proliferative contexts. Overall, ribosome biogenesis and rRNA processing best explain the shared functions among these proteins.","confidence":"High","size":28,"edges":61,"triangles":52,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0048701","count":5},{"id":"GO:0032436","count":5},{"id":"GO:0000463","count":4}]},{"hash":"458302209965520635","title":"Unknown","description":"The top GO terms cover a wildly diverse set of processes (telomere maintenance, pH response, T cell proliferation, mitotic arrest, axon guidance, caveolin-mediated endocytosis, imprinting regulation, meiotic spindle attachment, NK T cell differentiation, and vaginal development), with no clear, shared biological function tying the cluster together. This makes it inappropriate to assign a coherent, specific label beyond Unknown.","confidence":"","size":28,"edges":199,"triangles":576,"max_degree":25,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":28},{"id":"GO:0071469","count":28},{"id":"GO:0046641","count":28},{"id":"GO:0000751","count":28},{"id":"GO:0030517","count":28}]},{"hash":"703957513261038829","title":"DNA replication and repair machinery","description":"The top GO terms cluster around DNA replication (replication, primer synthesis, DNA unwinding, topological changes) and DNA repair (nucleotide-excision repair, SOS response), indicating proteins involved in genome maintenance. There is a minor signal for RNA surveillance (nonsense-mediated decay) and a developmental term (hair cell differentiation) that are less central, but do not override the predominant theme of replication and repair. Overall, this cluster most coherently reflects components of DNA replication and repair machinery.","confidence":"High","size":28,"edges":178,"triangles":641,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000184","count":13},{"id":"GO:0006268","count":12},{"id":"GO:0009432","count":12},{"id":"GO:0006306","count":11},{"id":"GO:0006260","count":11}]},{"hash":"921754860290675392","title":"Zinc Transport and Homeostasis in Development","description":"Dominated by zinc transport/homeostasis terms (zinc import, intracellular zinc homeostasis, detoxification) with two developmental terms (inner ear morphogenesis, limb development) suggesting zinc-related processes during organ/tissue development.","confidence":"Medium","size":28,"edges":70,"triangles":57,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0042472","count":2},{"id":"GO:0006831","count":2},{"id":"GO:0060173","count":2},{"id":"GO:0044749","count":2},{"id":"GO:1903615","count":2}]},{"hash":"2146403850934775960","title":"Unknown","description":"The top terms span brassinosteroid response, transcription regulation, vacuolar protein processing, light detection, xenobiotic response, and telomerase assembly, with no single shared function tying the 28 proteins together. The absence of meaningful edges further suggests heterogeneity, so a specific label cannot be justified.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009741","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006624","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0033160","count":1}]},{"hash":"798268484323322173","title":"Cell Cycle and Transcription Regulation","description":"Enriched for DNA-templated transcription and mitotic cell cycle/proliferation terms, with supporting signaling (kinase, GTPase regulation) and chromatin-related processes, indicating a cohesive module of transcriptional control coupled to cell-cycle progression and proliferation signals.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0071456","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008284","count":2}]},{"hash":"1781593581630337782","title":"Unknown","description":"The Top Terms span immune defense, neural development, transcription, and cell-cycle processes with no clear, unified function tying the proteins together. Several terms are obsolete, and there are no edges connecting members, suggesting a heterogeneous set rather than a coherent pathway or function. ","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050830","count":13},{"id":"GO:0022038","count":11},{"id":"GO:0014068","count":11},{"id":"GO:0006349","count":11},{"id":"GO:0001843","count":11}]},{"hash":"2142887508268835492","title":"Proteoglycan Metabolism and ECM Development","description":"The terms are dominated by proteoglycan biosynthesis/metabolic processes (heparan sulfate, dermatan sulfate) with supporting developmental signals such as chondrocyte development and ureteric bud formation, pointing to extracellular matrix proteoglycans and related development. A few unrelated terms (e.g., maltose transport, transcription regulation) appear, but the core pattern aligns with ECM proteoglycan metabolism and associated development.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0030202","count":1},{"id":"GO:0015014","count":1},{"id":"GO:0030208","count":1},{"id":"GO:0015768","count":1}]},{"hash":"960877058973974360","title":"Actin-driven cell migration and epithelial polarity","description":"The strongest recurring terms are establishment of epithelial cell polarity, cell migration, and actin filament bundle assembly, which together point to proteins coordinating actin cytoskeleton remodeling to promote movement and polarity in epithelial contexts. Some other terms (telomere maintenance, dendrite development, cytokine regulation) are less central and may reflect broader roles of individual proteins.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":8},{"id":"GO:0016477","count":8},{"id":"GO:0051017","count":8},{"id":"GO:0032212","count":7},{"id":"GO:0021707","count":7}]},{"hash":"1024853779324698273","title":"Unknown","description":"The top GO terms show a mix of telomere maintenance, cytoskeletal/mitotic assembly, RNA processing, ubiquitination, signaling, and neuronal differentiation, with no single unifying function. Several terms are broad or obsolete, and there are no obvious shared pathways connecting all members, so a cohesive functional label is not clear.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0051225","count":4},{"id":"GO:0006397","count":4},{"id":"GO:0090501","count":4}]},{"hash":"1428673664100547631","title":"TLR-driven antiviral innate immune signaling","description":"The top GO terms consistently point to innate immunity and antiviral responses: defense response to virus, innate immune response, Toll-like receptor signaling pathway (TLR8), interferon and IL-18 production, and inflammatory regulation. Despite no edges, the cohesive theme centers on Toll-like receptor\u2013mediated antiviral signaling, making this a concise, representative label.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":3},{"id":"GO:0045842","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0006469","count":2}]},{"hash":"1772847067962469845","title":"Ubiquitin-Dependent Stress and Innate Immune Signaling","description":"This cluster centers on ubiquitin-dependent protein turnover and innate immune pathways (NOD2 signaling; innate immune response), with additional cross-talk to signaling pathways (Wnt) and stress responses (mechanical stimuli, metal ion response, pinocytosis). The common thread is regulation of protein turnover and signaling under stress and immune contexts, suggesting a coherent theme of ubiquitin-mediated regulation linked to immune and stress-responsive signaling.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0016055","count":6},{"id":"GO:0032088","count":6},{"id":"GO:0000083","count":6},{"id":"GO:0071260","count":6}]},{"hash":"253142423471344163","title":"Signaling and Cytoskeletal Regulation","description":"The cluster includes proteins linked to multiple signaling pathways (Wnt, androgen receptor, insulin secretion) and cytoskeletal/architectural processes (myosin II assembly, cell polarity), with some roles in morphogenesis and vesicle signaling (Rab). Although the terms span diverse pathways, they collectively emphasize regulation of signaling and cell structure, suggesting a cohesive theme around how cells coordinate signals with their architecture.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0030521","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0035774","count":2},{"id":"GO:0032482","count":1}]},{"hash":"721784277973291712","title":"Fungal carbohydrate catabolism and cell wall remodeling","description":"The cluster shows enrichment for carbohydrate catabolic processes (xylan, cellulose, mannan) and for fungal-type cell wall disassembly along with biofilm formation, suggesting a theme of fungal polysaccharide degradation and cell-wall remodeling during growth or conjugation. Some GO terms (prostate gland development, male sex differentiation, steroid hormone receptor complex assembly) appear unrelated and may reflect annotation noise, but the dominant signals point to fungal metabolism and cell-wall dynamics.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0045493","count":3},{"id":"GO:0030850","count":3},{"id":"GO:0046661","count":3},{"id":"GO:0006463","count":3}]},{"hash":"1362391657269147094","title":"Plant light-sensing and chloroplast signaling","description":"The top GO terms cluster around chloroplast function and light sensing (phytochromobilin biosynthesis, chloroplast-nucleus signaling, photoinhibition), with some unrelated lipid/metabolic terms indicating noise; the dominant theme points to plant light response and pigment biosynthesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":2},{"id":"GO:0043085","count":2},{"id":"GO:0071432","count":2},{"id":"GO:0010024","count":1},{"id":"GO:0010019","count":1}]},{"hash":"817622678973220838","title":"Chromatin modification and transcription regulation","description":"This cluster features histone demethylation terms (H3-K4 and H3-K36) and regulation of transcription by RNA polymerase II, pointing to epigenetic control of gene expression as the core theme. Other terms (e.g., differentiation, metabolism) may reflect broader roles, but the chromatin/transcription connection is the most coherent link across the top terms.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0060997","count":3},{"id":"GO:0030961","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0045668","count":2}]},{"hash":"1909462542778882611","title":"Thermo-Mechanical Sensory Perception","description":"The dominant GO terms point to detection of mechanical stimuli (touch and pain) and thermosensation (heat/cold), including thermoception and responses related to capsazepine. Although a few terms (vasopressin secretion, chemokine production) are less related, the core cluster appears focused on sensory signaling pathways involving temperature and mechanical stimulus detection.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":5},{"id":"GO:0098914","count":5},{"id":"GO:0071651","count":5},{"id":"GO:0030103","count":5},{"id":"GO:0050966","count":5}]},{"hash":"1637275352684056290","title":"Phosphorylation Regulation and Stress Response","description":"This cluster shows a clear emphasis on control of phosphorylation, with terms for negative regulation of protein kinase activity and protein dephosphorylation, pointing to signaling regulation. It also includes stress- and development-related terms (response to X-ray, glucocorticoid, redox homeostasis, and G2/M cell cycle transition), suggesting a broader theme of signaling modulation under stress. A few terms (heart development, sensory perception of sound) may be incidental given the small, diverse set. Overall, the label reflects the dominant phosphorylation-centered signaling and stress-response signals.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0010165","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0007605","count":2}]},{"hash":"1962557423220886581","title":"ECM remodeling and kidney development","description":"The cluster\u2019s terms center on extracellular matrix (collagen fibril organization, collagen catabolism) and kidney morphogenesis (glomerular basement membrane development, metanephric mesenchymal cell migration). These points suggest a shared theme of ECM remodeling tied to kidney development, though a few terms (e.g., mitotic cycle, ossification, aldosterone regulation) are more peripheral, making the overall connection plausible but not perfect. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0001957","count":2},{"id":"GO:0045650","count":2},{"id":"GO:2000860","count":2}]},{"hash":"1711442259537695434","title":"Potassium Transport and Membrane Potential Homeostasis","description":"This cluster is dominated by GO terms describing potassium ion homeostasis, transmembrane transport, and membrane potential regulation, including import/export and stabilization/repolarization in cardiac cells. The co-occurrence of sensory touch response and cellular responses to signaling compounds (e.g., caffeine) suggests these proteins participate in modulating excitability and signaling through potassium dynamics. Overall, the proteins appear to coordinate potassium handling with maintaining resting and active membrane potentials. ","confidence":"High","size":27,"edges":105,"triangles":77,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":7},{"id":"GO:0097623","count":5},{"id":"GO:0030322","count":5},{"id":"GO:0060075","count":5},{"id":"GO:0050976","count":5}]},{"hash":"219880928137039506","title":"Presynaptic vesicle trafficking and autophagy","description":"The top GO terms cluster around synaptic vesicle priming, docking, and fusion, along with endomembrane organization (ER-Golgi), endosome transport, Golgi ribbon formation, and autophagosome maturation. This combination points to a cohesive role in vesicle trafficking at the presynaptic terminal and related autophagic/endolysosomal processes.","confidence":"High","size":27,"edges":28,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0097352","count":2},{"id":"GO:0045022","count":2},{"id":"GO:0010807","count":2},{"id":"GO:0097111","count":2},{"id":"GO:0006675","count":2}]},{"hash":"293842803459752382","title":"Centrosome and Cilium Biogenesis","description":"The top GO terms point to centriole replication, various aspects of cilium assembly (motile and non-motile), centrosome separation, astral microtubule nucleation, and microtubule polymerization, along with spindle pole body duplication and Hedgehog signaling via Smoothened. Together these terms indicate a coherent role in centrosome/cilium biogenesis and microtubule organization, supporting a unified label for this cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007099","count":1},{"id":"GO:0044458","count":1},{"id":"GO:1905515","count":1},{"id":"GO:0051299","count":1},{"id":"GO:0030954","count":1}]},{"hash":"1434492734090885129","title":"Mitochondrial metabolite transport","description":"This cluster centers on transport of various metabolites across the mitochondrial membrane (shuttles, cofactors, ions, nucleotides) and related membrane permeability regulation, with an accompanying oxidative stress response. The common theme is mitochondrial transmembrane transport of metabolites.","confidence":"High","size":27,"edges":17,"triangles":0,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0043490","count":3},{"id":"GO:1990616","count":3},{"id":"GO:1990544","count":3},{"id":"GO:0035349","count":3},{"id":"GO:0035435","count":3}]},{"hash":"1435501044522894136","title":"Stimulus-Driven Transcription Regulation","description":"The terms are dominated by RNA polymerase II\u2013driven transcription and its regulation in response to environmental and metabolic cues (lipid signals, carbon sources, and related metabolites), with a few terms tied to metabolism and immune cell differentiation. This suggests the proteins are enriched in transcriptional regulators that adjust gene expression based on nutrients and stimuli.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0032496","count":4},{"id":"GO:0046294","count":3},{"id":"GO:0019608","count":3},{"id":"GO:0030851","count":3}]},{"hash":"349624625032871728","title":"Ribosome Biogenesis and Ubiquitin-Proteasome Regulation","description":"The cluster is marked by strong signals for ribosome biogenesis and ribosomal subunit biogenesis, alongside multiple ubiquitin-related processes (autoubiquitination, K48-linked ubiquitination, and ubiquitin-dependent protein catabolic process including ERAD). These together suggest a functional link between ribosome assembly and ubiquitin\u2011mediated proteostasis. Additional terms related to TNF signaling, TGF-\u03b2 response, and skeletal muscle differentiation may reflect broader regulatory or context-dependent roles, but the core theme remains ribosome biogenesis with protein quality control. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070936","count":2},{"id":"GO:0042787","count":2}]},{"hash":"1520682618019401247","title":"Inner ear hair cell development and synaptic signaling","description":"The top GO terms cluster around auditory hair cells and inner ear morphogenesis (stereocilium organization, cochlea morphogenesis) plus neuronal synaptic features (glutamate secretion, receptor localization to synapse, dendritic spine morphogenesis) and actin cytoskeleton organization. This suggests proteins coordinating hair cell structural differentiation and synaptic transmission, with some peripheral terms (e.g., renal transport) likely reflecting shared epithelial pathways. Confidence: High","confidence":"","size":27,"edges":9,"triangles":0,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060088","count":5},{"id":"GO:0060997","count":5},{"id":"GO:0014047","count":5},{"id":"GO:0090103","count":5},{"id":"GO:0019933","count":5}]},{"hash":"240505081494553887","title":"Mitotic Regulation and Protein Phosphorylation","description":"The cluster shows strong enrichment for mitotic cell cycle, cell division, APC/C-dependent catabolic process, and regulation of serine/threonine kinase activity and autophosphorylation, indicating mitosis is the central theme. A few terms touch on hypoxia response, GTPase regulation, mRNA transport, or lens differentiation, but these do not override the main pattern.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0071456","count":6},{"id":"GO:0031954","count":6},{"id":"GO:0051301","count":6}]},{"hash":"1559587262776211512","title":"Detoxification and lipid/xenobiotic catabolism","description":"This cluster shows a convergence on metabolic breakdown and detoxification: multiple terms point to oxidation-reduction and cellular oxidant detoxification, response to toxic substances, and various catabolic processes for lipids and small molecules. While some terms (like antibiotic biosynthetic process and regulation of endocannabinoid signaling) are peripheral, the dominant theme is metabolism and detoxification, supporting the chosen label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0019433","count":7},{"id":"GO:0009636","count":7},{"id":"GO:0046272","count":6}]},{"hash":"1969226902351800243","title":"Transcription Regulation and Redox Response","description":"The top GO terms point to transcriptional regulation (DNA-templated transcription; negative regulation of transcription by RNA polymerase II) and redox/oxidative stress processes (cell redox homeostasis; cellular oxidant detoxification; cellular response to oxidative stress). This suggests a cluster of proteins involved in coordinating transcription control with cellular redox/homeostasis, despite some obsolete terms and a viral process annotation that may reflect annotation artifacts rather than a cohesive function. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0006662","count":2},{"id":"GO:0055114","count":2}]},{"hash":"867871529263388553","title":"Apoptosis Signaling and Kinase Regulation","description":"The top terms point to regulation of apoptotic signaling (including extrinsic pathways) and processes involving kinases and GTPases, with ceramide metabolism and morphogenesis-linked apoptosis also appearing. While some terms are more distant (transcription by RNA Pol III, meiotic regulation), the recurring theme is signaling control that modulates apoptosis, consistent with a cohesive biological function for this cluster.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":2},{"id":"GO:0043547","count":2},{"id":"GO:1903538","count":1},{"id":"GO:0000188","count":1},{"id":"GO:0000060","count":1}]},{"hash":"1865207400712099747","title":"Synaptic vesicle trafficking and glutamatergic signaling","description":"This cluster\u2019s top GO terms center on intracellular protein transport, synaptic vesicle maturation and fusion, and glutamatergic synaptic transmission, pointing to roles in presynaptic vesicle dynamics and neurotransmitter release. Additional terms involving Rho signaling and cell motility suggest cytoskeletal regulation that facilitates vesicle movement. Some terms like myoblast fusion or cortical migration may reflect shared components in cell fusion/migration but do not outweigh the core theme of synaptic vesicle trafficking and signaling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":4},{"id":"GO:0035023","count":3},{"id":"GO:0016188","count":2},{"id":"GO:0099526","count":2},{"id":"GO:0031340","count":2}]},{"hash":"184254057616246100","title":"Cell Growth and Gene Expression Machinery","description":"The cluster contains GO terms centered on transcription (DNA-templated transcription), ribosome biogenesis, and protein oligomerization/tetramerization, along with cell division and regulatory signaling (GTPase activity, peptidyl-tyrosine phosphorylation). This points to a cohesive theme of cellular growth, protein synthesis, and proliferation rather than a single specialized pathway. Brain development appears in the list but seems less central to the shared molecular functions, so the label emphasizes core growth and expression processes.","confidence":"Medium","size":27,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0050731","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0043547","count":2}]},{"hash":"2172747102076439500","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":10,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0048016","count":2},{"id":"GO:0006306","count":1},{"id":"GO:0006301","count":1}]},{"hash":"873009586243208686","title":"Metabolic Signaling via Phosphorylation","description":"The cluster is enriched for serine/threonine phosphorylation and kinase regulation terms, with signaling pathways such as Wnt, adiponectin-activated, and activin receptor signaling, plus glucose response and feeding regulation, pointing to a cohesive role in phosphorylation-driven metabolic signaling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080163","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0009749","count":1},{"id":"GO:0002023","count":1},{"id":"GO:0018105","count":1}]},{"hash":"1504565149304448010","title":"Cholesterol and lipoprotein metabolism","description":"The cluster shows strong signals for cholesterol storage, cholesterol homeostasis, VLDL particle assembly, and regulation of plasma lipoprotein levels, pointing to lipid transport and cholesterol regulation as the core theme. Additional terms like macrophage foam cell differentiation and amyloid precursor protein biosynthetic regulation tie into lipid-associated processes, while N-palmitoylation and the smoothened (Hedgehog) pathway hint at related lipid-modification biology. Overall, the proteins are best described as involved in lipid and cholesterol metabolism and lipoprotein handling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042121","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0010878","count":1},{"id":"GO:0034379","count":1},{"id":"GO:0042986","count":1}]},{"hash":"49848038941906261","title":"Regulators of stress response and cell fate","description":"The top GO terms point to regulatory roles across diverse but connected areas: oxidative stress response (cellular response to hydroperoxide), regulation of necroptosis and apoptosis, innate immune signaling (regulation of TLR pathways), transcriptional control, ubiquitin-mediated regulation, and cell cycle control. Although the specific processes vary, the unifying theme is modulation of stress responses and cell fate decisions rather than a single enzymatic activity. This justifies a label centered on regulatory roles in stress and survival pathways.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071447","count":1},{"id":"GO:1902083","count":1},{"id":"GO:1903204","count":1},{"id":"GO:0060544","count":1},{"id":"GO:0034121","count":1}]},{"hash":"841690291127710390","title":"Intracellular signaling and immune regulation","description":"The top GO terms center on intracellular signal transduction and immune-related regulation (e.g., regulation of IL-12, NF-kappaB activity, chemokine production), suggesting a shared theme of signaling control and immune modulation. Some terms about telomere maintenance and neuronal development appear, but the strongest cohesive signal is regulatory signaling and immune processes. The cluster has no edges, indicating it is not a tightly connected module, so the label is reasonable but not highly specific.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0021707","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0071651","count":2}]},{"hash":"833579516029188168","title":"Transcription and translation regulation","description":"The top GO terms emphasize regulation of transcription by RNA Pol II, transcription-coupled repair, and mRNA surveillance, alongside regulation of translation initiation and preinitiation complex formation, as well as chromatin-related processes. This points to a set of proteins involved in controlling gene expression across transcriptional, post-transcriptional, and translational steps.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0071033","count":1},{"id":"GO:0000188","count":1},{"id":"GO:0090052","count":1},{"id":"GO:0032436","count":1}]},{"hash":"904652150416714397","title":"Dopaminergic neuron development and signaling","description":"These terms cluster around dopamine-related neuronal processes: cellular response to dopamine and positive regulation of dopamine receptor signaling, plus related neural activity indicators like regulation of postsynaptic potential and neuron maturation. Additional terms touch broader cellular processes (mitosis, ubiquitination, chromatin localization, endosome-Golgi transport) that may be ancillary. The dominant signal is dopaminergic neuron development and signaling, justifying the label with high confidence.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014041","count":2},{"id":"GO:1905279","count":2},{"id":"GO:0071287","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0016336","count":2}]},{"hash":"1347696676124980432","title":"Unknown","description":"The Top Terms are highly heterogeneous, including DNA-templated transcription, ribosomal subunit export, DNA repair, brain development, viral processes, and diverse metabolic reactions. There is no clear single function or cohesive theme connecting these terms, suggesting the cluster does not share a specific, interpretable common role. Therefore, the label Unknown with no confidence is most appropriate.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0007420","count":1},{"id":"GO:0006110","count":1},{"id":"GO:0016032","count":1}]},{"hash":"500699502342304156","title":"Stress-Responsive Transcription and Signaling","description":"This cluster centers on regulation of DNA-templated transcription and various stress/immune signaling responses (cellular response to xenobiotic stimuli, cocaine exposure, IL-4 and type II interferon signaling) along with related cytoskeletal and protein quality-control processes (Rho signaling, aggresome assembly). The mix suggests a broad stress- and transcription-focused functional theme rather than a single pathway.","confidence":"Medium","size":26,"edges":55,"triangles":3,"max_degree":13,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0035690","count":2},{"id":"GO:0006656","count":2},{"id":"GO:0042220","count":2}]},{"hash":"629835268091507148","title":"Mitochondrial Transport and Metabolic Regulation","description":"The top GO terms cluster around mitochondrial membrane transport (ATP, phosphate, CoA, Mg2+, deoxynucleotides), energy metabolism (malate\u2013aspartate shuttle), and redox/insulin-related signaling, with a note on necroptosis regulation. This suggests a cohesive theme of mitochondrial transport coupled to metabolism and stress response.","confidence":"High","size":26,"edges":49,"triangles":0,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060546","count":14},{"id":"GO:0032869","count":13},{"id":"GO:0043490","count":12},{"id":"GO:1990616","count":12},{"id":"GO:1990544","count":12}]},{"hash":"1017235885873385807","title":"Metabolism and Transcription Regulation","description":"The cluster combines core metabolic processes (glycolysis and TCA cycle) with transcription-related terms (DNA-templated transcription and its regulation) and signaling/stress responses (response to glucose, cAMP, xenobiotic stimuli, and hydrogen peroxide), suggesting a theme where metabolic status interfaces with gene expression and stress signaling.","confidence":"Medium","size":26,"edges":188,"triangles":830,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006096","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1042052215963216164","title":"Organelle Fission and Cell Cycle","description":"The clearest recurring themes among the top GO terms are organelle fission (peroxisome and mitochondrial membrane fission) and core cell cycle/division processes. This suggests the proteins may participate in shaping organelles while driving cell proliferation. Some terms relate to hormone signaling and development, and a couple of outliers (photosynthesis, obsolete mitochondrial genome maintenance) may reflect annotation noise or cross-species annotations. Overall, the dominant signal points to organelle dynamics linked to cell cycle, so this label is a reasonable high-level summary.","confidence":"Medium","size":26,"edges":25,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016559","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0061179","count":2}]},{"hash":"1894742525382694462","title":"Redox Homeostasis and Stress Response","description":"The cluster centers on redox balance and cellular stress responses: GO:0045454 redox homeostasis, GO:0034599 cellular response to oxidative stress, GO:0034976 ER stress response, and GO:0080058 protein deglutathionylation, indicating a cohesive theme of redox regulation and stress signaling. Additional terms suggest broader regulatory connections to transcription and immune modulation, but the core signal remains redox-associated stress response.","confidence":"High","size":26,"edges":58,"triangles":21,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0000122","count":6},{"id":"GO:2000483","count":5},{"id":"GO:0016032","count":5}]},{"hash":"937069568894105291","title":"Unknown","description":"The top GO terms mix chromatin remodeling, G2/M cell cycle progression, kinase activity regulation, phototransduction, axonogenesis, and stress/viral processes, with several obsolete terms. There is no single coherent biological process linking these terms, and the cluster has no edges, suggesting dispersed, unrelated functions. Therefore, a meaningful, specific label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0007602","count":2},{"id":"GO:0007409","count":2}]},{"hash":"1995023974751054330","title":"Transcription Regulation and Cellular Signaling","description":"This cluster centers on broad regulatory roles across multiple cellular processes, dominated by transcriptional regulation (DNA-templated transcription and related gene expression regulation) and various signaling/regulatory activities (cellular response to pH, T cell proliferation regulation, endocytosis, spindle attachment regulation, and other regulatory terms). The diversity suggests a functional theme of general regulation rather than a single pathway, so a label emphasizing transcriptional regulation and signaling best captures the common thread.","confidence":"Medium","size":26,"edges":7,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":23},{"id":"GO:0006935","count":23},{"id":"GO:0032212","count":22},{"id":"GO:0071469","count":22},{"id":"GO:0046641","count":22}]},{"hash":"622306962028450378","title":"Genome Integrity: Replication and Splicing","description":"The cluster combines DNA replication and repair terms with spliceosomal processing, and includes PARP-related modification and localization to double-strand breaks, indicating a module centered on genome maintenance and RNA processing, likely reflecting coordinated DNA damage response activities.","confidence":"High","size":26,"edges":12,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0006271","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000245","count":1},{"id":"GO:0000012","count":1}]},{"hash":"2070954837771016011","title":"Neural development and visual signaling","description":"This cluster is dominated by terms related to neural development (axonogenesis) and vision (visual perception, phototransduction), suggesting a focus on the neural/visual system, even though a few outlier terms (e.g., cuticle development, spindle-related processes) appear.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0007409","count":4},{"id":"GO:0007601","count":3},{"id":"GO:0007602","count":3}]},{"hash":"1955450815595240404","title":"Unknown","description":"The top GO terms span signaling regulation (negative regulation of kinase activity and dephosphorylation) alongside unrelated processes (heat response, visual perception/phototransduction, nuclear import, and various development terms in different tissues), with few connections among them. There is no clear, cohesive function tying all 26 proteins together, so a precise, interpretable label is not justifiable.","confidence":"","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0009408","count":4},{"id":"GO:0060316","count":4},{"id":"GO:0006607","count":4},{"id":"GO:0006470","count":4}]},{"hash":"1388664096516939097","title":"Pigment, vitamin, and lipid metabolism","description":"The cluster is enriched for a set of biosynthetic and metabolic processes spanning pigments (melanin biosynthesis), vitamins (retinol metabolism, phylloquinone catabolic), and lipids (3-keto-sphinganine and PHB biosynthesis), with additional signals for antibiotic biosynthesis and response. This pattern points to a metabolic theme centered on pigment and vitamin/lipid pathways and related secondary metabolism, rather than a single linear pathway. An outlier term (lung development) is present but does not undermine the core association. ","confidence":"Medium","size":26,"edges":157,"triangles":362,"max_degree":20,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":24},{"id":"GO:0042619","count":22},{"id":"GO:0042376","count":21},{"id":"GO:0030324","count":21},{"id":"GO:0046677","count":21}]},{"hash":"1691102173917107043","title":"Auditory synaptic plasticity and vocalization behavior","description":"The cluster centers on neuronal synaptic regulation: long-term synaptic depression, dendritic spine morphogenesis, and positive regulation of excitatory postsynaptic potential and synapse structural plasticity, alongside auditory-related terms like sensory perception of sound and auditory receptor cell stereocilium organization. The presence of retrograde nitric oxide signaling and protein dephosphorylation further supports a dynamic synaptic signaling theme. The inclusion of social and vocalization behavior terms suggests relevance to vocal communication in an auditory context. Overall, these proteins likely participate in activity-dependent synaptic remodeling in hearing and related vocalization behaviors.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0060292","count":14},{"id":"GO:0060997","count":14},{"id":"GO:2000463","count":14},{"id":"GO:0051835","count":14},{"id":"GO:0007605","count":14}]},{"hash":"3541948473624350","title":"Neural development and synaptic signaling","description":"The cluster shows a clear signal for neuron formation and function: axonogenesis, long-term synaptic potentiation, excitatory postsynaptic potential, and visual perception. There are also hints of broader developmental regulation (myoblast fusion, mitotic cell cycle, and a plant ABA signaling term) that may reflect multi-function proteins or cross-pathway annotations, but the dominant theme aligns with neural development and synaptic signaling.","confidence":"Medium","size":26,"edges":7,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007520","count":8},{"id":"GO:0009738","count":8},{"id":"GO:0043065","count":8},{"id":"GO:0060291","count":8},{"id":"GO:0007601","count":7}]},{"hash":"717997375197631541","title":"Unknown","description":"The top GO terms are highly diverse, covering signaling (cAMP/cGMP), ion transport, metabolism, immune regulation, olfactory perception, and cardiac growth, with no dominant function tying all proteins together. Because there is no coherent shared process and the network has no edges, a single, intuitive label cannot be assigned.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016525","count":3},{"id":"GO:0071321","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0045013","count":3}]},{"hash":"821573494443706354","title":"Endocannabinoid signaling and lipid metabolism","description":"The cluster\u2019s top GO terms are dominated by regulation of endocannabinoid signaling pathway and several lipid catabolic processes (phosphatidylserine, monoacylglycerol, triglyceride), pointing to a shared function in lipid signaling and turnover. The brain development term provides a plausible neural context, while other scattered terms (antibiotic biosynthetic, stilbene, uracil catabolic, and obsolete terms) are likely incidental. Therefore, a lipid signaling/metabolic theme best fits the majority of annotations.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":6},{"id":"GO:0006660","count":6},{"id":"GO:0052651","count":6},{"id":"GO:0019433","count":6},{"id":"GO:0055114","count":5}]},{"hash":"427334260581351326","title":"Bacterial cell wall polysaccharide synthesis and glycosylation","description":"The top GO terms point to cell wall construction and related sugar-modification pathways: teichoic acid biosynthesis, UDP-glucose\u2013dependent polysaccharide synthesis, various O-linked glycosylation processes, and other polysaccharide biosynthesis activities. This pattern suggests proteins involved in assembling and glycosylating cell wall polymers typical of Gram-positive bacteria, with some annotations reflecting broader polysaccharide biosynthesis. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0008033","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0018243","count":2}]},{"hash":"1383486976582486295","title":"Steroid signaling and reproductive development","description":"The top GO terms are dominated by prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly, pointing to a cluster enriched for steroid signaling pathways driving male reproductive development. While other terms (cell division, cytokinin/GA signaling, innate immunity) appear, they seem peripheral or represent annotation noise, so the strongest thematic signal is steroid-mediated development, with some associated cell cycle regulation during development.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030850","count":8},{"id":"GO:0046661","count":8},{"id":"GO:0006463","count":8},{"id":"GO:0051301","count":7},{"id":"GO:0045842","count":6}]},{"hash":"853559202715478807","title":"RNA and Protein Methyltransferases","description":"The prominent GO terms point to methyltransferase activity across RNA (guanine-N7, tRNA, rRNA) and protein (peptidyl-lysine dimethylation). Additional terms reflect linked biosynthetic and xenobiotic-response processes often seen with methyltransferases in microbes. The clearest shared function is RNA and protein methylation, hence the name.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0036265","count":6},{"id":"GO:0030488","count":6},{"id":"GO:0070476","count":6},{"id":"GO:0018027","count":6}]},{"hash":"472162840627979562","title":"NOD2-NF-kappaB Innate Immune Signaling","description":"The top GO terms emphasize NOD2 signaling, NF-kappaB regulation, and IL-1 beta production, plus general intracellular signaling and transcriptional control, suggesting a cohesive theme of innate immune sensing and cytokine response. Some terms like cornea development and hypoxia detection may reflect broader functional contexts or annotation breadth.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0035556","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0050718","count":3}]},{"hash":"1876362486687155685","title":"Regulatory Signaling and Development","description":"The proteins show broad regulatory roles across signaling and developmental processes, including modulation of cardiac action potential regulation, muscle stretch response, neural differentiation, and immune signaling, plus telomere maintenance regulation. This combination points to a general regulatory function rather than a single specific pathway, so the label reflects the common theme of regulation in diverse contexts.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":21},{"id":"GO:0035994","count":21},{"id":"GO:0032212","count":20},{"id":"GO:0021707","count":20},{"id":"GO:1904355","count":20}]},{"hash":"953022556636370536","title":"Auditory hair cell development and synaptic signaling","description":"In this cluster, the dominant GO terms point to cochlea morphogenesis, stereocilium organization in auditory receptor cells, dendritic spine morphogenesis, glutamate secretion, and synaptic regulation (long-term depression and NO-mediated retrograde signaling). Together, these indicate proteins involved in the development and maturation of the auditory system and its synaptic connections, with Rho signaling likely supporting cytoskeletal remodeling in hair cells and synapses. A stray term on opsonization is less central. Overall, the theme is auditory system development and synaptic function.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0035023","count":14},{"id":"GO:0060088","count":13},{"id":"GO:0098924","count":13},{"id":"GO:0006470","count":13},{"id":"GO:0035640","count":13}]},{"hash":"223104500563694113","title":"DNA-Templated Transcription Regulation","description":"The Top Terms are dominated by DNA-templated transcription (GO:0006351) and regulation of DNA-templated transcription (GO:0006355), indicating the proteins mainly function as transcriptional regulators. Development-related terms (brain, uterus, multicellular organism development) likely reflect downstream roles of transcriptional control in development. Despite no edges shown, the GO enrichment strongly ties the cluster to transcription regulation.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":15},{"id":"GO:0006355","count":13},{"id":"GO:0010735","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0060065","count":2}]},{"hash":"1492211358040634742","title":"Glutamatergic synaptic vesicle trafficking","description":"The cluster\u2019s top GO terms are dominated by glutamatergic synaptic activity and vesicle dynamics (synaptic transmission, glutamatergic; synaptic vesicle maturation; positive regulation of vesicle fusion; presynapse to nucleus signaling). These point to a common function in glutamatergic synapse vesicle cycling and signaling, with additional supporting terms related to intracellular transport and GTPase regulation that fit the trafficking machinery. Some terms reflect broader or unrelated processes, but the strongest signal is neuronal vesicle trafficking at the synapse.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":3},{"id":"GO:0043087","count":3},{"id":"GO:0016188","count":2},{"id":"GO:0099526","count":2},{"id":"GO:0031340","count":2}]},{"hash":"961881662921917090","title":"Chromatin Regulation and Ubiquitin Signaling in Plant Immunity","description":"The top GO terms point to chromatin-level control of gene expression (nucleosome assembly, DNA-templated transcription, regulation of transcription) plus ubiquitin-centric signaling and protein turnover (K63-linked ubiquitination, ubiquitin-dependent sorting). The presence of innate immune response and secondary cell wall biogenesis terms suggests a plant defense/development nexus where chromatin state and ubiquitin pathways coordinate transcriptional responses. Overall, this cluster likely reflects chromatin-regulated transcriptional responses coupled with ubiquitin signaling in plant immunity and cell-wall related processes.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0006334","count":4},{"id":"GO:0030154","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0045087","count":3}]},{"hash":"277013059360156324","title":"Epigenetic Regulation in Development","description":"This cluster's top GO terms center on epigenetic control of gene expression (DNA methylation, histone catabolic process, epigenetic programming) and developmental processes (uterus morphogenesis, uterine gland development, embryonic cytokinesis, Purkinje cell maturation). The shared theme is regulation of gene expression via epigenetic mechanisms during development, justifying this label.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061038","count":1},{"id":"GO:0010426","count":1},{"id":"GO:0002674","count":1},{"id":"GO:0040029","count":1},{"id":"GO:0021691","count":1}]},{"hash":"1490691400217798326","title":"Gene Expression and Proteostasis","description":"The cluster centers on gene expression control (DNA-templated transcription, histone H3 acetylation) and protein turnover (polyubiquitination, SCF-proteasomal degradation), with supporting signals from mitotic spindle orientation and microtubule severing that connect to cell-cycle coordination. This combination suggests a cohesive theme of transcriptional regulation coupled with proteostasis during cell division.","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:0051013","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0035948","count":3}]},{"hash":"430785251595839229","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0046726","count":1},{"id":"GO:0006294","count":1},{"id":"GO:0016055","count":1}]},{"hash":"1303382473881304802","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning immune signaling (interleukin-1 response), viral processes, plant hormone response (abscisic acid), ERAD-related ubiquitin pathways, peroxisome protein import, translesion synthesis, RNA modification, cell division, and synapse assembly. With only a few terms supporting any coherent shared function and a sparse interaction pattern, there isn\u2019t a clear, unified theme tying these proteins together. Thus, Unknown with no confident label.","confidence":"","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071347","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0009737","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0016562","count":2}]},{"hash":"1152376101216801182","title":"Triglyceride Mobilization and Lipid Remodeling","description":"The top GO terms cluster around triglyceride mobilization, catabolic processes, and acyl-chain remodeling of triglycerides, along with phosphatidylethanolamine catabolism, indicating a lipid metabolism/remodeling theme. Extra terms point to regulatory and stress-related signaling (e.g., PKA activity, cadmium response), but the dominant signal is triglyceride/lipid metabolism.","confidence":"Medium","size":25,"edges":33,"triangles":1,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":2},{"id":"GO:0070208","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0006642","count":2},{"id":"GO:0019433","count":2}]},{"hash":"2241109804989678626","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009113","count":1},{"id":"GO:0006751","count":1},{"id":"GO:0052699","count":1},{"id":"GO:0006189","count":1},{"id":"GO:0052704","count":1}]},{"hash":"870395182717603480","title":"Growth control and neural development","description":"This cluster is enriched for growth-regulating pathways (Hippo signaling, positive regulation of Wnt signaling) and processes that restrain or coordinate proliferation (negative regulation of cell proliferation, CDK activity, apoptosis), indicating a core theme of growth control and cell cycle regulation. The presence of neural development terms (cerebellar cortex formation, regulation of axon regeneration) suggests additional emphasis on neural development and repair. Insulin signaling contributes to growth and metabolic control, while kinetochore localization points to mitotic coordination. Together, these terms portray proteins involved in coordinating growth signals, cell fate, and neural development.","confidence":"High","size":25,"edges":112,"triangles":247,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035329","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0060044","count":8},{"id":"GO:0045736","count":8},{"id":"GO:0048679","count":8}]},{"hash":"1686234301575337796","title":"TLR-mediated innate immune signaling and inflammation","description":"The GO terms cluster around innate immune recognition and response: Toll-like receptor signaling (including TLR8), cellular responses to lipopolysaccharide, positive regulation of inflammatory and interferon/IL-18 production, and antimicrobial peptide biosynthesis, with links to autophagy. These collectively point to a cohesive module of pathogen recognition and downstream inflammatory/antimicrobial defense.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071222","count":8},{"id":"GO:0006469","count":6},{"id":"GO:0032741","count":6},{"id":"GO:0034158","count":6},{"id":"GO:0050729","count":6}]},{"hash":"22791223636336929","title":"Mitochondrial Transport and Energy Metabolism","description":"Dominated by mitochondrial transport and energy-related functions (malate-aspartate shuttle, ATP transport, CoA, phosphate, nucleotide transport) with redox/membrane-regulation contexts.","confidence":"High","size":25,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":10},{"id":"GO:0000002","count":10},{"id":"GO:0043490","count":9},{"id":"GO:1990616","count":9},{"id":"GO:1990544","count":9}]},{"hash":"510579058157889509","title":"Methylation Enzymes and Cofactor Biosynthesis","description":"This cluster is characterized by a strong representation of methylation-related GO terms (tRNA wobble uridine modification, tRNA methylation, N-terminal peptidyl-serine trimethylation, histone methylation) alongside biosynthetic processes for cofactors such as ubiquinone and vitamin E, as well as xenobiotic and antibiotic biosynthesis. The common theme appears to be enzymes involved in methylation modifications and the biosynthesis of key cofactors, suggesting coordinated roles in metabolic regulation and RNA/DNA modification.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":3},{"id":"GO:0035573","count":3},{"id":"GO:0010189","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0017000","count":3}]},{"hash":"1088568347306891519","title":"Ribosome biogenesis and translation control","description":"The cluster is enriched for ribosome-related processes: formation of the translation preinitiation complex, translation reinitiation, and maturation of rRNA species, pointing to ribosome biogenesis and protein synthesis regulation. TORC1 signaling and regulation of GTPase activity further suggest growth-regulatory coordination with ribosome production. While some terms touch on cytoskeletal and organismal growth aspects, the dominant theme is ribosome biogenesis and translation control.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0051013","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000463","count":3}]},{"hash":"1557408225500782722","title":"RNA Processing and Translation Initiation","description":"The top GO terms prominently feature translation initiation complex formation and translation reinitiation, alongside mRNA export from the nucleus and a mitosis-associated DNA replication process. This suggests a core theme around RNA metabolism and the initiation of translation, with ancillary links to cell cycle\u2013related processes. Some terms appear unrelated (e.g., pancreatic juice secretion, synaptic plasticity), likely reflecting annotation breadth rather than a single cohesive pathway, but the dominant signal supports an RNA processing/translation initiation cluster.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":7},{"id":"GO:0002188","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0006406","count":5},{"id":"GO:1903461","count":5}]},{"hash":"1783272266710629528","title":"Unknown","description":"The terms span DNA replication, vesicle transport, meiotic DNA repair, metabolism, and diverse stress/physiological responses (morphine, lead ion, locomotion, cardiac hypertrophy). There isn\u2019t a single cohesive GO-based function linking these proteins, so a specific thematic label isn\u2019t warranted.","confidence":"","size":25,"edges":192,"triangles":712,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0006888","count":8},{"id":"GO:1990918","count":8},{"id":"GO:1900486","count":7},{"id":"GO:0043278","count":7}]},{"hash":"468097525344528981","title":"Muscle and heart development with transcriptional regulation","description":"This cluster is dominated by GO terms tied to developmental processes and gene expression control, including DNA-templated transcription, multicellular organism development, mitotic cell cycle, angiogenesis, skeletal system development, and cardiac-related regulation. The prominence of muscle/heart (cardiac muscle proliferation, skeletal development) alongside angiogenesis suggests a cohesive module of transcriptional regulation guiding muscle and vascular/musculoskeletal development in a multicellular context. While neuronal signaling terms appear, the overall theme centers on developmental growth and tissue formation driven by transcriptional programs.","confidence":"High","size":25,"edges":28,"triangles":6,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":19},{"id":"GO:0007275","count":18},{"id":"GO:0000278","count":18},{"id":"GO:0014850","count":18},{"id":"GO:0006349","count":17}]},{"hash":"1117307539751857097","title":"DNA Damage Response and NFAT Signaling","description":"The cluster prominently features GO terms tied to DNA damage response (DNA damage checkpoint signaling; signal transduction in response to DNA damage) and regulation of calcineurin-NFAT signaling, which aligns with NFAT-related developmental and immune processes (heart morphogenesis, neutrophil extravasation). While there are metabolism-related terms (energy homeostasis, glucose metabolic process) suggesting broader roles, the strongest cohesive theme appears to be DNA damage signaling connected to NFAT pathway modulation, with ancillary links to development and metabolism.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":2},{"id":"GO:0032095","count":2},{"id":"GO:2001108","count":2},{"id":"GO:0097009","count":2},{"id":"GO:0072672","count":2}]},{"hash":"1974642261305172557","title":"Plant Stress Response and Cell Wall Biogenesis","description":"In this cluster, several prominent terms point to plant-specific responses to environmental cues (response to abscisic acid; response to osmotic stress) and remodeling of growth-related structures (positive regulation of secondary cell wall biogenesis). These together suggest a cohesive module governing stress adaptation and cell wall dynamics, with other terms like viral process or telomere-related activities likely reflecting broader or incidental annotations rather than a single overriding function. The connections among these terms imply a plant-centered stress-growth regulatory theme.","confidence":"Medium","size":25,"edges":72,"triangles":82,"max_degree":15,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0016032","count":11},{"id":"GO:0009737","count":11},{"id":"GO:1901348","count":9},{"id":"GO:1905778","count":9},{"id":"GO:0035066","count":9}]},{"hash":"362301958976675695","title":"Metal and xenobiotic transmembrane transporters","description":"The top GO terms are dominated by transmembrane transport across a variety of substrates (cadmium and cobalt ions, nitrite, amino acids, vitamins, and xenobiotics), pointing to a cluster of transporter proteins with broad substrate specificity. Occasional SOS response and nucleotide-excision repair terms likely reflect stress related to metal exposure rather than core cluster function. Overall, the theme is metal/xenobiotic transport rather than DNA repair. ","confidence":"Medium","size":25,"edges":36,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0070574","count":4},{"id":"GO:0015707","count":3},{"id":"GO:0006824","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2}]},{"hash":"1634197263270339716","title":"Yeast Filamentous Growth and Gene Expression","description":"This cluster centers on filamentous growth and invasive behavior in response to glucose limitation (pseudohyphal growth, invasive growth), coupled with transcription/translation processes, suggesting coordinated gene expression changes during morphological switching. Some terms about telomere maintenance and nuclear transport appear, but the core theme is nutrient-driven morphogenesis and associated gene expression.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0001502","count":2},{"id":"GO:0071230","count":2},{"id":"GO:0007124","count":2}]},{"hash":"941184955762614977","title":"Proteostasis and Unfolded Protein Response","description":"This cluster is strongly enriched in motifs related to protein quality control, folding, and handling of misfolded proteins (e.g., unfolded protein response, chaperone-assisted refolding, misfolded protein transport, redox homeostasis). The combination points to proteostasis mechanisms that manage protein folding stress, with supporting terms like protein complex oligomerization. Some incidental terms (e.g., tRNA import) appear unrelated to core folding functions. Overall, the theme aligns with proteostasis and unfolded protein response.","confidence":"High","size":25,"edges":143,"triangles":306,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032781","count":5},{"id":"GO:0070389","count":5},{"id":"GO:0006986","count":5},{"id":"GO:0006469","count":4},{"id":"GO:0045454","count":4}]},{"hash":"377096265306529376","title":"Diverse catabolic detoxification","description":"This cluster is dominated by GO terms tied to breakdown and detoxification of a wide range of substrates (cellular oxidant detoxification and oxidation\u2013reduction processes) and multiple substrate-specific catabolic pathways (triglyceride, chlorophyll, uracil, stilbene, 3-phenylpropionate catabolic processes), with one term touching regulatory signaling. Together, these point to a general theme of diverse catabolic metabolism and detoxification rather than a single, specific pathway.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":7},{"id":"GO:0019433","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0046272","count":6}]},{"hash":"756339218351830091","title":"Unknown","description":"The top terms cover a broad and disparate mix: vitamin biosynthesis (cobalamin, biotin), isoprenoid precursor biosynthesis (DMAPP), translation and RNA-templated transcription, redox-related processes, and even neuronal signaling terms. This lack of a single, cohesive function or pathway makes it hard to assign a specific, representative label, so I\u2019d mark this cluster as Unknown with no clear representative function.","confidence":"","size":25,"edges":299,"triangles":2277,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0098869","count":2}]},{"hash":"172409006409028040","title":"Neural development and metabolism","description":"This cluster is enriched for neural development terms such as spinal cord development, proximal/distal pattern formation, and neural precursor cell proliferation, suggesting a core neural development theme. It also includes metabolic pathway terms (TCA cycle, amino acid biosynthesis, GABA catabolism), indicating a metabolic context accompanying development. An inflammatory response term to LPS is present but less central. Overall, the proteins appear to connect neural development with metabolic processes, justifying the label.","confidence":"Medium","size":25,"edges":115,"triangles":228,"max_degree":17,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0007568","count":5},{"id":"GO:0009097","count":5},{"id":"GO:0006099","count":4},{"id":"GO:0032496","count":4}]},{"hash":"476919661182743725","title":"Immune signaling and neural development regulators","description":"The top GO terms point to modulation of immune signaling (negative regulation of IL-12 production, NF-kappaB-related activity, chemokine production, and vitamin D response) and neural development (cerebellar granule cell differentiation and negative regulation of dendrite development). Additional terms about telomere regulation and protein ADP-ribosylation suggest broader regulatory roles in signaling and chromatin/post-translational modification. Together, these indicate a cluster of proteins that regulate signaling in immune and neural contexts, with auxiliary chromatin/ modification functions.","confidence":"Medium","size":25,"edges":22,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0021707","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071651","count":3},{"id":"GO:0007253","count":3}]},{"hash":"2065003847394465015","title":"Unknown","description":"The top terms are a\u6df7 blend of unrelated processes (seedling development, rRNA maturation, receptor recycling, endosome size, Rho signaling, transcription regulation) with several obsolete GO IDs, indicating no single cohesive function ties these proteins together. Therefore, Unknown with None confidence.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0090351","count":1},{"id":"GO:0000470","count":1},{"id":"GO:0000466","count":1}]},{"hash":"590443443167418622","title":"Neural development and synaptic signaling","description":"Because the top GO terms cluster around dendritic spine morphogenesis, trans-synaptic signaling, and retinal ganglion cell axon guidance, pointing to neural development and synaptic specialization. Additional terms involve retinoic acid response and Hedgehog signaling, developmental pathways commonly coordinating neural circuit formation. While some terms also cover broader morphogenesis, the strongest signal is neural connectivity and synaptic maturation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060997","count":2},{"id":"GO:0051291","count":2},{"id":"GO:0070212","count":2},{"id":"GO:0050798","count":1},{"id":"GO:0099557","count":1}]},{"hash":"2126567551453874374","title":"cAMP/cGMP signaling and potassium transport","description":"GO terms show recurring themes of cellular response to cAMP, cGMP biosynthesis, and potassium ion transmembrane transport, suggesting a cluster centered on cyclic nucleotide signaling and ion transport. Other listed terms (endosomal acidification, visual perception, kidney development) appear less directly connected but may reflect broader roles in signaling or endosomal processes, providing context rather than a core function. Overall, the label captures the strongest shared function among the terms. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0048388","count":1}]},{"hash":"659001866321672389","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms related to ribosome biogenesis and ribosomal subunit biogenesis, along with cytoplasmic translation and tRNA modification, and even export of ribosomal subunits from the nucleus. While a few terms touch on cell cycle or conjugation, the strongest signal centers on ribosome assembly and protein synthesis, indicating a cohesive group of proteins involved in ribosome formation and function.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006400","count":3},{"id":"GO:0002181","count":3},{"id":"GO:0090529","count":3},{"id":"GO:0007049","count":3}]},{"hash":"511009380285119329","title":"Xenobiotic and vitamin membrane transport","description":"This cluster is dominated by GO terms for transmembrane transport of vitamins and xenobiotics (and related compounds like antibiotics, lipoproteins, and fatty acids), plus organelle-specific transport (peptide export from mitochondrion, peroxisomal fatty acid import). These collectively indicate a membrane transport/function theme rather than a single metabolic enzyme. An outlier term about antigen processing is peripheral and not enough to redefine the core function.","confidence":"High","size":25,"edges":21,"triangles":6,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":14},{"id":"GO:0006855","count":14},{"id":"GO:0042891","count":12},{"id":"GO:0090374","count":8},{"id":"GO:0072089","count":8}]},{"hash":"1802048301084479327","title":"GPCR Signaling and Immune Regulation","description":"The top terms are dominated by GPCR signaling (GO:0007205) and immune-regulatory processes (GO:0045083, GO:0071651), including negative regulation of kinase activity (GO:0071901) and cytokine/chemokine production, which together point to modulation of signaling pathways and immune responses. There are additional terms related to neuronal differentiation and telomere maintenance, suggesting broader regulatory roles, but the strongest cohesive theme is regulation of signaling and immune functions.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":11},{"id":"GO:0098907","count":9},{"id":"GO:0032212","count":6},{"id":"GO:0021707","count":6},{"id":"GO:1904355","count":6}]},{"hash":"1810579009698278986","title":"Regulatory signaling and neural development","description":"Based on the top GO terms, the proteins appear enriched for regulation-focused processes spanning signaling pathways, gene expression (mRNA processing and kinase activity regulation), neural development (cerebellar granule cell differentiation and dendrite development), and broader genome/immune regulation (telomere maintenance, NF-kappaB-related regulation, cytokine activity). The mix suggests a cluster of regulatory proteins with roles in neural development and modulation of cellular signaling rather than a single, cohesive enzymatic function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":6},{"id":"GO:0006397","count":6},{"id":"GO:0032212","count":5},{"id":"GO:0021707","count":5},{"id":"GO:1904355","count":5}]},{"hash":"972348091038725353","title":"Protein turnover and cellular stress responses","description":"This cluster centers on protein processing and degradation (dephosphorylation, proteolysis, autophagy) and includes stress-response terms such as xenobiotic stimulus response and DNA damage checkpoint signaling regulation; some metabolic terms (gluconeogenesis, pentose-phosphate shunt) may support energy/redox balance during stress, suggesting a broad theme of maintaining protein homeostasis under cellular stress.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0006470","count":4},{"id":"GO:0006508","count":4},{"id":"GO:0016311","count":3},{"id":"GO:0006094","count":3},{"id":"GO:0010666","count":3}]},{"hash":"909623190764092905","title":"Spindle-Microtubule Attachment and Chromatid Biorientation","description":"The prominent terms describe positive regulation of spindle microtubule attachment to kinetochores, mitotic sister chromatid biorientation, and mitotic metaphase chromosome recapture, pointing to a coherent mitotic spindle\u2013related function; a few unrelated terms exist but do not outweigh the mitotic signal.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051987","count":2},{"id":"GO:1990758","count":2},{"id":"GO:1905185","count":2},{"id":"GO:0031116","count":2},{"id":"GO:1990942","count":2}]},{"hash":"2236589941277789332","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043113","count":3},{"id":"GO:0007266","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0060997","count":3},{"id":"GO:0035418","count":3}]},{"hash":"661303988435092593","title":"Developmental Regulation and Epigenetic Control","description":"The top GO terms point to broad developmental processes (brain development, cerebellar Purkinje cell maturation, uterus morphogenesis, embryo zygote cytokinesis) as well as epigenetic mechanisms (epigenetic regulation of gene expression, DNA methylation). Neural-related functions (feeding behavior) also appear, suggesting a general theme of developmental regulation with epigenetic control across systems. The lack of network edges implies this cluster reflects a broad, non-pathway-specific collection centered on development and gene regulation rather than a single cohesive process.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0060296","count":1},{"id":"GO:0018095","count":1},{"id":"GO:2000253","count":1},{"id":"GO:0061038","count":1}]},{"hash":"158990479746566379","title":"Nuclear chromatin and transcription regulation","description":"Most terms revolve around chromatin state and transcription control in the nucleus: subtelomeric heterochromatin formation, telomeric region localization, and negative regulation of transcription by RNA polymerase II, along with RNA surveillance and nucleosome-related processes. A few terms outside this theme (defense response, fertilization, osteoblast differentiation) are present but do not define the cluster; overall the shared signal points to nuclear chromatin dynamics and transcription control.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031509","count":1},{"id":"GO:0050830","count":1},{"id":"GO:0007338","count":1},{"id":"GO:1900446","count":1},{"id":"GO:0001649","count":1}]},{"hash":"1440693944938732138","title":"Innate Immune Signaling (NOD2/NF-kB)","description":"The cluster\u2019s top GO terms include innate immune response (GO:0005087) and the NOD2 signaling pathway (GO:0070431), as well as a (now obsolete) GO term related to NF-kappaB transcription factor activity (GO:0032088). Together, these point to a core theme of immune signaling, particularly pathways that regulate NF-kB and innate immune responses. The presence of other terms like cellular response to mechanical stimulus or plant hormone signaling may reflect annotation noise or cross-species annotations, but the dominant signal favors innate immune signaling. Confidence in the loan of an immune-focused label is therefore Moderate, given some noise in the term set.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0071260","count":4},{"id":"GO:0046827","count":3},{"id":"GO:0045087","count":3}]},{"hash":"2301364139304840798","title":"Ammonium/Nitrogen Transport and Utilization","description":"The cluster's GO terms concentrate on ammonium and broader nitrogen transport and utilization (ammonium transmembrane and transepithelial transport, methylammonium transport, nitrogen utilization), with related transporters for carbon dioxide and iron homeostasis. Some growth-related terms may reflect nutrient-response phenotypes, but the shared theme is transporter-mediated nitrogen handling. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0007124","count":4},{"id":"GO:0006808","count":4},{"id":"GO:0080181","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0019740","count":4}]},{"hash":"2160226514199672063","title":"TLR signaling and inflammatory response","description":"The top GO terms cluster around Toll-like receptor signaling (especially TLR8) and Toll pathway activity, with strong links to positive regulation of inflammatory processes, interferon-alpha production, and interleukin-18 production, plus antimicrobial peptide biosynthesis and autophagy regulation. The presence of cell surface receptor tyrosine kinase signaling supports a theme of receptor-mediated innate immune sensing leading to inflammation and antimicrobial defenses. Confidence: High","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007169","count":5},{"id":"GO:0006469","count":4},{"id":"GO:0032741","count":4},{"id":"GO:0034158","count":4},{"id":"GO:0050729","count":4}]},{"hash":"2104214773005885620","title":"Telomere Regulation & Neuronal Development","description":"The top GO terms are dominated by telomere maintenance regulation (positive regulation of telomere maintenance via telomerase and positive regulation of telomere capping), suggesting a telomere-regulatory theme. There are also signals of neuronal development (cerebellar granule cell differentiation, negative regulation of dendrite development) and immune signaling modulation (IL-12 and NF-kappaB related). This points to a cluster of regulatory proteins spanning telomere biology and neuronal development pathways, rather than a single, cohesive function. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":10},{"id":"GO:0021707","count":10},{"id":"GO:1904355","count":10},{"id":"GO:0071651","count":10},{"id":"GO:0007253","count":10}]},{"hash":"958485200950127405","title":"Pol II Transcription Regulation","description":"This cluster is dominated by GO terms about regulation of transcription from RNA polymerase II promoter under various conditions (oleic acid, nonfermentable carbon sources, etc.), with a secondary signal about mRNA stability regulation. The recurring theme points to transcriptional control as the core function, though the lack of edges and presence of some obsolete terms suggest annotation noise or dispersed signals. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":2},{"id":"GO:0035969","count":2},{"id":"GO:1904741","count":2},{"id":"GO:0061429","count":2},{"id":"GO:0061415","count":2}]},{"hash":"501188945982938122","title":"Translational Regulation and mRNA Processing","description":"This cluster shows a clear theme around translation initiation and preinitiation complex formation, plus spliceosome-related RNA processing and mRNA stabilization; together these terms point to coordinated RNA-level control of gene expression, spanning both translation and splicing regulation. While a few terms are odd/outlier, the dominant signal is RNA processing and translational control.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0001825","count":1}]},{"hash":"2065814857383029692","title":"Neuronal synaptic development and plasticity","description":"The cluster is enriched for neuronal synapse-related terms such as dendritic spine morphogenesis, regulation of synapse structure and excitatory postsynaptic potential, along with sensory perception and social behavior. Additional terms like TORC1 signaling, GTPase regulation, and mRNA transport suggest supporting roles in growth signaling and mRNA dynamics that influence neuronal function. Together, these functions point to a coherent theme of neuronal synaptic development and activity-dependent plasticity.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0038202","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0051028","count":3}]},{"hash":"969968901928948074","title":"Unknown","description":"The GO terms are highly diverse, spanning DNA-templated transcription, signaling (Rho, cAMP), metabolism (folic acid biosynthesis), and organismal traits (social behavior, heart morphogenesis), with no single unifying function evident across the 24 proteins. Edges are zero, suggesting no cohesive interaction module, so a single representative function cannot be inferred.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035176","count":2},{"id":"GO:0071481","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0046656","count":2}]},{"hash":"1159799745309161476","title":"Unknown","description":"The top GO terms span redox processes, nitrate assimilation, ion transport, kidney development, immune activation, and hormonal regulation, with no single cohesive function across the cluster. There isn't a clear shared theme binding these proteins, so Unknown is the appropriate label.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0001957","count":1}]},{"hash":"1877736108001475070","title":"Auditory synaptic signaling and cochlea morphogenesis","description":"These proteins cluster around neural communication in the auditory system: glutamate secretion, dendritic spine morphogenesis, and long-term synaptic depression point to synaptic transmission, while auditory receptor stereocilium organization and cochlea morphogenesis indicate development of the hearing apparatus. A secondary term on NO-mediated retrograde signaling fits with synaptic modulation. Overall, the dominant theme is hearing-related synaptic signaling and cochlear development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070433","count":2},{"id":"GO:0060088","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0035640","count":1}]},{"hash":"1330416387575774931","title":"Bacterial biosynthesis and redox balance","description":"These proteins are enriched for biosynthetic processes (biotin, PHB, antibiotic biosynthesis) and redox/oxygen homeostasis terms (oxidation-reduction, intracellular oxygen), suggesting a core theme of metabolism with redox regulation. Some terms relate to protein modification and translation regulation, indicating broader metabolic/protein-processing roles but not a single unified signaling pathway. Overall, the cluster likely reflects bacterial biosynthetic capacity tied to redox balance.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0006449","count":2}]},{"hash":"800267153818305055","title":"Regulation of RNA Polymerase II Transcription","description":"Most of the top GO terms describe transcription from the DNA template and regulation of transcription by RNA polymerase II, including both positive and negative regulation. The clustering of proteins with these terms suggests a shared theme of transcriptional control rather than a metabolic or biosynthetic function, indicating a regulatory module focused on RNAP II\u2013mediated transcription.","confidence":"High","size":24,"edges":152,"triangles":768,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0006355","count":7},{"id":"GO:0000122","count":5},{"id":"GO:0035969","count":4},{"id":"GO:1904741","count":4}]},{"hash":"1457914546180312409","title":"Regulatory Signaling and Gene Expression","description":"This cluster's top GO terms indicate a broad involvement in regulating signaling pathways and transcription. Terms include positive regulation of transcription, GPCR signaling, GTPase and kinase activity regulation, and processes like myoblast fusion, vesicle exocytosis, cytokinesis, and apoptosis. This suggests a general regulatory role over signaling and gene expression rather than a single specific function.","confidence":"Medium","size":24,"edges":88,"triangles":109,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045944","count":8},{"id":"GO:0007205","count":7},{"id":"GO:0098907","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0006469","count":6}]},{"hash":"1682072332857255664","title":"Interferon-Responsive Innate Immunity","description":"The cluster's top GO terms are dominated by innate immune response and cellular response to type I interferon, including negative regulation of defense response to virus by host, which points to antiviral signaling as the core function. While there are additional terms related to development and RNA processing, these appear ancillary and not central to the main immune-focused theme.","confidence":"High","size":24,"edges":76,"triangles":46,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030850","count":6},{"id":"GO:0046661","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0071357","count":5}]},{"hash":"730735627435149189","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":198,"triangles":880,"max_degree":23,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":19},{"id":"GO:0043547","count":19},{"id":"GO:0007601","count":17},{"id":"GO:0000278","count":17},{"id":"GO:1905869","count":16}]},{"hash":"1166552883829463706","title":"Synaptic vesicle trafficking and transmission","description":"The top GO terms cluster around presynaptic vesicle maturation and fusion, regulation of GTPase activity tied to vesicle trafficking, and synaptic transmission (glutamatergic), plus related intracellular transport and activity-dependent signaling from presynapse to nucleus, suggesting a cohesive neuronal synapse function. Some terms about development appear but do not outweigh the dominant synaptic vesicle theme.","confidence":"High","size":24,"edges":194,"triangles":752,"max_degree":23,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043087","count":9},{"id":"GO:0016188","count":8},{"id":"GO:0099526","count":8},{"id":"GO:0031340","count":8},{"id":"GO:2000235","count":8}]},{"hash":"1526106612217855746","title":"Lipid metabolism and small-molecule catabolism","description":"The top GO terms highlight lipid-related catabolic and regulatory processes (e.g., triglyceride catabolism, phospholipid dephosphorylation, regulation of endocannabinoid signaling) along with detoxification and broader organic compound catabolism (stilbene, uracil, phenylpropionate). This suggests a general metabolic cluster centered on breakdown and processing of lipids and various small molecules, rather than a single precise function.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:2000124","count":10},{"id":"GO:0019433","count":10},{"id":"GO:0055114","count":8},{"id":"GO:0017000","count":8},{"id":"GO:0046272","count":8}]},{"hash":"928590885201358527","title":"Vision and Development Regulators","description":"This cluster shows strong enrichment for phototransduction and visual perception, indicating involvement in eye-related sensory pathways. It also includes developmental processes such as limb development and skeletal muscle fiber development, along with thyroid hormone metabolic processes, suggesting coordination of growth and differentiation. Additional terms like positive regulation of DNA binding and negative regulation of protein kinase activity point to transcriptional and signaling regulation activities that may govern these developmental/vision pathways. The presence of some non-developmental terms (vacuole fusion, platelet degranulation) indicates functional diversity, but the core signal centers on vertebrate development with an eye/vision emphasis.","confidence":"Medium","size":24,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043388","count":3},{"id":"GO:0007602","count":3},{"id":"GO:0042403","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0060173","count":3}]},{"hash":"1475120277857934205","title":"Lymphocyte signaling and cytoskeletal dynamics","description":"The cluster shows prominent immune signaling terms (NK T cell differentiation, antigen receptor signaling, B cell homeostasis, hemopoiesis, integrin activation) together with cytoskeletal/motility terms (microtubule-based movement, lamellipodium assembly). A few metabolic/trafficking terms appear (ceramide transport, fatty acid import regulation), but the dominant theme is lymphocyte signaling intertwined with cytoskeletal remodeling.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007018","count":3},{"id":"GO:0001865","count":3},{"id":"GO:0050851","count":3},{"id":"GO:0001782","count":3},{"id":"GO:0035621","count":3}]},{"hash":"1188176107311042992","title":"Ubiquitination and ER quality control","description":"The top GO terms point to ubiquitin-related processes (K63-linked ubiquitination, mono-/autoubiquitination) and ER-associated degradation and protein folding in the endoplasmic reticulum, suggesting proteins that participate in ubiquitin-mediated regulation and ER quality control. Some terms appear obsolete or incidental (e.g., otolith development) but do not override the dominant theme. Therefore, a label emphasizing ubiquitination coupled with ER quality control is most representative.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030579","count":2},{"id":"GO:0006513","count":2}]},{"hash":"1903710373491621142","title":"Steroid hormone signaling in male reproduction","description":"This cluster\u2019s top terms cluster around prostate development, male sex differentiation, and steroid hormone receptor complex assembly, pointing to steroid hormone signaling governing male reproductive development. Some ER-related processing and transport terms appear, but the dominant signal is hormone-receptor\u2013mediated differentiation in male tissues.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0042098","count":2},{"id":"GO:0007029","count":1}]},{"hash":"2242550780074374606","title":"Unknown","description":"The terms span muscle attachment, nerve structure, vascular morphogenesis, and various regulatory/migration-related processes with no single cohesive function uniting the cluster, so a specific, representative label isn\u2019t apparent.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016203","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0014809","count":2},{"id":"GO:0021629","count":2},{"id":"GO:2000235","count":1}]},{"hash":"776603079755737375","title":"Unknown","description":"Top terms span insulin secretion regulation, calcium transport, sperm development, interferon production, hearing sensation, nucleotide and amino acid biosynthesis, and lipid storage, showing no single cohesive function. With no edges or clustering signal, this cluster lacks a unifying theme, so a specific label cannot be assigned.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035774","count":2},{"id":"GO:0070588","count":2},{"id":"GO:0007291","count":1},{"id":"GO:0007288","count":1},{"id":"GO:0032608","count":1}]},{"hash":"52991602475108842","title":"Plant reproductive development and gene regulation","description":"The cluster's top GO terms are dominated by plant reproductive processes (flower development, pollen maturation, inflorescence development) and regulatory mechanisms (miRNA transcription, K11-linked ubiquitination), suggesting a cohesive theme around plant reproductive development and its regulation, despite a few outlier terms that may reflect broad or cross-species annotations.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009911","count":2},{"id":"GO:0010152","count":1},{"id":"GO:0070979","count":1},{"id":"GO:0061614","count":1},{"id":"GO:0010229","count":1}]},{"hash":"188548521272879971","title":"Chloroplast RNA Processing and Organelle Translation Regulation","description":"This cluster is dominated by terms about chloroplast RNA processing/modification and regulation of mitochondrial translation, with a notable emphasis on chloroplast\u2013nucleus signaling. Although a few terms touch on antibiotic response or unrelated processes, the strongest signal ties to organelle RNA maturation and the control of translation within chloroplasts and mitochondria, suggesting a coherent theme around organelle RNA metabolism and inter-organelle communication.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007406","count":2},{"id":"GO:0070129","count":1},{"id":"GO:0010019","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0017000","count":1}]},{"hash":"1427549054429380876","title":"Paraxial Mesoderm and Somitogenesis","description":"The GO terms show strong enrichment for mesoderm-related development, including paraxial and axial mesoderm development and somitogenesis, with circulatory system development as a downstream theme, indicating a cohesive module of proteins involved in early vertebrate body plan formation.","confidence":"High","size":24,"edges":237,"triangles":1312,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0015031","count":2},{"id":"GO:0007601","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0001756","count":1}]},{"hash":"488688502191398190","title":"Developmental signaling and apoptosis regulation","description":"The cluster\u2019s top GO terms point to key growth and fate\u2011determining signaling pathways (Hippo, Wnt, GTPase regulation) and processes tied to differentiation and development (keratinocyte differentiation, trophoblast migration, mating projection growth) along with apoptosis. This suggests a cohesive theme around controlling cell growth, differentiation, and programmed cell death via signaling cascades, despite the diversity of terms. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0035329","count":7},{"id":"GO:0090263","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0060044","count":7}]},{"hash":"718310740532872331","title":"Developmental Transcription and Epigenetic Regulation","description":"GO terms point to developmental programs and transcriptional/epigenetic control, including pituitary gland development, embryonic development, neural maturation, hormone biosynthesis, and transcription regulation (DNA-templated). This suggests the cluster represents broad regulators of development and lineage specification, with epigenetic modulation (histone methylation) shaping gene expression. Some terms like fungicide response and dihydrolipoamide metabolism are peripheral noise.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":10},{"id":"GO:0051572","count":10},{"id":"GO:0006355","count":10},{"id":"GO:0045654","count":9},{"id":"GO:0046886","count":9}]},{"hash":"654226317452820925","title":"Regulation of synaptic vesicle exocytosis","description":"Most GO terms cluster around neuronal vesicle trafficking and release, including regulation of synaptic vesicle exocytosis, vesicle maturation and fusion, and Golgi-to-plasma membrane transport, with supporting hints from brain development and presynaptic signaling. The overall pattern suggests a module centered on regulated vesicle trafficking in neurons.","confidence":"Medium","size":24,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031384","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0043087","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0007420","count":3}]},{"hash":"614928080258723447","title":"Unknown","description":"The GO terms span telomere maintenance and capping, neuronal differentiation and dendrite development, immune signaling regulation (IL-12, NF-kB), chemokine production, vitamin D response, and kinase activity regulation, with no clear unifying function. The lack of edges and the eclectic mix prevent a cohesive, specific label.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":18},{"id":"GO:0032212","count":17},{"id":"GO:0021707","count":17},{"id":"GO:1904355","count":17},{"id":"GO:0071651","count":17}]},{"hash":"2187805695601497","title":"Vesicle trafficking and proteasomal degradation","description":"This cluster shows a clear grouping of terms for intracellular transport (intracellular protein transport, Golgi-to-ER retrograde transport, COPII cargo loading) and ubiquitin-proteasome\u2013dependent protein degradation (SCF-dependent proteasomal ubiquitin-dependent catabolic process), suggesting a shared function in moving and turnover of proteins within the cell. Some virus/host interaction terms and defense annotations likely reflect broader roles in vesicle trafficking during immune or viral processes, but the dominant theme remains trafficking coupled to degradation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0044829","count":1}]},{"hash":"182089448489541083","title":"Plant hormone-regulated transcription","description":"Dominant GO terms are DNA-templated transcription and its regulation, with cytokinin-activated signaling implying plant hormone\u2013controlled transcription; together these suggest a cluster of plant transcriptional regulatory proteins. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0006355","count":8},{"id":"GO:0009736","count":4},{"id":"GO:0000413","count":3},{"id":"GO:0035969","count":2}]},{"hash":"1928726068401280636","title":"Cochlear hair cell morphogenesis and auditory synapse function","description":"The dominant GO terms point to cochlea morphogenesis, auditory receptor stereocilium organization, glutamate secretion, and synaptic signaling components such as dendritic spine morphogenesis, long-term synaptic depression, and nitric oxide\u2013related retrograde signaling, together describing development and function of hair cell synapses in the auditory pathway. The focus on structural hair-cell components and glutamatergic signaling supports a label for cochlear hair cell development and auditory synaptic communication.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0060088","count":5},{"id":"GO:0098924","count":5},{"id":"GO:0006470","count":5},{"id":"GO:0035640","count":5},{"id":"GO:0060292","count":5}]},{"hash":"1090571435352113750","title":"Mechanotransduction and stress signaling","description":"The cluster is enriched for GO terms tied to sensing and responding to mechanical stimuli (cellular response to mechanical stimulus, detection of mechanical stimulus involved in sensory perception of pain) and related stress responses (response to cold), plus regulatory processes like ubiquitination and transcription. The co-occurrence of vasopressin secretion and chemokine production suggests neuroendocrine and inflammatory modulation downstream of mechanical signaling. Together, these points support a theme of mechanosensory signaling coupled with stress-regulatory regulation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3}]},{"hash":"1712285237960462928","title":"Telomere maintenance and DNA damage response","description":"The top GO terms point to telomere maintenance (via telomerase and capping) and localization to double-strand break sites, plus PARP-related modification, suggesting a cohesive focus on telomere protection and DNA damage repair. Some terms like androgen metabolism and smooth muscle development may be peripheral noise, but the telomere/DSB-related signals predominate, supporting a label centered on telomere biology and DNA damage response.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0048745","count":1},{"id":"GO:1990166","count":1},{"id":"GO:1904908","count":1}]},{"hash":"2060942438614168237","title":"Developmental Regulation and Signaling","description":"These proteins are annotated with growth and development-related processes (multicellular organism development, brain development, cystoblast division) as well as transcriptional regulation (DNA-templated transcription) and signaling/modulation (regulation of GTPase activity, focal adhesion assembly). The shared emphasis on development, adhesion, and signaling suggests a cohesive role in developmental regulation rather than a single, narrow pathway. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0051893","count":2},{"id":"GO:0035948","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043547","count":2}]},{"hash":"2209713329214015769","title":"TLR signaling and innate inflammatory response","description":"This cluster is dominated by GO terms for Toll-like receptor signaling (TLR2/8), positive regulation of inflammatory responses, interferon production, antiviral/antibacterial defenses, and responses to dsRNA and fungi. Together they point to a cohesive theme of innate immune sensing and the ensuing inflammatory and antimicrobial responses.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032741","count":2},{"id":"GO:0034158","count":2},{"id":"GO:0050729","count":2},{"id":"GO:0045356","count":2},{"id":"GO:0008063","count":2}]},{"hash":"1665882823056671078","title":"Neuronal signaling and brain development","description":"The top GO terms cluster around regulation of neuronal signaling (Rho signaling, glutamatergic synaptic transmission) and brain development, with supporting references to receptor recycling and endosome size that indicate trafficking in neural cells. This combination suggests a functional theme focused on neural communication and development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0060316","count":1},{"id":"GO:0006355","count":1}]},{"hash":"371309428551195986","title":"Unknown","description":"The GO terms are highly heterogeneous (visual perception, cerebellar Purkinje cell layer structure, plant hormone biosynthesis, chromatin silencing, transcription regulation, and miRNA processing), with no clear shared function tying the proteins together. A concise, representative label cannot be confidently assigned.","confidence":"","size":23,"edges":28,"triangles":5,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:1903468","count":3},{"id":"GO:0090055","count":3},{"id":"GO:0090419","count":3},{"id":"GO:0021693","count":3}]},{"hash":"151995025609703863","title":"RNA processing and translation regulation","description":"The cluster shows proteins linked to RNA metabolism and control of gene expression at multiple levels: translation initiation and preinitiation complex formation, small-subunit processome assembly (ribosome biogenesis), splicing regulation (spliceosome-associated terms), miRNA-mediated translational repression, and mRNA stabilization. This combination suggests a cohesive function in coordinating RNA processing with translation control.","confidence":"High","size":23,"edges":153,"triangles":506,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0001825","count":2}]},{"hash":"1816903692738549442","title":"RNA Methylation and Splicing","description":"The top GO terms are dominated by RNA-related methylation and processing: protein methylation, tRNA methylation, tRNA wobble uridine modification, and alternative mRNA splicing via spliceosome. While there are also broader metabolic and xenobiotic-response terms, the strongest signal centers on RNA modification and splicing machinery, justifying this label.","confidence":"Medium","size":23,"edges":31,"triangles":9,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006479","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0030488","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0002098","count":2}]},{"hash":"2116160158268951518","title":"Eye and neural development","description":"Dominant terms point to eye and neural development (optic nerve morphogenesis, camera-type eye morphogenesis; dendritic spine morphogenesis; positive regulation of synapse assembly; ephrin receptor signaling), suggesting a cluster of proteins involved in visual system formation and neuronal connectivity. A few immune or hormonal terms appear as less central outliers, but the core signal is developmental/neural.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":4},{"id":"GO:0060997","count":3},{"id":"GO:0021631","count":3},{"id":"GO:0042403","count":3},{"id":"GO:2000525","count":3}]},{"hash":"356991694012521286","title":"Developmental signaling and transport regulators","description":"The cluster centers on developmental processes (brain and skin development, multicellular organism development) and includes terms for intracellular transport and regulation of signaling pathways (kinase activity, GTPase activity, autophosphorylation), indicating proteins that modulate development via signaling and trafficking.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":7},{"id":"GO:0006886","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0031954","count":5},{"id":"GO:0000278","count":5}]},{"hash":"738291219742671961","title":"Neuronal transcription and spine morphogenesis","description":"Top GO terms center on DNA-templated transcription and its regulation, indicating a transcriptional control theme. Also prominent are neuronal synaptic features (dendritic spine morphogenesis, protein localization to synapse, receptor clustering) and Rho-mediated signaling, linking transcriptional regulation to activity-dependent synaptic remodeling. A few outliers (kinetochore localization, cardiac differentiation) are less consistent, but the dominant signal points to transcriptional regulation in neuronal spine development.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0060292","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0035418","count":2}]},{"hash":"830494263059904965","title":"Gene Expression: Transcription and Translation Initiation","description":"The cluster is dominated by GO terms for translation initiation (preinitiation complex formation, reinitiation, IRES-dependent initiation) and DNA-templated transcription, indicating a core module of gene expression machinery. Other terms like cilium assembly and TGF-beta signaling appear less central, suggesting these proteins mainly relate to transcription/translation control with possible peripheral roles in signaling or ciliary processes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006446","count":2},{"id":"GO:0051209","count":2}]},{"hash":"56837806687928374","title":"Unknown","description":"The top GO terms span telomere maintenance, pH response, T cell proliferation, mitotic arrest, axon extension regulation, caveolin-mediated endocytosis, imprinting regulation, meiotic spindle attachment, NK T cell differentiation, and vagina development, which are highly diverse with no clear unified function tying the cluster together. There isn\u2019t a single dominant biological theme among the proteins, so a cohesive label cannot be assigned with confidence.","confidence":"","size":23,"edges":207,"triangles":994,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":23},{"id":"GO:0071469","count":23},{"id":"GO:0046641","count":23},{"id":"GO:0000751","count":23},{"id":"GO:0030517","count":23}]},{"hash":"108111900626028250","title":"Lipid, saccharide, and plant metabolite biosynthesis","description":"The top GO terms cluster around biosynthetic processes across lipids, sugars, and plant-derived compounds (ether lipid biosynthesis, lipopolysaccharide biosynthesis, dTDP-rhamnose and GDP-mannose pathways) as well as plant secondary metabolites (phenylpropanoid, anthocyanin, sporopollenin). This suggests a broad biosynthetic theme rather than a single specific function.","confidence":"Medium","size":23,"edges":8,"triangles":0,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0008611","count":2},{"id":"GO:1902987","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1936685718036780421","title":"Osmotic stress and carbohydrate metabolism","description":"The cluster is enriched for response to water deprivation and osmolyte responses (sorbitol, mannitol, sucrose) as well as sugar metabolic processes (glucose, sucrose). The presence of bacillithiol and mycothiol biosynthetic processes suggests redox/osmotic protection roles. Together, these terms indicate a theme of osmotic stress adaptation linked to carbohydrate metabolism.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":3},{"id":"GO:0072708","count":3},{"id":"GO:0010555","count":3},{"id":"GO:0009744","count":3},{"id":"GO:0005985","count":3}]},{"hash":"1303255690732704206","title":"Regulated neuronal signaling and endosomal trafficking","description":"The top GO terms cluster around regulation of signaling pathways (Rho), receptor recycling and endosome size, synaptic transmission (glutamatergic), autophagy, and ubiquitination, suggesting a group of proteins coordinating signaling and membrane trafficking in neuronal contexts.","confidence":"Medium","size":23,"edges":4,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035023","count":8},{"id":"GO:0006355","count":5},{"id":"GO:1902499","count":5},{"id":"GO:0006349","count":4},{"id":"GO:0016239","count":4}]},{"hash":"2052645753362246641","title":"DNA Transcription Regulation and RNA Methylation","description":"The cluster is dominated by processes related to transcription control and chromatin state (DNA-templated transcription, regulation of transcription, and rDNA heterochromatin formation, plus negative regulation of RNA Pol II transcription). It also shows RNA modification activity (rRNA and tRNA methylation), pointing to a coherent theme around transcriptional regulation coupled with RNA processing/modification. While other terms like cell growth and immune signaling appear, the strongest signal ties to transcriptional regulation and chromatin-associated processes.","confidence":"High","size":23,"edges":124,"triangles":366,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000183","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0009236","count":4},{"id":"GO:0000122","count":4}]},{"hash":"1815885330370742820","title":"Unknown","description":"The terms span telomere maintenance, pH response, T cell proliferation and differentiation, pheromone-induced cell-cycle arrest, axon growth regulation, caveolin-mediated endocytosis, meiosis spindle regulation, and vaginal development, with no single unifying function. Therefore there is no coherent label beyond Unknown.","confidence":"","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":23},{"id":"GO:0071469","count":23},{"id":"GO:0046641","count":23},{"id":"GO:0000751","count":23},{"id":"GO:0030517","count":23}]},{"hash":"865285325909098647","title":"RNA Processing & Cell Cycle Regulators","description":"This cluster centers on RNA modification and ribonucleoprotein assembly (snRNA pseudouridine synthesis, snoRNA-guided rRNA pseudouridylation, telomerase RNA stabilization, telomerase holoenzyme assembly) and overlaps with cell division/mitotic cell cycle processes, suggesting proteins that coordinate RNA processing with genome maintenance and cell-cycle progression. Some features like brain development and mitochondrial distribution are peripheral, but the core signal is RNA processing linked to cell-cycle control.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0031120","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0051291","count":2}]},{"hash":"808927148439562806","title":"DNA Replication and Cell Cycle Regulation","description":"Most of the top GO terms describe DNA replication and regulation of the cell cycle (DNA replication, centrosome cycle, mitotic cell cycle arrest, telomere maintenance), indicating a core theme of proliferation control. Other terms (developmental morphogenesis, endocytosis, immune cell proliferation) are secondary or broader context, but do not outweigh the cell-cycle signal. ","confidence":"High","size":23,"edges":220,"triangles":1299,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":22},{"id":"GO:0006260","count":22},{"id":"GO:0007098","count":22},{"id":"GO:0048701","count":22},{"id":"GO:0032212","count":21}]},{"hash":"2166415605131725449","title":"Developmental signaling and morphogenesis","description":"This cluster is dominated by terms related to tissue development and morphogenesis (angiogenesis, embryonic cranial skeleton morphogenesis, keratinocyte differentiation) and major signaling pathways (Hippo, Wnt, insulin), with supporting cues from DNA replication and apoptosis that reflect cell proliferation and turnover during development. The ensemble points to a coherent theme of growth, differentiation, and tissue patterning governed by signaling networks.","confidence":"High","size":23,"edges":13,"triangles":6,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001525","count":13},{"id":"GO:0006260","count":10},{"id":"GO:0035329","count":9},{"id":"GO:0090263","count":9},{"id":"GO:0060044","count":9}]},{"hash":"865197336049371392","title":"Inflammatory and innate immune signaling","description":"The cluster\u2019s prominent GO terms center on immune signaling and inflammation, including TLR8 signaling, IL-18 production, interferon-alpha production, and positive regulation of inflammatory responses, plus regulation of protein kinase activity that modulates signaling. While bone development and axonogenesis appear, the core theme is immune response regulation and inflammatory signaling.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":14},{"id":"GO:0007409","count":12},{"id":"GO:0019800","count":10},{"id":"GO:0060348","count":10},{"id":"GO:0016525","count":10}]},{"hash":"1896215202332668528","title":"Actin filament assembly and contractile ring formation","description":"The Top Terms are dominated by actin-related processes (actin nucleation, actin filament network formation, and actomyosin contractile ring actin filament bundle assembly), indicating a cohesive theme around actin filament organization and cytokinesis. Peripheral terms like histamine response or meiosis chromosome movement are less central to the core function. Thus, labeling the cluster as actin filament assembly and contractile ring formation best represents the shared function.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051758","count":1},{"id":"GO:0071420","count":1},{"id":"GO:0061164","count":1},{"id":"GO:0010467","count":1},{"id":"GO:0071519","count":1}]},{"hash":"1835706900829350914","title":"Mitotic Ubiquitin-Proteasome Degradation","description":"The top GO terms point to ubiquitin-dependent protein catabolic processes, including SCF- and APC/C-dependent pathways, as well as general protein ubiquitination, and are linked to cell division and the mitotic cell cycle. This suggests the cluster comprises proteins involved in targeted proteolysis during mitosis, organizing progression through cell cycle phases via ubiquitin tagging and proteasomal degradation. The presence of heterooligomerization signals may reflect multi-subunit E3 ligases and proteasome-associated factors that coordinate mitotic protein turnover.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0016567","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0030433","count":5}]},{"hash":"2239198426160279079","title":"Unknown","description":"The provided GO terms span several unrelated areas: antibiotic and menaquinone/biotin biosynthesis (bacterial metabolism), DNA transcription and transcription regulation, cell cycle progression, telomere maintenance, and neuronal differentiation. With 0 edges and no cohesive functional theme across these terms, there isn't a clear common function binding these proteins into a single biological cluster.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016049","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0000082","count":3}]},{"hash":"1518813378259162368","title":"Mitochondrial Transport and Redox Response","description":"This cluster centers on transport across mitochondrial membranes and associated metabolic shuttles (malate-aspartate shuttle, ATP/ADP, CoA, phosphate, deoxynucleotide transport), along with magnesium export and regulation of membrane permeability, plus a redox/oxidative stress component (response to superoxide). Although liver regeneration and pregnancy terms appear, the common thread is mitochondrial transport and redox homeostasis, suggesting roles as mitochondrial transporters or membrane regulators. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":3},{"id":"GO:0007565","count":3},{"id":"GO:0043490","count":2},{"id":"GO:1990616","count":2},{"id":"GO:1990544","count":2}]},{"hash":"371798499744085109","title":"Unknown","description":"The top GO terms span telomere maintenance and capping, neural development (cerebellar granule cell differentiation, dendrite development), immune signaling (IL-12 production, NF-kappaB activity), vitamin D response, and post-translational modification (ADP-ribosylation; kinase activity). This wide mix does not point to a single coherent biological function for the cluster, suggesting either pleiotropic roles or annotation noise. Therefore, a concise, specific label cannot be assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":18},{"id":"GO:0021707","count":18},{"id":"GO:1904355","count":18},{"id":"GO:0071651","count":18},{"id":"GO:0007253","count":18}]},{"hash":"29373130372534336","title":"Membrane transport and lipid metabolism","description":"The GO terms are dominated by various membrane transport processes (glycolipid and glycosphingolipid transport, polyol/organic cation/ammonium transport) and lipid metabolism, with additional regulatory cues for signaling pathways (JNK, Rho) and synapse organization, suggesting a cluster centered on membrane trafficking and lipid regulation with potential neuronal signaling involvement.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046328","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0050808","count":2},{"id":"GO:0035023","count":2},{"id":"GO:1904781","count":2}]},{"hash":"1009492188254738180","title":"Somatosensory and Pain Perception","description":"Dominant GO terms include sensory perception of pain, mechanosensation (touch), thermoception, and cold response, pointing to a somatosensory/nociceptive function. Some unrelated terms (vasopressin secretion, chemokine production) suggest broader neuroendocrine or immune links, but the core theme across the cluster is somatosensory signaling and nociception.","confidence":"Medium","size":23,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0019233","count":6},{"id":"GO:0050976","count":6},{"id":"GO:0098914","count":6},{"id":"GO:0071651","count":6}]},{"hash":"416418447335496858","title":"GTPase and kinase signaling regulators","description":"The top GO terms emphasize regulation of GTPase activity, regulation of serine/threonine kinase activity (both positive and negative), as well as related processes like cell migration, ubiquitination, and nuclear import, suggesting a set of regulatory proteins that modulate signaling cascades and trafficking rather than fixed structural roles. The mix of activatory and inhibitory terms points to dynamic control of signaling pathways and cellular movement across this cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0007205","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0071902","count":4},{"id":"GO:0006607","count":4}]},{"hash":"543166577068892598","title":"Immune and neural development regulation","description":"The top GO terms point to immune signaling modulation (negative regulation of IL-12, NF-\u03baB cytoplasmic sequestration, chemokine production) and neural development processes (cerebellar granule cell differentiation, negative regulation of dendrite development). Additional terms on protein kinase activity regulation and vitamin D response suggest a broader signaling regulation theme. Although telomere maintenance terms appear, they do not define a single functional axis. Overall, the cluster seems characterized by regulation of signaling in immune and neural contexts.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":11},{"id":"GO:0032212","count":10},{"id":"GO:0021707","count":10},{"id":"GO:1904355","count":10},{"id":"GO:0071651","count":10}]},{"hash":"291521590797766464","title":"Unknown","description":"The terms span telomere maintenance, muscle development, neural signaling, transcription, and immune responses, with no clear single function tying the cluster together, so a confident specific label cannot be assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0099557","count":2}]},{"hash":"1275316890684227009","title":"Hypoxia-Responsive Transcription and Signaling","description":"The terms point to hypoxia-induced transcriptional regulation and signaling, with linked processes in the cell cycle and cytoskeletal dynamics (actin filament depolymerization) and kinase/GTPase signaling, reflecting coordinated stress response and proliferation control.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0071456","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0014898","count":3},{"id":"GO:0008284","count":3}]},{"hash":"1696492955210037160","title":"Unknown","description":"The top terms are a heterogeneous mix including lipid metabolism, brain development, RNA transcription termination, and general metabolic processes, with no single dominant function linking the proteins. Given zero edges and lack of a cohesive theme, there isn\u2019t a clear label to assign beyond Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0019433","count":5},{"id":"GO:2000124","count":4},{"id":"GO:0016311","count":4},{"id":"GO:0042619","count":3}]},{"hash":"469116371544375288","title":"Unknown","description":"The top GO terms are highly diverse (response to morphine, photosynthesis, mitotic cell cycle transition, ubiquitination, unfolded protein response, protein isomerization, metal ion response, etc.), with a mix of current and obsolete terms and no clear single biological theme connecting all proteins. This makes it not possible to assign a specific, representative label for the cluster.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043278","count":2},{"id":"GO:0007091","count":2},{"id":"GO:0015979","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0030850","count":2}]},{"hash":"79976710738782235","title":"Unknown","description":"The top terms span telomere maintenance and capping, neural differentiation, immune signaling, vitamin D response, and post-translational modification, with no single cohesive function tying all terms together. Hence no clear high-level label can be assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":7},{"id":"GO:0021707","count":7},{"id":"GO:1904355","count":7},{"id":"GO:0071651","count":7},{"id":"GO:0007253","count":7}]},{"hash":"2222453807491472282","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0070129","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0016554","count":2}]},{"hash":"760379179115742998","title":"Chromatin regulation and telomere maintenance","description":"The cluster\u2019s top GO terms cluster around DNA-templated transcription, chromatin organization (heterochromatin formation, histone modification regulation), and telomere-associated processes, suggesting a cohesive nuclear role in transcriptional control and telomere maintenance. A few peripheral terms (osmotic stress, viral process) are present but do not override the central theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000183","count":4},{"id":"GO:1901348","count":3},{"id":"GO:1905778","count":3},{"id":"GO:0035066","count":3}]},{"hash":"1066536508109586923","title":"Multisystem Developmental Morphogenesis","description":"Based on GO terms spanning axonogenesis, metanephric kidney development, lymph vessel and skin development, and regulation of signaling pathways, this cluster appears to group proteins involved in developmental signaling and tissue morphogenesis across multiple organs rather than a single tissue-specific function. The combination of morphogenesis and regulatory signaling terms supports a broad developmental role.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0007409","count":4},{"id":"GO:0072205","count":3},{"id":"GO:0060315","count":3},{"id":"GO:0007205","count":3}]},{"hash":"2167915080655527722","title":"Nutrient-responsive RNA Pol II transcription regulation","description":"The dominant GO terms are about DNA-templated transcription and regulation of transcription from RNA polymerase II promoters, including responses to various nutrient- and metabolic signals (oleic acid, carbon sources, starvation). This points to a cluster of proteins involved in regulating transcription in response to metabolic cues, with only a minor outlier like microtubule severing that may reflect indirect associations. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0006355","count":5},{"id":"GO:0035948","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0035969","count":1}]},{"hash":"1996792024745492245","title":"Cell Cycle and Innate Immunity","description":"This cluster is dominated by terms tied to cell division and mitotic regulation (cell division; metaphase/anaphase transition) alongside innate immune signaling (type I interferon response; innate immune response; defense response to virus). The presence of K11-linked ubiquitination suggests ubiquitin-mediated regulation relevant to both cell cycle control and immune pathways. A few terms (gluconeogenesis regulation; prostate gland development) seem less connected and may reflect annotation noise, but the core theme points to coupling of cell cycle processes with antiviral immune signaling.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":14},{"id":"GO:0071357","count":13},{"id":"GO:0090526","count":13},{"id":"GO:0045087","count":12},{"id":"GO:0050689","count":12}]},{"hash":"408110064460647457","title":"Ion transport and membrane potential regulation","description":"This cluster is dominated by GO terms for ion transport across the plasma membrane (calcium, magnesium, manganese, sodium, potassium) and membrane hyperpolarization, plus intracellular ion homeostasis, pointing to a group of transporters/channels governing ion balance and membrane potential. The presence of kidney and multicellular development terms may reflect tissue-specific roles where ion handling is crucial, but the unifying theme is ion transport and membrane potential maintenance.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019233","count":7},{"id":"GO:0060081","count":7},{"id":"GO:0010961","count":6},{"id":"GO:0098703","count":6},{"id":"GO:0006828","count":6}]},{"hash":"514003925458682349","title":"Ion transport and calcium signaling cluster","description":"The top GO terms point to ion movement across membranes (sodium import, potassium export) and regulation of calcium-release channels, which together suggest a core focus on ion homeostasis and calcium signaling. While other terms touch on skin and kidney development or stress responses, these appear secondary to the dominant ion transport theme, so the label emphasizes the most represented function. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903244","count":3},{"id":"GO:0098719","count":3},{"id":"GO:0097623","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0072205","count":2}]},{"hash":"876079115710235185","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":58,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0034221","count":2},{"id":"GO:0036085","count":2},{"id":"GO:0072334","count":2},{"id":"GO:0015786","count":2},{"id":"GO:1990569","count":2}]},{"hash":"758696726171821975","title":"Male Reproductive Development and Steroid Signaling","description":"Top terms include prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly, indicating a core theme of androgen-driven development and steroid signaling. Additional terms relate to innate immune responses and cell division, which may reflect broader cellular roles of the proteins or data noise. Overall, the cluster seems best characterized by steroid-mediated male reproduction with secondary immune/cell cycle associations.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030850","count":9},{"id":"GO:0046661","count":9},{"id":"GO:0006463","count":9},{"id":"GO:0071357","count":7},{"id":"GO:0051301","count":7}]},{"hash":"1478951417247234789","title":"Ribosome biogenesis and translation initiation","description":"The proteins cluster around ribosome assembly and translation initiation: ribosome biogenesis, formation of translation preinitiation complex, and translation reinitiation are all represented. These shared functions suggest a cohesive role in ribosome production and initiation of protein synthesis, despite a few unrelated terms appearing as minor noise.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0050830","count":2}]},{"hash":"1175972543078300221","title":"Redox balance and oxidative stress response","description":"The cluster\u2019s top GO terms cluster around oxidation-reduction processes, cellular oxidant detoxification, and redox homeostasis (e.g., cellular oxidant detoxification, cell redox homeostasis, and response to hydrogen peroxide). This points to a shared function in maintaining redox balance and detoxifying reactive oxygen species, with some members also linked to protein repair and related post-translational modifications. Some annotations are obsolete or mixed (viral process, glycerol ether metabolism), but the dominant theme supports redox regulation as the core function of the cluster.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0098869","count":3},{"id":"GO:0030091","count":3},{"id":"GO:0018401","count":3},{"id":"GO:0009086","count":2}]},{"hash":"1608098107138446372","title":"Protein Translation Machinery and Regulation","description":"The cluster is dominated by translation-related GO terms\u2014initiation, elongation, termination, cytoplasmic and mitochondrial translation\u2014as well as regulation and fidelity of translation. This suggests the proteins function together in protein synthesis and its control; a non-core term like glial cell proliferation may be incidental noise. Confidence in this label is High.","confidence":"","size":22,"edges":227,"triangles":1464,"max_degree":21,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0006449","count":5},{"id":"GO:1902802","count":5},{"id":"GO:2000767","count":5},{"id":"GO:0014009","count":5}]},{"hash":"2282867454364989408","title":"Developmental Cell Cycle and Transcription","description":"The cluster is dominated by nuclear processes like DNA replication and DNA-templated transcription, along with mitotic cell cycle and multicellular development terms (e.g., neural tube closure). While some terms touch on stress responses, the common thread is regulation of gene expression and cell division during development, justifying this label.","confidence":"Medium","size":22,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0070059","count":6},{"id":"GO:0006349","count":5},{"id":"GO:0001843","count":5}]},{"hash":"1869957052336380380","title":"Mitotic spindle dynamics and microtubule regulation","description":"The top GO terms are dominated by mitosis- and microtubule-related processes (spindle-kinetochore attachment, spindle pole separation, metaphase chromosome alignment, nuclear migration along microtubules, and actomyosin ring assembly), with some neuronal and stem-cell context terms that still align with cytoskeletal regulation. This suggests a cohesive theme around microtubule dynamics essential for cell division and cytoskeletal organization, justifying a label focused on mitotic spindle and microtubule regulation.","confidence":"High","size":22,"edges":169,"triangles":838,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0099607","count":12},{"id":"GO:1990535","count":12},{"id":"GO:0001560","count":12},{"id":"GO:0000073","count":12},{"id":"GO:0007080","count":12}]},{"hash":"1187578075414894618","title":"RNA Pol II Transcription Regulation","description":"Most terms center on DNA-templated transcription, regulation of transcription, initiation complex assembly, and elongation by RNA polymerase II, suggesting this cluster groups transcription regulation machinery; a few other terms appear as outliers but do not override the dominant transcription-focused signal.","confidence":"High","size":22,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0031564","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0032968","count":2},{"id":"GO:0051123","count":2}]},{"hash":"256351081600238839","title":"DNA-templated transcription regulation and ubiquitin signaling","description":"Top terms center on DNA-templated transcription and its regulation, indicating transcriptional regulators. Also present are ubiquitination-related terms (autoubiquitination, ERAD), suggesting post-translational control of these regulators. Stress/immune response terms (lipopolysaccharide, herbicide) and apoptosis imply these proteins participate in stress-induced transcriptional programs and cell fate decisions. Some obsolete terms may reflect annotation noise, but the core theme is transcription regulation linked with ubiquitin signaling.","confidence":"Medium","size":22,"edges":18,"triangles":0,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0032496","count":4},{"id":"GO:0006633","count":3}]},{"hash":"4886218262259728","title":"Bacterial amino-acid metabolism and antibiotic response","description":"The top terms point to amino-acid catabolism and related biosynthetic processes (L-alanine, L-serine, kynurenine), alongside diverse metabolism and secretion-related activities (lipopolysaccharide biosynthesis, oxalic acid secretion, organic phosphonate catabolism). The presence of antibiotic biosynthetic and antibiotic-response terms suggests antimicrobial-related functions, while Notch signaling appears as an outlier more typical of eukaryotes, likely a misannotation. Overall, the cluster seems to reflect metabolic versatility in bacteria with emphasis on amino-acid utilization and antibiotic-related responses.","confidence":"Medium","size":22,"edges":190,"triangles":1064,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":9},{"id":"GO:0097053","count":9},{"id":"GO:0007219","count":9},{"id":"GO:0017000","count":8},{"id":"GO:0009103","count":7}]},{"hash":"1321340620132706590","title":"Unknown","description":"The top terms cover plant-specific leaf senescence, DNA methylation regulation, peroxisomal protein import, protein oligomerization, oxidative stress response, mitochondrial DNA replication, chromatin assembly, and chaperone-mediated assembly, which do not converge on a single coherent function for this cluster. With no edge connections and only single-term annotations, there is insufficient signal to define a meaningful label beyond Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900056","count":1},{"id":"GO:0044030","count":1},{"id":"GO:0016558","count":1},{"id":"GO:0032463","count":1},{"id":"GO:0070407","count":1}]},{"hash":"1293125980093414223","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090162","count":3},{"id":"GO:0009408","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0071847","count":2}]},{"hash":"477500640974708311","title":"Cranial development and Wnt signaling","description":"Based on the prominent GO terms for cranial ganglion development, cranial skeletal system development, dorsal identity determination, and canonical Wnt signaling, the cluster appears to reflect cranial patterning and signaling pathways that regulate cell fate; while terms like GTPase activity and mitochondrial calcium regulation are general cellular processes, they do not negate the cranial development theme.","confidence":"Medium","size":22,"edges":126,"triangles":562,"max_degree":17,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0043547","count":12},{"id":"GO:0006607","count":11},{"id":"GO:0051561","count":11},{"id":"GO:0043065","count":11},{"id":"GO:0042144","count":11}]},{"hash":"1462547327107778299","title":"ECM Remodeling and Tissue Morphogenesis","description":"The top GO terms cluster around extracellular matrix components and tissue development\u2014collagen fibril organization, basement membrane development, and morphogenesis of tissues like bone and vasculature (intramembranous ossification, aorta smooth muscle morphogenesis, glomerular basement membrane). Additional ECM-related processes such as collagen catabolic activity and cuticle development support this theme. Some terms are less directly connected (immune regulation, aldosterone secretion), but the dominant signal points to ECM remodeling and tissue morphogenesis across organs.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001957","count":2},{"id":"GO:0045650","count":2},{"id":"GO:2000860","count":2},{"id":"GO:0032836","count":2},{"id":"GO:0001867","count":2}]},{"hash":"1460627647129629622","title":"RNA Pol II Transcription Regulation","description":"The top GO terms are centered on DNA-templated transcription and regulation of transcription from RNA polymerase II promoter, including condition-specific regulatory terms (e.g., oleic acid, carbon source). This points to a cohesive set of transcriptional regulators rather than metabolic enzymes, with minority biosynthetic terms likely incidental. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":18},{"id":"GO:0006355","count":15},{"id":"GO:0035969","count":3},{"id":"GO:1904741","count":3},{"id":"GO:0061429","count":3}]},{"hash":"1104462732062988475","title":"Mitochondrial Translation and Respiration","description":"Several terms point to mitochondria: tRNA aminoacylation for glycyl and prolyl pairs, selenocysteine biosynthesis, and general translation, plus the respiratory electron transport chain. This suggests the proteins cluster around mitochondrial protein synthesis and energy production. While some terms (DNA biosynthesis, embryonic development) are more general, the dominant theme is mitochondrial translation and respiration.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015966","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0097056","count":2},{"id":"GO:0070150","count":2},{"id":"GO:0001701","count":2}]},{"hash":"1886190928283319086","title":"Cardiac calcium signaling and small GTPase pathways","description":"This cluster is dominated by terms related to heart function and calcium dynamics (cardiac muscle contraction, heart development, detection of calcium ion, regulation of RyR calcium-release channel activity) as well as signaling via small GTPases (Rho and Ras pathways, NF-kappaB signaling). While some terms are more general (nuclear import, insulin secretion), the strongest signal ties cardiac calcium handling to GTPase-driven signaling pathways, suggesting a heart-centric calcium/GTPase regulatory theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060048","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1114566627884139808","title":"Redox stress and transcription regulation","description":"The cluster centers on redox/oxidative stress management (cellular oxidant detoxification and redox homeostasis) and transcriptional control (DNA-templated transcription, negative regulation of transcription by RNA polymerase II). Although some terms are obsolete, the recurring themes point to a functional link between oxidative stress response and transcription regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0016032","count":2}]},{"hash":"2299597627021804854","title":"DNA-Templated Transcription Regulation","description":"The dominant GO terms (regulation of DNA-templated transcription, DNA-templated transcription, and negative regulation of transcription by RNA polymerase II) indicate a transcription regulatory function, with a few minor terms related to chromatin modification and trafficking that are less representative.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0006351","count":4},{"id":"GO:0035023","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0007517","count":2}]},{"hash":"737642866847970681","title":"Cell wall biosynthesis and secretory pathway","description":"The top GO terms point to cell wall biosynthesis (cell wall organization; UDP-glucose metabolism) and the secretory pathway (SRP-dependent cotranslational targeting to membrane), suggesting a functional theme around producing and exporting cell wall components. There are some translation regulation and stress-related terms, but the strongest signals cluster around wall formation and membrane targeting. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0006011","count":2},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0045900","count":1}]},{"hash":"1977330532786568397","title":"Nitric oxide signaling and nitrosylation","description":"This cluster centers on NO-related biology: retrograde trans-synaptic signaling by nitric oxide, NO biosynthesis regulation, and nitrosylation, with gasotransmitter context (e.g., hydrogen sulfide biosynthesis). Peripheral terms such as blood pressure regulation and serotonin uptake can be linked to NO pathways, and xenobiotic catabolism may reflect broader metabolic regulation tied to NO signaling. Overall, the dominant theme is NO signaling and related post-translational modification.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098924","count":2},{"id":"GO:1901206","count":2},{"id":"GO:0051612","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0003100","count":1}]},{"hash":"918041266044773342","title":"Bone Remodeling and Dentinogenesis","description":"The dominant terms describe bone resorption and osteoclast differentiation, and odontogenesis (tooth/dentin formation), with epithelial morphogenesis also relevant to tooth development. Supporting terms about pH regulation, bicarbonate transport, and estrogen signaling may influence mineralization in bone and teeth. Together these indicate a functional module in skeletal/dental development and remodeling, hence 'Bone Remodeling and Dentinogenesis'. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043627","count":1},{"id":"GO:2001150","count":1},{"id":"GO:0009268","count":1},{"id":"GO:0045672","count":1},{"id":"GO:0015701","count":1}]},{"hash":"353829890868240217","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042744","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0009664","count":1}]},{"hash":"2085648046966501523","title":"Unknown","description":"The Top Terms include rRNA processing, chromatin modification, DNA repair, microtubule movement, and developmental processes (lens fiber differentiation, neural tube closure), with several obsolete annotations. This mix spans disparate cellular functions and lacks a clear unifying theme, so a single cohesive label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0070306","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0032995","count":3}]},{"hash":"174745929065118853","title":"Phosphorylation-driven signaling and transcription regulation","description":"Based on GO terms emphasizing serine/threonine phosphorylation, regulation of kinase activity, and control of transcription, the cluster likely groups proteins involved in phosphorylation-dependent signaling that modulates gene expression, including hormone-related pathways (adiponectin, activin receptor) and testosterone response. Some terms are obsolete, but the core theme is kinase-mediated signaling linked to transcriptional regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0018105","count":1},{"id":"GO:0010862","count":1},{"id":"GO:0045859","count":1},{"id":"GO:0033211","count":1}]},{"hash":"632066744515322542","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0090617","count":2},{"id":"GO:0090615","count":2},{"id":"GO:0010019","count":2},{"id":"GO:0009451","count":2}]},{"hash":"1026637583658491943","title":"Osteoclast differentiation and bone resorption regulation","description":"The cluster is dominated by GO terms related to osteoclast differentiation and bone resorption (positive regulation of osteoclast differentiation and positive regulation of bone resorption), suggesting a core function in bone remodeling. Additional terms touch on acid-base transport and pH response, which can influence osteoclast activity, and estrogen response is closely linked to bone remodeling, supporting the overall theme. Some unrelated terms (epithelium morphogenesis, fluid shear stress) may reflect broader tissue remodeling contexts but do not outweigh the bone-resorption signal.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015670","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0043627","count":1},{"id":"GO:2001150","count":1},{"id":"GO:0009268","count":1}]},{"hash":"1712781130878295068","title":"Auditory hair cell synapse formation and plasticity","description":"The top GO terms point to cochlear/hair cell development (cochlea morphogenesis, stereocilium organization) and synaptic function (glutamate secretion, dendritic spine morphogenesis, long-term synaptic depression, NO-mediated retrograde signaling), indicating a cohesive theme of auditory neuron synapse formation and plasticity.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":2},{"id":"GO:0098924","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0060292","count":2}]},{"hash":"2003906647154012887","title":"Cardiac gene regulation and ventricular electrophysiology","description":"The dominant terms are DNA-templated transcription and its regulation, with several entries related to ventricular cardiac muscle cell action potential, membrane repolarization, and vasoconstriction, suggesting a transcriptional control layer tied to cardiac electrophysiology. A few metabolism/brain-related terms appear but are less represented. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0007216","count":1},{"id":"GO:0002024","count":1},{"id":"GO:0032342","count":1}]},{"hash":"1706407719346101528","title":"Developmental transcriptional regulation","description":"The top terms point to DNA-templated transcription and chromatin-related regulation (histone methylation), plus multiple development-related processes (cerebellar cortex, hippocampus, heart development). This suggests a cluster of proteins involved in controlling gene expression during development, even though some terms (like plant auxin signaling) may reflect annotation noise. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080182","count":2},{"id":"GO:0021695","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0033138","count":2}]},{"hash":"576647607278752587","title":"Glycosylation and secreted glycoprotein processing","description":"The cluster\u2019s top GO terms cluster around protein O-linked glycosylation (GalNAc-mediated) and processes related to secretion of glycoproteins, including extracellular matrix components and immunoglobulin production. While there are a few carbohydrate-catabolic terms that are more general sugar metabolism, the strongest common theme appears to be glycosylation and secretion of glycoproteins, suggesting a functional group focused on post-translational modification and export. ","confidence":"Low","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030592","count":1},{"id":"GO:0006683","count":1},{"id":"GO:0046373","count":1},{"id":"GO:0070278","count":1},{"id":"GO:0016266","count":1}]},{"hash":"1703770677035367287","title":"Autophagy and ribosome regulation in yeast","description":"The top terms center on autophagy (ribophagy, engulfment by autophagosome) and ribosome-related processes (tRNA processing, ribosomal subunit export), with supportive yeast-specific regulatory themes (mating projection growth) and related lipid biosynthesis pathways, suggesting a cohesive cluster of autophagy and ribosome turnover control in yeast.","confidence":"High","size":21,"edges":14,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034517","count":4},{"id":"GO:2000235","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0046642","count":3},{"id":"GO:0061736","count":3}]},{"hash":"2281094187337273781","title":"Ribosome Biogenesis and rRNA Processing","description":"This cluster is dominated by GO terms for maturation of SSU/LSU rRNA, ribosome assembly, and preribosome large subunit formation, indicating a common role in ribosome biogenesis. Other terms like nonsense-mediated decay reflect RNA quality control contexts but do not override the ribosome-centric theme.","confidence":"High","size":21,"edges":36,"triangles":23,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000184","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0045056","count":2},{"id":"GO:0090263","count":2}]},{"hash":"1192423763203456686","title":"Cell cycle progression and TORC1 signaling","description":"This cluster is dominated by GO terms for mitotic cell cycle, cell division, and positive regulation of cell proliferation, with TORC1 signaling linking growth control to division. The inclusion of mRNA transport and GTPase activity regulation fits broader cellular regulation during proliferation, while defense-related terms appear as less central outliers. Overall, the theme centers on cell-cycle control and growth signaling.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0071456","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0043547","count":4}]},{"hash":"1256873199091642083","title":"Mesodermal development and osteoblast differentiation regulators","description":"The top GO terms center on DNA-templated transcription and its regulation, with strong links to mesodermal development processes (paraxial mesoderm, somitogenesis, circulatory system development) and osteoblast differentiation. This suggests a cluster of transcriptional regulators guiding mesodermal differentiation and bone formation, with additional general cellular processes (ribosome biogenesis, nutrient/xenobiotic responses) reflecting broader transcriptional activity in development. Confidence: High","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0001649","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0042254","count":2}]},{"hash":"200384789695131038","title":"Plant transcriptional regulation and chromatin remodeling","description":"The cluster is enriched for DNA-templated transcription and its regulation, plus chromatin remodeling and histone modification terms, which together point to transcriptional control mechanisms. The presence of ABA and osmotic-stress response terms supports a plant stress-responsive transcriptional regulation theme, and a few terms related to development (e.g., cell differentiation, secondary cell wall biogenesis) align with transcriptional programs governing growth. Some terms (like viral process or obsolete annotations) may reflect noise. Overall, the proteins likely participate in transcriptional regulation via chromatin remodeling in plants.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0006355","count":12},{"id":"GO:0009737","count":3},{"id":"GO:0043044","count":3},{"id":"GO:1901348","count":2}]},{"hash":"495916890833596076","title":"Mitochondrial translation and tRNA charging","description":"The dominant GO terms are translation and mitochondrial tRNA aminoacylation (lysyl-, asparaginyl-, and aspartyl-tRNA charging), indicating mitochondria-associated protein synthesis and tRNA charging. Some unrelated or obsolete terms are present, but the core pattern supports a mitochondrial translation focus.","confidence":"High","size":21,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0017000","count":4},{"id":"GO:0070154","count":4},{"id":"GO:0070145","count":4},{"id":"GO:0071915","count":4}]},{"hash":"2029453388627648149","title":"Nuclear RNA processing and chromatin regulation","description":"The terms cluster around nuclear RNA processing and chromatin dynamics, including spliceosome-mediated mRNA splicing, spliceosomal complex assembly, transcription termination, and import into the nucleus, as well as histone mRNA metabolism and pericentric heterochromatin formation. The presence of abiotic-stress responses (abscisic acid, water deprivation) and cell-cycle regulation suggests an integrated nucleus-centered program linking RNA processing, chromatin state, and growth/stress signaling in plants.","confidence":"Medium","size":21,"edges":163,"triangles":692,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0070317","count":2},{"id":"GO:1990141","count":2},{"id":"GO:0042633","count":2}]},{"hash":"756757070418480096","title":"Membrane Proteolysis and Protein Autoprocessing","description":"This cluster's top GO terms center on proteolytic processing: membrane protein proteolysis and protein autoprocessing, with proteolysis as a general theme. Other terms appear more diverse (xenobiotic transport, development, immune responses), suggesting a noisy cluster with a proteolysis-focused core.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0033619","count":1},{"id":"GO:0002018","count":1},{"id":"GO:0070305","count":1},{"id":"GO:0042985","count":1}]},{"hash":"484607565212194311","title":"Unknown","description":"The set shows highly diverse GO terms (redox homeostasis, DNA transcription, cytochrome complex assembly, ER targeting, ABA homeostasis, chloroplast movement, and developmental processes) with no single dominant function linking all proteins. This makes it unclear to assign a cohesive, specific label beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0017004","count":2},{"id":"GO:0006465","count":1},{"id":"GO:0045047","count":1}]},{"hash":"275062092247717463","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0009103","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0080110","count":3}]},{"hash":"81163055464210225","title":"Unknown","description":"The 21 proteins carry a highly diverse set of GO terms (transcription, ubiquitination, heart development, oligodendrocyte differentiation, immunoglobulin class switching, cell cycle, mRNA processing, lipid catabolism) with no clear shared pathway or interaction pattern (edges/triangles = 0), so a single cohesive function is not apparent.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0035544","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0003290","count":2},{"id":"GO:0048709","count":2}]},{"hash":"826367289926744978","title":"Cell signaling and cytoskeleton regulation","description":"This cluster shows enrichment for insulin receptor signaling, actin cytoskeleton organization, regulation of Rho signaling, GTPase activation, and microtubule-based movement, which together point to signaling pathways that coordinate cytoskeletal dynamics. Some terms like xenobiotic response and sterol biosynthesis are more peripheral, but the dominant theme is signaling linked to cytoskeletal regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0090630","count":2}]},{"hash":"539902278156309386","title":"Unknown","description":"The terms span diverse and largely unrelated processes (osmotic stress response, root meristem growth, cell wall biogenesis, viral processes, telomere regulation, and a DNA repair term), with several terms obsolete and no edges linking proteins. There isn\u2019t a clear common function to bind the cluster, so it\u2019s labeled Unknown with no confidence.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901348","count":1},{"id":"GO:1905778","count":1},{"id":"GO:0035066","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0016032","count":1}]},{"hash":"1880566537273384810","title":"Unknown","description":"The terms span diverse processes\u2014plant development (root meristem growth, secondary cell wall biogenesis, cell differentiation), chromatin regulation and telomere/DSB repair, osmotic stress response, and even viral processes\u2014without a single cohesive function to tie the cluster together.","confidence":"","size":21,"edges":19,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1901348","count":1},{"id":"GO:1905778","count":1},{"id":"GO:0035066","count":1},{"id":"GO:0006970","count":1},{"id":"GO:0016032","count":1}]},{"hash":"1843898351661261947","title":"Cochlear hair cell synapse development","description":"The GO terms cluster around cochlear morphogenesis and stereocilium organization, plus synaptic signaling (glutamate secretion, dendritic spine morphogenesis, long-term synaptic depression, NO retrograde signaling), indicating proteins involved in cochlear hair cell development and synaptic function.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0060088","count":2},{"id":"GO:0098924","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0035640","count":2}]},{"hash":"743467179096720272","title":"Mitochondrial respiration and proton transport","description":"The top GO terms are dominated by mitochondrial electron transport (GO:0006122), proton transmembrane transport (GO:1902600), and aerobic respiration (GO:0009060), which together point to oxidative phosphorylation and energy production in mitochondria. The other terms (DNA methylation regulation, chromatin assembly, senescence) are less clearly connected to this core function and may reflect broader annotation noise. Overall, the cluster is best described as mitochondrial energy metabolism.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006122","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0044030","count":1},{"id":"GO:0032463","count":1}]},{"hash":"1077256692386824762","title":"IRES-Dependent Translation Initiation","description":"The top GO terms are dominated by translation initiation and preinitiation complex assembly, plus translation reinitiation and IRES-dependent viral initiation, indicating the cluster centers on initiation control of translation (including viral IRES modes). A few outliers (splicing, processome, blastocyst formation) are likely secondary or annotation noise, but the main signal supports an initiation/translation-focused cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075522","count":2}]},{"hash":"1055275501398070689","title":"Redox Homeostasis and Stress Response","description":"Most terms cluster around oxidation-reduction processes, redox homeostasis, and cellular detoxification (oxidants, lipopolysaccharide, corticosterone, etc.), with supporting signals of metabolic and xenobiotic response (ethanol, selenium, thiamine biosynthesis). This pattern suggests a functional theme of maintaining redox balance and defending against oxidative and chemical stress, rather than a single specific pathway. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0045454","count":6},{"id":"GO:0009228","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0042420","count":4}]},{"hash":"1734348216103896634","title":"Neuronal development and synaptic vesicle regulation","description":"The cluster shows enrichment for brain development (GO:0007420), regulation of synaptic vesicle exocytosis (GO:2000300), synaptic vesicle maturation (GO:0016188), and presynapse to nucleus signaling (GO:0099526), all pointing to neuronal development and presynaptic synaptic function. While a couple of terms are broader or less related (e.g., ossification, mating projection growth), the dominant theme is neuronal growth and synaptic vesicle dynamics.","confidence":"High","size":21,"edges":70,"triangles":68,"max_degree":12,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043087","count":6},{"id":"GO:0007420","count":6},{"id":"GO:2000300","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0031384","count":5}]},{"hash":"80120602807116165","title":"Unknown","description":"The top GO terms span telomere maintenance, cerebellar neuron differentiation, dendrite development, GPCR signaling, immune cytokine regulation, and vitamin D response, which are diverse and lack a single cohesive biological theme; with no network edges tying them together, the cluster does not point to a specific shared function. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":9},{"id":"GO:0032212","count":7},{"id":"GO:0021707","count":7},{"id":"GO:1904355","count":7},{"id":"GO:0071651","count":7}]},{"hash":"1505152029183219045","title":"Epigenetic transcription regulation and chromatin remodeling","description":"Main terms cluster around DNA-templated transcription and chromatin regulation (histone deacetylation, chromatin silencing, rDNA heterochromatin). Some terms indicate stimulus-responsive transcription control (circadian rhythm, dopamine, glucose, methylglyoxal). The presence of obsolete terms reflects historical annotations but the core theme is epigenetic regulation of transcription. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042754","count":3},{"id":"GO:0006351","count":2},{"id":"GO:1903351","count":2},{"id":"GO:0031937","count":2},{"id":"GO:1901675","count":2}]},{"hash":"1041999111019388718","title":"Nervous-Muscular System Development and Structure","description":"The top GO terms cluster around nervous system development (brain development, olfactory nerve organization) and muscle-related processes (calcium-regulated contraction, muscle attachment), suggesting a shared theme of nervous and muscular system development and function. However, several terms point to unrelated processes (ribophagy, tRNA processing, immune regulation), indicating some heterogeneity. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0014809","count":2},{"id":"GO:0016203","count":2},{"id":"GO:0021629","count":2}]},{"hash":"1209546402335328154","title":"Cell cycle and membrane trafficking","description":"The top GO terms show a focus on cell division and cell cycle processes (cell division, cell cycle, nuclear membrane reassembly) alongside vesicle trafficking and membrane remodeling (Golgi retention, ESCRT-mediated viral budding, multivesicular body sorting). This suggests proteins coordinating division with membrane trafficking events, with some tissue-specific development context (egg chamber stalk formation). Therefore, a label emphasizing both cell cycle and membrane trafficking is appropriate.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0045053","count":4},{"id":"GO:0030713","count":3}]},{"hash":"288076687355111672","title":"Developmental Cell Cycle Signaling","description":"The top GO terms cluster around mitotic cell cycle and multicellular development (including neural tube closure), suggesting roles in embryonic development and cell division. Additional signaling-related terms indicate context-dependent signaling during development and stress. Although the proteins show no apparent direct interactions in this cluster, they collectively point to developmental processes intertwined with cell cycle regulation, justifying a label focused on developmental cell cycle signaling.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0072428","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0001843","count":2}]},{"hash":"1654487882181697258","title":"Plant cell wall remodeling and plasmodesmata organization","description":"The cluster is enriched for plant cell wall\u2013related terms, including cell wall modification, regulation of cellulose biosynthesis, and plasmodesma organization, pointing to roles in plant cell wall architecture and intercellular transport. A few unrelated terms appear (e.g., telomere regulation, piRNA processing, synaptic terms) which may be noise in this set.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009831","count":2},{"id":"GO:2001009","count":2},{"id":"GO:0009663","count":2},{"id":"GO:0006486","count":2},{"id":"GO:0036065","count":2}]},{"hash":"1512012999796885685","title":"Transcription Regulation and Signaling Regulators","description":"A core pattern in the listed terms is regulation of gene expression (regulation of DNA-templated transcription, DNA-templated transcription) with accompanying signaling and developmental processes (Wnt signaling, cerebellar granule cell differentiation, epithelial polarity, and actin organization). While there are some outliers (catecholamine metabolism, salicylic acid signaling, telomere maintenance, proteasome assembly), the cluster appears to assemble proteins involved in controlling transcription and various signaling pathways rather than a single metabolic or structural function. Confidence in a cohesive single-function label is moderate due to this heterogeneity.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006584","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0051017","count":1}]},{"hash":"898042423668158377","title":"Deubiquitinases suppressing innate immune signaling","description":"The GO terms converge on deubiquitination at specific lysine linkages (K27, K33) and on negative regulation of innate immune and inflammatory pathways (TLR3/TLR5 signaling, NF-kappaB), as well as related cellular processes like endothelial apoptosis, B cell homeostasis, and hepatocyte proliferation. This suggests a theme where deubiquitinases dampen immune signaling and inflammatory responses, possibly affecting chromatin ubiquitination as well.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990168","count":1},{"id":"GO:1990167","count":1},{"id":"GO:2000352","count":1},{"id":"GO:0001922","count":1},{"id":"GO:0002677","count":1}]},{"hash":"1429173526477791717","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (sensory perception, spindle organization, axon guidance, organelle transport, budding growth, peroxisome inheritance, cell migration), indicating no single functional theme tying these proteins together.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0007051","count":2},{"id":"GO:0016198","count":2},{"id":"GO:0051904","count":2},{"id":"GO:0007118","count":2}]},{"hash":"1593663001204683150","title":"Transcriptional Regulation and Chromatin Assembly","description":"The top terms are dominated by DNA-templated transcription and its regulation (GO:0006351, GO:0006355), with substantial involvement of nucleosome assembly (GO:0006334), indicating a core function in transcriptional control and chromatin organization. A few terms relate to heart development and cardiac muscle regulation, suggesting a potential cardiac context, but the overall signal centers on transcriptional regulation; the cardiac terms may reflect shared regulatory networks rather than a heart-specific cluster. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0006355","count":10},{"id":"GO:0006334","count":2},{"id":"GO:0007507","count":2},{"id":"GO:1901898","count":1}]},{"hash":"72834425926221633","title":"Neural development and axon guidance","description":"The top GO terms point to neural development and connectivity, including axonal fasciculation, corpus callosum development, and synapse assembly, with supporting neuronal signaling (cAMP/cGMP). Some terms like cell wall organization and urinary bladder development appear incidental, but the dominant theme is neural development and axon guidance.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0060157","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0016266","count":2},{"id":"GO:0051965","count":2}]},{"hash":"2204775295625813451","title":"Unknown","description":"The top GO terms are highly diverse (metal/ion transport, immunoglobulin production, plant hormone signaling, alkaloid response, learning, lipid metabolism, sugars biosynthesis) with no shared function, and the cluster has no edges or connectivity. This suggests no cohesive theme to label; Unknown with None confidence.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015693","count":1},{"id":"GO:0002377","count":1},{"id":"GO:0006817","count":1},{"id":"GO:0043279","count":1},{"id":"GO:0009939","count":1}]},{"hash":"1018627561611158797","title":"Glutamatergic signaling, Rho regulation, and endosomal trafficking","description":"The top terms focus on glutamatergic synaptic transmission, regulation of Rho signaling, and processes like receptor recycling and endosome size, which together suggest a module coordinating neuronal signaling with endosomal trafficking and cytoskeletal dynamics. While a few transcription-related and stress-response terms appear, they are less central to this cluster. Therefore, the label captures the main functional theme with reasonable confidence.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0035249","count":5},{"id":"GO:0001881","count":4}]},{"hash":"1375530354411670807","title":"Nuclear transcription regulation and RNA surveillance","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, plus RNA surveillance pathways (non-stop decay and no-go decay), as well as transcription termination. These features point to a core theme of nuclear gene expression control and RNA quality control, with additional, broader developmental terms (MET and stem cell maintenance) that may reflect ancillary roles in development. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0071025","count":1},{"id":"GO:0070481","count":1}]},{"hash":"361029836781380120","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning telomere maintenance, cytoskeleton and spindle assembly, RNA processing, signaling pathway regulation (BMP/TGF-\u03b2), photosystem adjustment, and meristem maintenance. With no clear shared function or interaction pattern among the proteins, there isn\u2019t a coherent biological theme to label a specific cluster. None","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0051225","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0090501","count":1}]},{"hash":"1334438121871069570","title":"Nutrient signaling and vesicle trafficking regulation","description":"The terms cluster around responses to glucose and fatty acids (nutrient signaling) together with negative regulation of vesicle trafficking processes (exocytosis, pinocytosis, phagocytosis) and protein complex oligomerization, plus a phosphorylation term related to signaling. This suggests a theme of coordinating nutrient sensing with control of vesicle trafficking, even though the associations are not exceptionally tight. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030819","count":1},{"id":"GO:0071398","count":1},{"id":"GO:0071333","count":1},{"id":"GO:0051259","count":1},{"id":"GO:0018106","count":1}]},{"hash":"2109480380430659617","title":"Mitotic Spindle and Cytoskeletal Organization","description":"The top GO terms emphasize microtubule-based mitosis (nuclear migration along microtubules, spindle-kinetochore attachment, chromosome alignment, spindle pole separation) and actomyosin ring assembly, pointing to cytoskeletal dynamics during cell division. Some neuronal terms reflect broader cytoskeletal roles in neurons, suggesting a theme of cytoskeleton organization with emphasis on mitosis and cell shape maintenance.","confidence":"Medium","size":20,"edges":94,"triangles":276,"max_degree":15,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0030473","count":5},{"id":"GO:0099607","count":4},{"id":"GO:1990535","count":4},{"id":"GO:0001560","count":4},{"id":"GO:0000073","count":4}]},{"hash":"594487086582880953","title":"Ribosome biogenesis and translation initiation","description":"This cluster's GO terms cluster around translation machinery, including formation of the translation preinitiation complex, regulation of translational initiation, and small-subunit processome assembly, pointing to roles in ribosome biogenesis and initiation of protein synthesis. Some metabolic terms appear but are less coherent with the main theme, so the core signal is the protein synthesis machinery.","confidence":"Medium","size":20,"edges":71,"triangles":77,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0005989","count":2},{"id":"GO:0009437","count":1},{"id":"GO:1902270","count":1},{"id":"GO:1900751","count":1}]},{"hash":"1049337742445790443","title":"Tissue Morphogenesis and ECM Organization","description":"This cluster\u2019s top GO terms cluster around tissue development and morphogenesis (skin, eye, bone via intramembranous ossification, kidney basement membrane development) and extracellular matrix organization (collagen fibril organization), indicating a shared theme of tissue formation and matrix remodeling. Immune regulation and endocrine-related terms appear but are ancillary to the main morphogenesis/ECM signal.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043589","count":3},{"id":"GO:0043588","count":3},{"id":"GO:0048593","count":3},{"id":"GO:0001957","count":2},{"id":"GO:0045650","count":2}]},{"hash":"2066612649369602232","title":"Zinc Ion Transport and Homeostasis","description":"The top GO terms cluster around zinc import across membranes, zinc ion homeostasis, detoxification, and responses to zinc ion starvation, indicating a zinc metabolism/transport module. Some outliers like limb development and LPS biosynthesis appear but do not define the core function; the dominant signal is zinc handling and transport.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006882","count":3},{"id":"GO:0006831","count":2},{"id":"GO:0060173","count":2},{"id":"GO:0044749","count":2},{"id":"GO:1903615","count":2}]},{"hash":"842784618128667519","title":"T Cell Development and Signaling","description":"This cluster is dominated by T cell development and signaling terms (beta selection, NK T cell differentiation, T cell proliferation) and includes several signaling pathways (Wnt, Kit, PDGF) and signaling complex assembly, suggesting a cohesive theme of immune cell development and signaling, with a few broader developmental terms present as context.","confidence":"High","size":20,"edges":14,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090263","count":18},{"id":"GO:0071469","count":17},{"id":"GO:0046641","count":17},{"id":"GO:0001865","count":17},{"id":"GO:0060068","count":17}]},{"hash":"938224625894608273","title":"Mitochondrial fission and muscle development","description":"This cluster shows strong signals for mitochondrial dynamics (mitochondrial fission, positive regulation of fission, mitochondrion localization via microtubules) and muscle-related processes (myoblast fusion, adult locomotory behavior, heart contraction), suggesting a shared function in coordinating mitochondrial behavior with muscle/heart development and function. Some cell-cycle or aging terms are present but less central to the main theme.","confidence":"Medium","size":20,"edges":33,"triangles":31,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0007062","count":1},{"id":"GO:0090141","count":1},{"id":"GO:0090529","count":1}]},{"hash":"1894319088237639937","title":"Transcription Regulation & Protein Modification","description":"The cluster's top GO terms center on regulation of DNA-templated transcription, transcription processes, and post-translational modifications (ubiquitination, phosphorylation, PARylation) along with proteasome assembly. This points to a cohesive theme of gene-expression control via protein modification and degradation, with support from telomere maintenance and neural differentiation terms that can relate to chromatin regulation and stress responses.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":3},{"id":"GO:0061408","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0016567","count":3}]},{"hash":"1580644230377966179","title":"Nuclear transcription regulation and developmental signaling","description":"The top terms cluster around regulation of gene expression and developmental or cellular signaling processes, including telomerase holoenzyme assembly and regulation of DNA-templated transcription, as well as root meristem growth, neuroblast polarity, auxin and cytokinin signaling, and glucocorticoid signaling. This suggests proteins that function in controlling transcription and coordinating cell fate, polarity, and signaling during development, rather than core metabolic roles. While some terms are species-specific, the common theme is regulatory control of transcription and development-related signaling.","confidence":"Medium","size":20,"edges":22,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1905323","count":2},{"id":"GO:0006355","count":2},{"id":"GO:2000012","count":1},{"id":"GO:1905793","count":1},{"id":"GO:0010449","count":1}]},{"hash":"2135168757964950103","title":"Bacterial Metabolism and Cell Envelope Biosynthesis","description":"This cluster shows enrichment for core biosynthetic and metabolic pathways typical of bacteria, including fructose and fructose-6-phosphate metabolism, the non-oxidative pentose-phosphate shunt, serine biosynthesis, and chorismate (aromatic amino acid precursor) biosynthesis, alongside lipopolysaccharide biosynthesis and cadmium ion transport. These terms collectively point to metabolic processes underpinning cell envelope construction and nutrient processing, with LPS biosynthesis being a hallmark of Gram-negative bacteria. A couple of terms like intestinal epithelial cell development may reflect cross-species annotation noise, but the dominant theme is bacterial metabolism and envelope biosynthesis. Confidence: Medium","confidence":"","size":20,"edges":21,"triangles":2,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006000","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0070574","count":2}]},{"hash":"1452159679868884509","title":"Hippo-Wnt signaling and apoptosis in cell fate","description":"This cluster is dominated by terms for hippo signaling and positive regulation of canonical Wnt signaling, both central to controlling cell proliferation, growth, and fate decisions. Additional terms on apoptosis, cell cycle arrest, and differentiation (keratinocyte differentiation) support a cohesive theme of cell fate regulation and growth control, with ancillary roles in nuclear transport and telomere maintenance that can influence long-term cellular outcomes.","confidence":"High","size":20,"edges":183,"triangles":1020,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035329","count":19},{"id":"GO:0090263","count":19},{"id":"GO:0060044","count":19},{"id":"GO:0006915","count":19},{"id":"GO:0046827","count":19}]},{"hash":"2259390154877990204","title":"Mitochondrial translation and mitophagy","description":"Dominant terms center on mitochondrial ribosome maturation and translation (LSU/5.8S rRNA), mitochondrial autophagy (mitophagy), and protein targeting to mitochondrion. This points to a cluster of mitochondria-associated translation and quality-control processes. The remaining terms (glycolytic regulation, gluconeogenesis, insulin secretion, cardiac apoptosis) are energy/metabolism-related, reinforcing a mitochondria-centered functional context. Therefore the label reflects a mitochondrial translation/mitophagy\u2013related cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":1},{"id":"GO:1903146","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000466","count":1},{"id":"GO:1903955","count":1}]},{"hash":"1701574058896482442","title":"Auditory hair cell synapse formation and function","description":"Most terms cluster around auditory hair cell biology (stereocilium organization, cochlea morphogenesis) and synaptic signaling (glutamate release, LTD, dendritic spine morphogenesis, NO-mediated signaling). This implies the proteins function in development and transmission at auditory synapses.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090141","count":2},{"id":"GO:0060088","count":2},{"id":"GO:0098924","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0035640","count":2}]},{"hash":"2135589369766680728","title":"Translation initiation and rRNA processing","description":"This cluster\u2019s top terms cluster around translation initiation (translation reinitiation and formation of translation preinitiation complex) and rRNA processing, pointing to involvement in protein synthesis initiation and ribosome maturation. A few terms pertain to development or other processes, which may reflect multifunctional proteins or annotation noise, but the dominant signal is translation-related.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0002188","count":11},{"id":"GO:0001731","count":11},{"id":"GO:0070306","count":9},{"id":"GO:0000447","count":9},{"id":"GO:0006349","count":9}]},{"hash":"159146701672189973","title":"LPS-TLR innate immune signaling","description":"Most terms describe lipopolysaccharide recognition and signaling through Toll-like receptors (TLR4 and TLR8), triggering innate immune and inflammatory responses. A few terms touch on broader kinase regulation and cell cycle, but the dominant theme is LPS-driven innate immunity.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031663","count":3},{"id":"GO:0032497","count":3},{"id":"GO:0071222","count":3},{"id":"GO:0034142","count":3},{"id":"GO:0045087","count":3}]},{"hash":"2260732158777115009","title":"Energy Metabolism and Signaling Cluster","description":"The proteins are enriched for core metabolic processes (TCA cycle, glyoxylate cycle, CoA biosynthesis) and phosphorylation, with additional GO terms related to cGMP signaling and olfactory perception, suggesting a group of metabolic enzymes intertwined with signaling functions. Some terms (embryonic development, redox) are less cohesive, but the dominant themes point to energy metabolism coupled with signal transduction, justifying the label.","confidence":"Medium","size":20,"edges":21,"triangles":1,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0015937","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0006097","count":3}]},{"hash":"1462801046711554059","title":"Small-molecule biosynthesis and catabolism","description":"The GO terms point to biosynthesis of vitamins and quinones (ascorbic acid, menaquinone, phylloquinone) along with antibiotic biosynthesis, and to catabolic pathways for aromatic and fatty acid compounds (phenylacetate, naphthalene, valine) plus general oxidation-reduction processes. This combination suggests a cluster focused on diverse small-molecule metabolism, including both synthesis and breakdown pathways. ","confidence":"Medium","size":20,"edges":27,"triangles":3,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0009234","count":2},{"id":"GO:0042372","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0006635","count":2}]},{"hash":"227131676349197081","title":"Molybdenum cofactor biosynthesis and sulfur metabolism","description":"The cluster is driven by terms related to the biosynthesis of cofactors (molybdopterin MoCo, molybdenum incorporation, FAD, glutathione) and sulfur metabolism (sulfate assimilation, hydrogen sulfide biosynthesis), suggesting a cohesive role in cofactor assembly and sulfur pathways. A couple of receptor clustering terms appear but do not define the overall function.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032324","count":1},{"id":"GO:0006747","count":1},{"id":"GO:0072579","count":1},{"id":"GO:0018315","count":1},{"id":"GO:0070814","count":1}]},{"hash":"1034297408237203032","title":"Unknown","description":"The top terms are a mix of RNA metabolism (miRNA catabolic process, splicing regulation), translation/ ribosome biogenesis (translation initiation, preinitiation complex, small-subunit processome), and viral-related processes (virion assembly, proviral latency, ESCRT-mediated budding), with no single unifying function across them. Because the terms do not cohere into a specific biological theme, a concise, accurate label cannot be established beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0033120","count":1},{"id":"GO:0039702","count":1},{"id":"GO:0006446","count":1}]},{"hash":"594122685591875639","title":"GTPase-Driven Cytoskeleton and Synaptic Signaling","description":"The cluster is dominated by GO terms pointing to small GTPase signaling (Rho, Ras, activation/regulation) and actin cytoskeleton organization, alongside synaptic processes (synaptic vesicle priming, long-term synaptic depression) and sensory-related terms. This suggests a coherent module where GTPase signaling regulates cytoskeletal dynamics essential for synaptic function, possibly in sensory neurons or synapses, with centrosome localization appearing as a related cellular architecture aspect. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0060292","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0090630","count":2}]},{"hash":"1949581619380130166","title":"Unknown","description":"The top terms are a mix of metabolism (methionine/threonine salvage), stress/defense (response to antibiotic, innate immune response), signal transduction (phosphorylation), and ciliopathy-related processes (sperm axoneme assembly, regulation of axon extension, protein polyglycylation) with no clear unifying function. The lack of shared pathway or coherent theme, plus zero edges, makes a specific, representative label unlikely.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0019284","count":2}]},{"hash":"1171153773922083532","title":"Ciliary and flagellar assembly and motility","description":"This cluster is driven by GO terms tied to axoneme assembly, flagellated sperm motility, and cilium movement, indicating a shared function in constructing and driving motile cilia/flagella. Additional terms on protein oligomerization and regulated export from the nucleus may reflect the complex assembly and regulation of these structures.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0007288","count":1}]},{"hash":"2072934252977739763","title":"Diverse metabolism and detoxification","description":"These proteins span a mix of metabolic biosynthesis and catabolic pathways (antibiotic biosynthesis, menaquinone and phenylpropionate catabolism) and detoxification, plus occasional signaling regulation (endocannabinoid regulation, strigolactone response). The common thread is broad metabolic processing and chemical-response functions rather than a single cohesive pathway, so a broad metabolism-focused label fits best.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:1902348","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0006212","count":3}]},{"hash":"719794077063095363","title":"Neural and Lens Development","description":"This cluster is most strongly associated with neural and ocular development, as indicated by GO terms like brain development, neural tube closure, and lens fiber cell differentiation. While some terms point to broader nuclear and ribosomal processes (transcription, rRNA processing, histone modification, DNA repair), the dominant signal centers on neural and lens tissue formation, suggesting a developmental regulatory theme in neural/eye contexts.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0001843","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0070306","count":2},{"id":"GO:0000447","count":2}]},{"hash":"1708377335759463324","title":"Unknown","description":"The top GO terms span telomere maintenance, neuronal differentiation, immune signaling, NF-kB regulation, dendrite development, kinase activity regulation, vitamin D response, and post-translational modification, indicating a highly diverse and unconnected set of functions with no single dominant theme. Therefore a cohesive label is not apparent.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":6},{"id":"GO:0021707","count":6},{"id":"GO:1904355","count":6},{"id":"GO:0071651","count":6},{"id":"GO:0007253","count":6}]},{"hash":"1404697863106443122","title":"Transcriptional, Signaling, and Proteostasis Regulation","description":"The cluster is enriched for terms spanning transcription (DNA-templated transcription, mRNA transport), signaling (positive regulation of GTPase activity, TORC1 signaling, peptidyl-serine dephosphorylation), and protein turnover (SCF-dependent ubiquitin-protein catabolic process). This suggests proteins involved in coordinating gene expression with signaling and proteostasis, rather than a single linear pathway. The diverse yet regulatory nature justifies a label centered on transcriptional and signaling control with proteostasis influence.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0031146","count":5}]},{"hash":"461989852937883647","title":"Developmental signaling and morphogenesis","description":"Represents processes driving organism development and tissue morphogenesis, highlighted by multicellular organism development, Wnt signaling, and lens fiber differentiation, plus cytoskeletal dynamics (microtubule movement) and mechanical signaling; some other terms appear to be unrelated background annotations.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0097284","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0070306","count":2}]},{"hash":"1315307492242347912","title":"Unknown","description":"The GO terms span a mix of processes from cell wall organization and DNA metabolism to signaling responses (cAMP, peptide hormones) and mRNA stability, with even renal water transport and lipid signaling; there's no single cohesive function tying all proteins together, so a general Unknown label is most appropriate.","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0045454","count":4},{"id":"GO:2001153","count":4},{"id":"GO:0046856","count":4},{"id":"GO:0006308","count":4}]},{"hash":"75419291029169549","title":"Antiviral innate immune response","description":"The cluster shows strong enrichment for innate immune response and defense response to virus, suggesting proteins function in antiviral defense signaling. While other terms touch on cell cycle regulation and cytokinin signaling, the dominant theme is innate antiviral defense. Confidence: High","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045842","count":6},{"id":"GO:0051607","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0009736","count":5},{"id":"GO:0071260","count":4}]},{"hash":"470271493935673431","title":"Exocytosis and vesicle trafficking regulation","description":"This cluster is dominated by GO terms related to vesicle trafficking and secretion, including negative regulation of SNARE complex assembly, exocytosis, and exocyst localization, suggesting a core theme of regulating vesicle fusion and targeting. Additional terms on GTPase activity regulation and ubiquitin/proteasomal turnover fit with the control of trafficking machinery, while development and immune signaling terms appear as broader context or secondary connections.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0046827","count":2}]},{"hash":"1113832634703160525","title":"Unknown","description":"The terms span telomere maintenance, neuronal differentiation, immune signaling, and various regulatory processes with no single, cohesive biological function that ties the cluster together.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:0021707","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0071651","count":4},{"id":"GO:0007253","count":4}]},{"hash":"2303837555709496360","title":"Neuronal differentiation and signaling regulation","description":"This cluster features terms tied to neuronal development (cerebellar granule cell differentiation, negative regulation of dendrite development) and regulation of signaling pathways (negative regulation of protein serine/threonine kinase activity), suggesting roles in fine-tuning neural signaling. The presence of immune-regulatory terms (NF-kappaB sequestration, negative regulation of IL-12 production, chemokine production, and vitamin D response) indicates broader regulatory signaling context that may intersect with neural development. Telomere maintenance terms are present but less central. Overall, the core theme appears to center on neuronal differentiation processes and the regulation of signaling cascades.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0021707","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0071651","count":2}]},{"hash":"1770206103313134477","title":"TLR signaling and inflammatory response","description":"These terms collectively reflect innate immune signaling: TLR8 signaling and Toll pathway engagement, upregulation of inflammatory cytokines (IFN-\u03b1, IL-18) and antibacterial peptides, and activation of autophagy. The overall theme is a TLR-driven inflammatory response and antimicrobial programs. The collagen fibril organization term likely reflects tissue context rather than core signaling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":1},{"id":"GO:0032741","count":1},{"id":"GO:0034158","count":1},{"id":"GO:0050729","count":1},{"id":"GO:0045356","count":1}]},{"hash":"529116394166873405","title":"Neuronal phototransduction and calcium signaling","description":"The cluster includes terms centered on phototransduction and calcium signaling (phototransduction; cellular response to calcium ion), with supporting neural context such as CNS development and ion transport. Additional terms cover broad signaling and detoxification, but the strongest shared theme is neural/light-sensing signaling and calcium-mediated responses, suggesting a neuronal photoreceptor\u2013like functional theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0001516","count":2},{"id":"GO:0034220","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0007602","count":2}]},{"hash":"1668951986211151062","title":"Unknown","description":"The top terms span ubiquitination, cell proliferation, kinase regulation, sensory processes, and various developmental pathways across different tissues (eye, kidney, muscle, insect cuticle). This heterogeneity suggests no single cohesive function for the cluster. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008284","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0006469","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0002576","count":1}]},{"hash":"413553994419292128","title":"Mitochondrial translation and respiration","description":"This cluster is dominated by GO terms tied to mitochondria: mitochondrial-specific tRNA aminoacylation (gly-, pro-, his-tRNAs), translation, and the respiratory electron transport chain, plus related mitochondrial morphogenesis. These together suggest a cohesive theme around mitochondrial protein synthesis and energy production, despite a few outlier terms. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007044","count":2},{"id":"GO:0015966","count":1},{"id":"GO:0071897","count":1},{"id":"GO:0070150","count":1},{"id":"GO:0001701","count":1}]},{"hash":"1837906282154736874","title":"Cell Cycle and Immune Signaling Regulators","description":"The top GO terms point to mitotic processes and regulation of cytokinesis, plus transcriptional regulation, NF-kappaB signaling, and interferon response, with additional hints of RNA processing and unfolded protein stress. This combination suggests a set of regulatory proteins that coordinate cell division with immune signaling and gene expression control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0032465","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0006355","count":1}]},{"hash":"1142728744246938911","title":"Unknown","description":"The top terms point to scattered regulatory processes, including negative regulation of phosphatase and kinase activities, and muscle-related maintenance/differentiation, with other unrelated chemical response terms and several obsolete GO terms. This mix lacks a single coherent function or pathway that ties the cluster together, so a reliable intuitive name cannot be assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010923","count":1},{"id":"GO:0006469","count":1},{"id":"GO:0051154","count":1},{"id":"GO:0014834","count":1},{"id":"GO:1904772","count":1}]},{"hash":"909831063288256421","title":"Unknown","description":"The terms are highly heterogeneous (NAD+ catabolic process, viral process, various developmental and imprinting-related terms) with only single counts and several obsolete annotations, and there are no edges linking the proteins. This provides no coherent shared function to name the cluster.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019677","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0018120","count":1},{"id":"GO:0071660","count":1},{"id":"GO:0009405","count":1}]},{"hash":"840405104242489311","title":"Nutrient-Regulated RNA Pol II Transcription","description":"Top GO terms indicate a common theme of DNA-templated transcription and regulation of transcription from the RNA polymerase II promoter in response to nutrients and metabolites (oleic acid, carbon sources). While a few biosynthetic processes appear, the predominant signal is transcriptional regulation linked to nutrient cues, supporting a cohesive label for a transcription-focused cluster without strong interaction evidence. High","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035969","count":3},{"id":"GO:1904741","count":3},{"id":"GO:0061429","count":3},{"id":"GO:0061415","count":3}]},{"hash":"1841266508840576647","title":"Nociception and Thermosensation","description":"This cluster is dominated by GO terms tied to pain and temperature sensing\u2014nociception, thermoception, cold response, and mechanical pain detection\u2014with an additional note of TRP/capsazepine-related signaling. While there are ancillary inflammatory signals present, the core pattern points to sensory pain and thermal perception pathways, justifying a label like nociception and thermosensation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007216","count":4},{"id":"GO:0071651","count":4},{"id":"GO:0030103","count":4},{"id":"GO:0050966","count":4},{"id":"GO:0009409","count":4}]},{"hash":"671014380524622612","title":"Ribosome Biogenesis and Translation","description":"Top GO terms cluster around ribosome production and function: tRNA modification, cytoplasmic translation, ribosome biogenesis, and export of the large subunit from the nucleus. There are also related cell-cycle and cytokinesis terms, which can co-occur with growth-related ribosome activity. Therefore, the label Ribosome Biogenesis and Translation captures the primary function of this cluster.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0055072","count":1},{"id":"GO:0007049","count":1}]},{"hash":"39605450582323557","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms for ribosome biogenesis and maturation of rRNA (large and small subunit), as well as formation of the translation preinitiation complex and translation reinitiation, indicating a cohesive theme around ribosome assembly and initiation of translation. Some RNA processing terms (mRNA splicing, RNA methylation) appear but are secondary to the ribosome-focused functions.","confidence":"High","size":19,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000463","count":3}]},{"hash":"939532914288027506","title":"Ammonium and Nitrogen Transport","description":"This cluster centers on transport and utilization of nitrogenous compounds, especially ammonium (ammonium transmembrane and transepithelial transport, methylammonium transport) and nitrogen utilization terms. The few growth-related GO terms (pseudohyphal growth, invasive growth in response to glucose limitation) suggest nutrient-limitation\u2013driven development, consistent with a theme of nutrient uptake and adaptation. Overall, ammonium/nitrogen transport and utilization best explains the shared functions in this set.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007124","count":1},{"id":"GO:0006808","count":1},{"id":"GO:0080181","count":1},{"id":"GO:0001403","count":1},{"id":"GO:0019740","count":1}]},{"hash":"913397188168778636","title":"Retina and photoreceptor development","description":"The top GO terms point to eye-specific biology: retina development, photoreceptor cell maintenance, and receptor localization to cilia, with supporting signals related to neural/craniofacial development such as ganglion and neurocranium morphogenesis, suggesting a cohesive theme of eye/retina morphogenesis and photoreceptor function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097500","count":1},{"id":"GO:0006910","count":1},{"id":"GO:0045494","count":1},{"id":"GO:0060348","count":1},{"id":"GO:1901621","count":1}]},{"hash":"563204327308215471","title":"DNA replication and cell cycle regulation","description":"The top GO terms are dominated by DNA replication, positive regulation of the nuclear cell cycle, and the centrosome cycle, with additional signals for mitotic cell cycle and telomere maintenance, indicating a cohesive theme around genome duplication and cell division. Some developmental terms (embryonic cranial skeleton morphogenesis and visual perception) may reflect broader roles or annotation overlap, but the core signal remains cell-cycle\u2013related functions.","confidence":"Medium","size":19,"edges":24,"triangles":3,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":17},{"id":"GO:0006260","count":17},{"id":"GO:0007098","count":17},{"id":"GO:0048701","count":17},{"id":"GO:0007601","count":15}]},{"hash":"508966040958322667","title":"Membrane transporters and synaptic vesicle loading","description":"The top GO terms show diverse membrane transport activities (sodium, sialic acid, xenobiotic, vitamin, phosphate, nitrite, fucose) along with neuronal-specific roles like neurotransmitter secretion and neurotransmitter loading into synaptic vesicles. The common thread is membrane transport proteins involved in substrate translocation and vesicular neurotransmission, making this cluster best described as membrane transporters with synaptic vesicle loading tendency.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0007269","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0098700","count":2}]},{"hash":"1893865394416651354","title":"Unknown","description":"The top GO terms span immune response, stress responses (cold), apoptosis, neural development, reproductive processes, transcription regulation, and hematopoietic differentiation, indicating no single cohesive function tying all proteins together. Because the cluster does not converge on one clear biological theme, a generic unknown label is most appropriate.","confidence":"","size":19,"edges":6,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0032496","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0009409","count":7},{"id":"GO:0048240","count":7}]},{"hash":"143481688109876033","title":"Hippo\u2013Wnt signaling and differentiation","description":"This cluster shows enrichment for Hippo signaling (GO:0035329) and positive regulation of canonical Wnt signaling (GO:0090263), along with related processes like DNA-templated transcription, apoptosis, dendrite morphogenesis, and keratinocyte differentiation. These terms together point to signaling networks that regulate development, tissue growth, and cell fate decisions, rather than a single isolated function. Potassium ion transport and some other terms are present but less central to the main theme. Overall, the proteins appear to participate in developmental signaling and differentiation regulation.","confidence":"Medium","size":19,"edges":75,"triangles":114,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006813","count":9},{"id":"GO:0035329","count":8},{"id":"GO:0090263","count":8},{"id":"GO:0060044","count":8},{"id":"GO:0006351","count":8}]},{"hash":"1510598329422721389","title":"Synaptic development and axon guidance","description":"Dominant terms describe neuronal connectivity: dendritic spine morphogenesis, synapse assembly, trans-synaptic signaling, and axon guidance of retinal ganglion and sensory neurons. The retinoic acid response further supports neuronal differentiation. While there are a few other morphogenesis terms (mouth and digestive tract) present, they are less central to this cluster's prevailing theme. Overall, the cluster most plausibly reflects synaptic development and neuronal pathfinding.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060997","count":9},{"id":"GO:0045880","count":9},{"id":"GO:0051965","count":9},{"id":"GO:0097155","count":9},{"id":"GO:0050798","count":8}]},{"hash":"1131619384714269264","title":"Unknown","description":"Top terms cover antibiotic response, tRNA modification, various biosynthetic processes, and transcription regulation, with no single cohesive function linking the proteins; the diversity suggests no clear cluster-specific theme.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0071320","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0005978","count":2}]},{"hash":"1005124983550975276","title":"Ion Transport Across Membranes","description":"The cluster's top GO terms are dominated by proton, sodium, and monoatomic ion transmembrane transport, indicating membrane ion transporters as the common function. A few terms about phototransduction, insulin secretion, and transcription regulation appear but are less frequent and could reflect annotation breadth; overall the theme centers on ion movement across membranes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015992","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0034220","count":1},{"id":"GO:0018298","count":1},{"id":"GO:0007602","count":1}]},{"hash":"63590575191121184","title":"ECM Remodeling and Tissue Morphogenesis","description":"This cluster centers on extracellular matrix (ECM) organization and remodeling, as reflected by collagen fibril organization and collagen catabolic process, along with basement membrane development. It also includes tissue morphogenesis terms (aorta smooth muscle tissue morphogenesis, intramembranous ossification) and cuticle-related development, suggesting a cohesive theme around ECM-driven tissue formation. Immune-related terms appear but are not dominant.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001957","count":1},{"id":"GO:0045650","count":1},{"id":"GO:2000860","count":1},{"id":"GO:0032836","count":1},{"id":"GO:0001867","count":1}]},{"hash":"2297485363336755882","title":"Transcription Regulation and Translation Control","description":"The cluster shows a clear enrichment for transcription-related GO terms (DNA-templated transcription, regulation of DNA binding, negative regulation of RNA polymerase II regulatory region DNA binding, and thyroid hormone metabolic processes) and for translation regulation (regulation of translation, cytosolic ribosome assembly). While a couple of transport/osmotic stress terms are present, the dominant theme is gene expression control at both transcriptional and translational levels, suggesting proteins involved in nuclear regulation of transcription and protein synthesis. Confidence: Medium","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042403","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0006919","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1847013797507153942","title":"Ubiquitin-Proteasome and Autophagy Network","description":"This cluster's top GO terms cluster around protein quality control: proteasome-mediated ubiquitin-dependent protein catabolic process, ERAD pathway regulation, deubiquitination regulation, and autophagosome assembly, all core components of proteostasis. Additional terms like Golgi organization and nuclear membrane reassembly suggest coordinated membrane/organelle remodeling linked to turnover and trafficking during quality control and cell cycle. While some terms such as ascospore formation and NF-kappaB sequestration are less central, the dominant theme is protein degradation and autophagy pathways that maintain protein homeostasis. The absence of edges does not negate this functional theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043161","count":1},{"id":"GO:0030437","count":1},{"id":"GO:0031134","count":1},{"id":"GO:1904293","count":1},{"id":"GO:0000045","count":1}]},{"hash":"44076128509145532","title":"Cytoskeletal dynamics and cell migration","description":"This cluster is dominated by GO terms tied to cell movement and actin-driven structures, notably cell migration (GO:0016477) and lamellipodium assembly (GO:0030032), with several entries linked to Rho and Ras signaling (GO:0035023, GO:0046580), which regulate cytoskeletal remodeling. While other terms touch on broader signaling (insulin receptor, GPCR pathways) and immune-related responses, the core signal revolves around cytoskeletal dynamics enabling cell motility, especially in migratory or immune contexts.","confidence":"Medium","size":19,"edges":29,"triangles":6,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0045843","count":2},{"id":"GO:0006376","count":2},{"id":"GO:0001865","count":2},{"id":"GO:0030032","count":2}]},{"hash":"652838023965484437","title":"Cell Growth and Transcription Regulation","description":"The top GO terms point to growth control and gene expression regulation, including cell growth, DNA-templated transcription, and regulation of translation, along with cell cycle processes like mitotic cell cycle and cytokinesis. Additional signals such as NF-kappaB signaling, protein ubiquitination, and xenobiotic response suggest a broader regulatory network coordinating growth, division, and transcription under stress.","confidence":"Medium","size":19,"edges":152,"triangles":697,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0006351","count":2},{"id":"GO:2001015","count":2},{"id":"GO:1902527","count":2}]},{"hash":"443727475081120614","title":"TLR-Driven Inflammatory Signaling","description":"This cluster is dominated by GO terms tied to Toll-like receptor signaling and inflammatory responses, including TLR8 signaling, Toll signaling, interferon-\u03b1 and IL-18 production, and antibacterial peptide biosynthesis. The recurring emphasis on innate immune sensing and downstream inflammatory pathways suggests proteins function together in pathogen recognition and initiating defense responses, with supporting roles in autophagy and extracellular matrix remodeling. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":1},{"id":"GO:0032741","count":1},{"id":"GO:0034158","count":1},{"id":"GO:0050729","count":1},{"id":"GO:0045356","count":1}]},{"hash":"618458502540554771","title":"Unknown","description":"The top GO terms span telomere maintenance, neuronal differentiation, immune signaling, vitamin D response, kinase regulation, and post-translational modification, with no single shared function tying them together. This heterogeneity suggests there is no coherent, common theme for the cluster. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":9},{"id":"GO:0021707","count":9},{"id":"GO:1904355","count":9},{"id":"GO:0071651","count":9},{"id":"GO:0007253","count":9}]},{"hash":"1454149160113628567","title":"Auditory hair-cell synapse and cochlea morphogenesis","description":"This cluster is dominated by GO terms tied to the auditory system and synaptic function, including stereocilium organization, cochlea morphogenesis, glutamate secretion, and synaptic plasticity (dendritic spine morphogenesis, long-term synaptic depression), indicating proteins involved in hair-cell synapses and cochlear development. Some terms appear unrelated (opsonization, exploration behavior), likely representing noise in the annotation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":3},{"id":"GO:0098924","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0035640","count":3},{"id":"GO:0060292","count":3}]},{"hash":"1597805350027143642","title":"Unknown","description":"The top GO terms are a mix of transport-related processes (folate, methotrexate, ion and proton transport) with several outliers (phototransduction, swimming, glucosinolate catabolic process, ubiquitination), offering no single cohesive function for the entire cluster. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015885","count":1},{"id":"GO:0051958","count":1},{"id":"GO:0034220","count":1},{"id":"GO:0018298","count":1},{"id":"GO:0007602","count":1}]},{"hash":"1146529556339103536","title":"Meiosis and germ cell genome maintenance","description":"The top GO terms cluster around germ cell development and meiotic processes (germ cell development, gene conversion at mating-type locus, meiotic mismatch repair), along with DNA damage response and repair (p53-mediated signaling, interstrand cross-link repair). Immunoglobulin diversification terms (somatic hypermutation, IgA switching) hint at recombination-related processes but fit under the broader theme of genome maintenance during meiosis and germ cell development. Therefore, the label Meiosis and germ cell genome maintenance is appropriate.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007281","count":2},{"id":"GO:0016446","count":2},{"id":"GO:0061500","count":2},{"id":"GO:0007050","count":2},{"id":"GO:0006119","count":2}]},{"hash":"1829070953768225348","title":"Developmental Gene Regulation","description":"The cluster centers on developmental processes (skin development, multicellular organism development, blastocyst development) and transcriptional control (DNA-templated transcription, regulation of DNA binding), with accompanying signaling regulation (kinase activity, autophosphorylation, GTPase activity) that typically modulates gene expression during development. This combination suggests proteins functioning in developmental gene regulation and signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043588","count":5},{"id":"GO:0031954","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0071902","count":4},{"id":"GO:0007275","count":4}]},{"hash":"1140545465396827307","title":"Brain-region neural development","description":"The cluster shows multiple brain-region development terms (cerebellar cortex, striatum, thalamus, olfactory bulb mitral cell layer development), suggesting a theme of neural development across brain regions. Some metabolic or generic terms (TCA cycle, oxidation-reduction, chloramphenicol response) appear incidental and do not define a cohesive alternative function, so the neural development signal is the most representative theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072747","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0010510","count":1},{"id":"GO:0016114","count":1}]},{"hash":"1947649136709095654","title":"Light-Responsive Photosynthesis and Light Harvesting","description":"These proteins are linked by GO terms describing light perception and the core photosynthetic machinery, including responses to red/blue light, high/low light, nonphotochemical quenching, and light harvesting in photosystems I and II. This pattern points to a cohesive group involved in photoreception and photosynthetic light reactions, with possible association to chlorophyll/chromophore linkage and phytol biosynthesis. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0010114","count":3},{"id":"GO:0071486","count":3},{"id":"GO:0010196","count":3},{"id":"GO:0009645","count":3},{"id":"GO:0009769","count":3}]},{"hash":"1634531004614338176","title":"Unknown","description":"The terms include Wnt signaling, telomere maintenance, cerebellar granule cell differentiation, immune regulation, and vitamin D response, with no single dominant function tying the proteins together. Because the cluster spans development, telomere biology, and immune signaling, a cohesive label cannot be assigned.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1}]},{"hash":"527684048064455878","title":"Regulators of GTPase signaling, cell cycle, and RNA processing","description":"This cluster centers on regulators of signaling and cell cycle, with emphasis on GTPase activity, serine/threonine kinase regulation, and mitosis, plus RNA processing (splicing and transport) and cytoskeleton organization, indicating a broad regulatory module rather than a single pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0071456","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0008284","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1382153414450155576","title":"Cardiac development and stress signaling","description":"The Top Terms include heart development (GO:0007507) and cardiac muscle hypertrophy in response to stress (GO:0014898), indicating a cardiac-focused theme. Additional context from related signaling and regulatory processes (protein ubiquitination, negative regulation of kinase activity, GPCR signaling) supports a cluster tied to cardiac signaling and remodeling under stress. While other terms touch on brain differentiation or telomere regulation, the heart-related terms are the strongest signal for this cluster.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1866440291617216001","title":"TLR signaling and inflammatory response","description":"The GO terms cluster around Toll-like receptor signaling (TLR8 and Toll pathway), positive regulation of inflammatory responses, interferon and IL-18 production, and antimicrobial peptide biosynthesis, indicating a cohesive Toll-like receptor\u2013driven immune/inflammatory module. A few terms like collagen fibril organization appear peripheral to this core theme. Overall, the cluster reflects inflammation-associated signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":1},{"id":"GO:0032741","count":1},{"id":"GO:0034158","count":1},{"id":"GO:0050729","count":1},{"id":"GO:0045356","count":1}]},{"hash":"1155304668145892550","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034965","count":1},{"id":"GO:1905267","count":1},{"id":"GO:0000294","count":1},{"id":"GO:0001682","count":1},{"id":"GO:1904876","count":1}]},{"hash":"535618949309966591","title":"Neuronal synapse development and spine morphogenesis","description":"The top GO terms converge on neural development and synaptic structure, including glutamatergic transmission, dendritic spine morphogenesis, and striatal neuron differentiation, with related signaling regulation (p38MAPK, ubiquitination) and immunological synapse formation, suggesting a cluster of proteins involved in shaping and regulating neural synapses and spines.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071847","count":1},{"id":"GO:1904888","count":1},{"id":"GO:0051968","count":1},{"id":"GO:0060997","count":1},{"id":"GO:0001771","count":1}]},{"hash":"712373036857123665","title":"Mechanosensation and Cardiac Signaling","description":"The GO terms show strong representation of mechanosensation (skin development and detection of mechanical stimulus) alongside cardiac electrophysiology (atrial/ventricular action potentials) and vasoconstriction, with a background of GPCR signaling. This pattern suggests the proteins participate in mechanotransduction that influences cardiac and vascular signaling more than a single isolated pathway. Some metabolic terms appear but are less central to the cluster\u2019s core theme.","confidence":"Medium","size":18,"edges":35,"triangles":17,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":12},{"id":"GO:0050976","count":12},{"id":"GO:0098914","count":12},{"id":"GO:0007216","count":11},{"id":"GO:0002024","count":11}]},{"hash":"954073385056816764","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0006605","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0000717","count":2}]},{"hash":"1438921109954979252","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":135,"triangles":600,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006369","count":14},{"id":"GO:0048701","count":14},{"id":"GO:0006260","count":14},{"id":"GO:0048026","count":14},{"id":"GO:0006306","count":13}]},{"hash":"1512428930663691646","title":"Unknown","description":"The top GO terms span diverse processes\u2014from ribosome biogenesis and DNA-templated transcription to brain development, lens fiber differentiation, and even ubiquitin-mediated proteolysis and chromatin modification\u2014without a single unifying function. This breadth suggests no coherent, specific cluster-level function can be confidently assigned beyond Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1}]},{"hash":"1197593317040518129","title":"Unknown","description":"The GO terms show broad and conflicting themes (cell division/mitosis, RNA processing/snoRNP assembly, unfolded protein response, morphine response, interferon response, photosynthesis) with several obsolete terms, indicating no cohesive biological function for the whole cluster. Hence no reliable, single label can be assigned.","confidence":"","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051348","count":4},{"id":"GO:0006986","count":4},{"id":"GO:0000492","count":3},{"id":"GO:0071357","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1013200767608564626","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":76,"triangles":164,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0097011","count":10},{"id":"GO:0001525","count":10},{"id":"GO:0050853","count":10},{"id":"GO:0051092","count":10},{"id":"GO:0070935","count":10}]},{"hash":"1719743525290890314","title":"Dendritic spine morphogenesis and synaptic signaling","description":"This cluster is dominated by terms related to spine formation, synapse localization, receptor clustering, and trans-synaptic signaling, indicating a core role in neuronal synapse development and communication; the additional terms (retinoic acid response, T cell proliferation, hypersensitivity) appear as broader or secondary associations.","confidence":"High","size":18,"edges":26,"triangles":8,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060997","count":13},{"id":"GO:0035640","count":7},{"id":"GO:0035418","count":7},{"id":"GO:0043113","count":7},{"id":"GO:0008285","count":7}]},{"hash":"2070362703996687747","title":"Golgi-Dependent Secretion and Transport","description":"The top terms point to Golgi-related trafficking and secretory activity (retrograde transport from endosome to Golgi, Golgi-to-plasma membrane transport, and Golgi ribbon formation) along with secretion-related processes like mucus secretion and neutrophil degranulation. Although some terms relate to development or chromatin modification, the dominant signal is the secretory/Golgi transport theme, suggesting proteins acting in the Golgi-mediated secretory pathway.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042147","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0006893","count":2},{"id":"GO:1903709","count":2},{"id":"GO:0032635","count":2}]},{"hash":"713132206516625361","title":"Unknown","description":"The terms are very diverse: histone demethylation, fatty acid and methyl-branched fatty acid metabolism, ectoine and verruculogen biosynthesis, and unrelated developmental/regulatory processes (uterus morphogenesis, transcriptional regulation under hypoxia). The coexistence of such disparate functions, plus several obsolete terms, makes a coherent shared function unlikely. Therefore, Unknown with None.","confidence":"","size":18,"edges":27,"triangles":7,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034720","count":5},{"id":"GO:0070544","count":5},{"id":"GO:0001561","count":4},{"id":"GO:0019491","count":4},{"id":"GO:0042400","count":4}]},{"hash":"694247310661108378","title":"Ubiquitin-Proteasome and Autophagic Antiviral Defense","description":"The terms cluster around ubiquitin-dependent proteolysis (SCF, sumoylation), autophagy, and innate immune signaling (I-kappaB regulation, antiviral defense, chemokine production, NO regulation), suggesting a module that links protein turnover with antiviral innate immunity via ubiquitin-proteasome and autophagy pathways.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0031146","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0045087","count":5},{"id":"GO:0045623","count":3}]},{"hash":"238990323511108594","title":"Sugar and ion transmembrane transporters","description":"The proteins in this cluster are dominated by diverse transmembrane transport GO terms, including D-glucose and D-xylose transport, sodium and potassium ion transport, phosphate ion transport, trehalose transport, nitrate assimilation, and related osmotic-stress responses, pointing to a cohesive group of membrane transport proteins with multiple substrate specificities.","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":3},{"id":"GO:0006970","count":2},{"id":"GO:0015753","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0035435","count":2}]},{"hash":"470652544305102733","title":"Mitochondrial proteostasis and degradation","description":"The listed GO terms cluster around mitochondrial maintenance (e.g., complex III assembly, inner membrane insertion, mtDNA regulation) and protein quality control/degradation pathways (protein processing/unfolding, ERAD, proteasome assembly, autophagosome maturation, aggresome formation), suggesting a cohesive theme of mitochondrial protein homeostasis and turnover.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034551","count":1},{"id":"GO:0097352","count":1},{"id":"GO:0070842","count":1},{"id":"GO:0045899","count":1},{"id":"GO:0032979","count":1}]},{"hash":"467806215649167187","title":"Neuronal signaling and lens morphogenesis","description":"The top GO terms emphasize neurotransmitter secretion and glutamatergic synaptic transmission, plus lens fiber cell morphogenesis, suggesting roles in neural communication and eye development. Additional terms point to growth factor responses and GTPase regulation, supporting a signaling-centric cluster, though some terms (piRNA processing, telomere maintenance) are less clearly connected.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0007269","count":3},{"id":"GO:0070309","count":3},{"id":"GO:0071363","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1542178843554726943","title":"Neural Development and Axon Guidance","description":"The proteins are enriched for neural development and wiring processes, including axon fasciculation, retinal ganglion cell axon guidance, dendritic spine morphogenesis, corpus callosum development, and trans-synaptic signaling, with supporting signals from retinoic acid and Hedgehog pathways; while a few morphogenesis terms appear, the dominant theme is CNS patterning and synaptic wiring.","confidence":"Medium","size":18,"edges":48,"triangles":27,"max_degree":10,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045880","count":16},{"id":"GO:0097155","count":16},{"id":"GO:0050798","count":15},{"id":"GO:0099557","count":15},{"id":"GO:0060021","count":15}]},{"hash":"903834787607467938","title":"Immune and Metabolic Signaling Regulation","description":"The top GO terms point to immune processes (defense against Gram-positive bacteria, T cell proliferation), metabolic signaling (response to glucose), and growth-related processes (angiogenesis), with additional ion transport and morphogenesis terms suggesting broader regulatory roles. This pattern implies a cluster of proteins that modulate signaling across immune, metabolic, and growth pathways rather than a single specific function.","confidence":"Medium","size":18,"edges":108,"triangles":311,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0043552","count":17},{"id":"GO:0006813","count":17},{"id":"GO:0048813","count":17},{"id":"GO:0014068","count":16},{"id":"GO:0071333","count":16}]},{"hash":"505006386352558789","title":"Cyclic nucleotide signaling and ion transport","description":"The cluster is driven by GO terms for cellular responses to cGMP and cAMP and regulation of guanylyl cyclase signaling, suggesting a core cyclic nucleotide signaling module. Additionally, multiple terms describe membrane ion transport (potassium and sodium), indicating a link to membrane transport processes. Other terms (lipopolysaccharide response, lipid catabolism) are present but less central, so the main theme centers on cyclic nucleotide signaling with associated ion transport.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071321","count":4},{"id":"GO:0007608","count":4},{"id":"GO:0010754","count":4},{"id":"GO:0046827","count":4},{"id":"GO:0071222","count":3}]},{"hash":"1320084777457809246","title":"Calcium signaling and transcription regulation","description":"This cluster centers on Ca2+-related signaling (release of sequestered Ca2+ into cytosol; calcineurin-NFAT signaling) and downstream transcriptional regulation (positive regulation of transcription by RNA Pol II), with supporting hints from Wnt signaling and cytokine production, suggesting a cohesive theme of Ca2+-mediated signal transduction leading to gene expression changes. Some terms like digestion or SA node regulation may be broader or secondary annotations, but the core connection is calcium-linked signaling and transcription control.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051209","count":3},{"id":"GO:0071651","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0098907","count":3},{"id":"GO:2000340","count":3}]},{"hash":"88290439595203683","title":"Developmental transcription and differentiation","description":"The cluster shows enrichment for brain-, skin-, and lens fiber cell differentiation, along with DNA-templated transcription and broader gene expression regulation, pointing to proteins involved in developmental transcriptional programs and differentiation processes. Some terms (e.g., imprinting regulation, fungal cell wall biogenesis) are less coherent with this theme and may reflect noise or cross-functional annotations, but the central signal centers on developmental transcriptional activity and differentiation. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035948","count":7},{"id":"GO:0007420","count":7},{"id":"GO:0043588","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0070306","count":6}]},{"hash":"473206480088880552","title":"Unknown","description":"The GO terms span telomere maintenance, neuronal differentiation, vitamin D response, and immune signaling, with no single unifying function across the proteins. The lack of edges and the scattered terms make it unclear what shared biology defines this cluster, so Unknown with confidence None.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":6},{"id":"GO:0032212","count":5},{"id":"GO:0021707","count":5},{"id":"GO:1904355","count":5},{"id":"GO:0071651","count":5}]},{"hash":"1876981176128152272","title":"Regulatory Signaling Modulators","description":"These terms point to regulatory roles across signaling pathways (GPCR/PKC), kinase activity control, immune signaling (IL-12), NF-kappaB regulation, neuronal development, and telomere maintenance, suggesting a cluster of proteins that mainly modulate signaling and gene regulation rather than a single, cohesive function. The lack of network connectivity and the mix of neuronal, immune, and telomere-related terms support a broad regulatory theme. Therefore the label is plausible but broad, with Medium confidence.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0021707","count":2},{"id":"GO:1904355","count":2}]},{"hash":"797101235931611161","title":"Mitochondrial Transporters","description":"These proteins cluster around transport across mitochondrial membranes: malate-aspartate shuttle, ATP, CoA, nucleotide, phosphate, magnesium export, and other transmembrane transport processes, with notes on membrane permeability and oxidative-stress response. This cohesive theme supports labeling the group as mitochondrial transporters or mitochondrial metabolite transporters.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043490","count":14},{"id":"GO:1990616","count":14},{"id":"GO:1990544","count":14},{"id":"GO:0035349","count":14},{"id":"GO:0035435","count":14}]},{"hash":"1100741052291957113","title":"Ubiquitin-Mediated Protein Degradation","description":"This cluster is dominated by GO terms tied to ubiquitination and proteostasis (protein ubiquitination, polyubiquitination, and ubiquitin-dependent ERAD pathway), along with cell cycle and growth signaling (mitotic cell cycle, cell division, TORC1 signaling). While a Gram-positive defense term appears, the strongest signal is ubiquitin-dependent modification and degradation, linking protein quality control to cell cycle regulation and stress responses. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0016567","count":5}]},{"hash":"789007779959134712","title":"Unknown","description":"GO terms span vascular morphogenesis, platelet degranulation, visual perception/phototransduction, memory, cuticle development, kidney development, and signaling regulation, with no connectivity tying them into a single coherent function. This heterogeneity makes it unlikely to assign a specific common function to the cluster.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0002576","count":2},{"id":"GO:0007602","count":2}]},{"hash":"1368914882101557277","title":"Translation initiation and reinitiation control","description":"The top GO terms cluster around translation initiation and reinitiation (preinitiation complex formation, regulation of translational initiation, translation reinitiation, and IRES-dependent viral translation), suggesting these proteins mainly regulate ribosome recruitment and start of translation, including viral contexts. Some ancillary terms (ubiquitination, GTPase regulation, ncRNA-mediated silencing) may reflect broader regulatory roles but do not diminish the strong translational signal.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0002188","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1069369701190203410","title":"Yeast Autophagy and Ribosome Regulation","description":"The top GO terms cluster around autophagy-related processes (ribophagy; engulfment by autophagosome) and ribosome biology (tRNA processing regulation; ribosomal large subunit export from nucleus), with yeast-specific lipid metabolism and mating-related processes (ergosterol biosynthesis, dolichyl phosphate biosynthesis, mating projection growth). This combination suggests a cohesive yeast-centered module linking autophagy with ribosome turnover and membrane/lipid pathways.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000235","count":2},{"id":"GO:0031384","count":2},{"id":"GO:0034517","count":2},{"id":"GO:0046642","count":2},{"id":"GO:0061736","count":2}]},{"hash":"1065998570691532589","title":"Calcium-Regulated Muscle Contraction","description":"This cluster is dominated by GO terms linking calcium signaling to muscle activity, including regulation of cardiac muscle contraction via calcium release, positive regulation of heart force, and skeletal muscle fiber development, suggesting a shared theme of calcium-dependent muscle function across cardiac and skeletal contexts (with some related sensory calcium signaling terms as ancillary connections).","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0010881","count":2},{"id":"GO:0005513","count":2}]},{"hash":"578140105524512585","title":"Developmental transcription initiation and chromatin modification","description":"The cluster prominently features transcription initiation processes (RNA Pol II preinitiation complex assembly, DNA-templated transcription initiation), plus Notch target transcription regulation and chromatin modification signals (historically histone H3 acetylation). The accompanying development-related terms (kidney, spinal cord, skin, follicle cell of egg chamber) suggest a theme of gene expression control during development. Despite no observed edges, the recurring transcriptional and chromatin-associated terms provide a coherent cohesive function for the group.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0001822","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0030307","count":1}]},{"hash":"1963411529482168692","title":"Unknown","description":"The top terms span diverse and only loosely related processes, including post-translational modifications (peptidyl-arginine hydroxylation, peptidyl-tyrosine dephosphorylation), epigenetic regulation (obsolete histone demethylation terms), development (negative regulation of osteoblast differentiation), metabolism (purine nucleobase metabolism), stress response (arsenic-containing substance response), and host\u2013symbiont interactions (obsolete symbiont-mediated modification). With no cohesive functional theme and no network edges to support a specific function, there is no clear, representative label beyond Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030961","count":1},{"id":"GO:0034720","count":1},{"id":"GO:0045668","count":1},{"id":"GO:0070544","count":1},{"id":"GO:0006144","count":1}]},{"hash":"1210842021528300444","title":"Calcium signaling and vesicle trafficking at synapses","description":"The top terms cluster around regulation of calcium-release channels, Rho signaling, receptor recycling, endosome size, and glutamatergic synaptic transmission. Together these indicate a common theme of neuronal signaling and intracellular trafficking at synapses, with calcium dynamics driving vesicle release and receptor turnover. Some terms in the list (e.g., transcription regulation) are less directly connected to this core, but the strongest signal supports a calcium- and trafficking-focused function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0051036","count":3}]},{"hash":"352080238820188750","title":"Unknown","description":"The Top Terms show a highly diverse mix of processes (amino acid, lipid, inositol, and hormone biosynthesis; DNA replication regulation; transcriptional and chromatin regulation; brain structure; signaling), with no clear shared function or pathway tying the proteins together, and no interactions detected. Therefore there is no cohesive theme to assign a meaningful label.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075139","count":1},{"id":"GO:0000105","count":1},{"id":"GO:0008654","count":1},{"id":"GO:0006021","count":1},{"id":"GO:1903468","count":1}]},{"hash":"1625693737027729241","title":"Gene Expression Regulation (Transcription & Translation)","description":"These GO terms indicate involvement in gene expression regulation at both the nuclear transcription level (DNA-templated transcription, transcriptional regulation by RNA Pol II, preinitiation complex formation, chromatin-related processes) and the level of translation initiation and its regulation (translation preinitiation complex, translational initiation regulation), plus mRNA surveillance and proteasomal regulation. This points to a broad cluster coordinating transcriptional control with translational initiation and RNA processing, rather than a single narrow function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035914","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071033","count":1},{"id":"GO:0090052","count":1}]},{"hash":"1649880929375256606","title":"Unknown","description":"The terms include immune signaling (IL-12 regulation, NF-kappaB-related), neuronal development (cerebellar granule cell differentiation and dendrite development), telomere maintenance, and vitamin D response, showing broad and disparate functions. There is no clear, single biological process tying the cluster together, so a concise label cannot be confidently assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1}]},{"hash":"1385397486555584317","title":"Apoptosis and Autophagy Regulation","description":"The terms cluster around apoptotic signaling (intrinsic pathways, execution phase, germ cell apoptosis) and regulation of macroautophagy, with supporting references to protein processing. This indicates a cohesive theme of programmed cell death linked with autophagy, rather than disparate stress responses such as estradiol or antibiotic signaling.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0032355","count":3},{"id":"GO:0008627","count":3},{"id":"GO:0016241","count":3},{"id":"GO:2001269","count":3},{"id":"GO:0016485","count":3}]},{"hash":"665121159185437518","title":"Renal tubule morphogenesis and ciliary motility","description":"The cluster shows strong representation of kidney development terms (metanephric distal/proximal tubule morphogenesis) and nephron development, alongside ciliary-related terms (axoneme assembly, cilium movement) and mechanosensing, plus vasopressin-related renal processes. This combination points to proteins involved in renal tubule morphogenesis and primary cilium\u2013mediated motility/signaling in kidney cells.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072287","count":2},{"id":"GO:0016525","count":2},{"id":"GO:0036303","count":2},{"id":"GO:0072237","count":2},{"id":"GO:0016567","count":2}]},{"hash":"419885885617955376","title":"Secretory Pathway Proteins","description":"The top GO terms cluster around secretory processes (endosomal lumen acidification, secretory granule organization, saliva and pancreatic juice secretion), indicating vesicle trafficking and secretion roles. Some developmental terms appear (retinoic acid response, organ development), but the dominant signal is secretory pathway function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048388","count":2},{"id":"GO:0072239","count":2},{"id":"GO:0030157","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0006182","count":2}]},{"hash":"450684045032204724","title":"DNA Damage Response and Transcription Regulation","description":"This cluster is driven by GO terms linked to DNA-templated transcription, regulation of transcription, SOS response, and nucleotide-excision repair, indicating a core link between DNA damage response pathways and transcriptional control. Additional terms about competence for transformation and condition-dependent transcription suggest broader transcriptional regulation activity across contexts, but the dominant theme remains DNA repair and transcription regulation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0009432","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0019538","count":1}]},{"hash":"18299386316958537","title":"Transcription Regulation and GTPase Signaling","description":"This cluster is enriched for DNA-templated transcription and its regulation, along with intracellular signal transduction driven by small GTPases, indicating a theme of nuclear transcription control linked to membrane-to-nucleus signaling. Additional terms hint at cellular stress responses (heat), autophagy regulation, and phagocytosis, suggesting these proteins participate in stress-responsive signaling networks that converge on transcriptional regulation. Overall, the dominant signal is transcriptional regulation with coordinated signaling, giving medium confidence in the label.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007264","count":2},{"id":"GO:0035556","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0035176","count":2}]},{"hash":"159573237018852890","title":"Unknown","description":"The terms span metabolism, RNA processing, chromatin modification, and stress responses with no single unifying function. While there are RNA modification and ribosome export terms, they are mixed with ubiquinone/vitamin E/antibiotic biosynthesis, histone methylation, and senescence/xenobiotic response, giving no cohesive theme.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":1},{"id":"GO:0010189","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0002098","count":1}]},{"hash":"1855663553787653171","title":"Unknown","description":"The top GO terms cover telomere maintenance, transcription, RNA processing, and a diverse set of cellular processes (migration, differentiation, immune proliferation, pH response), with no clear unified function and no connecting edges. This makes it difficult to assign a single coherent theme to the cluster, so Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0035994","count":2}]},{"hash":"1931333697719366506","title":"Neural development and neuromuscular behavior","description":"The terms cluster around nervous system development (lateral ventricle development, axon target recognition, neural patterning) and neuromuscular function (neuromuscular process) with associated adult behaviors (walking, eating), suggesting a coherent theme of neural development and nervous-system\u2013driven behavior; some immune signaling terms appear as ancillary context but do not define the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021670","count":1},{"id":"GO:0007385","count":1},{"id":"GO:0002931","count":1},{"id":"GO:0043407","count":1},{"id":"GO:0007628","count":1}]},{"hash":"95244941198181457","title":"Transcription Regulation and Development","description":"The cluster\u2019s terms are largely about DNA-templated transcription and its regulation, with additional development-related terms like lens fiber cell differentiation and neural tube closure, suggesting a theme of transcription control linked to developmental processes. Some obsolete or non-specific terms are present, but the dominant signal is regulation of transcription, potentially with developmental roles.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":1},{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0006349","count":1}]},{"hash":"798172436793839400","title":"Nuclear envelope dynamics and vesicle trafficking","description":"Top GO terms indicate cell cycle and transcription regulation, but multiple terms point to membrane organization and trafficking (nuclear membrane reassembly, ER targeting, ESCRT-mediated viral budding, multivesicular body sorting). This suggests a cluster of proteins coordinating nuclear envelope processes with membrane trafficking and protein sorting during the cell cycle.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0030713","count":1},{"id":"GO:1904669","count":1}]},{"hash":"2230683665790853163","title":"Mitosis and genome maintenance","description":"The strongest terms cluster around microtubule-based movement and mitotic cell cycle, with supporting signals from ubiquitin-proteasome\u2013dependent degradation and DNA repair, pointing to a cell-division/genome-stability program. Developmental terms appear less central, so the core theme aligns with mitosis and genome maintenance.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007018","count":4},{"id":"GO:0031146","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0070306","count":3},{"id":"GO:0000447","count":3}]},{"hash":"240272905971782356","title":"Cardiac potassium channel regulation and repolarization","description":"The top GO terms are dominated by regulation of heart rate by cardiac conduction, atrial cardiac muscle cell membrane repolarization, membrane hyperpolarization, and potassium ion export across the plasma membrane. These point to a common function in cardiac electrical activity and potassium channel modulation. A couple of terms\u2014protein homooligomerization and Rho signaling\u2014are more general, but could reflect subunit assembly of channels or signaling pathways that modulate excitability. Overall, the cluster appears to represent proteins involved in cardiac electrophysiology centered on potassium channel regulation and membrane potential changes.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:1902260","count":1},{"id":"GO:0044335","count":1},{"id":"GO:0086091","count":1},{"id":"GO:0035024","count":1}]},{"hash":"2010599839407733838","title":"Unknown","description":"The GO terms are too heterogeneous to define a single cohesive function for this cluster; they span eye and cranial skeletal development, extracellular matrix remodeling, endosome transport, membrane tubulation, secretory granule maturation, cytokinesis, and lipid biosynthesis, plus an obsolete plant auxin term. With 0 edges and only one annotation per term, there is no clear shared pathway or interaction to anchor a label, so Unknown is appropriate and there is no confidence.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001654","count":1},{"id":"GO:0022617","count":1},{"id":"GO:1904888","count":1},{"id":"GO:0031139","count":1},{"id":"GO:0045022","count":1}]},{"hash":"1794178708716382672","title":"TLR/NOD-like inflammatory signaling","description":"This cluster is dominated by innate immune signaling terms: Toll-like receptor pathways (TLR8 signaling and Toll signaling), NOD-like receptor signaling, and downstream inflammatory outputs such as IL-1 and IL-18 production, interferon-\u03b1 production, and overall inflammatory response. A connection to NF-kappaB regulation is also present, supporting a cohesive role in pattern-recognition receptor signaling and inflammatory activation. The occasional term about mechanical stimulus is less central and likely incidental. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0006469","count":1},{"id":"GO:0032741","count":1}]},{"hash":"2286777839067708140","title":"Unknown","description":"The top terms include amino acid and nucleotide biosynthesis (histidine, purine, tetrahydrofolate interconversion), transport (ammonium transport), signaling (response to cAMP, dopamine uptake), and a fungal developmental process (ascospore formation). These represent disparate processes across different organisms, with no single cohesive function tying all terms together, so there isn\u2019t a clear, specific label for this cluster.","confidence":"","size":17,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000105","count":2},{"id":"GO:0051583","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0070634","count":2}]},{"hash":"1371085246171379042","title":"Growth and development signaling","description":"Most terms center on growth and gene expression: TORC1 signaling, ribosome biogenesis, DNA-templated transcription, and cell division. Additional terms touch development (neural tube closure) and adaptive growth under stress (glucose limitation) as well as immune defense. Together they suggest a cluster that coordinates growth, development, and transcriptional control in response to environmental cues.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0060416","count":3},{"id":"GO:0006349","count":3}]},{"hash":"2056130820637570789","title":"Unknown","description":"There isn\u2019t a single cohesive theme connecting the top GO terms: the cluster includes core cellular processes (cell cycle, translation, telomere maintenance) alongside immune and neuroendocrine signaling (NF-kappaB sequestration, IL-12 regulation, chemokine production, vasopressin secretion). This mix suggests either diverse functions or annotation noise, so a concise, representative label cannot be confidently assigned.","confidence":"","size":17,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":6},{"id":"GO:0051301","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3}]},{"hash":"738161169428023505","title":"Nuclear gene expression & chromatin regulation","description":"This cluster centers on nuclear processes: regulation of DNA-templated transcription, transcription itself, chromatin organization, and mRNA export, with additional signals for kinetochore localization and ribosome biogenesis, indicating a cohesive set of proteins involved in gene expression control and chromatin maintenance. A few terms appear unrelated (e.g., glomerular filtration), but the dominant theme is nuclear gene expression and chromatin regulation.","confidence":"High","size":17,"edges":133,"triangles":638,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006406","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0006351","count":2}]},{"hash":"57685349690252080","title":"ER-Golgi vesicle transport","description":"This cluster is dominated by GO terms related to vesicle trafficking between the ER and Golgi, Golgi-associated vesicle fusion, and retrograde transport to the Golgi, with supporting small GTPase\u2013mediated signaling. While some developmental terms appear (eye morphogenesis, myelination) the shared function across proteins points to a common role in intracellular membrane trafficking and protein targeting. Confidence: Medium","confidence":"","size":17,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006623","count":2},{"id":"GO:0048280","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0000266","count":2}]},{"hash":"1827743972307291436","title":"Unknown","description":"The GO terms are highly diverse (synaptic terminal organization, immune differentiation, heart and skin development, erythrocyte differentiation, RNA localization and translation, mRNA decay, viral transcription, and FGF response), giving no clear, single shared function for the cluster.","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0072553","count":1},{"id":"GO:0061470","count":1},{"id":"GO:0003342","count":1},{"id":"GO:1902172","count":1},{"id":"GO:0045647","count":1}]},{"hash":"841009378271219024","title":"GPCR-driven cAMP/cGMP Signaling","description":"The cluster is dominated by GO terms tied to GPCR signaling and second messenger production: adenylate cyclase-activating adrenergic receptor signaling (cAMP), receptor guanylyl cyclase signaling (cGMP), and cAMP/cGMP biosynthesis, plus related intracellular signal transduction and blue light signaling, indicating a common theme of GPCR-mediated regulation of cyclic nucleotides and downstream transcription. ","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0009785","count":5},{"id":"GO:0035556","count":5},{"id":"GO:0071880","count":5},{"id":"GO:0052565","count":5}]},{"hash":"656671981834730418","title":"Translational Initiation and Cell Cycle Regulation","description":"The top GO terms cluster around translation initiation and preinitiation complex formation, plus regulation of CDK activity, suggesting a link between protein synthesis and cell cycle control. Some outlier terms (antigen processing, antibiotic response, etc.) may reflect broader or unrelated annotations, but the dominant theme points to translational control intertwined with cell cycle dynamics.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0045736","count":2},{"id":"GO:2001275","count":2}]},{"hash":"735154483424000733","title":"Ubiquitin-Mediated Transcription and Stress Response","description":"The cluster centers on transcriptional regulation (DNA-templated transcription and negative regulation of transcription elongation) and ubiquitin-related processes (K11- and K63-linked ubiquitination, autoubiquitination, ERAD). It also includes stress-related terms (unfolded protein response and redox homeostasis) and innate immune signaling, suggesting a module where ubiquitin signaling coordinates transcriptional control and protein quality control during cellular stress and immune responses. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0034244","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0006986","count":3}]},{"hash":"2262191062852750938","title":"RNA processing and transcription regulation","description":"The top GO terms cluster around transcription regulation by RNA polymerase II, various RNA processing steps via the spliceosome (mRNA splicing, cis splicing) and ncRNA-mediated silencing, plus translation and cytoplasmic stress granule localization, all suggesting a core theme of RNA metabolism and gene-expression control. Some terms like exocrine pancreas development and blood coagulation are less directly connected and may reflect broader or incidental annotations.","confidence":"Medium","size":17,"edges":17,"triangles":11,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3}]},{"hash":"1866300393701499070","title":"Auditory cochlear development and synaptic signaling","description":"The cluster is dominated by terms related to the auditory system and neural synaptic function: cochlea morphogenesis, stereocilium organization, receptor guanylyl cyclase signaling (sensory transduction), nitric oxide\u2013mediated retrograde signaling at synapses, glutamate secretion, dendritic spine morphogenesis, and long-term synaptic depression. These points together suggest roles in auditory development and synaptic communication, with exploration behavior reflecting neural circuitry engagement. A single outlier term about opsonization is noted but does not shift the overall theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0007168","count":6},{"id":"GO:0060088","count":5},{"id":"GO:0098924","count":5},{"id":"GO:0006470","count":5},{"id":"GO:0035640","count":5}]},{"hash":"2230632162898038701","title":"Mitochondrial redox balance and energy metabolism","description":"Most of the top GO terms describe mitochondrial processes: NADH to ubiquinone electron transport, 2-oxoglutarate metabolism, and dihydrolipoamide metabolic processes, as well as regulation of membrane potential and cellular redox homeostasis/detoxification. This points to a functional cluster centered on mitochondrial energy production and maintenance of redox balance. Some annotations, like sperm capacitation and DNA methylation involved in gamete generation, appear unrelated and are likely annotation noise or context-specific rather than core cluster functions.","confidence":"Medium","size":17,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":14},{"id":"GO:0055114","count":14},{"id":"GO:0098869","count":12},{"id":"GO:0043046","count":9},{"id":"GO:0009228","count":9}]},{"hash":"687402985616979114","title":"Transcription and Translation Initiation","description":"This cluster is dominated by GO terms for DNA-templated transcription and its regulation, plus translation and initiation complex formation, pointing to a gene expression module spanning transcriptional control and translation initiation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0001732","count":1},{"id":"GO:0006413","count":1}]},{"hash":"1413320795531767388","title":"Hair Follicle Development and Notch Regulation","description":"The strongest signals are hair follicle development and negative regulation of Notch signaling, which together point to hair follicle biology and modulation of Notch-driven differentiation. DNA-templated transcription supports a regulatory program, while prostaglandin biosynthesis, smooth muscle proliferation, and platelet aggregation hint at broader signaling in skin vasculature and inflammation, but the core theme remains hair follicle development with Notch pathway control.","confidence":"Medium","size":17,"edges":73,"triangles":196,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0001516","count":4},{"id":"GO:0051897","count":4},{"id":"GO:0048661","count":4},{"id":"GO:0042619","count":4}]},{"hash":"1639755118525771160","title":"Redox Homeostasis and Oxidative Stress Response","description":"This cluster is dominated by GO terms focused on redox biology, including cell redox homeostasis, oxidation-reduction processes, cellular response to oxidative stress, and oxidant detoxification, with supporting terms like protein deglutathionylation. These collectively point to a core theme of managing cellular redox state and defending against oxidative damage. A few terms related to development or transcriptional regulation may be incidental, but the redox-related terms strongly anchor the cluster's function. ","confidence":"High","size":17,"edges":17,"triangles":1,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0030416","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0009263","count":2}]},{"hash":"1450406488189437498","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0071951","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0006413","count":1}]},{"hash":"656247717326406438","title":"TLR Signaling and Innate Immune Activation","description":"The top GO terms cluster around Toll-like receptor signaling (TLR2, TLR3, TLR9), dsRNA response, LPS signaling, and downstream cytokine production (interferons, IL-18) and dendritic cell cytokines, indicating a cohesive program of innate immune sensing and inflammatory activation.","confidence":"High","size":17,"edges":16,"triangles":0,"max_degree":15,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032741","count":11},{"id":"GO:0050729","count":11},{"id":"GO:0045356","count":11},{"id":"GO:0034134","count":11},{"id":"GO:0043330","count":11}]},{"hash":"1201361770046920677","title":"Unknown","description":"The top terms are very heterogeneous: neural development (Purkinje cell layer morphogenesis), ubiquinone and tocopherol biosynthesis (cofactor/isoprenoid metabolism), lipid homeostasis, chloroplast protein import, plus miscellaneous processes like spindle elongation and Wnt signaling. This mix suggests no single cohesive function tying the cluster together, and terms appear to come from diverse organisms or annotations. Therefore, Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021692","count":2},{"id":"GO:1902171","count":2},{"id":"GO:1901006","count":2},{"id":"GO:0010795","count":2},{"id":"GO:0055088","count":2}]},{"hash":"635862825842810340","title":"Golgi Organization and Vesicle Trafficking","description":"These proteins are enriched for processes related to the Golgi apparatus and vesicle transport, including Golgi organization and bidirectional vesicle movement between the Golgi, ER, and other compartments, as well as Golgi-to-plasma membrane trafficking. Minor terms about regulation of kinase activity and protein complex formation may reflect regulation of trafficking machinery rather than a separate pathway, supporting a cohesive theme around Golgi function and vesicle transport.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007030","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0045859","count":2}]},{"hash":"1586031086579817533","title":"Ubiquitination-Linked Stress and Apoptosis","description":"This cluster centers on protein ubiquitination (GO:0016567) and various apoptotic and stress-related processes (ER stress response, hepatocyte and myeloid apoptosis), along with cell cycle and tissue remodeling features (epithelial polarity, angiogenesis, response to mechanical stimulus). The common theme appears to be regulation of cell fate and proteostasis under stress, with ubiquitination acting as a key regulatory mechanism bridging apoptosis, ER stress responses, and remodeling pathways. Given the diverse yet connected roles, the label is best described as ubiquitination-driven stress and apoptosis regulation, with moderate confidence due to functional breadth.","confidence":"Medium","size":17,"edges":13,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:2000171","count":3},{"id":"GO:0033028","count":3},{"id":"GO:0090162","count":3},{"id":"GO:0002040","count":3}]},{"hash":"839452920505383242","title":"Cytoskeletal dynamics in mitosis and neural maintenance","description":"This cluster centers on microtubule- and cytoskeleton-driven processes: mitotic spindle attachment and chromosome alignment, spindle pole separation, and nuclear migration along microtubules, plus actomyosin ring assembly for cytokinesis. It also includes neuronal maintenance terms like neuron projection maintenance and cerebellar Purkinje cell layer organization, suggesting shared cytoskeletal remodeling roles in neural contexts, with some signaling regulation (e.g., Rap). Overall, the proteins appear linked by cytoskeletal dynamics across cell division and neural structure maintenance. ","confidence":"High","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0099607","count":17},{"id":"GO:1990535","count":17},{"id":"GO:0001560","count":17},{"id":"GO:0000073","count":17},{"id":"GO:0007080","count":17}]},{"hash":"651163657778416068","title":"Developmental signaling and nuclear transport","description":"This cluster\u2019s top GO terms center on development (multicellular organism development, skin development, mitotic cell cycle) and signaling (positive regulation of GTPase activity, positive regulation of protein serine/threonine kinase activity), plus nuclear/cargo transport processes (mRNA transport, NLS-bearing protein import into nucleus). Together, they suggest proteins involved in coordinating signaling and gene expression during development, potentially linking kinase/GTPase signaling to nuclear transport and proliferation in developing tissues.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0051028","count":3},{"id":"GO:0006607","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0031954","count":2}]},{"hash":"732060316131386216","title":"Transcription and RNA Processing","description":"This cluster is dominated by transcription-related GO terms (DNA-templated transcription, transcription regulation, mitochondrial/plastid transcription) and RNA processing (RNA splicing), suggesting a core gene-expression function. A few metabolism and development terms appear but are less central.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903212","count":2},{"id":"GO:0090180","count":2},{"id":"GO:2001172","count":2},{"id":"GO:0007527","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1880270169173980847","title":"Neural and Eye Development with Growth Regulation","description":"This cluster prominently includes GO terms related to brain development, retina development, and lens fiber cell differentiation, suggesting a neural/eye development theme. It also includes more general cellular processes linked to growth and trafficking (ribosome biogenesis, cell division, TORC1 signaling, GTPase activity, ER-to-Golgi transport, actin remodeling), which provides a broader context of growth regulation. The combination points to development of neural/eye tissues coupled with cellular growth signaling pathways, though the functions are diverse, making the link partial but present.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0007420","count":4},{"id":"GO:1904263","count":4},{"id":"GO:0043547","count":4}]},{"hash":"1210352317447845786","title":"TLR-Mediated Inflammation and Interferon Signaling","description":"This cluster is strongly enriched for Toll-like receptor pathways and inflammatory responses, including Toll signaling, TLR8 signaling, and positive regulation of interferon-alpha and interleukin-18 production, suggesting a cohesive innate immune signaling module. Negative regulation of protein kinase activity aligns with signaling control within this network, while some bone development/axonogenesis terms may reflect shared developmental signaling components but are less central to the core immune theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":11},{"id":"GO:0007409","count":11},{"id":"GO:0019800","count":10},{"id":"GO:0060348","count":10},{"id":"GO:0016525","count":10}]},{"hash":"2222175601119292579","title":"Vesicle trafficking and exocytosis","description":"The top GO terms point to transport processes involving the plasma membrane and endomembrane system (plasma membrane to endosome transport, lysosomal transport, exocytosis, and negative regulation of protein localization to the cell surface). While some signaling terms appear, the dominant theme is vesicle movement and membrane trafficking. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":2},{"id":"GO:0032088","count":1},{"id":"GO:1902306","count":1},{"id":"GO:2000009","count":1},{"id":"GO:1902072","count":1}]},{"hash":"1638716574859292902","title":"Ubiquitin-regulated apoptosis and NF-\u03baB/JNK signaling","description":"The top terms cluster around ubiquitin-mediated processes (ubiquitin-dependent proteolysis, autoubiquitination, K48-linked ubiquitination) and signaling regulation (JNK cascade, I-kappaB phosphorylation, apoptotic regulation), indicating a coherent theme of ubiquitin-dependent control of cell death and NF-\u03baB/JNK signaling pathways, with some related immune and growth-regulatory terms.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0046621","count":4},{"id":"GO:1903721","count":4},{"id":"GO:0051865","count":4}]},{"hash":"83049102540135013","title":"Developmental morphogenesis and actin organization","description":"Multicellular organism development and actin cytoskeleton organization are the strongest shared themes in this cluster (both with two annotated proteins). Several terms point to tissue morphogenesis and structural organization (trigeminal nerve structural organization, dichotomous subdivision involved in salivary gland branching), supporting a cohesive developmental/morphogenesis focus. While a few metabolic or cell-cycle related terms appear, the dominant signal is development and cytoskeleton-associated processes, justifying this label. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0046239","count":1},{"id":"GO:0009229","count":1},{"id":"GO:0009228","count":1}]},{"hash":"814350991319850387","title":"Neural development and axon guidance","description":"The majority of top terms describe neural development and synaptic formation (dendritic spine morphogenesis, retinal ganglion cell axon guidance, optic nerve morphogenesis, corpus callosum development, trans-synaptic signaling, retinoic acid response, Hedgehog pathway regulation), suggesting proteins involved in neural patterning and connectivity. A single term on T cell proliferation is present but does not define the cluster's main function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050798","count":6},{"id":"GO:0099557","count":6},{"id":"GO:0060021","count":6},{"id":"GO:0060997","count":6},{"id":"GO:0048546","count":6}]},{"hash":"1791061396751115173","title":"Neural development and axon guidance","description":"The proteins cluster around neural development and connectivity: retinal ganglion cell axon guidance, optic nerve morphogenesis, corpus callosum development, dendritic spine morphogenesis, trans-synaptic signaling, and retinoic acid/Hedgehog pathway involvement, suggesting a cohesive theme of CNS development and visual system wiring. Some terms are broader morphogenesis, but the dominant signal is neural development and axon guidance.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050798","count":15},{"id":"GO:0099557","count":15},{"id":"GO:0060021","count":15},{"id":"GO:0060997","count":15},{"id":"GO:0048546","count":15}]},{"hash":"2253194204128855401","title":"Innate immune Toll-like signaling and cytokine production","description":"The GO terms cluster around Toll-like receptor pathways (TLR2, TLR8), inflammatory cytokine production (IL-1, IL-18, IFN-\u03b1), and positive regulation of inflammatory responses, plus antibacterial peptide biosynthesis. This points to a cohesive set of proteins coordinating innate immune sensing and cytokine-driven inflammation; actin filament remodeling may reflect cytoskeletal changes during immune activation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":3},{"id":"GO:0032741","count":2},{"id":"GO:0034158","count":2},{"id":"GO:0050701","count":2},{"id":"GO:0050729","count":2}]},{"hash":"579083350456806473","title":"Auditory Hair Cell Synaptic Signaling and Cochlear Morphogenesis","description":"The cluster\u2019s top GO terms center on hair cell and cochlear development (cochlea morphogenesis, stereocilium organization), along with synaptic functions (glutamate secretion, dendritic spine morphogenesis, long-term synaptic depression) and signaling pathways (GTPase activation, nitric oxide\u2013related retrograde signaling), indicating coordinated auditory synapse activity and cochlear structural formation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":3},{"id":"GO:0060088","count":2},{"id":"GO:0098924","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0035640","count":2}]},{"hash":"1546592124155710027","title":"Auditory Synapse Plasticity","description":"The top GO terms emphasize dendritic spine morphogenesis, synaptic plasticity (including long-term depression and regulation of excitatory postsynaptic potentials), and structural plasticity, all of which point to synapse formation and remodeling. The presence of sensory perception of sound and auditory receptor cell stereocilium organization ties the cluster to hearing-related synapses, with additional signaling via nitric oxide and protein dephosphorylation supporting synaptic communication processes. Some behavioral terms (social/vocalization) may reflect linked communication or context but do not contradict the main theme of hearing-associated synaptic plasticity.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060997","count":4},{"id":"GO:0060292","count":3},{"id":"GO:2000463","count":3},{"id":"GO:0051835","count":3},{"id":"GO:0007605","count":3}]},{"hash":"286887565136062497","title":"DNA-Templated Transcription Regulation","description":"This cluster is dominated by GO terms for regulation and transcription driven by DNA, especially GO:0006355 and GO:0006351, indicating transcriptional control as the shared function. The other terms (antibiotic biosynthesis, development) are relatively peripheral, suggesting some noise or mixed annotations. Overall, core function points to transcriptional regulation rather than a single biosynthetic or developmental process.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1901766","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0031342","count":1}]},{"hash":"182221408858471398","title":"Nigral Dopaminergic Development and Stress Response","description":"This cluster is most clearly linked by dopaminergic/nigral development (substantia nigra development) and dopamine catabolic processes, pointing to a nigrostriatal focus. The presence of oxidative stress and broader stress-response terms (hydrogen peroxide biosynthesis, corticosterone/ethanol response, heart development and hypertrophy in response to stress) suggests that the proteins participate in stress-related signaling with dopaminergic development as a core theme. Overall, a dopaminergic development with stress response interpretation fits best, though the heart-related terms imply a wider systemic stress program. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":2},{"id":"GO:0050665","count":2},{"id":"GO:0051412","count":2},{"id":"GO:0014898","count":2},{"id":"GO:0007507","count":2}]},{"hash":"510552778265781228","title":"Mitochondrial Metabolism and Protein Import","description":"Based on the GO terms, most entries relate to mitochondrial biology and energy metabolism (protein import into the mitochondrial matrix, regulation of mitochondrial membrane permeability, pyruvate metabolism, gluconeogenesis, and triglyceride biosynthesis). A few terms touch on unrelated processes like ciliary motility and cell cycle regulation, but the dominant theme is mitochondrial metabolism, so this label is representative. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903740","count":1},{"id":"GO:2000134","count":1},{"id":"GO:0046902","count":1},{"id":"GO:0070940","count":1},{"id":"GO:0010867","count":1}]},{"hash":"1000414671657052277","title":"Unknown","description":"Top terms span diverse processes such as immune signaling (NF-kappaB, NOD2), temperature sensation, morphine response, development, cell cycle, photosynthesis, and protein isomerization. The terms are disparate with no unifying pathway or function, and the interaction graph shows no edges, so there is no coherent functional theme to bind these proteins.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0050960","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0072205","count":2},{"id":"GO:0043278","count":1}]},{"hash":"1272363660869058190","title":"DNA Replication and Chromosome Maintenance","description":"The terms center on DNA replication, chromosome condensation and cohesion (mitotic and meiotic), cohesin loading, and DNA damage response (DSB repair and SOS). Despite a few obsolete or outlier terms, the dominant theme ties to genome maintenance and chromosome dynamics, justifying this label.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070058","count":1},{"id":"GO:0061780","count":1},{"id":"GO:0000733","count":1},{"id":"GO:0007076","count":1},{"id":"GO:0000724","count":1}]},{"hash":"401658697568873185","title":"Cardiac Action Potential Regulation","description":"The dominant GO terms center on cardiac muscle action potentials and their regulation (atrial repolarization, ventricular/contractile action potentials), indicating a cohesive theme of cardiac electrophysiology; peripheral terms like mechanosensation and hormonal pathways appear secondary and do not override this core function.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0050976","count":3},{"id":"GO:0098914","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0007216","count":2}]},{"hash":"1706201215297201760","title":"Chaperone-assisted protein folding and unfolded protein response","description":"The terms center on protein quality control under stress: unfolded protein response, misfolded protein transport, and chaperone-dependent refolding (even when some terms are obsolete). Additional terms like translation adjustment and redox homeostasis often accompany UPR, and protein complex oligomerization fits chaperone complex activity. Together they point to a cohesive theme of managing misfolded proteins via chaperones and the unfolded protein response.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0035719","count":1},{"id":"GO:1901621","count":1}]},{"hash":"536154330610520434","title":"Cardiac morphogenesis and conduction","description":"The cluster is driven by GO terms related to heart development, ventricular cardiac muscle morphogenesis, and regulation of cardiac conduction, including cell communication by electrical coupling in cardiac tissue, with supporting signals such as TGF-beta and smooth muscle contraction. While there are a few general cellular processes (protein refolding, sumoylation, redox response), the cardiac development/conduction theme is the strongest among terms.","confidence":"High","size":16,"edges":59,"triangles":94,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":1},{"id":"GO:0055010","count":1},{"id":"GO:1903779","count":1},{"id":"GO:0042026","count":1},{"id":"GO:0086064","count":1}]},{"hash":"346122825616328169","title":"Eye morphogenesis and transcription regulation","description":"The top GO terms point to eye development (lens fiber cell differentiation, compound eye morphogenesis, second mitotic wave in eye formation) and conserved transcriptional processes (DNA-templated transcription, RNA polymerase II transcription), suggesting a cluster of proteins coordinating transcriptional programs for eye morphogenesis plus associated cellular remodeling. Confidence in this label is High.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070306","count":2},{"id":"GO:0016330","count":2},{"id":"GO:0021654","count":2},{"id":"GO:0050873","count":2}]},{"hash":"266957047902226573","title":"Transmembrane Transporters","description":"Most of the top GO terms describe transmembrane transport of various substrates (protons, sodium ions, xenobiotics, vitamins), suggesting the cluster is enriched for membrane transporter proteins. While a few outliers reference signaling or other processes, the dominant theme is transport across membranes.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015992","count":3},{"id":"GO:0035725","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2}]},{"hash":"1930777228261736439","title":"Chromatin-Dependent Transcription Regulation","description":"This cluster is dominated by GO terms tied to RNA Polymerase II transcription control (elongation, termination, and negative regulation) and chromatin-associated processes (nucleosome density and histone modification). The presence of development-related terms likely reflects tissue-specific regulation linked to transcriptional control via chromatin state. Overall, the proteins appear connected through transcription regulation modulated by chromatin dynamics.","confidence":"Medium","size":16,"edges":21,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009416","count":1},{"id":"GO:0006368","count":1},{"id":"GO:0060303","count":1},{"id":"GO:0030540","count":1},{"id":"GO:0006369","count":1}]},{"hash":"1980418733855571457","title":"Developmental Gene Expression Machinery","description":"The set shows enrichment for translation initiation and reinitiation, transcription, and development-related processes (multicellular development, lens fiber differentiation), plus basic cellular functions like microtubule movement and rRNA processing. This points to a cluster of proteins involved in core gene expression with developmental roles, rather than a single, cohesive pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0032933","count":3}]},{"hash":"190745651258374165","title":"Lipid Biosynthesis and Remodeling","description":"The top GO terms are dominated by lipid metabolism and remodeling processes, including remodeling of phosphatidylinositol, cardiolipin, phosphatidylcholine, and ether lipids, along with triglyceride and CDP-diacylglycerol biosynthesis and platelet activating factor synthesis. This points to a cluster of proteins involved in lipid biosynthesis and membrane lipid remodeling rather than a single, tight functional module. Confidence: Medium","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036149","count":1},{"id":"GO:0010143","count":1},{"id":"GO:0035965","count":1},{"id":"GO:0006663","count":1},{"id":"GO:0008611","count":1}]},{"hash":"290170832587335936","title":"Photosynthesis Light Harvesting and Photoresponse","description":"The top GO terms cluster around light perception (red/blue light), responses to varying light intensities, nonphotochemical quenching, and core photosynthesis processes in photosystems I and II, plus phytol biosynthesis related to chlorophyll. This suggests proteins tied to light harvesting, photoreception, and light-driven photosynthetic activity, including photoprotection and regulation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010114","count":2},{"id":"GO:0071486","count":2},{"id":"GO:0010196","count":2},{"id":"GO:0009645","count":2},{"id":"GO:0009769","count":2}]},{"hash":"336400520331071219","title":"Inflammation and protein quality control","description":"The cluster is dominated by terms related to inflammatory signaling and TNF production, alongside protein folding/stabilization and refolding, suggesting a connection to immune response and protein homeostasis. A minority of terms reference membrane or virion-associated processes, which are less cohesive with the main theme but may reflect annotation noise or broader membrane-related roles. Overall, the label reflects inflammation plus protein quality control.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009395","count":2},{"id":"GO:1904469","count":1},{"id":"GO:0046931","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0051085","count":1}]},{"hash":"814330367956834269","title":"Unknown","description":"The TOP terms are highly heterogeneous (lens differentiation, rRNA processing, ubiquitin-dependent degradation, imprinting regulation, fungal cell wall biogenesis, microtubule movement, various histone modifications, neural tube closure, and DNA repair) with several obsolete annotations. There\u2019s no clear shared function or pathway linking these proteins, so the cluster cannot be coherently named beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:2000060","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1}]},{"hash":"1591775599343113978","title":"Ubiquitin-mediated protein degradation","description":"This cluster is dominated by ubiquitination-related terms: protein ubiquitination, ubiquitin-dependent protein catabolic process, and K48- and K6-linked ubiquitination, pointing to tag-and-degrade regulation of proteins as the central theme. While a few other terms (cobalamin/folic acid biosynthesis, histone catabolic process) appear, the ubiquitination signal is strong enough to name the cluster around protein turnover.","confidence":"High","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0006461","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0046656","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0070936","count":2}]},{"hash":"768672289296187197","title":"Pain and temperature sensing with calcium signaling","description":"The top GO terms cluster around nociception and thermoception (pain perception, mechanical stimulus detection, cold/thermoception) and also include ion transport (calcium and manganese) and regulated secretion (vasopressin, inflammatory chemokines), plus cardiac signaling (SA node action potential). This suggests a coherent theme of sensory perception linked to Ca2+-driven signaling and hormone/secretion pathways, rather than a single narrow function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098703","count":8},{"id":"GO:0071651","count":7},{"id":"GO:0030103","count":7},{"id":"GO:0006828","count":7},{"id":"GO:0050966","count":7}]},{"hash":"951501483065256845","title":"Isoprenoid biosynthesis","description":"This cluster's top GO terms cluster around biosynthesis and assembly of isoprenoids: geranyl diphosphate, farnesyl diphosphate, and geranylgeranyl diphosphate biosynthesis, plus monoterpene, cholesterol, and quinone biosynthesis. While a few terms relate to protein processing or transport, the dominant signal is shared involvement in terpenoid/isoprenoid metabolism.","confidence":"High","size":16,"edges":64,"triangles":108,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0006487","count":2},{"id":"GO:0051290","count":2},{"id":"GO:0043693","count":2},{"id":"GO:0033386","count":2}]},{"hash":"1614956854427196579","title":"Developmental Signaling and Immunity","description":"That cluster appears to be centered on cell signaling that guides development and interacts with immune responses. Key terms point to ephrin signaling, TGF-beta\u2013related responses, regulation of GTPases and cytoskeletal dynamics (actin capping), along with developmental processes like bone and lens morphogenesis, and a component of innate immunity. Therefore, a broad label like Developmental Signaling and Immunity best captures the shared function among these proteins.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0050731","count":2},{"id":"GO:0006915","count":2}]},{"hash":"708917927273120556","title":"Eye and neural morphogenesis with synapse formation","description":"The predominant GO terms point to development of neural and visual structures (optic nerve morphogenesis, camera-type eye morphogenesis, dendritic spine morphogenesis) and synaptic assembly/signaling (positive regulation of synapse assembly, ephrin receptor signaling). Supporting terms on cell migration and adhesion further align with morphogenetic processes in neural/eye tissues, making this a coherent developmental/synaptic cluster. ","confidence":"High","size":16,"edges":38,"triangles":65,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0002042","count":9},{"id":"GO:0034446","count":9},{"id":"GO:0051965","count":8},{"id":"GO:0051291","count":8},{"id":"GO:0042403","count":8}]},{"hash":"868023358101372294","title":"RNA and Histone Methylation","description":"This cluster is driven by methylation-related GO terms across substrates: RNA (rRNA methylation, tRNA wobble modification) and proteins (peptidyl-glycine, peptidyl-lysine dimethylation, peptidyl-arginine dimethylation) as well as histone methylation and rDNA heterochromatin formation, linking to chromatin regulation and senescence. Some terms (antibiotic biosynthetic process, tellurium ion response) are less central but can reflect broader methyltransferase roles. Overall a cohesive theme around methylation-based regulation of RNA, proteins, and chromatin. ","confidence":"High","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018013","count":6},{"id":"GO:0000183","count":6},{"id":"GO:0046690","count":5},{"id":"GO:0018027","count":5},{"id":"GO:0031167","count":5}]},{"hash":"494195514542753411","title":"tRNA modification and RNA processing with apoptosis links","description":"The top GO terms center on tRNA wobble uridine modification, regulation of translation initiation by tRNA modification, and mRNA processing/RNA repair, indicating a nuclear/cytosolic RNA maturation and translation-control module. The presence of DNA repair and mitochondrial permeability\u2013related death terms suggests additional stress-response links, but the core signal is RNA modification and processing with ties to cell death pathways.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006281","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0012501","count":2},{"id":"GO:0035553","count":2},{"id":"GO:0006307","count":2}]},{"hash":"1562451178445564372","title":"Chromatin remodeling and cell cycle regulation","description":"This cluster shows strong signals for chromatin remodeling and nucleosome dynamics (chromatin remodeling, nucleosome disassembly, centromere-related remodeling) and for cell-cycle control (regulation of nuclear DNA replication, G2/M transition), suggesting a core theme of chromatin-mediated cell cycle regulation. A few terms (social behavior, viral RNA replication via DNA intermediate, blastocyst hatching) appear anomalous or cross-species and are likely noise. Overall, the chromatin dynamics\u2013cell cycle connection best captures the group\u2019s function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035176","count":2},{"id":"GO:0039692","count":1},{"id":"GO:0043044","count":1},{"id":"GO:2000219","count":1},{"id":"GO:0000436","count":1}]},{"hash":"1572791223019718800","title":"Auditory system development and synaptic signaling","description":"This cluster centers on auditory system development (cochlea morphogenesis, stereocilium organization) and synaptic function/plasticity (glutamate secretion, dendritic spine morphogenesis, long-term synaptic depression, retrograde NO signaling), suggesting a cohesive role in auditory neuron development and synaptic regulation, despite a few outlier terms.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0060292","count":1}]},{"hash":"1003800414243058058","title":"Mitochondrial Transport and Redox Response","description":"The top GO terms point to various transmembrane transport processes across the mitochondrial membrane (malate-aspartate shuttle, ATP, CoA, phosphate, nucleotides, vitamins) plus regulation of membrane permeability and a superoxide response. This suggests a coherent theme of mitochondrial transporters with redox/oxidative stress involvement, justifying a label focused on mitochondrial transport and redox regulation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043490","count":14},{"id":"GO:1990616","count":14},{"id":"GO:1990544","count":14},{"id":"GO:0035349","count":14},{"id":"GO:0035435","count":14}]},{"hash":"1904453909036175497","title":"Steroid hormone and vitamin D metabolism","description":"The protein cluster shows strong enrichment for GO terms related to steroid/sex hormone metabolism (androgen metabolic process, female genitalia development) and secosteroid metabolism (response to vitamin D, vitamin D catabolic process, retinoic acid catabolic process) as well as oxidative lipid modification (lipid hydroxylation). These collectively point to enzymes involved in oxidative transformations of steroid hormones and vitamin D/retinoids. Some terms like macrolide biosynthetic process are outliers, but the core signal supports a steroid/vitamin D metabolic theme.","confidence":"Medium","size":16,"edges":15,"triangles":2,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":9},{"id":"GO:0008209","count":8},{"id":"GO:0042369","count":8},{"id":"GO:0002933","count":8},{"id":"GO:0010193","count":8}]},{"hash":"1260458117939795678","title":"Redox Homeostasis and Metabolic Pathways","description":"This cluster is enriched for redox-related GO terms (cell redox homeostasis, oxidation-reduction process, cellular oxidant detoxification) and core metabolic processes (tricarboxylic acid cycle, protein folding in endoplasmic reticulum). The dominant signal points to maintenance of cellular redox balance coupled with metabolism, with several development-associated terms (neural precursor proliferation, erythrocyte/megakaryocyte differentiation, in utero embryonic development) likely reflecting broader roles of metabolism/redox state in development or secondary associations.","confidence":"High","size":16,"edges":72,"triangles":206,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":9},{"id":"GO:0055114","count":7},{"id":"GO:0098869","count":6},{"id":"GO:2000179","count":5},{"id":"GO:0006099","count":5}]},{"hash":"1873533090481488247","title":"Cell Cycle Regulation and Kinetochore Localization","description":"This cluster is dominated by GO terms tied to cell cycle control: negative regulation of CDK activity, protein localization to the kinetochore, DNA replication, and control of cell proliferation, suggesting a core theme around mitotic progression and genome duplication. The other terms (morphogenesis, axon regeneration, cerebellar cortex formation, insulin signaling) may reflect additional roles or annotation cross-talk but do not outweigh the cell cycle signal.","confidence":"Medium","size":16,"edges":71,"triangles":164,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045736","count":11},{"id":"GO:0034501","count":11},{"id":"GO:0000902","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0007118","count":6}]},{"hash":"460771454824518565","title":"Pseudouridine Synthesis & Telomere Regulation","description":"The top GO terms cluster around pseudouridine synthesis across rRNA, tRNA, snRNA, and mRNA, indicating a core set of RNA modification enzymes. Additional signals for positive regulation of telomere maintenance via telomerase and telomere capping suggest a link between pseudouridylation machinery and telomere biology. A couple of outlier terms (cerebellar differentiation, chemokine production) are minor. Overall, the theme is RNA pseudouridylation with telomere regulatory roles.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:1990481","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1}]},{"hash":"1717622090190191174","title":"DNA-Templated Transcription Regulation and Chromatin Dynamics","description":"This cluster is enriched for DNA-templated transcription and regulation of transcription by RNA polymerase II, and it also includes a chromatin-related term (histone H3-S10 phosphorylation involved in chromosome condensation). Together these terms point to a core theme of transcriptional control tied to chromatin state. The remaining terms reflect broader signaling and cell-cycle contexts that can modulate transcription, supporting a label centered on transcription regulation with chromatin dynamics.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0007595","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006351","count":4},{"id":"GO:2000775","count":3},{"id":"GO:0000320","count":3}]},{"hash":"420344999196464209","title":"Ubiquitin-Proteasome Regulation of Innate Immunity","description":"The GO terms cluster around ubiquitin-dependent proteolysis and SCF-mediated degradation, together with innate immune signaling pathways (NOD2, TLR2) and cytokine production (IL-1, IL-18, IFN-\u03b1) and inflammatory responses, suggesting these proteins coordinate proteolysis to modulate inflammatory signaling and cytokine output in innate immunity.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:0032088","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0032741","count":3}]},{"hash":"2141693403421413468","title":"Metabolic biosynthesis and osmotic stress responses","description":"This cluster includes diverse biosynthetic processes (wybutosine biosynthesis, antibiotic biosynthesis, C-terminal protein methylation) alongside osmotic and sugar-related stress responses (response to water deprivation, sorbitol/mannitol/sucrose) and regulation of glucose metabolism, suggesting a broad mix of metabolic/biosynthetic activity with osmotic stress response rather than a single cohesive function.","confidence":"Low","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006481","count":1},{"id":"GO:0031591","count":1},{"id":"GO:0010906","count":1},{"id":"GO:0090266","count":1},{"id":"GO:1901106","count":1}]},{"hash":"30986459778613645","title":"Telomere Maintenance and Neural/Immune Signaling Regulation","description":"The cluster features regulatory GO terms for telomere maintenance and capping (telomerase-regulated maintenance; telomere capping), along with neural development (granule cell differentiation; dendrite development) and immune signaling (IL-12 regulation; chemokine production; NF-kappaB-related processes). It also includes broader signaling controls (protein kinase activity regulation; protein ADP-ribosylation) and vitamin D response. Together, these terms point to a broad regulatory module coordinating genome stability, neural development, and immune signaling.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0021707","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071651","count":3},{"id":"GO:0007253","count":3}]},{"hash":"715873706369728369","title":"Developmental morphogenesis and organogenesis","description":"The cluster\u2019s top GO terms cluster around developmental processes across tissues\u2014multicellular organism development, dendritic spine morphogenesis, lens fiber cell differentiation, and thyroid gland development\u2014plus supporting terms involving cytoskeletal movement and ubiquitin-related protein turnover. This points to a cohesive theme of developmental patterning and morphogenesis with roles in cellular architecture, despite a few outliers (e.g., rRNA processing).","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0045880","count":2},{"id":"GO:0030878","count":2},{"id":"GO:0070306","count":1}]},{"hash":"1785484776097975781","title":"Muscle Development and Lipid Signaling","description":"Most prominent GO terms connect skeletal muscle fiber development and lipid biosynthesis/signaling (phosphatidylethanolamine, phosphatidylserine, platelet activating factor), with additional cell-cycle related terms and signaling pathway hints. This suggests proteins in the cluster participate in muscle biology and membrane-associated signaling rather than a single enzyme, justifying the label.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0017186","count":1}]},{"hash":"1426978757793756057","title":"ER quality control and glycoprotein processing","description":"The dominant GO terms point to endoplasmic reticulum\u2013based proteostasis: retention of proteins in the ER lumen, retrograde ER-to-cytosol transport and ubiquitin-dependent ERAD, and N-glycan processing to lysosome. While a few terms touch on xenobiotic transport or organ development, the core signals converge on ER folding/maturation and glycan remodeling, suggesting a cohesive role in ER quality control and glycoprotein handling.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0010977","count":1},{"id":"GO:0072001","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0046835","count":1}]},{"hash":"869869346025159586","title":"Ubiquitin-dependent proteolysis","description":"The top GO terms are dominated by ubiquitin-related degradation pathways (ubiquitin-dependent ERAD, K48-linked ubiquitination, autoubiquitination, and ubiquitin-dependent protein catabolic process). These indicate a cohesive theme of tagging and degrading proteins via ubiquitin signaling, with a few other terms likely secondary annotations. Overall, the cluster appears to center on ubiquitin-mediated proteolysis.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0030433","count":7},{"id":"GO:0045087","count":6},{"id":"GO:0046621","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0070936","count":6}]},{"hash":"1598768872462801884","title":"Exocytosis and neural morphogenesis","description":"Top terms show a strong signal for Golgi to plasma membrane transport and exocytosis, suggesting involvement in vesicle trafficking. In addition, several terms pertain to neural and craniofacial morphogenesis and axon guidance (optic vesicle formation, trigeminal nerve organization, branchiomotor neuron guidance, axonogenesis, limb bud formation), pointing to roles in neural development that often rely on targeted secretion. Together, the terms align on a theme of secretory processes contributing to neural morphogenesis and patterning, hence the label Exocytosis and neural morphogenesis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":2},{"id":"GO:0006887","count":2},{"id":"GO:0021637","count":1},{"id":"GO:0060666","count":1},{"id":"GO:0021960","count":1}]},{"hash":"70503653676635276","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032298","count":1},{"id":"GO:1904876","count":1},{"id":"GO:0007175","count":1},{"id":"GO:1904744","count":1},{"id":"GO:1904751","count":1}]},{"hash":"1540923633906194493","title":"Diverse membrane transporters","description":"All top GO terms describe transmembrane transport across membranes for a wide range of substrates, from ions (sodium, potassium, nitrite, nitrate) to small molecules (fucose, vitamins) and even xenobiotics and neurotransmitter loading. This suggests the cluster is comprised of membrane transport proteins with broad substrate specificity rather than a single substrate type.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0035461","count":1}]},{"hash":"298072560947299117","title":"Male germ cell development and meiosis","description":"The terms strongly cluster around spermatogenesis and meiotic processes (spermatid differentiation, spermatocyte division, male meiosis cytokinesis, male germ-line cyst formation, meiotic chromosome condensation) with related mentions of cell cycle transitions. Some terms like viral process or lung development appear as noise, but the dominant theme is germ cell development and meiosis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000082","count":2},{"id":"GO:0007112","count":1},{"id":"GO:0045665","count":1},{"id":"GO:0048136","count":1},{"id":"GO:0016032","count":1}]},{"hash":"1820622826344141235","title":"Unknown","description":"The GO terms span fatty acid oxidation/metabolism and distinct biosynthetic processes for ectoine and verruculogen, with no shared function or network connectivity, making a cohesive functional theme unclear.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001561","count":1},{"id":"GO:0019491","count":1},{"id":"GO:0042400","count":1},{"id":"GO:1902181","count":1},{"id":"GO:0097089","count":1}]},{"hash":"288773531404710687","title":"GABAergic Synaptic Transmission and Plasticity","description":"The terms cluster around regulation of GABAergic synaptic transmission and neuronal plasticity (long-term potentiation, synaptic plasticity regulation, observational learning), with supporting roles from Rho signaling and manganese transport that can influence synapse remodeling. A couple of non-neuronal terms (placental/smooth muscle development) appear, likely incidental to the main neuronal theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0032228","count":2},{"id":"GO:0006828","count":2},{"id":"GO:0016525","count":2},{"id":"GO:0060291","count":2}]},{"hash":"864340867788871002","title":"Nuclear gene expression and mitosis regulation","description":"The top GO terms cluster around nuclear processes, including mitotic cell cycle, transcription, and regulation of gene expression, with additional signals for ubiquitin-dependent protein degradation and chromatin modification. A few terms are peripheral or obsolete (lens fiber differentiation, rRNA processing), but the dominant theme points to nuclear gene expression control linked to cell division. Overall, the cluster seems to represent proteins involved in transcriptional regulation and mitotic regulation, with some ancillary RNA processing roles.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1}]},{"hash":"1793456861838860789","title":"Unknown","description":"Top terms span transcription regulation, metabolic regulation, chromatin-related localization, tRNA modification, and development, with no single cohesive function tying all 16 proteins. The lack of edges and the diversity of GO terms suggest a mixed cluster without a clear common theme.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:1903212","count":2},{"id":"GO:0090180","count":2},{"id":"GO:2001172","count":2},{"id":"GO:0007527","count":2}]},{"hash":"54667790093147326","title":"Neuronal vesicle trafficking and signaling","description":"The top GO terms cluster around regulation of synaptic vesicle endocytosis and exocytosis and excitatory postsynaptic potentials, with substantia nigra development indicating dopaminergic neurons. While some terms (xenobiotic response, autophagy, cardiac hypertrophy) are broader, the dominant pattern is vesicle cycling and neuronal signaling, justifying this label.","confidence":"Medium","size":15,"edges":9,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":8},{"id":"GO:1900242","count":8},{"id":"GO:2000300","count":7},{"id":"GO:0021762","count":7},{"id":"GO:0060079","count":7}]},{"hash":"1943180673819173822","title":"Unknown","description":"The top GO terms are very diverse, spanning telomere maintenance, neural differentiation, immune signaling, vitamin D response, and post-translational modifications, with no single unifying pathway or function tying the proteins together; the sparse connectivity (1 edge, 0 triangles) supports lack of a cohesive cluster theme.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0007253","count":1}]},{"hash":"537160609316520715","title":"Ubiquitin-Dependent Cell Cycle Regulation","description":"The top GO terms are dominated by ubiquitination processes (K11-linked ubiquitination, polyubiquitination) and APC/C-dependent catabolic activity, along with cell division and related proteolysis. Chromatin remodeling and ERAD-linked pathways further point to coordinated protein turnover and gene-expression control linked to the cell cycle. Some stress-related signaling (GCN2) and glucose-limitation responses are present but secondary, reinforcing a theme of regulated proteolysis driving cell-cycle progression and chromatin state.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":2},{"id":"GO:0060765","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0070979","count":2}]},{"hash":"1147300822267236594","title":"Transcription and ribosome biogenesis","description":"The Top Terms show enrichment for DNA-templated transcription and ribosome biogenesis, along with rRNA maturation/processing steps (5.8S rRNA, ITS1 cleavage). This suggests a cluster focused on gene expression machinery\u2014transcriptional regulation coupled with ribosome assembly and rRNA processing. While some brain and lens development terms appear, they are less represented and do not define the cluster\u2019s core function.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0006355","count":2}]},{"hash":"1160821696625793070","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":19,"triangles":10,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0010610","count":4},{"id":"GO:0070935","count":3},{"id":"GO:0033129","count":3},{"id":"GO:0006355","count":3}]},{"hash":"355566822528035763","title":"Unknown","description":"The GO terms span transcription regulation, protein kinase activity regulation, redox homeostasis, tRNA import, and protein folding/transport, with no single cohesive function tying them together; the network is sparse (one edge, no triangles), so a clear, specific label is not supported.","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032782","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0045454","count":2}]},{"hash":"457096320389080048","title":"Transmembrane Ion and Metabolite Transporters","description":"The GO terms center on a broad set of transmembrane transport activities, especially ion transport (K+, Na+, phosphate regulation) and metabolite transport (malate, succinate, citrate), which together point to a cluster of membrane transporter proteins with diverse substrates. A minor term for nonsense-mediated decay appears incidental, not defining the cluster\u2019s main function. ","confidence":"High","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:2000185","count":4},{"id":"GO:0006813","count":4},{"id":"GO:0015700","count":4},{"id":"GO:0055085","count":4},{"id":"GO:0006814","count":4}]},{"hash":"187873287497695801","title":"Translation and tRNA processing","description":"GO terms strongly point to protein synthesis and RNA biology: translation (GO:0006412), tyrosyl-tRNA aminoacylation (GO:0006437), tRNA pseudouridine synthesis (GO:0031119), and regulation of translational fidelity (GO:0045903). These together indicate a core theme of the translation machinery and RNA processing; a few peripheral terms (e.g., development or metabolism) are less central to the cluster\u2019s main function.","confidence":"High","size":15,"edges":22,"triangles":8,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1903212","count":1},{"id":"GO:0090180","count":1},{"id":"GO:2001172","count":1}]},{"hash":"1975299363584307096","title":"Spliceosome-driven mRNA Splicing and RNA Processing","description":"The top GO terms cluster around spliceosome-mediated mRNA splicing, snoRNA involvement, and ncRNA-mediated regulation, with additional hints toward mRNA stability and localization (oskar mRNA). Together these indicate a cohesive group focused on post-transcriptional RNA processing and regulation rather than transcriptional control, hence the chosen name.","confidence":"High","size":15,"edges":40,"triangles":84,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0034247","count":5},{"id":"GO:0000398","count":5},{"id":"GO:0006378","count":5}]},{"hash":"1488141738381124052","title":"Unknown","description":"The terms span cell budding, immune homeostasis, DNA repair, signaling activities, isoprenoid biosynthesis, responses to morphine and lead, locomotion, and stress-related cardiac remodeling. There\u2019s no single unifying function or pathway tying these together, and with no edges linking the proteins, a cohesive label isn\u2019t supported.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007114","count":3},{"id":"GO:0043029","count":3},{"id":"GO:0006281","count":2},{"id":"GO:0016311","count":2},{"id":"GO:1900486","count":2}]},{"hash":"244207164750063063","title":"Nuclear mRNA/RNP export and mitosis","description":"The top GO terms are dominated by nuclear transport/export (mRNA export, ribosomal subunit export, hnRNP/snRNP/protein import into the nucleus), plus transcription regulation and mitotic chromosome dynamics (alignment and movement). Together these suggest a cohesive set of nuclear trafficking proteins with roles in transcriptional control and mitotic chromosome behavior, hence a label focused on nuclear transport and mitosis.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006406","count":7},{"id":"GO:0000055","count":6},{"id":"GO:0006609","count":5},{"id":"GO:0006608","count":5},{"id":"GO:0000060","count":5}]},{"hash":"1303878866901416872","title":"Transmembrane Ion and Nutrient Transport","description":"This cluster is dominated by GO terms for transmembrane transport of various ions and nutrients (sodium, potassium, phosphate, nitrate assimilation, sialic acid, vitamins) and includes a specific note on neurotransmitter loading into synaptic vesicles, suggesting a theme of membrane transport and vesicle-related processes. A heat-response term is present but less central, so the core signal is membrane transport. ","confidence":"High","size":15,"edges":22,"triangles":5,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2}]},{"hash":"544265114909488832","title":"Unknown","description":"The GO terms span DNA and protein modification (protein methylation, DNA methylation, restriction-modification), telomere-associated processes, basic metabolism (glucose and thiamine biosynthesis), a redox term, and cell size regulation, with no clear single pathway or function linking all proteins. The lack of edges and the presence of diverse, sometimes organism-specific terms suggest these proteins do not form a coherent functional cluster, so Unknown is most appropriate.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006479","count":3},{"id":"GO:0031848","count":2},{"id":"GO:0031627","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006006","count":2}]},{"hash":"142753346393566006","title":"Mitochondrial Transporters and Metabolic Shuttles","description":"The top GO terms point to mitochondrial processes: numerous transmembrane transports (ATP, CoA, phosphate, magnesium, deoxynucleotides, ornithine), the malate-aspartate shuttle, and regulation of mitochondrial membrane permeability, plus a response to oxidative stress. Together these indicate a cohesive theme of mitochondrial transport/metabolism rather than cytosolic functions, justifying a label focused on mitochondrial transport and metabolism.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":4},{"id":"GO:0043490","count":3},{"id":"GO:1990616","count":3},{"id":"GO:1990544","count":3},{"id":"GO:0035349","count":3}]},{"hash":"852892090375343877","title":"Translation initiation and cell cycle machinery","description":"The top GO terms point to translation initiation and formation of the preinitiation complex, combined with mitotic functions (cell division, microtubule severing, CENP-A chromatin assembly) and RNA processing/trafficking activities. This pattern suggests a cluster of proteins involved in core protein synthesis together with cell-cycle machinery, rather than a single specialized pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0002188","count":7},{"id":"GO:0001731","count":7},{"id":"GO:0051301","count":6},{"id":"GO:0051013","count":5},{"id":"GO:0030433","count":5}]},{"hash":"2246181408425723029","title":"Development and Organ Differentiation","description":"The cluster shows enrichment for developmental and tissue differentiation terms across multiple organs (inner ear, heart endocardial cushions, kidney proximal tubule) along with related processes like cell growth and migration, suggesting a theme around organ development and differentiation. Some terms (antibiotic biosynthetic process, tRNA wobble modification) appear as noise, but the dominant signal points to developmental biology.","confidence":"Medium","size":15,"edges":19,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0002098","count":2},{"id":"GO:0042491","count":2}]},{"hash":"1938610261220085707","title":"DNA Damage Response and Apoptosis","description":"These proteins show strong enrichment for DNA repair and replication processes (base-excision repair, DNA replication) and DNA-damage\u2013induced apoptotic signaling, with supporting roles for protein deubiquitination and inflammatory response. There are a few outliers (salivary gland morphogenesis, immunoglobulin hypermutation, ethanol response), but the dominant theme is genome integrity maintenance and programmed cell death, justifying the label.","confidence":"Medium","size":15,"edges":48,"triangles":65,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016446","count":2},{"id":"GO:0006286","count":2},{"id":"GO:0006284","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0016579","count":1}]},{"hash":"779714782271823180","title":"Ubiquitin-Driven Proteostasis and ERAD","description":"The cluster centers on ubiquitination and protein quality control, with multiple GO terms for ubiquitin-related processes (K63-linked ubiquitination, autoubiquitination, ubiquitin-dependent ERAD) and chaperone-mediated assembly, indicating coordination of proteostasis and degradation pathways. The inclusion of ERAD and proteasome-associated terms supports a cohesive theme around protein turnover and stress-responsive regulation, even though a few terms touch broader stress or apoptosis signaling.","confidence":"High","size":15,"edges":27,"triangles":15,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0070534","count":4},{"id":"GO:0090035","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0030579","count":4}]},{"hash":"1904281764988987512","title":"Hippo\u2013Wnt Growth and Differentiation Signaling","description":"The proteome is enriched for hippo signaling and positive regulation of canonical Wnt signaling, both central to controlling proliferation, apoptosis, and cell fate. Additional terms for transcription, cell cycle progression, and differentiation (keratinocytes) support a theme of growth control and lineage specification, with some tissue-specific morphogenesis signals.  ","confidence":"High","size":15,"edges":32,"triangles":30,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035329","count":7},{"id":"GO:0090263","count":7},{"id":"GO:0006915","count":7},{"id":"GO:0060044","count":7},{"id":"GO:0030216","count":7}]},{"hash":"1135378010052854393","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster is dominated by GO terms related to translation initiation and ribosome assembly (formation of preinitiation and initiation complexes, translation, and cytosolic ribosome assembly), indicating a core function in ribosome biogenesis and protein synthesis. A couple of peripheral terms (osmotic stress response, D-xylose transport) appear incidental and not central to the main theme.","confidence":"High","size":15,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0002176","count":1},{"id":"GO:0001732","count":1},{"id":"GO:0006413","count":1}]},{"hash":"1446343221046934390","title":"Autophagy and Protein Modification","description":"This cluster is driven by GO terms related to autophagy (macroautophagy, nucleophagy) and post-translational modifications (protein sumoylation, C-terminal lipidation). These suggest a cohesive theme around autophagy regulation and associated protein modifications. Some terms like defense response to fungus could reflect autophagy\u2019s role in immunity, while a few others (e.g., amygdala development, thiamine biosynthesis) may be annotation noise or broader cellular processes. Overall, the autophagy/PTM connection is the strongest signal.","confidence":"Medium","size":15,"edges":47,"triangles":77,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0050832","count":6},{"id":"GO:0045892","count":6},{"id":"GO:0016925","count":6},{"id":"GO:0018192","count":6},{"id":"GO:0061504","count":6}]},{"hash":"2132424891171875108","title":"Plant amino-acid catabolism with defense signaling","description":"The top terms highlight several amino-acid catabolic processes (alanine, kynurenine, lysine, threonine) and related metabolic steps, plus fatty acid homeostasis, alongside plant-specific defense and developmental signals (systemic acquired resistance and fruit ripening). Although a Notch signaling term is present, the dominant pattern is metabolic remodeling tied to plant defense and ripening processes. This label thus captures the cluster's core theme without overfitting to a single outlier term.","confidence":"Medium","size":15,"edges":75,"triangles":222,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":9},{"id":"GO:0097053","count":9},{"id":"GO:0007219","count":9},{"id":"GO:0033512","count":8},{"id":"GO:0034276","count":7}]},{"hash":"2207707719586859319","title":"Transcriptional Regulation in Development and Immune Signaling","description":"The cluster is dominated by GO terms for DNA-templated transcription and regulation of transcription, and development, suggesting a core role in transcriptional control during organismal development. The presence of several immune-related terms (innate immune response, IL-18/IL-1 production, Th17 differentiation, MHC I biosynthesis, and TLR3 signaling) indicates additional involvement in immune signaling pathways. Taken together, these proteins likely participate in transcriptional regulation that intersects with developmental processes and immune response modulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0098911","count":2},{"id":"GO:0045087","count":1}]},{"hash":"28936462265459578","title":"Unknown","description":"Top terms span visual perception/phototransduction, signaling regulation, platelet function, and disparate development processes, with no single unifying function. The proteins thus appear functionally heterogeneous.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":3},{"id":"GO:1903244","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0006469","count":2}]},{"hash":"1778761082256929124","title":"Innate immunity and proteostasis regulation","description":"These proteins center on antiviral defense, inflammatory signaling (NF-\u03baB/I\u03baB), and protein-homeostasis processes (ERAD, autophagy, sumoylation), suggesting a theme of innate immune signaling linked to proteostasis and transcriptional regulation. Although the interactions appear minimal (Edges 0), the GO terms converge on immune response and proteostasis functions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0031664","count":2},{"id":"GO:0045623","count":1},{"id":"GO:0016925","count":1}]},{"hash":"1452752484994253966","title":"Peroxisome Biogenesis and Oxidative Stress Response","description":"The cluster\u2019s top GO terms are dominated by peroxisome-related processes (organization, fission, size regulation) and oxidative stress/detoxification responses, indicating a functional grouping around peroxisome dynamics and cellular defense against oxidants. Some developmental terms appear, but they are likely ancillary or cross-species annotations; the core theme is peroxisome biology and oxidative stress response.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001824","count":2},{"id":"GO:0007031","count":1},{"id":"GO:0050873","count":1},{"id":"GO:0044375","count":1},{"id":"GO:0016559","count":1}]},{"hash":"1987396565295524559","title":"Unknown","description":"The GO terms are a random mix across reproductive development, hormone signaling, cell cycle, immunity, and even plant-specific photosynthesis, with deprecated terms and no connecting edges, giving no clear single function for the cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030850","count":6},{"id":"GO:0046661","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0045087","count":5}]},{"hash":"886723613594957160","title":"Cerebellar neural development and axon regeneration","description":"This cluster is dominated by GO terms tied to cerebellar development and neural differentiation, including cerebellar cortex formation, Bergmann glial cell differentiation, and regulation of axon regeneration. While other terms touch on signaling pathways (insulin signaling, T cell receptor signaling) and cell cycle regulation, the strongest and most coherent theme centers on cerebellar neural development and axon growth/repair. Confidence: Medium","confidence":"","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035335","count":9},{"id":"GO:0045736","count":9},{"id":"GO:0034501","count":9},{"id":"GO:0048679","count":8},{"id":"GO:0008286","count":8}]},{"hash":"1222633858420419680","title":"Nuclear transcription and cell cycle stress response","description":"Most terms point to nuclear gene expression (DNA-templated transcription) together with cell cycle processes (cell division, chromosome segregation) and stress responses (ER stress, oxidative stress), suggesting a cluster of genes involved in transcriptional control linked to cell cycle regulation and cellular stress signaling; a viral process term and some obsolete terms are less informative, but do not override the core theme. ","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:0051301","count":1},{"id":"GO:0007059","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0016032","count":1}]},{"hash":"178977411716538001","title":"Oxidative Metabolism and Xenobiotic Catabolism","description":"This cluster is dominated by GO terms for oxidation-reduction processes, cellular oxidant detoxification, and various catabolic pathways (stilbene, uracil, 3-phenylpropionate, epoxygenase P450, etc.), plus related detox and metabolite-biosynthetic processes. The recurring theme is metabolism of small molecules via redox reactions and xenobiotic processing, despite some disparate terms like endocannabinoid regulation. Overall, the proteins are best described as involved in oxidative metabolism and detox/catabolic pathways. ","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0046272","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0046839","count":2}]},{"hash":"1911355145965295732","title":"Ion Transport and Cardiac Electrophysiology","description":"The dominant GO terms point to membrane excitability and ion movement (sodium import, potassium export, repolarization, hyperpolarization) and cardiac action potentials, suggesting a core theme of membrane potential regulation and electrophysiology. Additional terms show related signaling and endocrine contexts (GPCR signaling, thermogenesis, aldosterone biosynthesis), which may reflect broader tissue signaling links, but the core cluster appears to center on ion transport and cardiac electrical activity.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":7},{"id":"GO:0098914","count":7},{"id":"GO:0060081","count":7},{"id":"GO:0098719","count":7},{"id":"GO:0097623","count":7}]},{"hash":"563124197162508257","title":"Unknown","description":"The GO terms are highly heterogeneous, including neuronal differentiation (cerebellar granule cell differentiation, dendrite development), telomere maintenance (telomere maintenance via telomerase, telomere capping), ubiquitination, and immune signaling regulation, with some terms labeled obsolete. There is no clear, unified biological process linking these terms, making it inappropriate to assign a specific, representative function beyond Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":8},{"id":"GO:0098907","count":8},{"id":"GO:0016567","count":8},{"id":"GO:0032212","count":7},{"id":"GO:0021707","count":7}]},{"hash":"2062051637155021331","title":"Cranial patterning and craniofacial development","description":"Dominant terms point to head morphogenesis, including cranial development, cranial skeletal system, cranial ganglion development, dorsal identity, and Wnt signaling in development, with adherens junction assembly supporting tissue morphogenesis. Some trafficking-related terms are present but appear tangential to the main cranial theme.","confidence":"High","size":15,"edges":101,"triangles":405,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0048496","count":7},{"id":"GO:0000011","count":7},{"id":"GO:0061550","count":6},{"id":"GO:0044336","count":6},{"id":"GO:1904888","count":6}]},{"hash":"1744508350065179810","title":"Unknown","description":"The GO terms span mechanosensory response, telomere maintenance regulation, immune signaling, neuroendocrine secretion, and development, with no clear shared function tying all proteins. This lack of a cohesive theme suggests the cluster cannot be assigned a specific biological label.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0032212","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0071651","count":4},{"id":"GO:0007253","count":4}]},{"hash":"2044235012461899162","title":"Vesicle trafficking regulation and signaling","description":"The top GO terms cluster around intracellular transport and vesicle regulation: ER-to-Golgi transport, protein targeting to vacuole, regulation of multivesicular body size, and regulation of synaptic vesicle exocytosis, all tied together by regulation of phosphatidylinositol dephosphorylation. Additional terms point to broader signaling and development roles (brain development, Wnt signaling, mating projection growth, mitotic processes), suggesting these proteins coordinate trafficking with growth and division. Confidence: Medium","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060304","count":2},{"id":"GO:0031384","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0010796","count":2},{"id":"GO:0007420","count":2}]},{"hash":"2203247292342189067","title":"TLR signaling and inflammation","description":"This cluster centers on Toll-like receptor pathways (TLR8, Toll signaling) and downstream inflammatory responses, including cytokine production (IL-18, interferon-\u03b1) and antibacterial peptide biosynthesis, with some emphasis on regulation of signaling via dephosphorylation and kinase activity control, plus autophagy. This combination points to a coherent innate immune signaling module activated by TLRs.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0006469","count":1},{"id":"GO:0032741","count":1},{"id":"GO:0034158","count":1},{"id":"GO:0050729","count":1}]},{"hash":"2169964818486136297","title":"Auditory hair cell morphogenesis and synaptic signaling","description":"This cluster centers on hearing-related processes: stereocilium organization and cochlea morphogenesis point to hair cell development, while glutamate secretion, long-term synaptic depression, and retrograde nitric oxide signaling indicate synaptic transmission and plasticity in auditory pathways. Dendritic spine morphogenesis and protein dephosphorylation further reflect neuronal signaling components, suggesting a cohesive theme of hair cell development coupled with synaptic signaling in the ear. Unknown terms like opsonization appear less connected and can be considered noise. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0060088","count":6},{"id":"GO:0098924","count":6},{"id":"GO:0006470","count":6},{"id":"GO:0035640","count":6},{"id":"GO:0060292","count":6}]},{"hash":"944636880767977280","title":"Unknown","description":"The top GO terms span ubiquinone and vitamin E biosynthesis, antibiotic biosynthesis, RNA and histone methylation, xenobiotic response, and cellular senescence, indicating a broad and heterogeneous set of functions without a single cohesive module; the lack of edges further supports labeling this cluster Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0010189","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0017000","count":1},{"id":"GO:1901052","count":1}]},{"hash":"157683564170640619","title":"Unknown","description":"The top terms span nuclear/chromatin-associated processes, DNA repair, viral processes, plant hormone response, neural development, and vesicular transport, with no clear single theme tying all proteins together. This lack of a cohesive functional pattern supports labeling the cluster as Unknown.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":3},{"id":"GO:1990414","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0014041","count":2}]},{"hash":"1892366635286873736","title":"Unknown","description":"The GO terms span telomere maintenance and capping, neural differentiation, immune signaling, and kinase regulation, with no single cohesive function tying the proteins together, so a specific, representative label cannot be determined.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0007253","count":1}]},{"hash":"672282371758798843","title":"Unknown","description":"The GO terms are very diverse (eye/retinal development, rRNA processing, ubiquitin-dependent proteolysis, chromatin modification, neural tube development, DNA repair, fungal cell wall regulation, microtubule movement) with little apparent unity, and several entries are marked obsolete. There is no clear common function linking these proteins into a single coherent biological theme.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:2000060","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1}]},{"hash":"31625321181394594","title":"Cell Cycle Regulation and Telomere Maintenance","description":"The dominant signals are cell division, CDK regulation, transcription control, telomere maintenance, and DNA damage response (site of double-strand breaks), suggesting a module tied to cell cycle progression and genome stability; a couple terms (androgen metabolism, smooth muscle development) appear peripheral. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0008209","count":1}]},{"hash":"98410686315758895","title":"Cell Division and Development","description":"The dominant signals are cell division and development: multiple terms refer to mitotic cell cycle, general cell division, and multicellular development (including skin and lens differentiation), with associated transcription activity. A coherent theme is regulation of cell proliferation and differentiation during organismal development.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007275","count":2}]},{"hash":"503680941687017271","title":"SNARE-mediated secretion and Golgi trafficking","description":"Based on the top GO terms, the cluster centers on secretory pathway activities: Golgi-to-plasma membrane transport, SNARE complex assembly, vesicle targeting, Golgi ribbon formation, and degranulation/mucus secretion. Although cerebral cortex development is listed, the dominant theme is vesicle trafficking and secretion, including endosome-to-Golgi retrograde transport and vacuole fusion, which ties these proteins to secretory processes. ","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0042147","count":1},{"id":"GO:0043312","count":1},{"id":"GO:0070254","count":1}]},{"hash":"1396872922763460518","title":"RNA processing and ribosome biogenesis","description":"The proteins in this cluster are enriched for RNA maturation processes\u2014splicing (mRNA via spliceosome, spliceosomal complex assembly), tRNA processing, and rRNA maturation\u2014as well as translation, indicating a shared role in RNA processing and ribosome assembly; additional terms for chromatin-related processes and hormone response appear less central to the core function.","confidence":"High","size":14,"edges":81,"triangles":267,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1000325286366028711","title":"Neuronal signaling and ion homeostasis","description":"The cluster shows strong enrichment for ion transport (potassium and sodium), membrane potential regulation, and signaling via cAMP/cGMP, pointing to nerve cell communication and ionic balance maintenance. While transcription-related terms appear, the dominant theme is neuronal signaling and ion homeostasis, with occasional developmental and pain perception associations.","confidence":"High","size":14,"edges":41,"triangles":50,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0019233","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0071321","count":3}]},{"hash":"1329826426362292022","title":"Cochlear development and synaptic organization","description":"The top GO terms point to inner ear formation (cochlea morphogenesis, stereocilium organization) and neuronal communication (dendritic spine morphogenesis, glutamate secretion), suggesting a cluster centered on auditory system development and synaptic function, with some generic cellular processes included as secondary themes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:1903220","count":1},{"id":"GO:0043278","count":1},{"id":"GO:0060997","count":1},{"id":"GO:0014047","count":1}]},{"hash":"452136902885871377","title":"Muscle fiber-type switching and cardiac stress signaling","description":"This cluster is enriched for muscle-related terms: transition between fast and slow fibers, calcium release via ryanodine receptors, and positive regulation of cardiac muscle hypertrophy in response to stress, plus locomotion. Other terms (DNA replication, ER-Golgi transport, xenobiotic/morphine response) appear as general cellular processes or stress responses but do not define the core theme. Thus, the dominant signal is muscle physiology and stress signaling. ","confidence":"Medium","size":14,"edges":26,"triangles":15,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0014883","count":4},{"id":"GO:0035690","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0006888","count":4},{"id":"GO:1900486","count":3}]},{"hash":"622863950322374253","title":"Immune cell activation and signaling","description":"The cluster\u2019s top GO terms include positive regulation of alpha-beta T cell proliferation and NK T cell differentiation, plus caveolin-mediated endocytosis and potassium ion transport, all pointing to immune signaling and activation processes. While some terms touch on cell cycle and other general processes, the immune-related terms provide a cohesive theme around adaptive immune function and membrane trafficking.","confidence":"Medium","size":14,"edges":70,"triangles":175,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006813","count":14},{"id":"GO:0032212","count":13},{"id":"GO:0071469","count":13},{"id":"GO:0046641","count":13},{"id":"GO:0000751","count":13}]},{"hash":"763070046416180437","title":"Unknown","description":"The GO terms are highly diverse, spanning transcription regulation, signal transduction, neural and sensory processes, development in multiple tissues, and immune-related functions, with no clear shared function tying the proteins together.","confidence":"","size":14,"edges":26,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0002576","count":2}]},{"hash":"216903602933697507","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":46,"triangles":64,"max_degree":12,"top_function":"autophagy","top_go_terms":[{"id":"GO:1902564","count":6},{"id":"GO:0070979","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0016032","count":4}]},{"hash":"696849267085687672","title":"Mitochondrial Metabolite Transporters","description":"The top GO terms are dominated by transmembrane transport into and out of mitochondria for a variety of substrates and cofactors (malate-aspartate shuttle, ATP, CoA, phosphate, dNTPs, TPP, thiamine-related compounds, ornithine), plus regulation of mitochondrial membrane permeability and a superoxide response. This points to a cohesive set of mitochondrial transport proteins handling diverse metabolite exchange and related redox regulation. ","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043490","count":3},{"id":"GO:1990616","count":3},{"id":"GO:1990544","count":3},{"id":"GO:0035349","count":3},{"id":"GO:0035435","count":3}]},{"hash":"2090651566555346932","title":"Ubiquitin-Driven Proteostasis and Innate Immunity","description":"The cluster\u2019s top GO terms cluster around ubiquitin-dependent protein turnover (ERAD and general ubiquitin-mediated proteolysis) and innate immune signaling (innate immune response, TNF-mediated signaling, defense against virus). While some terms are obsolete or peripheral (e.g., peroxisome import, miRNA silencing, plant cytokinin signaling), the recurring theme is proteostasis via ubiquitin pathways interconnected with immune response pathways, suggesting a functional group focused on protein quality control that feeds into immune signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0090073","count":2}]},{"hash":"2278595982558089618","title":"Energy metabolism and protein quality control across organelles","description":"Predominant terms point to energy production and transport (photosynthesis, mitochondrial ETC, proton translocation) with concurrent protein quality control roles (autoubiquitination, ERAD), and basic gene expression/repair processes; together they suggest a cluster of proteins tied to energy metabolism and proteostasis in organelles.","confidence":"Medium","size":14,"edges":10,"triangles":1,"max_degree":7,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0015979","count":3},{"id":"GO:0006122","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0006412","count":2}]},{"hash":"2182488194914136801","title":"Chromatin regulation and transcription control","description":"This cluster centers on DNA-templated transcription and chromatin-related processes: transcriptional regulation, histone modification (H3-K79 methylation), heterochromatin formation, and DNA damage tolerance. Additional terms for RNA guanine-N7 methylation and protein polyubiquitination reinforce a nuclear/chromatin maintenance theme. A few viral process terms (virion assembly/release) may reflect annotation noise or cross-annotation but do not dominate the cluster.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":3},{"id":"GO:0006301","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0036265","count":2}]},{"hash":"1682963814230372327","title":"Actin Dynamics and Cell Migration","description":"This cluster centers on actin cytoskeleton remodeling and how it drives cell movement and polarity. Enriched terms include barbed-end capping and actin crosslinking, GTPase regulation, TGF-beta signaling, cell migration, and epithelial polarity; with related roles in bone development and synaptic plasticity contextually linked to cytoskeletal dynamics.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0071560","count":2},{"id":"GO:0050731","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0090162","count":2}]},{"hash":"2099377250454235802","title":"Ribosome biogenesis and rRNA processing","description":"This cluster is dominated by GO terms for SSU-rRNA maturation and ITS1 cleavage, key steps in ribosome RNA processing and small subunit assembly, indicating a ribosome biogenesis-focused group; the other terms are less central or peripheral to this theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000462","count":7},{"id":"GO:0000724","count":7},{"id":"GO:0007064","count":7},{"id":"GO:0070306","count":6},{"id":"GO:0000447","count":6}]},{"hash":"623930396006192953","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0030422","count":1},{"id":"GO:0048136","count":1},{"id":"GO:0006446","count":1}]},{"hash":"1212761228226145521","title":"Nervous system development and microtubule dynamics","description":"The top GO terms point to neural development (Schwann cell development, substantia nigra development), neuronal signaling (excitatory postsynaptic potential), and cytoskeletal organization (microtubule nucleation, spindle-related processes). While there are some vascular/cardiac terms, the dominant theme is nervous system development together with cytoskeletal/microtubule dynamics, suggesting a cluster focused on CNS/PNS development with cytoskeletal regulation.","confidence":"Medium","size":14,"edges":79,"triangles":249,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0034501","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0014044","count":5},{"id":"GO:1903087","count":5},{"id":"GO:0007020","count":5}]},{"hash":"2103902856371711931","title":"DNA replication and cell cycle regulation","description":"The cluster is dominated by GO terms tied to DNA replication, nuclear cell cycle regulation, centrosome cycle, and mitotic control, pointing to a core function in cell division and genome maintenance. While there are additional terms related to development and endocytosis, they appear secondary to the primary theme of cell cycle control.","confidence":"Medium","size":14,"edges":69,"triangles":163,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":14},{"id":"GO:0006260","count":14},{"id":"GO:0007098","count":14},{"id":"GO:0048701","count":14},{"id":"GO:0032212","count":13}]},{"hash":"757765879943768478","title":"Unknown","description":"The Top Terms span plant development (auxin transport, root meristem growth, cytokinin signaling) and animal development/polarity (left/right asymmetry, neuroblast polarity) along with unrelated processes (telomerase assembly, glucocorticoid signaling). The lack of a coherent, single biological theme across kingdoms suggests no clear unifying function for this cluster, so Unknown is the most appropriate label.","confidence":"","size":14,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000012","count":1},{"id":"GO:1905793","count":1},{"id":"GO:0061371","count":1},{"id":"GO:0010449","count":1},{"id":"GO:0045201","count":1}]},{"hash":"157197897015694180","title":"Retinal phototransduction and calcium signaling","description":"Dominant themes are phototransduction and visual perception, with calcium-release regulation and exocytosis control, suggesting a retina-related signaling cluster. Some terms about metanephric development and cell cycle appear incidental rather than core; overall, the theme is vision-related calcium signaling.","confidence":"Medium","size":14,"edges":12,"triangles":0,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007602","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0072205","count":3},{"id":"GO:0060315","count":3}]},{"hash":"2248921370617150316","title":"Ion Transport Under Osmotic Stress","description":"This cluster shows enrichment for transmembrane transport of ions (potassium, sodium) and other solutes (D-xylose), with responses to osmotic stress and cold, pointing to a core theme of ion transport linked to stress adaptation. Additional terms for ubiquitin-dependent protein catabolic process, apoptotic process, and splicing/transcription suggest broader regulatory adjustments under stress. Overall, the dominant signal is ion transport tied to stress responses.","confidence":"Medium","size":14,"edges":17,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0009409","count":2}]},{"hash":"1908476878939529794","title":"Vision and neural signaling","description":"This cluster is dominated by vision-related processes, with visual perception and phototransduction as top terms, suggesting light sensing and processing roles. The presence of short-term memory and protein phosphorylation regulation terms supports a neural signaling context, while several outlier terms (cuticle and kidney development) may reflect annotation noise or multi-function proteins. Overall, the dominant theme is vision and neural signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060316","count":4},{"id":"GO:0006469","count":4},{"id":"GO:0031954","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0007602","count":3}]},{"hash":"57384548412116710","title":"Unknown","description":"The GO terms span reproductive hormone signaling (prostate gland development, male sex differentiation, steroid hormone receptor complex assembly), antiviral innate immunity (innate immune response, cellular response to type I interferon, cellular response to exogenous dsRNA, negative regulation of defense response to virus by host), and ciliopathy/retina-related processes (non-motile cilium assembly, protein localization to photoreceptor outer segment). There is no single cohesive function that links all terms clearly, so a single intuitive label is not warranted.","confidence":"","size":14,"edges":15,"triangles":0,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030850","count":7},{"id":"GO:0046661","count":7},{"id":"GO:0071357","count":7},{"id":"GO:0006463","count":7},{"id":"GO:0045087","count":6}]},{"hash":"734126454604930245","title":"DNA-Templated Transcription Regulation","description":"The most represented GO terms are regulation of DNA-templated transcription and DNA-templated transcription itself, indicating the cluster is centered on transcriptional control. Other terms (auxin/hormone biosynthesis, development, stress responses) appear less dominant, but do not override the clear transcription-focused signal.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0045654","count":3},{"id":"GO:0009851","count":3},{"id":"GO:0046886","count":3}]},{"hash":"1045581769217049868","title":"Cell Growth and Ribosome Biogenesis","description":"The top GO terms cluster around fundamental cellular growth and division processes (cell growth, cell division) and the production of ribosomes (ribosome biogenesis), plus RNA processing (RNA methylation) and genome maintenance (telomere maintenance, meiosis). While there are also terms related to cytoskeleton, polarity, and signaling, the dominant theme is core growth-related machinery and genome maintenance, justifying a label centered on growth and ribosome biogenesis.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0000747","count":3}]},{"hash":"1674928266933884163","title":"Ubiquitin-Proteasome Pathway","description":"The proteins are enriched for ubiquitin-dependent protein degradation (ERAD, K48-linked ubiquitination, autoubiquitination) and related regulatory signaling (apoptosis, JNK cascade), indicating a cohesive cluster centered on ubiquitin tagging for proteasomal degradation and its regulatory roles.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0046621","count":3},{"id":"GO:1903721","count":3},{"id":"GO:0051865","count":3}]},{"hash":"1047622764118829796","title":"Unknown","description":"The top GO terms describe a broad, inconsistent set of processes (positive regulation of GTPase activity; lens fiber cell differentiation; microtubule-based movement; neural tube closure; double-strand break repair via homologous recombination) and include several obsolete terms, with no observed edges linking the proteins. This indicates there is no single cohesive function or pathway tying these proteins together, so Unknown is the best label.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0070306","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0006349","count":3}]},{"hash":"1756616109492074802","title":"Unknown","description":"The GO terms cluster around telomere regulation, neural differentiation, immune signaling, and protein modification, with no single coherent function linking all terms. The lack of edges further suggests no cohesive pathway or process defines the set, so a precise label isn\u2019t supported.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":5},{"id":"GO:0021707","count":5},{"id":"GO:1904355","count":5},{"id":"GO:0071651","count":5},{"id":"GO:0007253","count":5}]},{"hash":"698616124738966190","title":"Translation Initiation and Ribosome Regulation","description":"Top GO terms converge on translation initiation and ribosome dynamics (preinitiation complex formation, IRES-dependent initiation, translation reinitiation, ribosome disassembly, regulation of translation, and translational fidelity), suggesting the proteins mainly participate in protein synthesis control. Some non-dominant terms (necroptosis regulation, insulin secretion) are present but do not define the cluster.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060546","count":2},{"id":"GO:0035774","count":2},{"id":"GO:0097274","count":2},{"id":"GO:0006417","count":1},{"id":"GO:0002192","count":1}]},{"hash":"1653860610329973775","title":"Genome maintenance and RNA processing","description":"Top GO terms center on nuclear genome integrity (telomere maintenance via recombination, interstrand cross-link repair, DNA incision, DNA-templated transcription) and RNA processing (tRNA processing). Although several annotations are labeled obsolete, the remaining terms collectively point to nuclear functions related to genome maintenance and RNA maturation rather than a single cytosolic pathway. The lack of edges suggests loose network connectivity, but the extracted themes justify this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0090342","count":1},{"id":"GO:0033683","count":1}]},{"hash":"351160977379142555","title":"Immune Activation and Cell Migration","description":"The top GO terms point to immune system relevance (NK T cell differentiation; antigen receptor-mediated signaling; B cell homeostasis; hemopoiesis) and overlap with cytoskeletal/motility processes (microtubule-based movement; lamellipodium assembly; integrin activation). This pattern suggests proteins that participate in immune cell activation together with adhesion and movement, with supporting roles in vesicle trafficking and broader signaling contexts.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007018","count":1},{"id":"GO:0001865","count":1},{"id":"GO:0050851","count":1},{"id":"GO:0001782","count":1},{"id":"GO:0035621","count":1}]},{"hash":"1011589185405677512","title":"Ubiquitin-Dependent Protein Degradation (ERAD)","description":"This cluster is dominated by GO terms for ubiquitination and protein catabolism (ubiquitin-dependent proteolysis, ERAD, autoubiquitination, K48-linked ubiquitination, and general protein ubiquitination), indicating a core function in targeted protein turnover. A peroxisomal matrix import term and a couple of indirect items reflect ubiquitin's broader roles, but the dominant pattern is ubiquitin-mediated degradation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0046621","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0070936","count":5}]},{"hash":"1061021467140375396","title":"Bacterial cell wall glycosylation and polysaccharide biosynthesis","description":"This cluster is dominated by GO terms tied to cell wall organization and glycosylation, including protein O-linked glycosylation, teichoic acid biosynthesis, cellulose biosynthesis, and UDP-glucose metabolism. These terms point to enzymes and pathways that build and modify bacterial cell wall polysaccharides. Some terms (e.g., hyaluronan and immunoglobulin production) are less directly connected, but the central theme remains glycosylation and cell wall biosynthesis. Overall, the label reflects the strongest shared function among the terms.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0016266","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0018243","count":2}]},{"hash":"1286178372458951461","title":"Unknown","description":"The top GO terms span diverse biological processes (immune response, virus defense regulation, photosynthesis, development in brain and prostate) and include obsolete annotations, implying no single cohesive function for this cluster.","confidence":"","size":14,"edges":11,"triangles":3,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":14},{"id":"GO:0050689","count":14},{"id":"GO:0006478","count":14},{"id":"GO:0043278","count":14},{"id":"GO:0007091","count":14}]},{"hash":"1580153542242859909","title":"Antiviral innate immune response","description":"The proteins cluster around innate antiviral signaling and defense, as shown by frequent GO terms like defense response to virus, innate immune response, TLR8 signaling, interferon-alpha production, and inflammatory response. While some terms touch on cell cycle regulation or neural development (e.g., mitotic transition, axonogenesis), the dominant theme is antiviral innate immunity and inflammatory signaling, consistent with antiviral defense mechanisms.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":8},{"id":"GO:0045842","count":7},{"id":"GO:0051607","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0007190","count":6}]},{"hash":"26198364734426752","title":"Cardiac and smooth muscle signaling","description":"Top GO terms highlight cardiac action potentials, membrane repolarization, smooth muscle contraction, and calcium signaling, indicating a cluster centered on muscle excitation-contraction signaling. While other terms touch endocrine and sensory pathways, the dominant theme is muscle electrophysiology and Ca2+-mediated signaling.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":10},{"id":"GO:0098914","count":10},{"id":"GO:0060083","count":10},{"id":"GO:0034465","count":10},{"id":"GO:0051592","count":10}]},{"hash":"2113688443566401065","title":"Ubiquitination-linked immune signaling regulators","description":"The cluster centers on protein ubiquitination and immune signaling regulation, with GO terms for protein ubiquitination, NF-kappaB cytoplasmic sequestration, negative regulation of IL-12, and production of chemokines. Together these point to roles in controlling inflammatory responses. Other terms (telomere maintenance, vasopressin secretion, pain perception) are less cohesively linked, so the core theme remains ubiquitination-associated immune signaling regulation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071651","count":3},{"id":"GO:0007253","count":3}]},{"hash":"667734455987858972","title":"Neural lipid signaling and brain development","description":"This cluster highlights lipid-related signaling pathways (triglyceride and diacylglycerol metabolism) and lipid signaling regulators (endocannabinoid, sphingosine-1-phosphate), coupled with brain development and vascular development, and an inflammatory component. The common theme appears to be neural lipid signaling intertwined with brain and blood vessel development, with modulation of inflammatory processes.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":3},{"id":"GO:2000124","count":2},{"id":"GO:0046339","count":2},{"id":"GO:0003376","count":2},{"id":"GO:2000064","count":2}]},{"hash":"873576332388291896","title":"Unknown","description":"The top GO terms are a mix of separate metabolic and regulatory processes (cholesterol biosynthesis, galactose metabolism, sorbitol biosynthesis, inositol catabolic process, hemopoiesis) plus some regulatory annotations, with no clear shared function or pathway linking the proteins. The cluster has no edges or consistent themes, suggesting heterogeneous composition; therefore there is no cohesive label beyond Unknown. ","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":1},{"id":"GO:0030097","count":1},{"id":"GO:0006061","count":1},{"id":"GO:0006012","count":1},{"id":"GO:0033673","count":1}]},{"hash":"827232167596771833","title":"Cilium assembly and axoneme movement","description":"The top GO terms center on axoneme assembly and cilium movement, indicating a ciliogenesis/motility theme for this cluster. The nucleotide phosphorylation terms are broader, less specific signals and don\u2019t detract from the clear cilia-related function. Therefore, labeling it as ciliogenesis and axoneme motility is appropriate.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061565","count":1},{"id":"GO:0061566","count":1},{"id":"GO:0061568","count":1},{"id":"GO:0061570","count":1},{"id":"GO:0061571","count":1}]},{"hash":"737295643868540728","title":"RNA Pol II Transcription Regulation","description":"Most of the top GO terms are centered on DNA-templated transcription and regulation of transcription from the RNA polymerase II promoter, indicating a shared function in transcription control. Aflatoxin biosynthetic and amino acid regulatory terms are minor/outliers and do not redefine the core theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0035969","count":1},{"id":"GO:1904741","count":1},{"id":"GO:0061429","count":1}]},{"hash":"401046863051036640","title":"Unknown","description":"The top GO terms span disparate areas, including GPCR signaling, ephrin signaling, synaptic plasticity, renin-angiotensin regulation, cGMP response, APP processing, MHC II antigen presentation, antibacterial peptide production, mesonephros development, and protein autoprocessing, with no single overarching function linking all proteins. This lack of a coherent shared theme makes it unclear what concise label best describes the cluster.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":2},{"id":"GO:1901187","count":2},{"id":"GO:1900383","count":2},{"id":"GO:0002018","count":1},{"id":"GO:0070305","count":1}]},{"hash":"1384275861711521004","title":"Unknown","description":"The top terms are highly heterogeneous, spanning growth hormone response, lens fiber differentiation, rRNA processing, imprinting regulation, fungal cell wall biogenesis, microtubule movement, histone modification, neural tube closure, and homologous recombination repair. With no clear shared function and no edges connecting the proteins, there is no coherent unifying theme to assign a specific label.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060416","count":3},{"id":"GO:0070306","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0032995","count":2}]},{"hash":"538527486975852933","title":"Vision and Synaptic Transmission","description":"Reason: The prominent terms point to vision and neural signaling\u2014visual perception, phototransduction, short-term memory, and synaptic vesicle exocytosis\u2014supported by cytoskeletal elements (myosin II) related to neurons. Some unrelated terms likely reflect annotation noise, but the core theme is sensory processing and synaptic transmission.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0006469","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0002576","count":1},{"id":"GO:0007602","count":1}]},{"hash":"307265556529145260","title":"Unknown","description":"The GO terms are highly diverse and span development (lens fiber differentiation, neural tube closure), RNA processing, ubiquitin-mediated proteolysis, histone acetylation, microtubule movement, DNA repair, and plant signaling. With no single cohesive function dominating, there is no clear theme tying these proteins together, so this cluster is labeled Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:2000060","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1}]},{"hash":"2248593135674459434","title":"Skeletal Muscle Regulation and Metabolism","description":"The terms point mainly to skeletal muscle biology: contraction regulation (especially fast-twitch fibers), muscle atrophy, and actin cytoskeleton associations, along with metabolic shifts toward lactate production. Wnt signaling links to muscle development/remodeling, and there is also coverage of vascular smooth muscle growth regulation. A couple of terms (tight junction localization, vagus nerve development) are less directly muscle-specific but can be related to broader tissue organization and development. Overall, the cluster centers on muscle function and its regulation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902396","count":1},{"id":"GO:0014732","count":1},{"id":"GO:0051666","count":1},{"id":"GO:0031448","count":1},{"id":"GO:1904025","count":1}]},{"hash":"726036889407648718","title":"Unknown","description":"The GO terms are highly diverse (innate immunity, ubiquitination, apoptosis, autophagy, calcium detection, tissue morphogenesis, membrane repair, ossification). No single shared function or pathway ties the proteins together, and there are no interactions to define a cohesive module. Therefore, Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":1},{"id":"GO:0070534","count":1},{"id":"GO:0097050","count":1},{"id":"GO:0046597","count":1},{"id":"GO:0005513","count":1}]},{"hash":"100695717365291154","title":"Cardiovascular Development and Hormonal Signaling","description":"Proteins in this cluster show clear enrichment for cardiac-related processes (cardiac muscle cell action potential, regulation of ventricular cardiac muscle cell action potential, vasoconstriction) and GPCR signaling, plus endocrine-hormonal contexts (aldosterone biosynthesis) and metabolic regulation (diet-induced thermogenesis). While some terms touch general development (multicellular organism development, skin development), the strongest, cohesive theme centers on cardiovascular signaling and hormone-driven regulation, supporting a label focused on heart-related development and hormonal signaling.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0007216","count":5},{"id":"GO:0002024","count":5}]},{"hash":"225228894098304120","title":"Unknown","description":"The Top Terms are highly heterogeneous, ranging from endosomal acidification and proton transport to differentiation, transcription termination, and motility, with no single overarching function or pathway that ties the cluster together. This suggests there is no coherent theme for a meaningful label.","confidence":"","size":13,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048388","count":1},{"id":"GO:0090463","count":1},{"id":"GO:0001649","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0071973","count":1}]},{"hash":"2291988363576843878","title":"Chaperone-assisted folding and microtubule organization","description":"Major GO terms cluster around protein quality control and cytoskeletal dynamics: chaperone-mediated protein complex assembly, protein folding, ubiquitin\u2013proteasome\u2013mediated cytoplasmic quality control, and tubulin complex assembly/microtubule organization. This suggests a core theme of ensuring proper protein folding and assembly of microtubule structures, with a few peripheral terms (telomere maintenance, cerebellar differentiation) likely reflecting broader or indirect functions. Confidence: Medium","confidence":"","size":13,"edges":57,"triangles":120,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0046475","count":2},{"id":"GO:0043622","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0071629","count":1},{"id":"GO:0007021","count":1}]},{"hash":"816651120956079049","title":"Signal transduction and sensory processes","description":"This cluster centers on signaling-related activities (protein phosphorylation and regulation of kinase activity) and sensory pathways (visual perception and phototransduction), suggesting proteins involved in stimulus response and regulation of gene expression via signaling cascades. Other terms (xenobiotic response, miRNA silencing, development terms) are more disparate but do not override the core signaling/sensory theme.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006468","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0035278","count":2},{"id":"GO:0006469","count":2}]},{"hash":"2100137710069619950","title":"Neural development and axon guidance","description":"The top GO terms are dominated by neuronal-related processes: regulation of neuronal synaptic plasticity, axon extension and guidance, and trigeminal nerve organization, pointing to a neural development/function theme. Additional terms like endosomal localization and glycosylation reflect supporting cellular processes; some terms (e.g., organ morphogenesis) widen to general development. Overall, the cluster appears to center on neural development and connectivity, with some broader developmental context.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048168","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0051260","count":2},{"id":"GO:1903244","count":2},{"id":"GO:0006487","count":1}]},{"hash":"2179887720009512610","title":"Diverse biosynthesis and protein modification processes","description":"The Top Terms span various biosynthetic pathways (novobiocin, cobalamin, lignin) alongside protein-centric modifications (methylation, O-linked glycosylation via mannose, GPI anchor biosynthesis) and related lipid metabolism (dolichol). This breadth indicates a cluster of proteins involved in diverse biosynthetic routes and post-translational modification processes rather than a single, cohesive function.","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043642","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0009809","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0032259","count":1}]},{"hash":"359778842423337019","title":"Organ morphogenesis and left-right patterning","description":"These terms cluster around developmental processes across multiple organs (kidney development: metanephric collecting duct, metanephric cortical collecting duct, mesonephric duct development; ear development: inner ear auditory receptor cell differentiation; heart morphogenesis: heart looping; left-right axis formation: determination of liver left/right asymmetry). While autophagosome maturation and stress/NO-related terms appear, the dominant theme is organogenesis and left-right patterning, suggesting a cohesive focus on morphogenesis across tissues.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097352","count":3},{"id":"GO:0042491","count":3},{"id":"GO:0071470","count":3},{"id":"GO:0045429","count":3},{"id":"GO:0072205","count":3}]},{"hash":"1598640133442768732","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0042255","count":1},{"id":"GO:0000480","count":1}]},{"hash":"2185889062185213361","title":"Genome maintenance and cell cycle","description":"The top terms cluster around DNA replication, DNA repair, mitotic cell cycle, and telomere maintenance, indicating a role in genome integrity and cell division. Some terms reflect other processes (endocytosis, signaling, pH response), but the dominant theme is genome stability and cell proliferation.","confidence":"High","size":13,"edges":37,"triangles":51,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007118","count":10},{"id":"GO:0006281","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0032212","count":8}]},{"hash":"200115484467397319","title":"DNA-templated transcription regulation cluster","description":"The majority of top GO terms point to transcription-related processes (regulation of DNA-templated transcription and DNA-templated transcription). A number of catabolic processes appear as well, but they are less dominant, suggesting the cluster is centered on transcription regulation with some heterogeneous metabolic annotations. Overall, the theme is transcription control.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0019380","count":2},{"id":"GO:0046272","count":2}]},{"hash":"1794905928541713310","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":25,"triangles":21,"max_degree":8,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":5},{"id":"GO:0046380","count":4},{"id":"GO:0016311","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0032361","count":4}]},{"hash":"499440552055143587","title":"Proteostasis and unfolded protein response","description":"This cluster is dominated by terms related to protein folding quality control: unfolded protein response, misfolded protein transport, chaperone-assisted refolding, and redox homeostasis, suggesting a group of proteins involved in maintaining proper protein folding. Some terms (DNA replication, tRNA import, and developmental signaling) appear peripheral, but do not override the primary proteostasis signal.","confidence":"Medium","size":13,"edges":18,"triangles":2,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0035719","count":3},{"id":"GO:1901621","count":3}]},{"hash":"2286703281380962349","title":"ER-Golgi Vesicle Trafficking and Localization","description":"The top terms cluster around ER-to-Golgi and Golgi-to-ER transport, ER lumen retention, and protein localization to membranes, suggesting a shared role in intracellular trafficking and membrane targeting; a few terms appear unrelated, likely reflecting broad annotations or incidental associations.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":1},{"id":"GO:0090004","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0071340","count":1},{"id":"GO:0006890","count":1}]},{"hash":"682705867450712005","title":"Hippo-Wnt Signaling and Growth Control","description":"The top GO terms indicate enrichment for Hippo signaling and positive regulation of canonical Wnt signaling, along with processes related to cell proliferation, apoptosis, and differentiation. This points to a cluster centered on developmental signaling pathways that govern growth, cell fate decisions, and survival. Confidence: Medium","confidence":"","size":13,"edges":28,"triangles":9,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":7},{"id":"GO:0035329","count":6},{"id":"GO:0090263","count":6},{"id":"GO:0060044","count":6},{"id":"GO:0006915","count":6}]},{"hash":"966346228674837345","title":"Synaptic Actin Remodeling and Adhesion Regulation","description":"Top terms indicate actin filament dynamics and focal adhesion control (positive/negative regulation of focal adhesion assembly, actin filament bundle assembly, cell adhesion) along with neuronal processes like synaptic plasticity and dendritic spine maintenance. This suggests a cohesive theme of actin cytoskeleton remodeling at synapses coupled with adhesion signaling, which can modulate spine structure and plasticity. Some immune-related terms (TNF/IL-6, defense response to fungus) appear but are less central to the core cytoskeletal/adherence theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051894","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0031915","count":1},{"id":"GO:0032232","count":1},{"id":"GO:0007162","count":1}]},{"hash":"273464497889246042","title":"Transmembrane Transport of Ions and Metabolites","description":"The top GO terms are all about moving various substrates across membranes\u2014ions (Na+, K+), nitrite/nitrate, sugars like fucose, sialic acid, vitamins, and xenobiotics\u2014alongside neurotransmitter loading into synaptic vesicles, suggesting a cohesive membrane transport function for this cluster.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0035461","count":1}]},{"hash":"872737121392281717","title":"RNA Pseudouridine Synthesis","description":"The top GO terms are centered on pseudouridine formation across RNA types (mRNA, snRNA, tRNA, rRNA) with a single entry for enzyme-directed rRNA pseudouridine synthesis, signaling a cohesive function in RNA modification. A translation term is present but likely secondary to the core pseudouridylation activity, suggesting the proteins cluster as RNA modification factors involved in pseudouridine synthesis. Confidence: High","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990481","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0090116","count":1}]},{"hash":"755737990297703696","title":"Fatty acid biosynthesis and acetyl-CoA metabolism","description":"The top GO terms are dominated by fatty acid metabolism (long-chain and very long-chain fatty acids) and acetyl-CoA\u2013related processes (acetyl-CoA biosynthesis from acetate, pyruvate fermentation to acetate), indicating a core theme of lipid biosynthesis and acetyl-CoA\u2013connected metabolism. A few terms such as DNA replication and seed coat development appear among the annotations, which may reflect background or cross-talk annotations rather than a shared function of the cluster. Overall, the cluster seems best characterized by lipid metabolism and acetyl-CoA\u2013linked pathways.","confidence":"Medium","size":13,"edges":20,"triangles":15,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006633","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0019290","count":2},{"id":"GO:0019654","count":2}]},{"hash":"234709204960254729","title":"Unknown","description":"The terms span metabolism (ethanol), mitochondrial ribosome assembly, various developmental and reproductive processes (uterus morphogenesis, uterine gland development, embryo sac cytokinesis, Purkinje cell maturation), epigenetic regulation (DNA methylation, epigenetic regulation of gene expression), and mitotic processes (mitotic DNA replication). Because these GO terms describe diverse, possibly species-specific processes with no clear shared function, there isn't a coherent unifying theme to define a precise biological role for this cluster.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006067","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0061038","count":1},{"id":"GO:0010426","count":1},{"id":"GO:0002674","count":1}]},{"hash":"2065562456291065394","title":"Cellular stress responses and apoptosis regulation","description":"The cluster\u2019s GO terms are dominated by stress-related processes (cellular response to xenobiotic stimulus, cellular response to mechanical stimulus) and apoptosis (myeloid and hepatocyte apoptotic processes), plus protein ubiquitination and cell cycle control, suggesting a shared theme of stress response and survival/death regulation. Some terms (gluconeogenesis, brain/dendrite development, epithelial polarity) appear more peripheral but do not outweigh the dominant stress/apoptosis signals. Confidence: Medium","confidence":"","size":13,"edges":38,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0007420","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0033028","count":2}]},{"hash":"1640222385456246592","title":"Core gene expression and metabolism","description":"The dominant terms point to basic gene expression machinery\u2014translation initiation, ribosome biogenesis, and transcription\u2014suggesting a core expression-focused theme. Additional terms for membrane transport and metabolism imply broader housekeeping roles, while a few outliers (e.g., nail development) may reflect annotation noise. With no edges tying the proteins, this cluster likely aggregates broadly related but not tightly connected functions, supporting a Moderate (Medium) confidence.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035725","count":1},{"id":"GO:0015992","count":1}]},{"hash":"1231390058619546786","title":"Unknown","description":"The terms cluster around ER stress and unfolded protein response with related translation regulation, but also include unrelated processes (photosynthesis, mitotic transition) and mixed immune-defense terms, indicating weak functional coherence. With only one edge and diverse GO annotations, there isn\u2019t a clear, representative function tying the group together.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006626","count":2},{"id":"GO:0045087","count":1},{"id":"GO:0050689","count":1}]},{"hash":"1184060838223504940","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0070129","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0010019","count":1}]},{"hash":"1345947224328418165","title":"Neuronal signaling and vesicle trafficking","description":"The top GO terms emphasize glutamatergic synaptic transmission, axonogenesis, receptor recycling, and endosome size regulation, with supporting hints from Rho signaling and transcription regulation. This combination points to neuronal communication and membrane trafficking at synapses. Some terms are obsolete, but the overall pattern suggests a neuron-specific trafficking and signaling role rather than generic cellular processes.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":7},{"id":"GO:0035023","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0001881","count":5},{"id":"GO:0051036","count":5}]},{"hash":"1433047665704419457","title":"Unknown","description":"The top GO terms span telomere maintenance, neural differentiation, immune signaling, vitamin D response, and protein modification, showing no single cohesive function binding the proteins. This diversity suggests there isn't a shared, interpretable pathway for the cluster, so a specific label isn\u2019t supported.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":8},{"id":"GO:0021707","count":8},{"id":"GO:1904355","count":8},{"id":"GO:0071651","count":8},{"id":"GO:0007253","count":8}]},{"hash":"731167595388091143","title":"Ion and nutrient transmembrane transporters","description":"The top GO terms are dominated by transmembrane transport activities for diverse substrates (phosphate ion, sodium, potassium, sialic acid, vitamin, nitrate, fucose), pointing to a shared function in transporting ions and nutrients across membranes. Some terms like lactation, liver regeneration, and female pregnancy are more contextual rather than core functions of the cluster. Overall, the predominant pattern is membrane transport of ions and nutrients.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0007595","count":2},{"id":"GO:0097421","count":2},{"id":"GO:0007565","count":2},{"id":"GO:0035725","count":2}]},{"hash":"1099967539460280059","title":"Neural signaling and vesicle exocytosis proteins","description":"The Top Terms cluster around neuronal signaling and vesicle trafficking: visual perception and phototransduction point to neural/retinal function, short-term memory to neural processes, and terms like regulation of synaptic vesicle exocytosis and myosin II filament assembly speak to vesicle transport and secretion. The presence of platelet degranulation also reflects a shared secretory mechanism. Some outliers (e.g., chitin-based cuticle development, metanephric collecting duct development) likely reflect broad GO annotations rather than a cohesive function, but the dominant theme is neural signaling and vesicle exocytosis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0002576","count":2},{"id":"GO:0007602","count":2},{"id":"GO:0072205","count":2}]},{"hash":"61272452027222260","title":"Ion and metabolite membrane transporters","description":"GO terms center on transmembrane transport of ions and metabolites (sodium, potassium, phosphate, nitrite, nitrate) and small molecules (sialic acid, vitamins, xenobiotics), plus neurotransmitter loading into synaptic vesicles, indicating a membrane transporter theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":1},{"id":"GO:0098700","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0035461","count":1}]},{"hash":"1789796270027732216","title":"Plant meristem and leaf development","description":"This cluster is strongly characterized by GO terms related to plant organogenesis, including regulation and development of leaf tissues, shoot apical meristem, and inflorescence meristem. Despite a few unrelated terms appearing once, the dominant theme ties to plant meristem regulation and leaf/inflorescence development, justifying a specific label around plant development in meristems.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000155","count":1},{"id":"GO:0071447","count":1},{"id":"GO:1902083","count":1},{"id":"GO:1903204","count":1},{"id":"GO:2000024","count":1}]},{"hash":"2131364032345546214","title":"Muscle energy metabolism and vascular remodeling","description":"The terms point to glycogen metabolism and its regulation, plus cardiac muscle hypertrophy in response to stress and branching in blood vessel morphogenesis, which together favor a theme of muscle energy use and vascular growth. Some items (e.g., ER-Golgi transport, isoprenoid biosynthesis) are more general cellular processes, so the connection is present but not exclusive, yielding a moderate level of confidence.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:1900486","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0010288","count":2}]},{"hash":"579983640226428617","title":"Vesicle trafficking and membrane fusion","description":"The top GO terms cluster around vesicle-related processes, including synaptic vesicle maturation, regulation of vesicle fusion, and intracellular protein transport, pointing to a shared role in membrane trafficking and fusion across cell types. Some terms are more divergent (e.g., mating projection regulation, B cell receptor signaling), likely representing annotation noise rather than core functions of the cluster. Overall, this suggests a membrane trafficking/fusion theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031384","count":3},{"id":"GO:0010796","count":3},{"id":"GO:0016188","count":2},{"id":"GO:0099526","count":2},{"id":"GO:0031340","count":2}]},{"hash":"288118452071700309","title":"Peroxisome Autophagy and Lipid Metabolism","description":"This cluster shows autophagy-related terms such as autophagy of the peroxisome, Cvt pathway, and phagophore assembly site localization, alongside lipid metabolism terms including fatty acid oxidation and regulation of triglyceride and cholesterol metabolism. Taken together, the data point to a theme of autophagy-related vesicle trafficking with lipid processing, though some terms (ectoine and verruculogen biosynthesis) are less connected to this theme, making the link moderate.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030242","count":1},{"id":"GO:0032258","count":1},{"id":"GO:0034497","count":1},{"id":"GO:0001561","count":1},{"id":"GO:0019491","count":1}]},{"hash":"1250218100295529098","title":"Membrane Transport and Trafficking","description":"This cluster centers on transport and trafficking processes across membranes and organelles, including vacuolar V-type ATPase assembly, amino acid and glucose transmembrane transport, chloroplast protein import, and dolichol-linked glycan biosynthesis (all tying to protein maturation and trafficking). A couple of terms (grooming behavior, lens development) appear incidental across species and do not define the core theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070072","count":1},{"id":"GO:0080144","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0060905","count":1},{"id":"GO:1904659","count":1}]},{"hash":"549872016102997842","title":"Unknown","description":"The terms span telomere maintenance, neural differentiation, immune signaling, vitamin D response, and protein ADP-ribosylation, with no obvious shared function. The absence of edges/triangles suggests no cohesive pathway ties these proteins together, so a specific, representative label isn\u2019t supported.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":8},{"id":"GO:0021707","count":8},{"id":"GO:1904355","count":8},{"id":"GO:0071651","count":8},{"id":"GO:0007253","count":8}]},{"hash":"742130531405962339","title":"Unknown","description":"The top GO terms are scattered across transcription, RNA processing, chromatin modification, development (lens differentiation and neural tube closure), and even DNA repair, with several entries marked obsolete. There is no single coherent biological process uniting these terms, and the cluster has no edges, suggesting a mix of loosely related or poorly annotated proteins. Therefore a single clear label is not justifiable.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0070306","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0032995","count":2}]},{"hash":"1548419281139926776","title":"Chromatin Regulation in Development","description":"The top GO terms point to DNA-templated transcription and multiple histone H3 methylation processes, indicating chromatin regulation. Developmental terms such as skin development and lens fiber differentiation support a theme of transcriptional control during organismal development.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0034729","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0051568","count":2}]},{"hash":"275523002476604868","title":"Diverse Small-Molecule Catabolism","description":"The top GO terms point to catabolic and detoxification activities across a range of substrates (stilbene, uracil, glucuronoside, prostaglandin), nitrogen utilization, and oxidative processes, indicating broad metabolic processing rather than a single pathway; this supports naming the cluster as diverse small-molecule catabolism.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019740","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009086","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0046272","count":2}]},{"hash":"2192412738849458783","title":"Intracellular signaling with immune and neuronal regulation","description":"This cluster centers on intracellular signal transduction and immune signaling (negative regulation of IL-12, NF-kappaB-related sequestration, and chemokine production) and also touches on neuronal development/differentiation (cerebellar granule cell differentiation, negative regulation of dendrite development). Additional terms about telomere maintenance/capping and vitamin D response suggest broader cellular regulation, but the strongest cohesive theme is signaling and immune/neural regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0021707","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071651","count":3}]},{"hash":"2033384426641688420","title":"Transcription Regulation and Signaling Proteins","description":"This cluster centers on GO terms for DNA-templated transcription and its regulation, alongside signaling processes (phosphatidylinositol signaling, GTPase regulation, GPCR pathways). Although a few terms touch on cell cycle, sporulation, or angiogenesis, the predominant themes are transcriptional control and signal transduction, suggesting the proteins act as regulators of gene expression and signaling cascades.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1528589358870553396","title":"Ion homeostasis and excitable-tissue signaling","description":"The cluster centers on membrane potential maintenance and ion transport (K+), with roles in cardiac and neuronal excitability (atrial repolarization, cardiac action potentials, resting potential stabilization). Additional GO terms for mechanosensation and GPCR glutamate signaling support sensory and neural excitability connections, while aldosterone biosynthesis and diet-induced thermogenesis reflect endocrine/metabolic links to electrolyte balance and energy regulation.","confidence":"Medium","size":12,"edges":16,"triangles":7,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0050976","count":12},{"id":"GO:0098914","count":12},{"id":"GO:0030322","count":11},{"id":"GO:0060075","count":11},{"id":"GO:0030007","count":11}]},{"hash":"1745787068416903821","title":"Terpenoid biosynthesis (MEP pathway)","description":"The top GO terms include two terpenoid biosynthetic process terms, one specifically mentioning the methylerythritol phosphate (MEP) pathway and a mevalonate-independent route, which strongly points to involvement in terpenoid/isoprenoid biosynthesis. The remaining terms are sparse or obsolete and don\u2019t form a cohesive alternative function, so the terpenoid biosynthesis theme best represents the cluster. Confidence: Medium","confidence":"","size":12,"edges":59,"triangles":159,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0051484","count":1},{"id":"GO:0051483","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0032480","count":1},{"id":"GO:0051085","count":1}]},{"hash":"2286830990284427298","title":"Vertebrate neural development and transcriptional regulation","description":"The set is enriched for neural and vertebrate development terms (forebrain development, neural tube closure, skeletal system development, multicellular organism development) and a DNA-templated transcription term, pointing to proteins involved in transcriptional regulation during neural/vertebrate development. Some terms like cell cycle, metal stress, and immune defense appear ancillary or broad.","confidence":"Medium","size":12,"edges":47,"triangles":85,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001501","count":2}]},{"hash":"936521619444873344","title":"Transcriptional and mitotic regulation","description":"The cluster\u2019s prominent terms include DNA-templated transcription, mitotic cell cycle, APC/C-dependent catabolic processes, and protein ubiquitination, withTORC1 signaling also present. This points to a cohesive theme where transcriptional control interfaces with mitotic progression and regulated protein degradation during cell division, reflecting coordinated growth and division control. ","confidence":"High","size":12,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1904263","count":2},{"id":"GO:0000209","count":2},{"id":"GO:0051301","count":2}]},{"hash":"999978570356318428","title":"Fungal cell wall biosynthesis and morphogenesis","description":"The cluster\u2019s terms cluster around fungal cell wall production and organization, including cell wall biogenesis, mannoprotein and GDP-mannose\u2013related biosynthesis, and processes linked to cell shape and morphogenesis, indicating a cohesive theme of fungal cell wall construction/remodeling. Some terms like rRNA methylation and transcription regulation are less central and likely background noise. ","confidence":"High","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0009298","count":2},{"id":"GO:0009103","count":2}]},{"hash":"2050287685169807388","title":"Virus replication, latency, and virion assembly","description":"The top GO terms point to viral life-cycle processes: host-mediated activation of viral genome replication, establishment of proviral latency, and virion assembly, plus membrane fusion between virus and host. Additional terms like P-body assembly and protein folding suggest viral manipulation of host RNA processing and protein homeostasis to facilitate replication. Overall, these terms cohere as a viral replication/assembly module with host interactions.","confidence":"High","size":12,"edges":40,"triangles":64,"max_degree":10,"top_function":"protein folding","top_go_terms":[{"id":"GO:0033962","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0006278","count":3},{"id":"GO:0044829","count":3},{"id":"GO:0019068","count":3}]},{"hash":"1537207745472176204","title":"Histone methylation and transcription regulation","description":"Based on the top GO terms, the cluster centers on chromatin modification via histone methylation (H3-K4/H3-K79) and on transcription control (DNA-templated transcription and its regulation). Other terms appear peripheral (rRNA processing, ubiquitin-dependent proteolysis, microtubule movement, lens differentiation), so the core theme is chromatin regulation and transcription control.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034729","count":3},{"id":"GO:0051568","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0070306","count":2}]},{"hash":"437332457013775286","title":"DNA Replication, Repair, and Stress Response","description":"The cluster centers on genome maintenance activities: DNA replication, nucleotide-excision repair, SOS response, and even viral genome replication. While there are also terms tied to transcription and splicing (RNA Pol II promoter clearance, prespliceosome assembly), these can be involved in coordinating gene expression with DNA damage and replication stress. A couple of terms reflect broader stress or developmental processes, but the dominant signal is genome maintenance and stress signaling.","confidence":"Medium","size":12,"edges":17,"triangles":6,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0048701","count":7},{"id":"GO:0019079","count":6},{"id":"GO:0006289","count":5},{"id":"GO:0009432","count":5}]},{"hash":"1481237233307382012","title":"Unknown","description":"The cluster's top GO terms are highly diverse and largely unrelated (cytochrome b6f complex assembly, redox processes, viral processes, tRNA import into nucleus, phosphorylation, protein complex oligomerization, etc.), and there are no edges or connections among proteins (Edges: 0, Triangles: 0, Max Degree: 0). Because there is no coherent shared function or pathway, there is no sensible, specific label beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010190","count":1},{"id":"GO:0006469","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0006662","count":1}]},{"hash":"879226463178932801","title":"Ribosome Biogenesis and Translation","description":"The terms are dominated by translation-related processes: translation itself, ribosome biogenesis, maturation of SSU rRNA, and initiation, plus regulation of translational fidelity and rRNA pseudouridylation, indicating a cluster of ribosome assembly and protein synthesis factors. A couple of terms about antibiotic response or apoptosis appear, but they are minor and do not override the translation-centered signal.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0006413","count":2},{"id":"GO:0045903","count":2}]},{"hash":"10962034727901817","title":"Diverse biosynthesis and modification pathways","description":"The GO terms cluster around biosynthesis of multiple compounds (ubiquinone, vitamin E, juvenile hormone, antibiotics, resorcinol) and various chemical modifications (N-terminal peptidyl-serine trimethylation, tRNA wobble uridine modification), with a note on cellular response to xenobiotics. This suggests a broad theme of biosynthetic and modification activities rather than a single specific function, hence a broad yet descriptive label.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":1},{"id":"GO:0035573","count":1},{"id":"GO:0010189","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0017000","count":1}]},{"hash":"763817262873585869","title":"Growth signaling and cell cycle regulation","description":"Top GO terms indicate involvement in insulin receptor signaling, glucose-mediated signaling, and regulation of nuclear DNA replication and the centrosome cycle, pointing to a core theme of growth-related signaling coordinating cell proliferation. Some terms are obsolete or peripheral (e.g., histone displacement, biofilm adhesion regulation), but the dominant pattern supports a label around growth signaling and cell cycle control.","confidence":"Medium","size":12,"edges":16,"triangles":12,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0010571","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0001207","count":2}]},{"hash":"43908696113289396","title":"Unknown","description":"The top GO terms span diverse, seemingly unconnected functions (tRNA modification, vitamin and ubiquinone biosynthesis, lipopolysaccharide biosynthesis, chromatin organization, collagen catabolism, N-terminal methylation), giving no single cohesive theme for a precise label.","confidence":"","size":12,"edges":52,"triangles":115,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0045226","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0035551","count":1}]},{"hash":"2152113247025630200","title":"Myoblast differentiation and protein oligomerization","description":"Top GO terms include positive regulation of myoblast differentiation and myoblast fusion, along with negative regulation of osteoblast differentiation, suggesting a muscle lineage\u2013related regulatory cluster. Additional terms for DNA-templated transcription and protein tetramerization/homooligomerization indicate involvement of transcriptional control and multi-subunit complexes. Some terms related to ERAD and Golgi retention hint at broader protein quality control and trafficking roles that can accompany regulatory programs. Overall, the cluster seems centered on muscle development with a notable emphasis on protein complex formation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0051262","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0070389","count":2}]},{"hash":"2039904389662905512","title":"Mitochondrial energy metabolism and protein turnover","description":"The top terms point to mitochondrial respiration (NADH to ubiquinone) and complex II assembly, indicating energy production. Additional terms involve protein modification and turnover (sumoylation and ubiquitin-dependent ERAD), suggesting a theme of proteostasis. Some transcription-related terms appear less connected to the main signal, likely representing multifunctional proteins or annotation noise. Overall, the cluster centers on mitochondrial energy metabolism with protein quality control.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":1}]},{"hash":"1732709772290705732","title":"Diverse solute transporters","description":"Based on the top GO terms, most proteins are tied to transport of various solutes (peptides, drugs, lipoproteins, fatty acids, ions, and lipids) across membranes or into organelles, suggesting a transporter-focused cluster. Immune processing and stem cell proliferation terms appear as outliers and do not define the main theme. Therefore, a concise label is \"Diverse solute transporters\" reflecting the transport-centric functions represented.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090374","count":2},{"id":"GO:0072089","count":2},{"id":"GO:1900753","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0019885","count":2}]},{"hash":"115814268852666755","title":"Zinc transport and homeostasis","description":"The GO terms are overwhelmingly centered on zinc ion import across membranes, intracellular zinc ion homeostasis, detoxification, and responses to zinc ion starvation, indicating proteins clustered around zinc uptake and regulation. A couple of outliers (lipid metabolism, limb development) exist but do not define the main theme. Thus, labeling this cluster as zinc transport and homeostasis captures the dominant function.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006629","count":1},{"id":"GO:0006831","count":1},{"id":"GO:0060173","count":1},{"id":"GO:0044749","count":1},{"id":"GO:1903615","count":1}]},{"hash":"1774345640816060654","title":"K63-linked ubiquitination and protein quality control","description":"The top GO terms are dominated by ubiquitination processes, especially K63-linked ubiquitination and autoubiquitination, along with ubiquitin-dependent ERAD pathways. This suggests a cluster of proteins involved in tagging and degrading proteins for quality control and proteostasis (with auxiliary links to chaperone-mediated assembly). Some terms related to stress or hormone signaling appear but do not override the central ubiquitination/proteostasis theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0070534","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0030433","count":7},{"id":"GO:0070535","count":5},{"id":"GO:0090035","count":5}]},{"hash":"332893460292803633","title":"Ribosome biogenesis and translational control","description":"Most of the top GO terms point to ribosome biogenesis and translation-related processes (preribosome/large subunit maturation, rRNA maturation, tRNA modification, and regulation of translation including mitochondrial translation). While there are a couple of transcription regulation terms present, the dominant theme across the cluster is assembly and control of the protein-synthesis machinery.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0046944","count":2},{"id":"GO:0006450","count":2},{"id":"GO:0009736","count":2}]},{"hash":"2279903461718119924","title":"Cardiac Electrophysiology and Vasoconstriction","description":"The cluster centers on terms involving cardiac electrical activity and regulation, including ventricular cardiac muscle cell action potential, membrane repolarization, and vasoconstriction, which together point to heart rhythm control and vascular tone as the main theme. Some terms (splicing, GPCR signaling, aldosterone biosynthesis, diet-induced thermogenesis) appear peripheral, but do not overshadow the strong cardiac-focused signal. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000349","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0007216","count":1},{"id":"GO:0002024","count":1},{"id":"GO:0032342","count":1}]},{"hash":"265114119421449548","title":"Unknown","description":"The GO terms listed span several unrelated processes (lipopolysaccharide biosynthesis, copper and zinc ion transport, dephosphorylation, P450 epoxygenase pathway, serine biosynthesis, stilbene catabolism) with no single cohesive function tying the cluster together. This diversity suggests there is no clear, unifying role for the protein group, so a precise, representative label cannot be inferred from the data.","confidence":"","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:0006874","count":3},{"id":"GO:0046272","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0046839","count":3}]},{"hash":"428173998663274712","title":"Prostaglandin-mediated neuroimmune signaling","description":"The GO terms center on prostaglandin biosynthesis and lipid mediator signaling, with supportive immune/regulatory (leukocyte proliferation, MCP-1 regulation) and redox/detoxification terms, plus neural context (CNS development, hormone responses). This pattern suggests a cohesive theme around prostaglandin-driven signaling that links neural and immune functions.","confidence":"Medium","size":12,"edges":12,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0032355","count":3},{"id":"GO:0070458","count":3},{"id":"GO:0007417","count":3}]},{"hash":"1739417623871265387","title":"Chloroplast Photosynthesis and Redox Maintenance","description":"The dominant GO terms point to chloroplast-associated processes: photosynthesis, nonphotochemical quenching (NPQ), proton transmembrane transport, and cell redox homeostasis/detoxification. These indicate a cluster of proteins involved in light energy capture and protection against oxidative stress, typical of chloroplast function. The presence of aromatic compound catabolic terms may reflect annotation noise or cross-annotation, but they do not define the core theme. Confidence reflects a strong alignment to chloroplast energy management and redox regulation.","confidence":"High","size":12,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":3},{"id":"GO:0010196","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0046381","count":2}]},{"hash":"401013140557357807","title":"RNA Pseudouridine Synthesis Cluster","description":"The GO terms converge on RNA modification by pseudouridine synthesis across mRNA, snRNA, and tRNA, pointing to RNA maturation roles. While a few terms pertain to other processes (transcription, cytoskeletal movement), the strongest signal is pseudouridylation-related activity.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090344","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1990481","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0031119","count":1}]},{"hash":"1669078923786541023","title":"Proteolysis and RAAS/Angiogenesis Signaling","description":"The top GO terms point to protein degradation (proteolysis) and peptide turnover, alongside angiotensin maturation and regulation of blood pressure via the renin-angiotensin system, plus angiogenesis. While other terms appear (immune antigen presentation, leukotriene synthesis), the strongest cohesive theme is proteolysis linked to cardiovascular signaling through RAAS and angiogenic processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000469","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0043171","count":1},{"id":"GO:0030154","count":1},{"id":"GO:0006508","count":1}]},{"hash":"1843042649774600339","title":"Plant cell wall biosynthesis and O-glycosylation","description":"The top GO terms cluster around plant cell wall construction and protein glycosylation, including homogalacturonan and glucuronoxylan biosynthesis, plant-type secondary cell wall biogenesis, mucilage biosynthesis, and O-linked glycosylation via GalNAc and mannose. This points to a cohesive role in assembling cell wall polysaccharides and modifying secreted glycoproteins.","confidence":"High","size":12,"edges":25,"triangles":20,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0016266","count":2},{"id":"GO:0006012","count":1},{"id":"GO:0010289","count":1},{"id":"GO:0043403","count":1}]},{"hash":"1134551947738607337","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":2},{"id":"GO:0071847","count":1},{"id":"GO:0016188","count":1},{"id":"GO:0048541","count":1},{"id":"GO:0016310","count":1}]},{"hash":"78790035986641807","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":7},{"id":"GO:0000278","count":7},{"id":"GO:1905869","count":5},{"id":"GO:0035330","count":5},{"id":"GO:0042068","count":5}]},{"hash":"338994240676397759","title":"Proteostasis and organelle quality control","description":"This cluster\u2019s terms center on protein folding stress responses (ER unfolded protein response), protein turnover (autophagosome maturation, oxidation-dependent degradation, ubiquitin-specific protease activity), and targeting/import into organelles (mitochondrial inner membrane insertion, peroxisome matrix import). Taken together, they point to cellular quality control of proteins and maintenance of organelle function, rather than a single signaling pathway or process. Some terms like transcription or cell division are broader but don\u2019t define the cluster\u2019s primary theme.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0030968","count":3},{"id":"GO:0045737","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0097352","count":2}]},{"hash":"1366546870847208008","title":"Innate Immune Signaling and Developmental Regulation","description":"The cluster is dominated by terms tied to innate immune responses and immune signaling (innate immune response, defense against virus, NF-kappaB signaling), with supporting links to receptor tyrosine kinase signaling and ubiquitination. Several development-related terms (multicellular organism development, axonogenesis, ossification) suggest these proteins may participate in broader regulatory networks that connect immune signaling to developmental processes.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0005513","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0043123","count":2}]},{"hash":"2139387361945935761","title":"Cardiac electrophysiology and vasoconstriction","description":"The dominant terms point to heart-specific functions: ventricular action potentials, membrane repolarization, and contraction, along with vasoconstriction and actin cytoskeleton organization in cardiac cells. Although there are a few metabolic terms (aldosterone biosynthesis, diet-induced thermogenesis), the cluster is best characterized by cardiac electrical activity and vascular tone regulation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0007216","count":2},{"id":"GO:0002024","count":2},{"id":"GO:0032342","count":2},{"id":"GO:0086002","count":2}]},{"hash":"1669098871975220577","title":"Embryonic Development and Tissue Morphogenesis","description":"The GO terms are dominated by various embryonic and tissue morphogenesis processes (hair follicle, trachea, hindlimb morphogenesis; heart looping; neural crest migration; skeletal development) and associated development-related regulation, indicating a cluster of proteins involved in broad embryonic development and morphogenesis across multiple tissues.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":1},{"id":"GO:0031069","count":1},{"id":"GO:0045109","count":1},{"id":"GO:0048706","count":1},{"id":"GO:2001054","count":1}]},{"hash":"1202456144658948752","title":"Gene Expression Regulation and RNA Processing","description":"The GO terms cluster around transcription (DNA-templated transcription), mRNA transport, and TORC1 signaling, with additional signals from rRNA processing and serine dephosphorylation, pointing to a broad theme of gene-expression control and RNA handling rather than a single, tight pathway. Some outlier terms (lens differentiation, fungal-type cell wall biogenesis) may reflect annotation noise rather than a cohesive functional group.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035948","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0038202","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0070262","count":3}]},{"hash":"1458511140791188052","title":"Metabolic energy and autophagy regulation","description":"This cluster centers on energy metabolism activities (gluconeogenesis, pentose phosphate pathway regulation, dephosphorylation) and on autophagy/mitophagy control, with additional signals of broader cellular stress responses (DNA damage signaling, xenobiotic response) and some tissue-context terms (brain development, cardiac apoptosis). The combination suggests a theme around how cells generate and manage energy while maintaining quality control under stress. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0010666","count":1},{"id":"GO:0043456","count":1},{"id":"GO:0006914","count":1}]},{"hash":"1124593102309815573","title":"TLR-Mediated Innate Immune Activation","description":"The proteins show a cohesive signal for innate immune sensing and Toll-like receptor\u2013driven inflammation, including detection of bacteria, MyD88-dependent and TLR3 signaling, and downstream cytokine production (IL-1, IL-18) with inflammatory response and antigen presentation components (MHC I) and Th17 differentiation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":1},{"id":"GO:0032741","count":1},{"id":"GO:2000321","count":1},{"id":"GO:0045345","count":1},{"id":"GO:0050701","count":1}]},{"hash":"1142091915918647467","title":"Unknown","description":"The GO terms cover transcription, mitotic spindle orientation, microtubule movement, development (lens fiber differentiation and neural tube closure), rRNA processing, histone modification, and DNA repair, with some obsolete terms and an unrelated fungal cell wall biogenesis item. Together they do not point to a single cohesive function, suggesting the cluster is heterogeneous or noisy.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0000132","count":4},{"id":"GO:0070306","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0006349","count":3}]},{"hash":"472152686595795651","title":"Unknown","description":"The GO terms are scattered across protein complex assembly, skin development, translation initiation, innate immune and virus responses, and lipid/cholesterol metabolism, with no clear single theme tying them together, and no edges among proteins. This suggests a functionally heterogeneous set rather than a cohesive cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070208","count":2},{"id":"GO:0043588","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0090502","count":1},{"id":"GO:0045087","count":1}]},{"hash":"1162923160956870120","title":"Unknown","description":"The terms span ubiquitination, synapse/corpus callosum development, mechanical sensing, plant polysaccharide metabolism, and immune signaling, with no single cohesive theme or connecting interactions among the proteins. No edges link them, so there is no clear shared function to label.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0051965","count":2},{"id":"GO:0022038","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0045490","count":2}]},{"hash":"1634564306452005402","title":"Unknown","description":"The top terms are a mix of placenta development, lipid biosynthesis regulation, vesicle transport, and general stress responses, with no single shared Biological Process or function linking the proteins. There are no edges or clustering signals to suggest a cohesive role, so a clear label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":1},{"id":"GO:0001890","count":1},{"id":"GO:1901352","count":1},{"id":"GO:2001247","count":1},{"id":"GO:0001892","count":1}]},{"hash":"1864981380160715961","title":"Unknown","description":"The GO terms span immune signaling (antigen receptor\u2013mediated signaling, B cell homeostasis, NK T cell differentiation, chemokine production) and also cardiac/endocrine/metabolic processes (cardiac muscle action potentials, aldosterone biosynthesis, diet-induced thermogenesis, GPCR glutamate signaling), with no clear single theme tying them together. ","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007216","count":1},{"id":"GO:0007018","count":1},{"id":"GO:0001865","count":1},{"id":"GO:0050851","count":1},{"id":"GO:0002024","count":1}]},{"hash":"1594148570423397051","title":"DNA Damage Response and RNA Processing","description":"This cluster centers on nucleic acid stress signals (SOS response, DNA replication, viral genome replication, antibiotic response) together with RNA processing activities (prespliceosome assembly, RNA exon ligation, rRNA catabolic process). The combination suggests a program coordinating DNA damage/replication stress with RNA metabolism. ","confidence":"Medium","size":11,"edges":11,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0019079","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0006306","count":3}]},{"hash":"1485006550796913171","title":"RNA processing and translational control","description":"This cluster is driven by terms related to translation initiation and preinitiation complex formation, as well as RNA processing steps like spliceosome-mediated splicing, miRNA-mediated translational silencing, and mRNA stabilization. The presence of small-subunit processome assembly also points to ribosome biogenesis, together with post-transcriptional regulation, indicating a cohesive theme of RNA metabolism coupled with control of translation.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1902625","count":5},{"id":"GO:0006446","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0034462","count":5},{"id":"GO:0001825","count":5}]},{"hash":"13916367562441902","title":"Salvage Metabolism and Galactose Response","description":"This cluster centers on salvage pathways for nucleotides and amino acids, plus related sugar metabolism. GO terms include AMP salvage, GDP-L-fucose salvage, and methionine salvage, along with L-threonine and L-homoserine biosynthesis. A note of galactose involvement appears via glycolytic processing from galactose and galactose-regulated transcription, linking salvage metabolism to sugar signaling. Together, these terms point to a metabolism-focused cluster driven by salvage and galactose-responsive steps.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":3},{"id":"GO:0046835","count":3},{"id":"GO:0019509","count":2},{"id":"GO:0019284","count":2},{"id":"GO:0034418","count":2}]},{"hash":"262432671117516902","title":"DNA replication and chromatin regulation","description":"The cluster is dominated by GO terms tied to DNA replication, centrosome cycle, and regulation of the nuclear cell cycle, along with chromatin-related processes such as histone exchange and heterochromatin formation, and nucleolar rRNA transcription. The presence of developmental morphogenesis terms likely reflects cell proliferation and chromatin-driven gene regulation during development. Overall, the core theme is DNA replication coupled with chromatin dynamics, with developmental processes as secondary associations.","confidence":"High","size":11,"edges":41,"triangles":72,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":11},{"id":"GO:0007098","count":11},{"id":"GO:0006260","count":10},{"id":"GO:0048701","count":10},{"id":"GO:0043486","count":6}]},{"hash":"1513224704474012852","title":"Methylation-Centric Biosynthesis","description":"The cluster is dominated by methylation-related GO terms (various RNA and protein methylations, rRNA modification) alongside several biosynthetic processes for vitamins and cofactors (cobalamin, ubiquinone, vitamin E) and antibiotic biosynthesis, suggesting a group of methyltransferases involved in diverse biosynthetic pathways, especially RNA/protein methylation steps linked to cofactor biosynthesis.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0018013","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0018027","count":4},{"id":"GO:0031167","count":4}]},{"hash":"447600285711761307","title":"mRNA processing and translation control","description":"This cluster is characterized by GO terms focused on translation initiation regulation, preinitiation complex formation, miRNA-mediated translation inhibition, mRNA stabilization, and splicing regulation via the spliceosome. Together these terms indicate post-transcriptional gene regulation, encompassing RNA processing and control of protein synthesis rather than transcriptional activity.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1902625","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0034462","count":3},{"id":"GO:0001825","count":3}]},{"hash":"1717244147879107926","title":"Ribosome biogenesis and translation","description":"This cluster's top GO terms are dominated by translation and ribosome-related processes (translation, ribosome biogenesis, maturation of LSU-rRNA, ribosomal large subunit assembly), indicating a cohesive role in ribosome production and protein synthesis. Ancillary terms such as protein stabilization and ubiquitin pathway regulation may reflect regulatory context rather than core function.","confidence":"High","size":11,"edges":44,"triangles":87,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042254","count":3},{"id":"GO:0000470","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0072717","count":1}]},{"hash":"4217257317712635","title":"Methyltransferases and chromatin methylation","description":"The top GO terms cluster around multiple methylation activities (peptidyl-lysine methylation, dimethylation, trimethylation, N-terminal glycine methylation, and rRNA methylation) and link to rDNA heterochromatin formation, indicating a core function as methyltransferases involved in chromatin and RNA modification. Some auxiliary terms (like cobalamin biosynthesis) are present but do not disrupt the main theme of methylation-related activities.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":4},{"id":"GO:0018023","count":4},{"id":"GO:0018027","count":4},{"id":"GO:0018013","count":4},{"id":"GO:0031167","count":4}]},{"hash":"562895849576238013","title":"Mitosis and Spindle Assembly","description":"This cluster\u2019s top GO terms center on cell division and microtubule-related processes (cell cycle, mitotic spindle pole body duplication, microtubule nucleation, cell division, septum assembly), suggesting a cohesive role in mitosis and cytoskeletal organization. The presence of translation regulation and ER stress terms may reflect broader cellular regulation but do not undermine the core theme of mitotic machinery.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090529","count":2},{"id":"GO:0007049","count":2},{"id":"GO:1903087","count":2},{"id":"GO:0007020","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1430165061675785620","title":"Signaling Pathway Regulators","description":"This cluster\u2019s top GO terms center on regulation of signaling pathways (negative regulation of protein kinase activity; regulation of VEGF receptor signaling; calcium-channel regulation; synaptic vesicle exocytosis) and related stress responses (apoptosis, cardiac hypertrophy). While other terms touch metabolism and cell cycle, the strongest common theme is modulation of signaling networks and cellular responses, suggesting these proteins act as regulators of signaling rather than core enzymes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000413","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0060316","count":2},{"id":"GO:2000300","count":2},{"id":"GO:1903244","count":2}]},{"hash":"976246526140329526","title":"RNA modification and translation","description":"The cluster is enriched for RNA modification (tRNA and rRNA pseudouridine synthesis) and for cytoplasmic and mitochondrial translation, indicating components of ribosome-associated RNA processing and protein synthesis. A few terms touch metabolism or signaling, but the dominant theme is RNA modification and translation machinery.","confidence":"High","size":11,"edges":15,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046391","count":1},{"id":"GO:0000162","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0002181","count":1}]},{"hash":"865478861719142598","title":"Ethanol and Alcohol Metabolism","description":"The cluster's top GO terms are dominated by ethanol oxidation and related catabolic processes (ethanol catabolic process, ethanol oxidation), plus sorbitol and other organic compound metabolisms (retinol, furaldehyde, Ehrlich pathway to alcohol). This pattern points to a cohesive theme of alcohol processing and related carbon-source catabolism, with sporulation and a broad respiratory term contributing less specifically. Confidence in this thematic labeling is Medium.","confidence":"Medium","size":11,"edges":25,"triangles":33,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0030435","count":4},{"id":"GO:0006069","count":4},{"id":"GO:0042572","count":4},{"id":"GO:0006068","count":4}]},{"hash":"1681462769998902785","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":4},{"id":"GO:0000122","count":2},{"id":"GO:0006796","count":1},{"id":"GO:0000447","count":1}]},{"hash":"199946417487181223","title":"Chaperone-driven proteostasis and chromatin regulation","description":"The GO terms cluster around chaperone function (Hsp90 deacetylation, aggresome assembly, chaperone-mediated protein complex assembly) and chromatin/epigenetic regulation (heterochromatin formation, nucleosome density, DNA methylation-dependent chromatin states), suggesting a coordinated role in protein quality control linked to chromatin state and transcriptional regulation under stress.","confidence":"High","size":11,"edges":51,"triangles":131,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070846","count":7},{"id":"GO:0070842","count":7},{"id":"GO:0090035","count":7},{"id":"GO:0060303","count":7},{"id":"GO:0061188","count":7}]},{"hash":"1393813724822375924","title":"Wnt signaling and embryonic morphogenesis","description":"The top terms cluster around developmental signaling and organogenesis, especially canonical Wnt signaling involved in tissue patterning and survival (negative regulation of apoptosis), cranial skeleton development, dorsal identity, and adherens junction assembly, plus organ formation processes like renal vesicle development and cardiac tissue patterning. While some terms reflect general cellular processes, the overarching theme is Wnt-driven embryonic morphogenesis across multiple tissues.","confidence":"Medium","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0048364","count":7},{"id":"GO:0044336","count":6},{"id":"GO:1904888","count":6},{"id":"GO:2000017","count":6},{"id":"GO:0034333","count":6}]},{"hash":"1845087380334829458","title":"Unknown","description":"The terms span highly diverse processes\u2014from saccharide and lipid biosynthesis to metal transport, calcium homeostasis, stilbene catabolism, and hormone response\u2014showing no single shared function that ties all proteins in this cluster together.","confidence":"","size":11,"edges":40,"triangles":74,"max_degree":10,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0046380","count":4},{"id":"GO:0016311","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0070574","count":4},{"id":"GO:0006874","count":4}]},{"hash":"1517190388363551677","title":"Mesodermal Muscle and Vasculature Differentiation Regulation","description":"The cluster is dominated by GO terms for mesodermal cell differentiation, myoblast differentiation, and positive regulation of vasculogenesis, with regulatory hints such as negative regulation of Notch signaling and transcriptional changes in hypoxia, indicating a coordinated mesodermal program directing muscle and vascular development.","confidence":"High","size":11,"edges":42,"triangles":91,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0048333","count":3},{"id":"GO:0034720","count":3},{"id":"GO:0070544","count":3},{"id":"GO:0061428","count":3},{"id":"GO:0042264","count":3}]},{"hash":"314576458786347589","title":"Redox-Linked Central Carbon Metabolism","description":"The GO terms center on core carbon metabolism (glycolysis, pyruvate and malate pathways, amino acid catabolism) and redox regulation (redox homeostasis, NADP metabolic regulation), with porphyrin biosynthesis suggesting NADPH-linked biosynthetic activity; together these imply a metabolic module focused on energy production and maintaining redox balance.","confidence":"High","size":11,"edges":18,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0042853","count":2}]},{"hash":"2190932436157828580","title":"Detoxification and xenobiotic metabolism","description":"The cluster shows enrichment for detoxification and diverse catabolic processes, including cellular oxidant detoxification and response to toxic substances, plus specific catabolic pathways (stilbene, uracil, glucuronoside) and nitrogen utilization. Some terms are obsolete or broad (oxidation-reduction, methionine biosynthetic), but overall the proteins appear linked to processing and neutralizing xenobiotics and plant-derived compounds rather than a single biosynthetic pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0098869","count":7},{"id":"GO:0009636","count":7},{"id":"GO:0019740","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0009086","count":6}]},{"hash":"2204274741247086044","title":"Transcription Regulation and Differentiation","description":"Most prominent GO terms are about transcription and its regulation (DNA-templated transcription; regulation of DNA-templated transcription; positive regulation of transcription by RNA polymerase II) along with cell-cycle control (G1/S transition; intra-S checkpoint). Differentiation-related terms (neuron and lung epithelium) and synapse organization further suggest developmental programs governed by transcriptional regulation. This points to a transcription-centric cluster with differentiation and cell-cycle links.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0031573","count":2},{"id":"GO:0030182","count":2},{"id":"GO:0060487","count":2},{"id":"GO:0000082","count":2}]},{"hash":"162431217482223641","title":"Synaptic signaling in auditory development","description":"Most top GO terms point to neural communication and synaptic plasticity (glutamate secretion, dendritic spine morphogenesis, long-term synaptic depression, and nitric oxide\u2013mediated signaling). Additionally, cochlea morphogenesis and auditory receptor stereocilium organization tie the cluster to the auditory system. A few terms (cell division, protein dephosphorylation, opsonization) are less indicative but do not override the prevailing synaptic-auditory theme. Confidence: Medium","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0060088","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0035640","count":1}]},{"hash":"2077366177132129425","title":"Unknown","description":"The Top Terms show a mix of disparate processes (photosynthesis, redox homeostasis, tRNA import, developmental signaling, protein folding/transport) and several obsolete annotations, with only a single edge connecting proteins. This lack of a cohesive shared function suggests the cluster does not represent a single, well-defined biological theme, so a specific label cannot be reliably assigned.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006469","count":1},{"id":"GO:0045454","count":1}]},{"hash":"1739605423731551662","title":"Protein oligomerization and mitochondrial respiration","description":"The cluster shows strong representation of protein complex assembly and oligomerization (homotetramerization, heterooligomerization, positive regulation of oligomerization) along with mitochondrial respiration/electron transport terms, suggesting a theme around assembling protein complexes and energy metabolism. While terms like viral process and symbiont entry appear, they seem less central to the core functions, likely reflecting broad or incidental annotations. Therefore the label emphasizes the main, coherent themes: protein oligomerization and mitochondrial respiration.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0032461","count":3},{"id":"GO:0006122","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0010992","count":3}]},{"hash":"55843675949319296","title":"Septin-based budding and cytokinesis","description":"The cluster shows strong enrichment for septin ring assembly, protein localization to the bud neck, and cell division/cytokinesis terms, which together point to the machinery governing budding yeast morphogenesis and cytokinesis. Some broader GO terms present likely reflect non-specific annotations, but the core theme is septin-structure\u2013driven budding division.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0071560","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0090090","count":2}]},{"hash":"1576169650602189490","title":"Rab-regulated autophagy and vesicle trafficking","description":"This cluster is dominated by GO terms tied to Rab signaling and intracellular vesicle transport, including phagophore assembly site localization, phagosome-lysosome fusion, and regulation of synaptic vesicle exocytosis. These point to a cohesive theme of Rab-mediated vesicle trafficking and autophagic processes, with additional terms hinting at neuronal morphology and microtubule-associated dynamics that can accompany vesicle movement. Overall, the cluster appears to reflect Rab-driven trafficking with autophagy-related functions, making this label representative.","confidence":"Medium","size":11,"edges":21,"triangles":6,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032482","count":5},{"id":"GO:0018125","count":5},{"id":"GO:0034497","count":5},{"id":"GO:0002093","count":5},{"id":"GO:0043497","count":5}]},{"hash":"1699184674112071316","title":"Mitochondrial Translation and Biosynthesis","description":"The cluster\u2019s terms cluster around biosynthetic and translation-related processes, with explicit mitochondrial involvement (mitochondrial glycyl-tRNA aminoacylation, mitochondrial morphogenesis) and related biosynthesis (heme, selenocysteine, DNA biosynthesis, gluconeogenesis). This pattern points to proteins linked to mitochondrial protein synthesis and associated metabolic pathways, rather than a single isolated function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0015966","count":1},{"id":"GO:0071897","count":1},{"id":"GO:0097056","count":1}]},{"hash":"81230943257341913","title":"Kinase Signaling and Actin Cytoskeleton Regulation","description":"The top GO terms cluster around phosphorylation-driven signaling (positive regulation of serine/threonine and tyrosine phosphorylation, autophosphorylation) and actin cytoskeleton dynamics (Arp2/3-mediated nucleation). Additional terms touch on GTPase regulation, GPCR signaling, and broader cellular processes like mitosis and hypoxia response, suggesting a cohesive theme of coordinated signaling that governs cytoskeletal remodeling and cell-cycle-related regulation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0051028","count":5},{"id":"GO:0007205","count":4},{"id":"GO:0098907","count":4}]},{"hash":"170088722529905227","title":"Unknown","description":"Top GO terms are diverse, including response to antibiotic, osmotic stress, redox homeostasis, regulation of protein activity, tRNA import, and even plant- and development-related terms, with no clear shared function or interaction pattern. Because there is no unifying theme among these terms, the cluster does not map to a coherent biological category.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032781","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006469","count":1},{"id":"GO:0045454","count":1},{"id":"GO:1901348","count":1}]},{"hash":"756006218878783839","title":"Mitochondrial maintenance and proteostasis","description":"This cluster features GO terms tied to mitochondrial function\u2014assembly of respiratory chain complex III, protein insertion into the mitochondrial inner membrane, and regulation of mtDNA replication\u2014along with protein quality control processes such as autophagosome maturation and aggresome formation/ERAD. The combination points to a cohesive module focused on maintaining mitochondrial integrity and cellular proteostasis, despite some noise from development- and transcription-related terms.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0001824","count":5},{"id":"GO:0034551","count":4},{"id":"GO:0097352","count":4},{"id":"GO:0070842","count":4}]},{"hash":"113069816199307002","title":"Cardiac contraction and cGMP signaling regulation","description":"The cluster\u2019s top GO terms predominantly point to regulation of cardiac muscle contraction and cGMP-related pathways (negative regulation of cardiac muscle contraction, regulation of cardiac muscle cell contraction, cellular response to cGMP, cGMP catabolic processes). This suggests proteins in this cluster are linked to modulating heart muscle function via cGMP signaling. A few terms are non-cardiac or obsolete, but the dominant theme remains cardiac function and cGMP signaling.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901898","count":6},{"id":"GO:0010753","count":6},{"id":"GO:0036006","count":6},{"id":"GO:0055118","count":6},{"id":"GO:0046069","count":6}]},{"hash":"217943925030176984","title":"ER-Golgi Vesicle Trafficking and Mitosis","description":"Proteins in this cluster are enriched for vesicle trafficking between the ER and Golgi (including COPII budding and ER-to-Golgi transport) and for related exocytosis processes, with additional signals of brain development and mitotic roles (spindle assembly, mitotic cell cycle). The common theme appears to be intracellular vesicle transport, potentially coupled to cell division, justifying a label that combines secretory pathway trafficking with mitotic processes.","confidence":"Medium","size":11,"edges":29,"triangles":23,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007420","count":6},{"id":"GO:2000300","count":4},{"id":"GO:0010796","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0031384","count":4}]},{"hash":"2109270188181565231","title":"Unknown","description":"The top terms span very different biological areas (RNA processing, development, chromatin modification, DNA repair, cell movement, and even fungal cell wall regulation), with several terms marked obsolete. There\u2019s no coherent, dominant function linking the proteins, so a single representative label isn\u2019t justifiable.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0070306","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0032995","count":3}]},{"hash":"317118724991017358","title":"Auditory hair cell synapse and cochlear morphogenesis","description":"The top terms cluster around inner-ear sensory biology, with emphasis on hair cell stereocilium organization, cochlear morphogenesis, glutamate secretion at hair cell synapses, and synaptic plasticity (long-term depression, dendritic spine morphogenesis). This points to a shared function in hair cell\u2013synapse formation and cochlear development, with a miscellaneous single immune-related term likely not core to the cluster.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0060292","count":1}]},{"hash":"2208344494014080139","title":"Unknown","description":"The top GO terms span development in multiple organs, lipid biosynthesis, neuronal signaling, stress responses, and apoptosis, with no clear shared process linking the proteins; several entries are obsolete, indicating a noisy or non-cohesive cluster.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072205","count":2},{"id":"GO:0042994","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0006646","count":2},{"id":"GO:2000300","count":2}]},{"hash":"663560078432272333","title":"Synaptic Vesicle Trafficking","description":"The top GO terms emphasize vesicle-related processes: synaptic vesicle maturation, presynapse signaling, and positive regulation of vesicle fusion, along with intracellular transport and cytoskeletal regulation (Rho signaling). These point to a shared function in vesicle trafficking and synaptic signaling. Other terms (tRNA processing regulation, B cell receptor signaling, myoblast fusion, cortical migration, phosphatidylcholine catabolism) are more peripheral but may reflect broader membrane dynamics, so the core theme remains vesicle trafficking in a neuronal/synaptic context. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0016188","count":2},{"id":"GO:0099526","count":2},{"id":"GO:0031340","count":2},{"id":"GO:2000235","count":2}]},{"hash":"2226238370038939950","title":"Muscle development and sarcomere organization","description":"Prominent terms are skeletal muscle tissue development and sarcomere organization, with swimming as supportive evidence of muscle-based locomotion. Some ubiquitination and transcription-regulation terms appear, but the strongest link is to muscle structure and development.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007519","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0036268","count":1},{"id":"GO:0070294","count":1},{"id":"GO:0019762","count":1}]},{"hash":"1916004631276379976","title":"Neural development and axon guidance (cranial nerves)","description":"This cluster\u2019s top GO terms cluster around neural development and connectivity: optic vesicle formation, branchiomotor neuron axon guidance, trigeminal nerve organization, anterior commissure morphogenesis, and positive regulation of axonogenesis, suggesting a coordination of neural patterning and nerve wiring. While there are broader developmental terms like limb bud formation and a cellular transport term, the dominant theme is neuronal development and axon pathfinding.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017009","count":1},{"id":"GO:0021637","count":1},{"id":"GO:0060666","count":1},{"id":"GO:0021960","count":1},{"id":"GO:0003403","count":1}]},{"hash":"388122563392647780","title":"Neuronal synaptic transmission and spine morphogenesis","description":"The top GO terms cluster around neuronal communication: neurotransmitter secretion, regulation of synaptic transmission, trans-synaptic signaling, and dendritic spine morphogenesis, with long-term synaptic depression indicating plasticity. A couple of terms are less related, but the dominant theme is synaptic signaling and spine development in neurons.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034396","count":1},{"id":"GO:0010815","count":1},{"id":"GO:1903895","count":1},{"id":"GO:0051968","count":1},{"id":"GO:0099557","count":1}]},{"hash":"541110718446794000","title":"Shikimate Pathway and Aromatic Amino Acid Biosynthesis","description":"The GO terms include shikimate metabolic process, chorismate biosynthetic process, and aromatic amino acid biosynthetic process, which together point to enzymes of the shikimate pathway that produce aromatic amino acids. A few unrelated terms (Golgi retention, mitophagy) are present but do not override the core biosynthetic theme. Overall, the cluster likely groups proteins involved in aromatic amino acid biosynthesis via the shikimate pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":1},{"id":"GO:1905090","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0046177","count":1},{"id":"GO:0019632","count":1}]},{"hash":"1542040218141948497","title":"Unknown","description":"The top GO terms are highly diverse, spanning redox processes, sensory organ morphogenesis (ear/eye/skin), platelet activation, photoprotection, proton transport, and xenobiotic/aromatic compound metabolism, with no connecting network edges to tie them into a single function. This lack of a cohesive theme makes a specific, representative cluster name infeasible.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0043589","count":2},{"id":"GO:0048593","count":2},{"id":"GO:0010572","count":2}]},{"hash":"2016729362274697030","title":"Aminoacyl-tRNA Synthetases","description":"The terms are dominated by aminoacyl-tRNA charging (methionyl-, leucyl-, isoleucyl-, valyl-, phenylalanyl-tRNA aminoacylation) and translation, including regulation of translational fidelity. This indicates core involvement in tRNA charging and protein synthesis, with a few peripheral metabolic terms likely unrelated noise. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006431","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006429","count":2},{"id":"GO:0006428","count":2},{"id":"GO:0006438","count":2}]},{"hash":"522044263847589112","title":"Ubiquitin-Proteasome System Regulation","description":"The Top Terms are centered on ubiquitin-related processes (ERAD, deubiquitination, ubiquitin-dependent degradation) and regulatory steps, with supporting themes like NF-kappaB sequestration and nuclear envelope dynamics during cell cycle stages. This suggests a cluster of proteins that modulate protein turnover and ubiquitin signaling, despite some peripheral terms, so a focused label on ubiquitin-proteasome system regulation fits best.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031134","count":1},{"id":"GO:1904293","count":1},{"id":"GO:1903094","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0031468","count":1}]},{"hash":"2077035156854292733","title":"Unknown","description":"The Top Terms span very diverse biological processes across different organisms: nitrogen fixation (bacteria-associated), porphyrin/heme biosynthesis, ER-to-cytosol retrograde transport, spermatid differentiation, compound eye cone cell fate commitment, EGFR ligand maturation, and NK cell activation regulation. With no connecting pathways or cellular context and no edges tying the proteins together, there is no cohesive theme to name a specific function for this cluster. Therefore, Unknown with None confidence.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009399","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0018160","count":1},{"id":"GO:0006782","count":1},{"id":"GO:0006783","count":1}]},{"hash":"2137350755608532492","title":"Innate Immune Signaling and Cytokine Production","description":"This cluster is dominated by GO terms related to innate immunity and cytokine production, including innate immune response, TLR3 signaling, IL-1 and IL-18 production, Th17 differentiation, and MHC class I biosynthesis, suggesting a cohesive role in immune activation and antigen presentation. A few terms about magnesium homeostasis and cell polarity appear less directly connected, but do not override the overall immune-focused theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010961","count":2},{"id":"GO:0000282","count":1},{"id":"GO:0061161","count":1},{"id":"GO:0045087","count":1},{"id":"GO:0032741","count":1}]},{"hash":"2023723998389183741","title":"RNA Pol II Transcription Regulation by Nutrient Signals","description":"Dominant GO terms center on transcription from RNA polymerase II and its regulation under various environmental cues (oleic acid, carbon sources, starvation). The unifying theme is transcriptional control rather than specific metabolic reactions, despite a few terms touching metabolism; overall the cluster appears to group proteins involved in regulating gene expression at the transcriptional level.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035969","count":1},{"id":"GO:1904741","count":1},{"id":"GO:0061429","count":1}]},{"hash":"1759061078553172520","title":"Unknown","description":"The top GO terms span nuclear RNA processing and DNA replication initiation, transcription regulation, translation, lipid biosynthesis, and sensory pathways, with no clear shared process. The lack of connectivity and the wide functional spread suggest no single cohesive theme for this cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032298","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000398","count":1},{"id":"GO:1903026","count":1},{"id":"GO:0002181","count":1}]},{"hash":"1218889727744136099","title":"Plant carbohydrate metabolism and redox regulation","description":"The cluster highlights carbohydrate-related biosynthesis (glucose, gluconate) and vitamin C (ascorbic acid) pathways, alongside regulatory processes affecting kinases/phosphatases and redox-related activity (SOD). This suggests a theme centered on carbon metabolism with a redox-regulatory layer in plant systems, justifying a label focused on carbohydrate metabolism and redox regulation rather than more specific or unrelated functions.","confidence":"Medium","size":10,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0046178","count":1},{"id":"GO:0019853","count":1},{"id":"GO:0010907","count":1},{"id":"GO:0006469","count":1}]},{"hash":"58257235259268729","title":"Cellular stress and host interaction","description":"The terms cluster around stress responses (hypoxia, oxidant detoxification, hydrogen sulfide biosynthesis) and various protein regulation/trafficking processes, plus a host-interaction term (symbiont entry into host cell). There isn\u2019t a single cohesive function linking all terms, so the label reflects a broad theme of cellular stress and regulatory processes with Medium confidence. ","confidence":"Medium","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0046718","count":3},{"id":"GO:0010710","count":3},{"id":"GO:0019433","count":3}]},{"hash":"1484610063053759597","title":"Potassium Transport and Membrane Potential Regulation","description":"The cluster is dominated by GO terms tied to membrane potential stabilization and regulation, potassium ion homeostasis and transport, and cardiac action potentials, pointing to cellular excitability and ion balance as the core function. While a few terms touch on mechanosensation, GPCR signaling, and hormonal/metabolic processes, these are less central to the primary theme. Thus, naming the cluster around potassium transport and membrane potential regulation best captures its shared biology.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030322","count":9},{"id":"GO:0060075","count":9},{"id":"GO:0030007","count":9},{"id":"GO:0050976","count":9},{"id":"GO:0098914","count":9}]},{"hash":"416175600103669195","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000447","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0000480","count":1}]},{"hash":"931832232516090359","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to ribosome assembly and function (cytoplasmic translation, ribosome biogenesis, tRNA modification, ribosomal subunit export), suggesting the proteins collectively contribute to protein synthesis machinery. While a few terms touch on other processes, the ribosome/translation theme is the strongest signal.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006400","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0055072","count":1}]},{"hash":"1953650730528112734","title":"Bacterial Osmotic Stress and Thiol Biosynthesis","description":"This cluster includes several stress and sugar-related GO terms: response to water deprivation, response to sorbitol/mannitol, response to sucrose, and sugar metabolism (glucose, sucrose). The presence of bacillithiol and mycothiol biosynthetic processes strongly points to bacterial redox maintenance systems. Taken together, the terms suggest a coherent theme of osmotic stress adaptation and carbohydrate metabolism coupled with thiol-based biosynthesis in bacteria.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":1},{"id":"GO:0072708","count":1},{"id":"GO:0010555","count":1},{"id":"GO:0009744","count":1},{"id":"GO:0005985","count":1}]},{"hash":"2039955612341442473","title":"DNA repair and RNA processing","description":"This cluster centers on nucleic acid metabolism: multiple GO terms point to DNA repair (single-strand break repair, regulation of homologous recombination, telomere protection from NHEJ) and telomere maintenance, alongside RNA-related processes (maturation and processing of rRNA, ribosome biogenesis). The presence of a DNA recombination term (V(D)J) further supports genome maintenance as a core theme. While these processes span DNA repair and RNA biology, the unifying thread is nucleic acid metabolism and genome stability. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071919","count":2},{"id":"GO:0033153","count":1},{"id":"GO:0000012","count":1},{"id":"GO:0061819","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1625893245284090220","title":"Photosynthesis light harvesting and photoprotection","description":"The cluster is dominated by GO terms tied to photosynthesis, light harvesting in photosystems I and II, and light-responsive processes (response to red light, high/low light intensity), along with nonphotochemical quenching for photoprotection and chlorophyll-related phytol biosynthesis. An outlier term on skin morphogenesis is likely noise; overall, the set points to light-driven photosynthetic and protective mechanisms.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043589","count":2},{"id":"GO:0010114","count":1},{"id":"GO:0071486","count":1},{"id":"GO:0010196","count":1},{"id":"GO:0009645","count":1}]},{"hash":"295247688818207000","title":"Growth signaling and transcription control","description":"This cluster highlights several regulators of cell growth and fate, with GO terms spanning DNA-templated transcription, Hippo signaling, and Wnt signaling, plus apoptosis, telomere maintenance, and differentiation processes. The combination suggests a cohesive theme around growth signaling converging on transcriptional control and cell fate decisions, rather than a single, narrowly defined function.","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:0035329","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0060044","count":4},{"id":"GO:0006915","count":4}]},{"hash":"1456994563483278889","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0006415","count":2}]},{"hash":"1890495754947216945","title":"Unknown","description":"The top GO terms are diverse: ER membrane localization and ERAD, endosome transport, ribosome-related processes (rRNA methylation, phenylalanyl-tRNA aminoacylation), and various transport activities, with no single dominant function across the cluster. This suggests the proteins do not share a cohesive cellular role based on current annotations.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010936","count":1},{"id":"GO:0097051","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0036010","count":1}]},{"hash":"743102393439651684","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms related to ribosome production and protein synthesis (translation, ribosome biogenesis, small subunit biogenesis/assembly, tRNA modification, nucleolus organization). These suggest proteins involved in ribosome assembly and the translation apparatus. A couple of terms like Notch signaling and brain segmentation are present but appear incidental to the main ribosome/translation theme.","confidence":"High","size":10,"edges":15,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0006378","count":2}]},{"hash":"1714778910941657094","title":"Regulatory Signaling and Metabolism","description":"The top GO terms cluster around broad regulatory roles\u2014not a single pathway\u2014covering regulation of kinase activity, transcription (Pol III), phosphorylation control of STAT, regulation of catalytic activity, protein catabolic regulation, and various metabolic processes (ceramide metabolism, amino acid\u2013related response). This mix suggests proteins that act as regulators in signaling and metabolism rather than components of one cohesive pathway, supporting a label of a general regulatory cluster. Confidence: Medium","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903538","count":2},{"id":"GO:0000188","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0006672","count":2},{"id":"GO:0045945","count":2}]},{"hash":"1540358310347302144","title":"Nuclear RNA Processing and Transcription Regulation","description":"The GO terms cluster around nuclear processes: RNA splicing and spliceosome assembly, transcription termination of RNA polymerase II, histone mRNA metabolism, and chromatin-related processes (pericentric heterochromatin formation). The presence of import into nucleus reinforces a nuclear role. Some terms also reflect plant stress-responsive transcriptional regulation (ABA and water deprivation), suggesting a broader role in gene expression control under stress. Overall, these proteins seem linked to nuclear RNA processing and transcription/chromatin regulation.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":1},{"id":"GO:1990141","count":1},{"id":"GO:0042633","count":1},{"id":"GO:0045292","count":1},{"id":"GO:0009737","count":1}]},{"hash":"1264033939606247822","title":"Transmembrane transporters (diverse substrates)","description":"The top GO terms cluster around transmembrane transport of a wide range of substrates\u2014vitamins, xenobiotics, sugars (sialic acid, fucose), and various ions (sodium, potassium, phosphate, nitrite, nitrate)\u2014as well as a vesicular neurotransmitter loading process. This points to a group of membrane transporter proteins handling diverse molecules and vesicular cargo, supporting the label Transmembrane transporters (diverse substrates). ","confidence":"High","size":10,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0015739","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0035725","count":3}]},{"hash":"812740171317312573","title":"Unknown","description":"The Top Terms are highly diverse, spanning cell cycle, neural sensing (visual perception, phototransduction, short-term memory), secretory/platelet functions, development (kidney collecting duct, insect cuticle), and cytoskeletal signaling. There isn\u2019t a clear, single biological theme linking all of these terms, so a coherent, specific label is not justifiable.","confidence":"","size":10,"edges":18,"triangles":13,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0002576","count":3},{"id":"GO:0007602","count":3}]},{"hash":"1688370284866544260","title":"Diverse chemical-response and developmental signals","description":"The cluster mixes GO terms for responses to xenobiotics and drugs (xenobiotic stimulus, morphine, lead ion) with tissue-development and remodeling processes (lymphangiogenesis, hepatocyte differentiation, cardiac hypertrophy in response to stress) and general cellular activities (mitotic cell cycle, isoprenoid biosynthesis). This suggests proteins involved in broad chemical-response signaling and developmental modulation rather than a single, cohesive molecular function, so the label reflects a general theme rather than a precise pathway.","confidence":"Medium","size":10,"edges":7,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001946","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0070365","count":2},{"id":"GO:1900486","count":2}]},{"hash":"171748034803285566","title":"Mitotic Chromosome Condensation and Transcription Regulation","description":"Top terms are dominated by mitosis- and chromatin-related processes (histone H3 S10 phosphorylation for chromosome condensation; re-entry into the mitotic cell cycle; syncytial mitotic cell cycles) and by transcription repression during mitosis (negative regulation of RNA Pol II). Although a few terms touch on stress responses or tissue-specific proliferation, the core signal ties to mitotic chromatin dynamics and transcription control, supporting this label.","confidence":"High","size":10,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000775","count":2},{"id":"GO:0000320","count":2},{"id":"GO:0019085","count":2},{"id":"GO:0071481","count":2},{"id":"GO:1905866","count":2}]},{"hash":"1358756854946331168","title":"Developmental transcription regulators","description":"The top GO terms cluster around transcription-related processes (DNA-templated transcription, regulation of transcription, RNA polymerase II regulation, heterochromatin formation) with several development-associated terms (brain development, brain segmentation, rhombomere development, gonad development, vitellogenesis, fertilization). This suggests proteins that regulate gene expression during development, possibly including transcription factors and chromatin modifiers involved in neurodevelopment and reproductive development. Therefore, a concise, representative label is Developmental transcription regulators.","confidence":"Medium","size":10,"edges":27,"triangles":36,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":3},{"id":"GO:0007338","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0000183","count":2}]},{"hash":"1218575035079560437","title":"Redox-Driven Organic Compound Catabolism","description":"This cluster centers on oxidation-reduction (redox) processes and the catabolism of various organic substrates (sorbitol, furaldehyde, ethanol, amino acids via the Ehrlich pathway, retinol), along with NADH oxidation and related energy metabolism. The convergence on redox-linked catabolic pathways plus respiratory processes supports a cohesive theme of redox-driven metabolism. ","confidence":"High","size":10,"edges":14,"triangles":8,"max_degree":6,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006062","count":4},{"id":"GO:0033859","count":4},{"id":"GO:0000947","count":4},{"id":"GO:0018119","count":4}]},{"hash":"2278637458708305426","title":"DNA-Templated Transcription Regulation","description":"Dominant GO terms point to DNA-templated transcription and its regulation, suggesting the proteins group around transcriptional control. The other terms (sorbitol/furaldehyde metabolism, nitrosylation, respiratory processes) are less consistent with the main theme and may reflect annotation noise or multifunctionality. Overall, the cluster is best described as a transcription regulation module, albeit with some metabolic annotations.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0061179","count":2},{"id":"GO:0006062","count":1}]},{"hash":"1219155002949685532","title":"Mitochondrial Redox and Energy Metabolism","description":"The top GO terms cluster around mitochondrial energy production and redox balance, including mitochondrial electron transport (NADH to ubiquinone), 2-oxoglutarate metabolic process, and dihydrolipoamide metabolism, along with regulation of membrane potential and redox homeostasis. Additional terms for cellular response to cAMP and xenobiotic stimulus suggest associated signaling and stress responses that can tie to mitochondrial function. A few terms related to sperm capacitation or gamete generation may reflect organism-specific contexts or incidental annotations, but do not override the central mitochondrial metabolism theme. Overall, the cluster is best described as mitochondrial energy metabolism with redox regulation.","confidence":"High","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0045454","count":7},{"id":"GO:0071320","count":6},{"id":"GO:0042493","count":6},{"id":"GO:0006103","count":6}]},{"hash":"359174512253064122","title":"Unknown","description":"The top GO terms are highly diverse, spanning cell division, DNA recombination, various stress responses (to hydrogen peroxide and lead ions), metabolism (glycolytic regulation, sucrose response), development (fat pad development), mitochondria distribution, and even morphine response. There is no single, coherent biological theme tying these proteins together, suggesting a mixed or non-specific set rather than a defined functional cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0009744","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0006110","count":2}]},{"hash":"503375018431961799","title":"Neuronal synaptic signaling and plasticity","description":"This cluster's top GO terms cluster around neuronal communication and synaptic remodeling: NO-mediated retrograde signaling, glutamate secretion, long-term synaptic depression, dendritic spine morphogenesis, and regulation of serotonin uptake. While a couple of terms are less connected (lipid A biosynthesis, exploration behavior), the dominant pattern points to proteins involved in neurotransmission and synaptic plasticity.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098924","count":3},{"id":"GO:1901206","count":3},{"id":"GO:0051612","count":3},{"id":"GO:0009245","count":2},{"id":"GO:0060088","count":2}]},{"hash":"1816517670195761093","title":"Unknown","description":"The top terms cover a wide and disparate set of regulatory processes (meiotic cell cycle regulation, kinase activity regulation, transcription regulation by RNA polymerase III, regulation of catalytic activity and protein turnover, and apoptotic processes in morphogenesis). This lack of a unifying function or pathway makes it inappropriate to assign a specific label, so Unknown is the most honest fit. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903538","count":1},{"id":"GO:0000188","count":1},{"id":"GO:0000060","count":1},{"id":"GO:0006672","count":1},{"id":"GO:0045945","count":1}]},{"hash":"1557021043525518096","title":"Ion Transport and Phototransduction Proteins","description":"This cluster is dominated by GO terms for monoatomic and proton transmembrane transport and phototransduction, suggesting membrane-associated transporters or channels involved in light-sensing pathways. The other terms are sporadic and less cohesive, so the core theme centers on ion transport and phototransduction rather than broader regulatory roles. Confidence: Medium","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0034220","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0007602","count":2},{"id":"GO:0015992","count":2},{"id":"GO:0006368","count":1}]},{"hash":"598802620633494504","title":"Mitochondrial respiration and protein oligomerization","description":"This cluster centers on mitochondrial electron transport and aerobic respiration, alongside protein oligomerization (homotetramerization/heterooligomerization), suggesting a role in assembling energy-production complexes. Some terms like viral process and symbiont entry appear tangential, but the core theme is energy metabolism and multimeric protein assembly.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0032461","count":2},{"id":"GO:0006122","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0010992","count":2}]},{"hash":"455368730800996743","title":"Unknown","description":"The GO terms span eye/vision processes (visual perception, phototransduction) and a mix of unrelated topics (platelet degranulation, kidney, muscle, insect cuticle, memory, mammary gland involution), with no shared biological function across the cluster. Given the lack of a cohesive theme and no edges linking proteins, a single representative label cannot be confidently assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0002576","count":2},{"id":"GO:0007602","count":2},{"id":"GO:0072205","count":2}]},{"hash":"1436582264942445113","title":"Mitotic spindle assembly and chromosome alignment","description":"The cluster is dominated by GO terms describing mitotic spindle microtubule attachments, pole separation, metaphase chromosome alignment, and microtubule-driven nuclear migration, indicating a core theme of mitosis and spindle dynamics. Some neuronal and tissue maintenance terms may reflect shared cytoskeletal roles, but the central signal is mitotic machinery. ","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0099607","count":9},{"id":"GO:1990535","count":9},{"id":"GO:0001560","count":9},{"id":"GO:0000073","count":9},{"id":"GO:0007080","count":9}]},{"hash":"1546528991519625735","title":"Polyamine and amino-acid metabolism with acetylation","description":"This cluster centers on metabolic pathways involving polyamines (spermidine acetylation, putrescine catabolic process) and amino acid biosynthesis (L-arginine biosynthesis), plus related acetylation and modifier processes (N-terminal acetylation, glucosamine metabolism, mycothiol biosynthesis). While some terms (angiogenesis, obsolete annotations) may be noise, the dominant theme is metabolic biosynthesis and protein/ metabolite acetylation across microbes. ","confidence":"Medium","size":10,"edges":8,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001525","count":6},{"id":"GO:0032918","count":4},{"id":"GO:0009447","count":4},{"id":"GO:0030435","count":4},{"id":"GO:0006526","count":4}]},{"hash":"563482843309793776","title":"Kinase Regulation and Cell Cycle Control","description":"The top GO terms emphasize negative regulation of kinase signaling (MAPK/ERK, tyrosine dephosphorylation, and broader kinase activity inhibition) together with cell cycle processes (CDK activity, cyclin regulation, and kinetochore localization). This points to a theme of dampening signaling pathways to control mitosis and cell cycle progression, with osmotic stress and synaptic vesicle clustering as related signaling contexts.","confidence":"Medium","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0070373","count":8},{"id":"GO:0050860","count":8},{"id":"GO:0000200","count":8},{"id":"GO:0007049","count":7},{"id":"GO:0035335","count":7}]},{"hash":"1422205036326819666","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":21,"triangles":19,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":10},{"id":"GO:0000278","count":10},{"id":"GO:1905869","count":9},{"id":"GO:0035330","count":9},{"id":"GO:0042068","count":9}]},{"hash":"130700207769186534","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":30,"triangles":37,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":10},{"id":"GO:0007601","count":8},{"id":"GO:1905869","count":8},{"id":"GO:0035330","count":8},{"id":"GO:0042068","count":8}]},{"hash":"1832092286660005236","title":"Unknown","description":"The GO terms show a mix of telomere maintenance regulation, neural development, immune signaling, and general regulation of enzymes and post-translational modification, with no single unifying process connecting them. The lack of a cohesive theme or pathway makes a specific, representative label unreliable.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0007253","count":1}]},{"hash":"1789320886013491525","title":"Unknown","description":"The top GO terms span GPCR/PKC signaling, cardiac action potential regulation, telomere maintenance, neural differentiation, and cytokine/immunity regulation, with no single cohesive function clearly tying the cluster together. This broad mix suggests no common theme beyond generic regulation, so Unknown is most appropriate.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":6},{"id":"GO:0098907","count":6},{"id":"GO:0032212","count":4},{"id":"GO:0021707","count":4},{"id":"GO:1904355","count":4}]},{"hash":"67489098337008295","title":"DNA-Templated Transcription Regulation","description":"The cluster is dominated by GO terms for regulation of DNA-templated transcription and DNA-templated transcription themselves (GO:0006355 and GO:0006351), indicating proteins primarily involved in transcriptional control. Other terms \u0627\u0634\u0627\u0631\u0647 to signaling and trafficking appear ancillary, but the strongest signal is transcription regulation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0060316","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0001881","count":3}]},{"hash":"1667560572775269088","title":"Unknown","description":"This cluster lacks a unifying function among its top GO terms. They cover diverse regulatory processes: telomere maintenance, cerebellar granule cell differentiation, regulation of chemokine production, NF-kappaB sequestration, IL-12 signaling inhibition, dendrite development, protein kinase activity regulation, vitamin D response, and protein ADP-ribosylation. With only scattered regulatory terms and a single edge linking the members, there is no clear common pathway or cellular process to name; thus Unknown with confidence None.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0007253","count":1}]},{"hash":"214916868240075939","title":"TLR Signaling and Inflammatory Response","description":"The main GO terms cluster around Toll-like receptor signaling (TLR8) and Toll signaling, with positive regulation of inflammatory responses, interferon-alpha and IL-18 production, and related pathways. This points to a coherent role in innate immune sensing and cytokine-driven inflammation. Additional terms about autophagy regulation and antibacterial peptide biosynthesis fit defense responses, while collagen fibril organization may reflect extracellular matrix remodeling during inflammation. Overall, the cluster represents Toll-like receptor\u2013driven innate immune signaling with inflammatory regulation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0032741","count":2},{"id":"GO:0034158","count":2},{"id":"GO:0050729","count":2},{"id":"GO:0045356","count":2}]},{"hash":"1659833550146190991","title":"Ubiquitin- and Autophagy-Mediated Protein Quality Control","description":"This cluster centers on pathways that govern protein turnover and quality control through ubiquitination (deubiquitination, sumoylation), aggresome formation, and autophagy/mitophagy regulation, as well as endocytosis modulation. Taken together, these terms point to a cohesive theme of proteostasis maintenance via ubiquitin-related modifications and autophagy-lysosome pathways, rather than a single metabolic process. ","confidence":"High","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904021","count":1},{"id":"GO:0016579","count":1},{"id":"GO:0070842","count":1},{"id":"GO:1900186","count":1},{"id":"GO:0016925","count":1}]},{"hash":"264161178756035630","title":"Sterol and lipid biosynthesis","description":"The top terms cluster around lipid and sterol metabolism: ergosterol and cholesterol biosynthesis, sterol oxidation, fatty acid and ether lipid metabolism, and sphingolipid-related processes. Although a couple terms pertain to tissue-specific processes (myelin maintenance, sebaceous gland differentiation) the dominant signal is lipid/sterol biosynthesis, suggesting these proteins function in lipid-related metabolic pathways.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006696","count":1},{"id":"GO:0006675","count":1},{"id":"GO:0033490","count":1},{"id":"GO:0032286","count":1}]},{"hash":"602781831821269452","title":"Unknown","description":"The TOP terms span a wide range of processes\u2014from cell division and mitotic transitions to immune response, hormone signaling, prostate and male development, ciliary and photoreceptor localization, and metabolism. There isn\u2019t a clear single biological theme tying these terms together, suggesting no cohesive function for this cluster beyond a broad panel of unrelated processes.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:1903646","count":8},{"id":"GO:0045842","count":8},{"id":"GO:0071357","count":8},{"id":"GO:0030850","count":8}]},{"hash":"397285861106312803","title":"Auditory hair cell morphogenesis and synaptic signaling","description":"The GO terms cluster around cochlear development, stereocilium organization, glutamate secretion, and receptor localization to synapses, indicating a shared role in auditory hair cell maturation and neuron\u2013hair cell communication.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:0048294","count":1},{"id":"GO:0060997","count":1},{"id":"GO:0014047","count":1},{"id":"GO:0090103","count":1}]},{"hash":"383224341235709591","title":"Collagen-ECM Organization and Tissue Morphogenesis","description":"The set shows strong representation of collagen fibril organization, basement membrane development, and various tissue morphogenesis processes (including aorta smooth muscle and intramembranous ossification), pointing to extracellular matrix remodeling and connective tissue formation as the core theme. A few terms (e.g., complement activation) are less aligned but do not override the dominant ECM/morphogenesis signal.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001957","count":1},{"id":"GO:0045650","count":1},{"id":"GO:2000860","count":1},{"id":"GO:0032836","count":1},{"id":"GO:0001867","count":1}]},{"hash":"1070362832980924435","title":"Innate immune defense with ubiquitin-mediated regulation","description":"This cluster is characterized by GO terms for innate immune response and defense against Gram-positive bacteria, plus ubiquitin-protein ligase activity and proteasomal degradation, suggesting a theme centered on innate immune signaling coupled with ubiquitin-regulated protein turnover. Some terms related to translation initiation or transcription may reflect shared cellular processes but do not override the immune/ubiquitin theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0001731","count":2}]},{"hash":"434306873151748857","title":"RNA processing and translation initiation regulation","description":"This cluster centers on RNA metabolism: regulation of splicing via the spliceosome, regulatory ncRNA-mediated gene silencing, and control of translational initiation with preinitiation complex and small-subunit processome assembly. While a few terms are less directly connected (some obsolete entries and development-related terms), the dominant signal ties to RNA processing and how translation is initiated or regulated.","confidence":"Medium","size":9,"edges":29,"triangles":44,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2}]},{"hash":"1671999802384007689","title":"Drosophila oogenesis and early embryogenesis","description":"This cluster centers on developmental regulation in Drosophila related to female germline development and early embryo formation, including egg chamber follicle relationships, germarium cyst encapsulation, syncytial nuclear migration, and regulation of the preblastoderm cell cycle and transcription. While a couple of terms pertain to broader vertebrate development, the dominant theme is Drosophila reproductive development and initial embryogenesis.","confidence":"Medium","size":9,"edges":26,"triangles":33,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":2},{"id":"GO:0030713","count":1},{"id":"GO:0048706","count":1},{"id":"GO:0045652","count":1},{"id":"GO:0006355","count":1}]},{"hash":"211478650232184486","title":"Immune activation and antigen presentation","description":"Most proteins in this cluster are linked to innate immune signaling, phagocytosis, dendritic cell chemotaxis, and MHC class I\u2013mediated antigen presentation (e.g., innate immune response-activating signaling pathway, positive regulation of phagocytosis, peptide antigen assembly with MHC class I). This points to a cohesive theme of immune cell activation and antigen processing/presentation. While there are a couple of terms less directly related (e.g., ER unfolded protein response, sperm\u2013zona pellucida binding, posterior lateral line development), the dominant pattern supports an immune-focused cluster.","confidence":"Medium","size":9,"edges":8,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048916","count":1},{"id":"GO:0002502","count":1},{"id":"GO:0033144","count":1},{"id":"GO:1901224","count":1},{"id":"GO:0010204","count":1}]},{"hash":"694407242130792637","title":"Autophagy-Linked Metabolic Catabolism","description":"Rationale: The cluster shows explicit autophagy-related terms (glycophagy; positive regulation of macroautophagy) alongside several carbohydrate and lipid catabolic processes (starch, maltose, glycerophospholipid catabolic processes) indicating a theme of autophagy coupled with energy substrate breakdown. Mitochondrial translation and mRNA decay hint at broader metabolism, but the strongest shared signal is autophagy-associated metabolism. Some terms (habituation, pole plasm localization) appear peripheral to this central theme.","confidence":"Medium","size":9,"edges":18,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0005983","count":1},{"id":"GO:0043609","count":1},{"id":"GO:0061723","count":1},{"id":"GO:0046475","count":1}]},{"hash":"1086298417380877398","title":"Viral life cycle and host entry","description":"The top GO terms point to key stages of viral infection and replication, including host entry, fusion of viral and host membranes, virion assembly, and the overall viral life cycle, with supporting processes like host-mediated replication activation and related cellular factors (lipid droplets and protein folding) that viruses commonly exploit. This suggests the cluster represents proteins involved in viral life cycle and host interactions.","confidence":"High","size":9,"edges":13,"triangles":9,"max_degree":6,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006278","count":4},{"id":"GO:0044829","count":4},{"id":"GO:0019068","count":4},{"id":"GO:0019064","count":4},{"id":"GO:0050714","count":4}]},{"hash":"1614433666358541222","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0001731","count":2}]},{"hash":"967129453117153792","title":"Cytoskeleton remodeling and Rho-GTPase signaling","description":"The top GO terms cluster around actin cytoskeleton organization, microtubule-based movement, and Rho-family GTPase signaling (activation of GTPase activity, regulation of Rho signaling), with a receptor guanylyl cyclase pathway also present. Together these point to a core theme of cytoskeletal dynamics coordinated by small GTPases and associated signaling. Some neural-related terms (spinal cord development, sensory perception of sound) may reflect tissue context rather than a central function of the cluster.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0007168","count":2},{"id":"GO:0030036","count":2}]},{"hash":"2205103456884295367","title":"Cytoplasmic translation and ribosome biogenesis","description":"The top GO terms are dominated by translation-related processes (translation, cytoplasmic translation) and ribosome biogenesis, with several entries on translational fidelity, suggesting the cluster centers on protein synthesis machinery and its quality control in the cytoplasm; transcription terms appear but do not define the core function.","confidence":"High","size":9,"edges":9,"triangles":2,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":4},{"id":"GO:0006353","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0002181","count":2}]},{"hash":"1663415426378117837","title":"Nuclear import and transcription regulation proteins","description":"The top GO terms point to import of nuclear proteins (hnRNPs, snRNPs, transcription factors) and regulation of transcription by RNA polymerase II, with a few mitotic chromosome movement and alignment terms. This suggests a cohesive theme around nuclear transport coupled to transcriptional regulation, with ancillary cell-cycle-related associations; some terms are flagged as obsolete, but the core signal remains nuclear import and gene regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000060","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006609","count":1},{"id":"GO:0006608","count":1},{"id":"GO:0007080","count":1}]},{"hash":"725262133175060645","title":"Biosynthesis and biomolecule modification","description":"Top GO terms are dominated by diverse biosynthetic processes (ubiquinone, vitamin E, antibiotic, juvenile hormone) with additional protein and RNA modification activities (N-terminal peptidyl-serine trimethylation; tRNA wobble uridine modification). A few terms relate to xenobiotic or metal ion stress responses, suggesting a cluster of proteins involved in production and chemical modification of biomolecules rather than a single tightly linked pathway.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0035573","count":2},{"id":"GO:0010189","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0017000","count":2}]},{"hash":"503280331871328836","title":"Wnt signaling and cell adhesion in development","description":"The Top Terms point to embryonic development themes (cranial skeletal system development, dorsal identity, renal vesicle formation) and signaling with a noticeable emphasis on the canonical Wnt pathway and its regulation of apoptosis, along with adherens junction assembly. While other terms (GTPase activity regulation, nuclear import, mitochondrial calcium, vacuole fusion) are present, the developmental and cell-adhesion/signaling signals are most prominent, supporting a label focused on Wnt-related developmental signaling and cell adhesion.","confidence":"Medium","size":9,"edges":8,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0006607","count":4},{"id":"GO:0051561","count":4},{"id":"GO:0043065","count":4},{"id":"GO:0042144","count":4}]},{"hash":"80580077539119525","title":"Unknown","description":"The terms are diverse and largely unrelated functionally; some pertain to innate immune responses to dsRNA, but others refer to development, cell cycle regulation, and photosynthesis. With no coherent shared pathway or interaction (no edges/triangles), a single representative function cannot be assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071360","count":2},{"id":"GO:0045087","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0006478","count":1},{"id":"GO:0072189","count":1}]},{"hash":"600553834020408502","title":"Osmotic Stress Response and Thiol Biosynthesis","description":"This cluster centers on osmotic/osmoprotectant responses, highlighted by GO terms for water deprivation and responses to sorbitol, mannitol, and sucrose, as well as sugar metabolism. The presence of bacillithiol and mycothiol biosynthetic processes suggests a thiol-based redox/osmotic protection theme common to bacteria. Some terms (like feeding behavior) may be less related, but the core signals point to osmotic stress management and thiol biosynthesis.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0072708","count":3},{"id":"GO:0010555","count":3},{"id":"GO:0009744","count":3}]},{"hash":"2185488595919443386","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":14,"triangles":8,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0002188","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1130656274652446345","title":"RNA processing and translation initiation","description":"The top GO terms cluster around translational initiation regulation, preinitiation complex formation, and small-subunit processome assembly, with additional splicing-related terms (spliceosome regulation, alternative splicing, and mRNA processing). This combination suggests proteins involved in RNA maturation and early translation steps, i.e., RNA processing and translation initiation machinery.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1902625","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0034462","count":3},{"id":"GO:0001825","count":3}]},{"hash":"2248168719485423594","title":"Redox Homeostasis and Oxidative Stress Response","description":"The top GO terms are dominated by redox-related processes: cellular redox homeostasis, cellular oxidant detoxification, oxidative stress response, and deglutathionylation, indicating an antioxidant defense/regulatory cluster. A few terms (RNA polymerase II regulation, methylamine metabolism, neural crest migration) appear less connected and may reflect multifunctional proteins or annotation noise, but the core theme centers on maintaining redox balance and detoxification of reactive species.","confidence":"Medium","size":9,"edges":9,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0080058","count":3}]},{"hash":"2175475096092957790","title":"Chromatin remodeling and histone modification","description":"The top terms cluster around chromatin dynamics: nucleosome disassembly, histone displacement, and especially N-terminal peptidyl-lysine acetylation, which points to histone modification and chromatin remodeling as the core theme. While a couple terms touch on development or other processes, these are likely ancillary annotations; the recurrent signals most strongly support chromatin regulation as the shared function of this protein group.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0030490","count":2},{"id":"GO:0018076","count":2},{"id":"GO:0001207","count":2},{"id":"GO:0031496","count":2}]},{"hash":"753629458770014194","title":"Developmental Transcription and Cell Cycle Regulation","description":"This cluster is dominated by GO terms pointing to vertebrate development (neural tube closure, forebrain and skeletal system development, multicellular organism development) and transcriptional control (DNA-templated transcription), with supporting signals for cell proliferation (mitotic cell cycle) and ER-stress\u2013related apoptosis. A few terms related to immunity appear sparsely, but the central theme remains developmental regulation and transcriptional control.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006349","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0000278","count":4}]},{"hash":"701365110615278740","title":"Unknown","description":"The terms span nuclear cell-cycle/DNA replication, centrosome dynamics, morphogenesis (dendrite and cranial skeleton), ion transport, telomere maintenance, pH response, and immune proliferation, with no single unifying function linking all proteins. This heterogeneity makes a coherent, specific cluster label infeasible.","confidence":"","size":9,"edges":27,"triangles":38,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":7},{"id":"GO:0007098","count":7},{"id":"GO:0043552","count":7},{"id":"GO:0006813","count":7},{"id":"GO:0048813","count":7}]},{"hash":"953370737098918199","title":"Neural and Embryonic Development with Transcriptional Regulation","description":"The terms point to developmental and neural contexts (neural tube closure, forebrain development, multicellular organism development, skeletal system development) with a core emphasis on DNA-templated transcription, suggesting a module of developmental transcriptional programs. Additional terms indicate proliferation (mitotic cell cycle) and stress/apoptotic responses (ER stress\u2013related apoptosis) that can accompany development. An immune defense term appears less central and may reflect cross-talk rather than a core function. Overall, this cluster seems to represent neural/embryonic development tied to transcriptional regulation and associated growth and stress responses.","confidence":"Medium","size":9,"edges":23,"triangles":33,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006349","count":9},{"id":"GO:0001843","count":9},{"id":"GO:0050830","count":9},{"id":"GO:0001403","count":9},{"id":"GO:0000278","count":9}]},{"hash":"174701577790491083","title":"RNA Modification and Transcription Regulation","description":"Top GO terms indicate a core role in tRNA methylation/modification and in DNA-templated transcription and its regulation, suggesting RNA processing and transcription control as the central theme of this cluster. The presence of several metabolic biosynthesis terms may reflect multifunctional proteins or annotation noise, but the strongest signal remains RNA metabolism and transcription regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0019475","count":1},{"id":"GO:0009234","count":1}]},{"hash":"949642592355431407","title":"Neuronal development and synaptic signaling","description":"The top GO terms cluster around neural development and synaptic function: dendritic spine morphogenesis, retinal ganglion cell axon guidance, ephrin receptor signaling, and trans-synaptic signaling related to synaptic transmission. Additional development-related terms (roof of mouth development, digestive tract morphogenesis, and focal adhesion regulation) support a broader developmental theme, with one outlier term on T cell proliferation. Overall, the dominant signal points to neuronal development and synaptic connectivity.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":8},{"id":"GO:0048013","count":8},{"id":"GO:0051893","count":8},{"id":"GO:0050798","count":7},{"id":"GO:0099557","count":7}]},{"hash":"1436415936310431863","title":"Unknown","description":"The Top Terms span neural crest differentiation, rRNA maturation, multiple DNA replication and repair processes, and antigen processing/presentation, showing no single cohesive function for the cluster. A generic Unknown label is the most appropriate given the diverse annotations.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014033","count":1},{"id":"GO:0000462","count":1},{"id":"GO:1903459","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1903460","count":1}]},{"hash":"1960635631666313104","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006368","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0001711","count":1},{"id":"GO:0090262","count":1},{"id":"GO:0009910","count":1}]},{"hash":"583611527562511121","title":"Spliceosome-Mediated Splicing and Stress Granule Regulation","description":"The cluster is enriched for GO terms tied to mRNA splicing via the spliceosome, including regulation of spliceosomal activity and alternative splicing, as well as stress-related RNA processing such as localization to cytoplasmic stress granules and stress-responsive RNA regulation. This points to a coherent theme of RNA metabolism centered on splicing and stress-induced regulation, with additional broad RNA silencing links that fit within the regulatory RNA landscape.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":6},{"id":"GO:0010610","count":5},{"id":"GO:0048026","count":4},{"id":"GO:1903608","count":3},{"id":"GO:0075522","count":3}]},{"hash":"1330112388589722360","title":"RNA and Protein Methylation","description":"The cluster includes several GO terms tied to methylation: rRNA methylation, peptidyl-lysine dimethylation and trimethylation, and N-terminal peptidyl-glycine methylation, suggesting a coherent theme of methyltransferase activity affecting both RNA and proteins. Additional terms related to chromatin modification and sporulation support a broader link to epigenetic regulation, though some terms appear more peripheral to the core methylation theme.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":4},{"id":"GO:0018027","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0000183","count":2},{"id":"GO:0018023","count":2}]},{"hash":"1060000874860798263","title":"Muscle calcium signaling and redox homeostasis","description":"This cluster's top GO terms center on redox balance and detoxification (cell redox homeostasis, cellular oxidant detoxification, L-ascorbic acid metabolic process) and on calcium signaling related to muscle function (regulation of ryanodine-sensitive calcium-release channel activity, positive/negative regulation of skeletal muscle contraction by calcium release). Together they point to proteins involved in managing oxidative stress while modulating Ca2+-dependent muscle contraction. Some metabolic terms are broader, but the redox and calcium-muscle theme is the strongest linkage.","confidence":"Medium","size":9,"edges":33,"triangles":65,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0071243","count":5},{"id":"GO:0019852","count":5},{"id":"GO:0060316","count":5}]},{"hash":"1753219562084276931","title":"Organogenesis and developmental regulation","description":"The top GO terms point to organ development across multiple tissues (heart morphogenesis, hindbrain development, pituitary gland development, optic cup morphogenesis), suggesting a general theme of organogenesis. The presence of protein autoubiquitination hints at regulatory control common in developmental processes. A couple of outlier terms (some obsolete or metabolic) temper the signal, but the dominant pattern supports a developmental organogenesis theme. ","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0019285","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0030902","count":1}]},{"hash":"772615441643458511","title":"Unknown","description":"The GO terms cover a wide, disparate range of metabolic processes (antibiotic and antibiotic response, vitamin/phytochemistry, pigment and lipid metabolism, steroid hormone metabolism, development), with no single unifying function linking the proteins. ","confidence":"","size":9,"edges":32,"triangles":58,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0042619","count":5},{"id":"GO:0042376","count":4},{"id":"GO:0030324","count":4}]},{"hash":"1431143898302543293","title":"Diverse small-molecule biosynthesis and metabolism","description":"The terms center on biosynthetic and metabolic processes for various small molecules (retinol, fructose, prostaglandin, ascorbic acid, androgen) with accompanying redox activity and some signaling regulation (PI3K/Akt) and cell proliferation effects. This points to a broad, heterogeneous metabolic cluster rather than a single pathway, so the label emphasizes diversity in small-molecule biosynthesis and metabolism.","confidence":"Medium","size":9,"edges":20,"triangles":23,"max_degree":7,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0042572","count":6},{"id":"GO:0046370","count":6},{"id":"GO:0001516","count":5},{"id":"GO:0051897","count":5}]},{"hash":"572206048478312564","title":"Glycan biosynthesis and metal ion transport","description":"The cluster shows strong representation of glycan-related biosynthetic processes, including lipopolysaccharide biosynthesis and N-acetylglucosamine/N-acetylneuraminate biosynthesis, which points to glycan production at the cell surface. Copper ion transport and calcium ion homeostasis provide a metal ion handling context that often accompanies membrane- and cell-wall related metabolism. Some terms like phospholipid dephosphorylation and epoxygenase pathways are more peripheral, but do not override the dominant glycan-centric signal. This label is a reasonable, domain-aligned summary of the core functions, hence Medium confidence. ","confidence":"Medium","size":9,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":4},{"id":"GO:0016311","count":3},{"id":"GO:0006874","count":2},{"id":"GO:0006045","count":2},{"id":"GO:0019700","count":2}]},{"hash":"1214945678098021494","title":"Plant metabolism and SA-mediated defense signaling","description":"The cluster includes multiple biosynthetic processes (porphyrinogen IX, biotin, kynurenic acid, sphingomyelin, fatty acids) alongside plant-specific functions such as systemic acquired resistance and fruit ripening, indicating a group of proteins tied to core metabolism with SA-dependent defense signaling in plants.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006782","count":5},{"id":"GO:0009102","count":5},{"id":"GO:0034276","count":4},{"id":"GO:0055089","count":4},{"id":"GO:0042218","count":4}]},{"hash":"1010476387357499214","title":"Unknown","description":"The top GO terms span redox homeostasis, hormone/peptide signaling, ion/water transport, DNA metabolism, RNA stability, and skin development, with no clear shared function or pathway tying the cluster together. The absence of edges suggests the proteins do not form a cohesive interaction module, so a single representative label isn\u2019t evident beyond an overall \u201cunknown/diverse functions\u201d category.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:2001153","count":3},{"id":"GO:0046856","count":3},{"id":"GO:0006308","count":3},{"id":"GO:0080111","count":3}]},{"hash":"1206640746434264484","title":"Mitochondrial dynamics and ribosome biogenesis","description":"The cluster\u2019s strongest signals are mitochondrial fission, establishment of mitochondrion localization via microtubules, and ribosome biogenesis, which together point to a theme of organelle dynamics coupled with protein synthesis. Other terms like cobalamin biosynthesis and cell septum assembly appear more peripheral or context-specific, likely reflecting annotation noise or broader cellular functions. Overall, the core connection seems to be mitochondrial dynamics intertwined with ribosome assembly.","confidence":"Medium","size":9,"edges":16,"triangles":14,"max_degree":7,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0006461","count":5},{"id":"GO:0009236","count":5},{"id":"GO:0090529","count":2},{"id":"GO:1901741","count":2},{"id":"GO:0034643","count":2}]},{"hash":"1370530767520236263","title":"Lipid metabolism and membrane organization","description":"The cluster is dominated by lipid-related processes (fatty acid catabolic, triglyceride and galactolipid biosynthesis) and membrane/organellar architecture (lipid droplet organization, ER organization, nucleus organization, lamin depolymerization), pointing to a cohesive role in lipid handling and nuclear/ER membrane dynamics; a few terms (viral process, transcription regulation) are less central and may reflect broader regulatory contexts.","confidence":"Medium","size":9,"edges":25,"triangles":30,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0009062","count":3},{"id":"GO:0006997","count":3},{"id":"GO:0007078","count":3}]},{"hash":"1102081753315765891","title":"Unknown","description":"The terms include metabolism (gluconeogenesis and PPP regulation), dephosphorylation, autophagy, DNA damage response, xenobiotic response, and development/apoptosis terms (brain development, cardiac muscle cell apoptosis), which do not point to a single cohesive function for the cluster. Hence no specific shared theme can be inferred.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":3},{"id":"GO:0030420","count":3},{"id":"GO:0006094","count":2},{"id":"GO:0010666","count":2},{"id":"GO:0043456","count":2}]},{"hash":"1430172799696031354","title":"Ubiquitin-mediated protein degradation","description":"The cluster is dominated by GO terms related to ubiquitination and protein degradation, including K63-linked ubiquitination, protein autoubi quitination, and ubiquitin-dependent ERAD pathways, suggesting a core role in tagging proteins for turnover and quality control. Other terms (hormone responses and chaperone assembly regulation) appear peripheral or context-dependent, but do not override the central theme of ubiquitin-mediated degradation.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0033280","count":2},{"id":"GO:0090035","count":2}]},{"hash":"1732572525332967116","title":"Unknown","description":"The top GO terms span neural development, sensory perception, pigmentation, and assorted cellular transport/localization processes, with no single cohesive function tying all proteins together. This scattered set makes a concise, representative label unreliable.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022008","count":1},{"id":"GO:0006409","count":1},{"id":"GO:0019233","count":1},{"id":"GO:0018063","count":1},{"id":"GO:0048069","count":1}]},{"hash":"194382151933388476","title":"Neural development and dendritic spine morphogenesis","description":"The top GO terms cluster around central nervous system development, optic nerve morphogenesis, and dendritic spine morphogenesis, indicating proteins involved in neural patterning and synaptic structure formation. Although some terms relate to ECM and cell adhesion, the strongest signal is CNS development and dendritic spine formation, supporting a label focused on neural development.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007417","count":4},{"id":"GO:1902948","count":4},{"id":"GO:2001108","count":4},{"id":"GO:0048710","count":4},{"id":"GO:0060997","count":4}]},{"hash":"1230882413275138525","title":"RNA processing and translation regulation","description":"The cluster\u2019s GO terms are dominated by RNA metabolism and translation control functions, including regulation of translational initiation, formation of translation preinitiation complex, small-subunit processome assembly, negative regulation of mRNA splicing, and miRNA-mediated inhibition of translation. While a few terms pertain to polysaccharide metabolism or development, the strongest and most consistent signal centers on RNA processing and translation regulation, suggesting proteins here are involved in RNA processing and translation control pathways. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":1},{"id":"GO:0042121","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1976663898442548231","title":"ECM remodeling and basement membrane development","description":"The cluster shows a strong signal for extracellular matrix biology, with collagen fibril organization and collagen catabolic processes, and basement membrane development (glom\u00aderular basement membrane). These points suggest ECM assembly/remodeling as the core theme, complemented by related processes like ossification and kidney development, but the dominant pattern remains ECM-related.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":2},{"id":"GO:0001957","count":1},{"id":"GO:0045650","count":1},{"id":"GO:2000860","count":1},{"id":"GO:0032836","count":1}]},{"hash":"527389798040164174","title":"Cardiac electrophysiology and vascular regulation","description":"This cluster\u2019s top GO terms cluster around heart muscle electrical activity and vascular control, including ventricular action potential regulation, membrane repolarization, vasoconstriction, and vasopressin/aldosterone-related hormonal signaling, with additional links to stress-induced cardiac hypertrophy. These themes point to coordinated cardiac electrophysiology and vascular tone regulation as the core function of the proteins.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007216","count":3},{"id":"GO:0002024","count":3},{"id":"GO:0032342","count":3},{"id":"GO:0086002","count":3},{"id":"GO:0071651","count":3}]},{"hash":"1710099195686307528","title":"GPI-anchor biosynthesis and lipid metabolism","description":"The cluster features direct GPI-anchor related terms (biosynthesis and attachment) and several lipid-related processes (fatty acid transmembrane transport, sphingosine biosynthesis), suggesting a membrane-associated biosynthesis/signaling theme. While some terms (fungal/plant cell wall organization, mechanosensory detection, and JAK-STAT regulation) are less tightly connected, they may reflect broader membrane-related functions or signaling contexts. Overall, the common thread appears to be membrane-anchored biosynthesis and lipid signaling processes.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0016255","count":1},{"id":"GO:0046425","count":1},{"id":"GO:0031505","count":1}]},{"hash":"1405045337886848831","title":"Unfolded protein response and chaperone-mediated folding","description":"This cluster centers on responses to misfolded or unfolded proteins, chaperone-dependent refolding, and quality control pathways (unfolded protein response, misfolded protein transport, and protein folding maintenance), with supporting signals from redox homeostasis. Some terms (tRNA import, frameshifting, development signaling) are less connected but do not outweigh the main theme of protein folding stress and quality control.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0035719","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0051259","count":2}]},{"hash":"2301186773526725963","title":"Mitochondrial Transporters and Redox Regulation","description":"The cluster centers on mitochondrial membrane transport of metabolites and ions (malate-aspartate shuttle, ATP, CoA, phosphate, deoxynucleotides, magnesium, ornithine) and on regulation of mitochondrial permeability, with accompanying redox-related responses (superoxide) and a link to energy/metabolic signaling (insulin secretion). This cohesive theme supports labeling as mitochondrial transport and redox-related processes.","confidence":"High","size":9,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061179","count":5},{"id":"GO:0043490","count":4},{"id":"GO:1990616","count":4},{"id":"GO:1990544","count":4},{"id":"GO:0035349","count":4}]},{"hash":"1941978229429869563","title":"Xenobiotic and immune stress response","description":"The top GO terms converge on responses to antibiotics, xenobiotics, estradiol, lipopolysaccharide, and amino acids, plus transcription regulation and signaling pathways related to NF-kappaB and apoptosis. Taken together, these proteins appear to participate in cellular defense and stress signaling triggered by diverse external stimuli, 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:0046677","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0032355","count":2},{"id":"GO:0071285","count":2}]},{"hash":"948476681525162901","title":"Sterol/Lipid Homeostasis and Vesicle Transport","description":"This cluster is anchored by multiple GO terms related to sterol biosynthesis, sterol transport, and cellular cholesterol response, along with triglyceride storage regulation and post-Golgi vesicle transport. These collectively point to a theme of lipid (sterol/triglyceride) homeostasis and the trafficking processes that manage lipid-containing membranes, with some additional context from cell polarity and autophagy-related terms. Confidence: Medium","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030011","count":1},{"id":"GO:0010922","count":1},{"id":"GO:0010891","count":1},{"id":"GO:0016126","count":1},{"id":"GO:0015918","count":1}]},{"hash":"1880394660999970902","title":"Unknown","description":"These nine proteins show a scattered collection of regulatory GO terms: negative regulation of interferon production, regulation of ERK signaling, ubiquitin-protein transferase activity, chromatin-related processes (heterochromatin formation, histone methylation), protein stabilization and isomerization, and negative regulation of cell motility. There is no clear, unique shared biological process or molecular function linking them beyond general regulatory concepts. Therefore, I cannot assign a specific functional label beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032480","count":1},{"id":"GO:0051085","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0051443","count":1},{"id":"GO:0080182","count":1}]},{"hash":"724767106634552985","title":"Visual system development and phototransduction","description":"The top GO terms are dominated by axonogenesis, visual perception, and phototransduction, pointing to proteins involved in visual system development and sensory signaling. There is some supporting context from related signaling modulation (negative regulation of protein kinase activity), though several terms appear broader or unrelated (nuclear import, spindle duplication, cuticle development, thyroid metabolism, cardiac contraction). Overall, the core theme centers on vision-related neuronal function, justifying a Medium confidence. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":7},{"id":"GO:0007409","count":7},{"id":"GO:0007601","count":6},{"id":"GO:0007602","count":6},{"id":"GO:0008365","count":6}]},{"hash":"1717405414705802895","title":"Unknown","description":"The terms point to multiple unrelated processes (telomere maintenance, cell cycle regulation, migration/adhesion, muscle stretch response, adipogenesis, RNA processing, pH response). There is no clear, single shared function tying these proteins together, so a cohesive label is not justifiable.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0045736","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0035994","count":4}]},{"hash":"1925215332418349547","title":"TGF-\u03b2/BMP signaling regulators","description":"Proteins in this cluster are enriched for GO terms describing negative regulation of BMP signaling, negative regulation of TGF-\u03b2 receptor signaling, and cellular responses to TGF-\u03b2 stimulus, including SMAD-related processes. This indicates a coherent theme of modulating TGF-\u03b2/BMP pathway activity. A few terms such as maintenance of meristem identity and photosystem stoichiometry adjustment appear peripherally, possibly reflecting organism-specific roles or broader regulatory links, but the central signal points to TGF-\u03b2/BMP pathway regulation.","confidence":"Medium","size":9,"edges":32,"triangles":60,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":8},{"id":"GO:0030512","count":8},{"id":"GO:0080005","count":8},{"id":"GO:0071560","count":8},{"id":"GO:0010074","count":8}]},{"hash":"1621269762058483595","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904158","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0035719","count":1},{"id":"GO:0070843","count":1},{"id":"GO:0006458","count":1}]},{"hash":"344399620636720445","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0022417","count":1},{"id":"GO:0051084","count":1},{"id":"GO:0033617","count":1}]},{"hash":"896412467768557317","title":"Synaptic vesicle trafficking and GPCR endocytosis","description":"The top GO terms point to neuronal vesicle cycling and receptor trafficking, including clathrin-dependent endocytosis, synaptic vesicle budding, endosome organization, and GPCR internalization, with neuronal behavior terms (sound perception, locomotion) supporting a neural context. Cytoskeletal/cytoskeleton-related processes (Rho signaling) and mitochondrial fission may accompany these vesicle dynamics at synapses, suggesting a cohesive role in neuronal synaptic vesicle recycling and GPCR endocytosis.","confidence":"High","size":9,"edges":7,"triangles":0,"max_degree":4,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0000266","count":5},{"id":"GO:1901998","count":5},{"id":"GO:0007605","count":5},{"id":"GO:0072583","count":5}]},{"hash":"956697172756686269","title":"Organelle Protein Import and Respiratory Complex Assembly","description":"Based on the GO terms, the proteins cluster around targeting and import into mitochondria and chloroplasts (chloroplast stroma, mitochondrial matrix, inner membrane) and the assembly of respiratory chain components (e.g., complex IV) along with related regulation of mitochondrial translation. Although some terms are obsolete, the overarching theme is import machinery and assembly of organelle respiratory complexes, making this an intuitive label.","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0032094","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0030150","count":1}]},{"hash":"1190823979823083986","title":"Ubiquitin-regulated membrane trafficking in germline development","description":"The terms point to ubiquitin-related regulation (negative regulation of ubiquitination, ubiquitin-dependent endocytosis) together with membrane targeting and trafficking processes, tied to germline development events such as egg chamber formation and follicle cell dynamics. A few terms (sperm individualization) extend the theme to gametogenesis in general, suggesting a broader role for ubiquitin-mediated trafficking in reproductive development.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0030713","count":1},{"id":"GO:0031397","count":1},{"id":"GO:0007293","count":1},{"id":"GO:2000397","count":1}]},{"hash":"1701097155427200913","title":"Membrane Transport and Neural Signaling","description":"These proteins show several GO terms for membrane transport (pyruvate, antimonite, arsenite, sodium-dependent organic anion transport) alongside neural/synaptic terms (auditory receptor stereocilium organization, retrograde nitric oxide signaling, long-term synaptic depression). The shared thread appears to be membrane transport processes that enable or modulate neural signaling and synaptic regulation. Some terms are broader phenotypes (exploration behavior, ectopic germ cell programmed cell death) and may reflect downstream or context-specific roles. Overall, there is a plausible but not tight link between transport and neural signaling.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006849","count":1},{"id":"GO:0015699","count":1},{"id":"GO:0043251","count":1},{"id":"GO:0015700","count":1},{"id":"GO:0060088","count":1}]},{"hash":"1688350813395923853","title":"Unknown","description":"The GO terms are a mix of diverse processes from different organisms (hormone metabolism, bacterial LPS, plant sporopollenin and phylloquinone biosynthesis, melanin, antibiotic responses), with no unifying function or pathway linking the proteins. No coherent theme emerges to name the cluster.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0042376","count":1},{"id":"GO:0030435","count":1}]},{"hash":"2140101475043609771","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning lens development, rRNA processing, imprinting regulation, fungal cell wall biogenesis, microtubule movement, histone modification (obsolete terms), neural tube closure, homologous recombination repair, and TGF-beta signaling. This lack of a cohesive, shared function or pathway suggests no single theme tying the proteins together, beyond random annotation noise, so I label the cluster Unknown with low evidential support.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0070306","count":5},{"id":"GO:0000447","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0032995","count":5},{"id":"GO:0007018","count":5}]},{"hash":"1553657470346835491","title":"Unknown","description":"The top GO terms span DNA replication, telomere maintenance, cell cycle arrest, spindle dynamics, endocytosis, imprinting regulation, synaptic signaling, and NFAT pathway modulation, which are disparate processes. This lack of a single cohesive theme means a reliable, specific label cannot be assigned.","confidence":"","size":8,"edges":17,"triangles":20,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0032212","count":6},{"id":"GO:0000751","count":6},{"id":"GO:0030517","count":6},{"id":"GO:0072584","count":6}]},{"hash":"1466854378908532055","title":"SR Ca2+ Release and Signaling","description":"The cluster is dominated by terms tying to calcium ion handling via the sarcoplasmic reticulum and ryanodine receptor\u2013mediated calcium release (including regulation of RyR activity and SR Ca2+ release), plus a cellular calcium response and heart development context, suggesting a cohesive function in calcium signaling and SR calcium cycling.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0042994","count":2}]},{"hash":"1753679406090152979","title":"DNA DSB repair and meiotic recombination","description":"Most top terms cluster around DNA double-strand break processing and repair via homologous recombination, including meiotic DSB formation, indicating a genome maintenance/recombination theme. Some terms are unrelated or obsolete (peroxisome import, developmental terms) but the core signal is DNA repair and recombination.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043951","count":8},{"id":"GO:0010390","count":8},{"id":"GO:0000729","count":8},{"id":"GO:0016562","count":8},{"id":"GO:0042138","count":8}]},{"hash":"1939004641504258706","title":"Ribosome biogenesis and translation","description":"The top GO terms cluster around ribosome production and assembly: ribosome biogenesis, maturation of LSU-rRNA, and assembly of the large subunit precursor of the preribosome, plus translation. These indicate participation in ribosomal subunit processing/assembly and protein synthesis, with a few ancillary terms that are less central. Overall, the dominant signal is ribosome-related processes.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0031496","count":2}]},{"hash":"6520696320609293","title":"Translational initiation and mRNA regulation","description":"The top GO terms cluster around translation initiation and reinitiation (formation of translation preinitiation complex, translation reinitiation, regulation of translational initiation) and related mRNA stability and silencing processes (mRNA stabilization, miRNA-mediated gene silencing by inhibition of translation). Small-subunit processome assembly links to ribosome biogenesis, reinforcing a shared focus on ribosome production and use. While a few terms touch development or splicing, the dominant signal is translation control and post-transcriptional regulation.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:1902625","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0034462","count":3}]},{"hash":"1795970080307625768","title":"Transcription Regulation and RNA Modification","description":"Several terms point to transcription and RNA metabolism (DNA-templated transcription, negative regulation of transcription by RNA polymerase II, tRNA methylation, tRNA wobble uridine modification). A weaker signal for xenobiotic stress response and various biosynthetic processes suggests additional, indirect roles in stress and metabolism, but the strongest theme is transcription control and RNA processing.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0035690","count":3},{"id":"GO:0006744","count":2},{"id":"GO:0010189","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1984660402302383156","title":"Protein acetylation and amino acid metabolism","description":"The cluster is enriched for acetylation-related GO terms (spermidine acetylation, N-terminal peptidyl-glutamic acid acetylation, peptidyl-lysine N6-acetylation, histone H4 acetylation), indicating a common theme of acetyltransferase activity and protein modification. Associated metabolic processes such as arginine biosynthesis, putrescine catabolism, glucosamine metabolism, and mycothiol biosynthesis suggest linked amino-acid and cofactor metabolism, supporting a cohesive label around acetylation and related metabolism.","confidence":"High","size":8,"edges":23,"triangles":31,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":7},{"id":"GO:0009447","count":7},{"id":"GO:0006526","count":7},{"id":"GO:0018002","count":7},{"id":"GO:0006041","count":7}]},{"hash":"611263074840960972","title":"Mitochondrial translation and tRNA aminoacylation","description":"Based on the top GO terms, the cluster is dominated by translation and multiple mitochondrial tRNA aminoacylation processes (glycyl-, threonyl-, alanyl-, and selenocysteinyl-tRNA biosynthesis). This points to a cohesive function in mitochondrial protein synthesis and tRNA charging, with a few auxiliary terms (e.g., DNA biosynthesis, embryonic development) that are less central to the main theme. Overall, the data support a mitochondrion-centered translation/tRNA-aminoacylation role.","confidence":"High","size":8,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0015966","count":2},{"id":"GO:0071897","count":2},{"id":"GO:0097056","count":2},{"id":"GO:0070150","count":2}]},{"hash":"924792113803511771","title":"Nuclear DNA replication and RNA processing","description":"Dominant terms are DNA replication/recombination and RNA processing (prespliceosome assembly, RNA exon ligation, rRNA maturation), pointing to a nuclear complex coordinating genome duplication with ribonucleic acid maturation. The viral genome replication term is likely incidental.","confidence":"High","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006310","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0019079","count":6},{"id":"GO:0006306","count":5},{"id":"GO:0070417","count":5}]},{"hash":"644300790760127226","title":"Unknown","description":"The Top Terms are highly heterogeneous, spanning nuclear export regulation, synaptic localization, embryonic mesoderm formation, various metabolic regulations, and even plant hormone signaling, with no clear, shared function linking the proteins. The cluster has no edges, suggesting little direct interaction or a unifying pathway, so a single meaningful label cannot be determined.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0035418","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0006110","count":1},{"id":"GO:0009740","count":1}]},{"hash":"420790987068582082","title":"Ion and nutrient transmembrane transporters","description":"The set is dominated by transmembrane transport GO terms for ions (Na+, K+, phosphate, nitrate) and nutrients/vitamins (D-xylose, L-ascorbic acid), plus xenobiotic transport. An accompanying osmotic stress response term supports a role in osmoregulation via transporter activity. This combination suggests a cohesive cluster of membrane transport proteins.","confidence":"High","size":8,"edges":15,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":8},{"id":"GO:0006855","count":8},{"id":"GO:0006970","count":5},{"id":"GO:0015753","count":5},{"id":"GO:0035725","count":5}]},{"hash":"1829820872503789268","title":"Unknown","description":"Top GO terms are highly diverse, spanning proteolysis and ubiquitin-dependent protein turnover, glutathione metabolism, lens fiber differentiation, rRNA processing, microtubule-based movement, and fungal cell wall regulation. This broad mix indicates no cohesive functional module or shared pathway, so a specific, representative label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901750","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0006751","count":1},{"id":"GO:0006750","count":1},{"id":"GO:0070306","count":1}]},{"hash":"269866149949771280","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0007190","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0007409","count":2}]},{"hash":"1867950669396818378","title":"Developmental differentiation and chromatin regulation","description":"The terms point to developmental processes (lens fiber differentiation, neural tube closure, TGF-beta response) and chromatin/gene expression regulation (histone acetylation/methylation, imprinting-related regulation, DNA repair). Some other GO terms like rRNA processing or fungal cell wall biogenesis seem less connected and may reflect annotation noise or broader functional links. Overall, a theme around development and epigenetic regulation best fits the cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0070306","count":5},{"id":"GO:0000447","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0032995","count":5},{"id":"GO:0007018","count":5}]},{"hash":"2094459479566225477","title":"Auditory synapse formation and cochlear morphogenesis","description":"The terms cluster around cochlear development (cochlea morphogenesis, stereocilium organization) and synaptic signaling/plasticity (glutamate secretion, long-term synaptic depression, dendritic spine morphogenesis, nitric oxide retrograde signaling, protein dephosphorylation), suggesting a module dedicated to maturation and function of auditory synapses. Some unrelated terms exist (e.g., opsonization), but the core theme is auditory structure development and synaptic signaling. ","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":3},{"id":"GO:0098924","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0035640","count":3},{"id":"GO:0060292","count":3}]},{"hash":"1434951203623238157","title":"DNA-templated transcription","description":"The cluster centers on DNA-templated transcription (GO:0006351) with several proteins annotated to transcription, suggesting a transcription-related group; the presence of several obsolete or diverse metabolic terms likely reflects annotation noise rather than a coherent metabolic module. ","confidence":"Medium","size":8,"edges":14,"triangles":12,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0033512","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0018272","count":2},{"id":"GO:0034276","count":2}]},{"hash":"1492625330521294836","title":"Translational initiation and mRNA processing","description":"The top GO terms cluster around translation initiation and preinitiation complex formation, ribosome biogenesis (small-subunit processome), miRNA-mediated translational repression, and RNA processing/splicing regulation, plus mRNA stabilization. This indicates a post-transcriptional gene expression module focused on controlling translation and RNA maturation rather than a single pathway.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0001825","count":2}]},{"hash":"1679339873113877704","title":"Mitochondrial translation and ribosome biogenesis","description":"This cluster is dominated by GO terms for translation and its regulation, plus rRNA maturation and transcription antitermination, collectively pointing to ribosome assembly and protein synthesis in mitochondria. Supporting terms like cristae formation and ATP synthesis driven by proton motive force further emphasize a mitochondrial context, particularly inner-membrane organization and energy production. Some outliers (response to virus, cell cycle regulation) are less representative but do not negate the core mitochondria-focused function.","confidence":"High","size":8,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045787","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0009615","count":1},{"id":"GO:0099132","count":1}]},{"hash":"1906171878856326669","title":"Nuclear DNA transcription and replication regulation","description":"The dominant GO terms are DNA-templated transcription and DNA replication, with additional signals pointing to genome maintenance (telomere maintenance via telomerase) and cell-cycle related processes (mitotic arrest, spindle attachment). While other terms touch on endocytosis and neuronal development, the strongest and most consistent theme across terms is nuclear genome expression and replication regulation, justifying this label. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0071469","count":4},{"id":"GO:0046641","count":4}]},{"hash":"1763786753743722331","title":"Regulators of cell proliferation and morphogenesis","description":"The GO terms cluster around controlling growth and development\u2014negative regulation of Wnt signaling and cell proliferation, positive regulation of apoptosis, and processes like cell migration and morphogenesis\u2014along with DNA replication and telomere maintenance, which tie to genome integrity during division. Although a cocaine-response term appears, the dominant pattern is growth/shape control and developmental regulation rather than a single pathway, making this label representative of the cluster\u2019s function.","confidence":"Medium","size":8,"edges":13,"triangles":8,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090090","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0000902","count":3}]},{"hash":"1917983529704199970","title":"Gram-negative cell envelope biosynthesis","description":"This cluster is dominated by GO terms for cell wall and outer membrane assembly in Gram-negative bacteria, notably lipopolysaccharide (LPS) and O-antigen biosynthesis and cell wall organization. Additional terms for amino acid catabolism and proteolysis appear less cohesive, but the envelope biosynthesis signal is the strongest.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":4},{"id":"GO:0031564","count":4},{"id":"GO:0071555","count":2},{"id":"GO:0009243","count":2},{"id":"GO:0009103","count":2}]},{"hash":"2111319625202542605","title":"Post-transcriptional RNA processing and translation control","description":"The terms point to RNA metabolism and post-transcriptional regulation: regulation of translational initiation, preinitiation complex formation, small-subunit processome assembly, spliceosome-related splicing regulation, miRNA-mediated translation inhibition, and mRNA stabilization. This suggests a cohesive theme around RNA processing and control of translation, spanning both nuclear RNA processing and cytoplasmic translation regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0001825","count":1}]},{"hash":"1673602427905594156","title":"Unknown","description":"These proteins carry GO terms from both bacterial cell wall biosynthesis and antigen production, retinoid/retinal metabolism, and several vertebrate developmental processes (heart morphogenesis, hindbrain, pituitary, and optic cup morphogenesis). The terms do not reveal a single cohesive function or pathway linking all members, so a clear, representative label cannot be inferred. ","confidence":"","size":8,"edges":12,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0042572","count":2},{"id":"GO:0042574","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009246","count":2}]},{"hash":"1829719589816418844","title":"Chromatin and rRNA methyltransferases","description":"The cluster\u2019s top terms center on methylation activities: rRNA methylation, rDNA heterochromatin formation, and various protein methylations (N-terminal glycine, lysine methylations). This points to enzymes that modify chromatin state and ribosomal RNA, impacting transcription and gene expression. Additional developmental GO terms likely reflect broader regulatory roles rather than a separate function of the cluster. Overall, a cohesive theme is chromatin- and RNA-modifying enzymes.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0018023","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0031167","count":2}]},{"hash":"2064577775365964846","title":"Viral translation initiation and reinitiation","description":"The predominant GO terms cluster around regulation and formation of the translation preinitiation complex, translation initiation and reinitiation, including IRES-dependent viral initiation, indicating a shared role in controlling translation, especially in viral contexts. Other terms (mRNA splicing, transcription regulation) appear less central to the cluster\u2019s main signal.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0075522","count":2}]},{"hash":"2256690974597077046","title":"Unknown","description":"Top GO terms span DNA replication, development, proteasomal regulation, and diverse cellular stress responses (to LPS, virus, ionomycin, arsenite) as well as telomere maintenance. There is no single coherent function tying these eight proteins together, and the lack of interactions further supports an absence of a clear theme. Therefore, Unknown with None.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0032435","count":4},{"id":"GO:0071222","count":4},{"id":"GO:0098586","count":4}]},{"hash":"1995956243863638901","title":"Renal water balance and urine regulation","description":"The cluster shows strong kidney/urinary system signals: GO terms like response to water deprivation, regulation of urine volume, and inner medullary collecting duct development suggest a shared role in renal water handling and urine concentration. While other terms (e.g., certain metabolic processes) appear, they are less cohesive with this central renal theme, supporting a label focused on renal water balance.","confidence":"High","size":8,"edges":13,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":3},{"id":"GO:0019853","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0018931","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1241231411279781718","title":"Kidney water handling and urine regulation","description":"The top GO terms cluster around renal physiology\u2014regulation of urine volume, response to water deprivation, and inner medullary collecting duct development\u2014supporting a focus on kidney water balance and collecting duct function. Some terms (like cholesterol catabolic and retinoic acid-related processes) seem peripheral or incidental, indicating possible broader metabolic roles or annotation noise within the cluster.","confidence":"Medium","size":8,"edges":19,"triangles":23,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":5},{"id":"GO:0019853","count":4},{"id":"GO:0008209","count":4},{"id":"GO:0018931","count":4},{"id":"GO:0055114","count":4}]},{"hash":"313604429667563312","title":"Glycolysis and Gluconeogenesis","description":"The cluster is dominated by terms tied to central carbohydrate metabolism, especially glycolysis and gluconeogenesis, including canonical glycolysis, gluconeogenesis, and fructose-related catabolic/metabolic processes. Although there are some stress- and signaling-related terms (response to hydrogen peroxide, antibiotic response, growth hormone response), the strongest signals are on energy metabolism and fructose-based pathways, with regulatory processes like ATP-dependent activity and potential enzyme oligomerization supporting metabolic control.","confidence":"High","size":8,"edges":9,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0060416","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0051289","count":2}]},{"hash":"834193908977625180","title":"Chromatin regulation and transcription control","description":"Dominant themes are chromatin state regulation and transcription control: heterochromatin formation/maintenance, nucleosome density, and histone deacetylation, with DNA-templated transcription; metabolic terms likely reflect broader cellular coupling rather than core function.","confidence":"High","size":8,"edges":23,"triangles":30,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2000648","count":4},{"id":"GO:0060303","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0034983","count":3}]},{"hash":"1194064305989483998","title":"RNA processing and translation initiation","description":"The GO terms cluster around RNA metabolism and control of gene expression at the level of RNA processing and translation: regulation of translational initiation, formation of the translation preinitiation complex, small-subunit processome assembly, mRNA splicing regulation, miRNA-mediated inhibition of translation, and mRNA stabilization. Collectively these point to RNA processing and translation control as the core theme. A single term about chromosome segregation is less related and may reflect a multifunctional protein or annotation noise. Overall, the cluster represents RNA processing and translation regulation.","confidence":"High","size":8,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007059","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0034462","count":2}]},{"hash":"2160078516550806583","title":"Actin Cytoskeleton Remodeling in Immune Signaling","description":"This cluster is dominated by GO terms for actin cytoskeleton organization, lamellipodium assembly, and Rho GTPase activation, plus microtubule-based movement, pointing to dynamic cytoskeletal remodeling. The presence of immune-related terms such as antigen receptor-mediated signaling, B cell homeostasis, and NK T cell differentiation suggests these actin-regulatory proteins function within immune cell activation contexts. Some terms (sensory perception of sound, ceramide transport) are less directly connected and may reflect broader cellular roles or annotation noise, but the core theme centers on actin dynamics coordinating signaling in immune cells.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0007018","count":1}]},{"hash":"1253677550558899232","title":"Proteostasis and Unfolded Protein Response","description":"The GO terms are dominated by protein folding/refolding, misfolded protein transport, and response to unfolded protein, along with chaperone-related activities and protein maturation processes, pointing to a proteostasis/quality-control theme. A few peripheral terms (tRNA import, developmental signaling) exist but do not override the central proteostasis signal.","confidence":"Medium","size":8,"edges":20,"triangles":30,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0035719","count":6},{"id":"GO:1901621","count":6},{"id":"GO:0051259","count":6}]},{"hash":"69066192561429637","title":"Secretory vesicle trafficking","description":"The terms cluster around secretory pathways (pancreatic juice and saliva secretion; secretory granule organization) and vesicle/endo-lysosomal functions (endosomal lumen acidification), with additional signals related to sensory development (retinoic acid response, visual perception) and nephrogenesis (metanephric kidney development). This suggests a group of proteins involved in secretory/vesicular trafficking, with broader developmental signaling links.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":2},{"id":"GO:0048388","count":1},{"id":"GO:0072239","count":1},{"id":"GO:0030157","count":1},{"id":"GO:0007601","count":1}]},{"hash":"473837443665404705","title":"Steroid receptor signaling and chaperone activity","description":"The top GO terms center on steroid hormone receptor complex assembly and prostate/male differentiation, pointing to steroid signaling. Additional terms like protein refolding and cellular response to hydrogen peroxide suggest chaperone-mediated protein folding involved in receptor maturation. Some heart development terms are plausible downstream effects of steroid signaling, which supports a cohesive theme despite the absence of network edges.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":4},{"id":"GO:0046661","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0033197","count":3}]},{"hash":"247024737692449048","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0070129","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0010019","count":1}]},{"hash":"1038538260109522147","title":"Wnt-regulated morphogenesis and craniofacial development","description":"The top GO terms cluster around developmental morphogenesis and Wnt pathway regulation (negative regulation of canonical Wnt signaling; cranial skeletal system development; dorsal identity; renal vesicle formation). Also includes adherens junction assembly and cell migration, indicating roles in cell adhesion and movement during tissue shaping. Together these suggest a theme of Wnt-guided morphogenesis, particularly in craniofacial and related organ development.","confidence":"High","size":8,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":5},{"id":"GO:0043065","count":5},{"id":"GO:0008285","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0090090","count":5}]},{"hash":"967656917906467949","title":"DNA replication and RNA processing","description":"This cluster centers on nucleic acid metabolism: multiple GO terms point to DNA replication and related processes (unwinding, replication, and chromatin-associated steps) alongside diverse RNA processing activities (prespliceosome assembly, RNA exon ligation, rRNA maturation, and nuclear RNA decay). A few terms like cellular response to cold or viral genome replication may be incidental noise, but the core theme is nuclear nucleic acid metabolism and processing.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0006306","count":2},{"id":"GO:0070417","count":2},{"id":"GO:1903241","count":2}]},{"hash":"190726549006644156","title":"DNA-Templated Transcription Regulation","description":"These proteins are mainly linked to DNA-templated transcription and its regulation, indicating a nuclear transcription regulatory function. With equal representation of the transcription and regulation terms (GO:0006351 and GO:0006355) and only a minor, non-defining RNA decay term, the cluster appears to group transcription regulators rather than RNA processing or other pathways.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0000184","count":1},{"id":"GO:0032508","count":1}]},{"hash":"1535161802771018885","title":"Plant hormone signaling and stress response","description":"The top GO terms include cytokinin-activated signaling (plant hormone), ubiquitin-dependent protein turnover, chromatin remodeling, innate immune response, defense regulation, and photosynthesis. This pattern suggests a cluster anchored in plant hormone signaling (cytokinin) with links to protein turnover, chromatin regulation, and defense/stress responses, even though some terms may reflect annotation noise. Overall, a coherent theme around plant signaling and stress responses best fits the set.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0045087","count":2}]},{"hash":"2211856685029930309","title":"Neuronal Spine Morphogenesis and Rac Signaling","description":"This cluster is driven by terms related to dendritic spine development and morphogenesis, Rac-mediated signal transduction, and actin-driven structures like lamellipodia and filopodia (ruffle assembly), with hippocampus development indicating neuronal context. While there are a couple of cell cycle terms present, the strongest theme is neuronal cytoskeleton remodeling and spine formation governed by Rac signaling.","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045792","count":4},{"id":"GO:0090307","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0060999","count":3},{"id":"GO:0016601","count":3}]},{"hash":"1642274086961403218","title":"Ribosome biogenesis via rRNA and tRNA methylation","description":"This cluster is characterized by RNA methylation processes linked to ribosome assembly: tRNA methylation, rRNA guanine-N7 methylation, and maturation of SSU and LSU rRNA, with an additional methylation-related activity (peptidyl-glutamine methylation). The presence of innate immune terms appears incidental. The dominant pattern points to ribosome biogenesis driven by RNA modification.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0030490","count":1},{"id":"GO:0000470","count":1},{"id":"GO:0018364","count":1}]},{"hash":"886828075230207062","title":"Proteasome-ubiquitin\u2013mediated antigen processing","description":"The cluster centers on proteasome core assembly and ubiquitin-dependent protein degradation, which underpin peptide generation for MHC class I antigen presentation (TAP-dependent). The presence of SCF ubiquitination, deubiquitination, and related immune signaling terms (T cell and Fc receptor pathways) supports a cohesive theme of proteasome- and ubiquitin-mediated antigen processing and immune activation.","confidence":"High","size":8,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":3},{"id":"GO:0002479","count":3},{"id":"GO:0016579","count":3},{"id":"GO:0080129","count":3},{"id":"GO:0038095","count":3}]},{"hash":"1012475620697861792","title":"Renal and craniofacial morphogenesis","description":"The top GO terms point to kidney development (renal vesicle formation, metanephros morphogenesis) and craniofacial skeletal development, complemented by adherens junction assembly and EMT/Wnt signaling aspects. This suggests a cohesive developmental/morphogenesis module focusing on organ formation and epithelial organization in renal and craniofacial contexts, rather than a single metabolic or signaling pathway.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0044336","count":6},{"id":"GO:1904888","count":6},{"id":"GO:2000017","count":6},{"id":"GO:0034333","count":6},{"id":"GO:0072033","count":6}]},{"hash":"287712115737213778","title":"DNA Double-Strand Break Repair and Recombination","description":"This cluster is dominated by GO terms for DNA double-strand break processing and homologous recombination repair, including meiotic DSB formation and repair via HR. While there are a few peripheral terms related to development or peroxisomal processes, the strongest signal is DNA damage response and recombination, justifying the DSB repair/recombination label.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043951","count":8},{"id":"GO:0010390","count":8},{"id":"GO:0000729","count":8},{"id":"GO:0016562","count":8},{"id":"GO:0042138","count":8}]},{"hash":"130779027187188562","title":"Unknown","description":"The top GO terms are highly diverse, including chromosome segregation and meiosis, telomerase assembly, immune-related processes, metabolism, placenta development, and sensory detection, with no single coherent theme linking all proteins. Confidence: None","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001890","count":2},{"id":"GO:0007059","count":2},{"id":"GO:0071353","count":1},{"id":"GO:0033160","count":1},{"id":"GO:0016446","count":1}]},{"hash":"1669129460909644513","title":"DNA Damage Repair and Stress Response","description":"The top GO terms point to genome maintenance (base-excision repair, DNA recombination, DNA alkylation repair) and responses to various stimuli (xenobiotic, light, estradiol), suggesting a theme of DNA repair coupled with environmental signaling. While terms like cell wall organization and mucilage biosynthesis appear, they are less central to the main signal and may reflect plant-specific regulatory contexts co-occurring with stress responses. Overall, the cluster seems best described by DNA repair and stress-response functions.","confidence":"Medium","size":8,"edges":13,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0007114","count":2}]},{"hash":"391538116341577953","title":"Methylation enzymes and cofactor biosynthesis","description":"Based on the frequent methylation-related GO terms (rRNA methylation, rRNA modification, various protein methylations) and multiple biosynthetic processes for cofactors (biotin, cobalamin, menaquinone) as well as antibiotic biosynthesis, the cluster appears to group methyltransferases linked to biosynthetic pathways in bacteria.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0018027","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0009234","count":2}]},{"hash":"1655814847000164851","title":"RNA Pol II Transcription Regulation and Chromatin Remodeling","description":"The top GO terms are centered on DNA-templated transcription and regulation of RNA polymerase II promoter activity, with chromatin remodeling frequently implicated. While some metabolism-related or obsolete terms appear, the consistent theme is transcriptional control linked to chromatin state, justifying a label focused on transcription regulation and chromatin remodeling.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0035969","count":2},{"id":"GO:1904741","count":2},{"id":"GO:0061429","count":2}]},{"hash":"506680112429914974","title":"Synaptic vesicle maturation and transmission","description":"This cluster is dominated by GO terms related to synaptic vesicle maturation, presynaptic signaling, vesicle fusion, and glutamatergic transmission, pointing to a neuronal synaptic function and vesicle trafficking theme. Some terms (tRNA processing, B cell signaling, myoblast fusion, cortical migration) appear as outliers, but the core signal centers on synaptic vesicle dynamics and neurotransmission, supporting a neuronal/synaptic label. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016188","count":2},{"id":"GO:0099526","count":2},{"id":"GO:0031340","count":2},{"id":"GO:2000235","count":2},{"id":"GO:0050861","count":2}]},{"hash":"3520104479142269","title":"Chromatin Remodeling and RNA Processing Regulation","description":"This cluster centers on nuclear processes such as chromatin remodeling, snoRNA localization/assembly, histone deacetylation regulation, and regulation of tRNA processing, pointing to chromatin state control and RNA processing as the core theme. Some terms related to cell motility or morphogenesis appear peripheral and may reflect broader regulatory contexts, but the primary signal is chromatin and RNA processing regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0031063","count":1},{"id":"GO:0000492","count":1},{"id":"GO:2000235","count":1}]},{"hash":"620540064389599485","title":"Craniofacial and ectodermal development","description":"Most terms converge on craniofacial and ectodermal development, including cranial ganglion and skeletal formation, along with Wnt signaling\u2013related dorsal identity and junction/morphogenesis processes. This suggests a coherent developmental module governing craniofacial patterning and tissue morphogenesis, possibly regulated by Wnt signaling and cell adhesion.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0061550","count":5},{"id":"GO:0044336","count":5},{"id":"GO:1904888","count":5},{"id":"GO:2000017","count":5},{"id":"GO:0071255","count":5}]},{"hash":"1083724530881509","title":"Rab-regulated autophagy and phagosome maturation","description":"The terms cluster around Rab signaling and autophagy-related processes, including phagophore assembly, phagosome-lysosome fusion, and phagosome acidification, pointing to a role in membrane trafficking and autophagic degradation. Some peripheral terms (auditory receptor morphogenesis, spindle-kinetochore regulation) are less connected to the core theme but don\u2019t override the dominant Rab/autophagy signal.","confidence":"High","size":8,"edges":8,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032482","count":8},{"id":"GO:0018125","count":8},{"id":"GO:0034497","count":8},{"id":"GO:0002093","count":8},{"id":"GO:0043497","count":8}]},{"hash":"1829105553661921173","title":"Cardiac Electrophysiology and Vascular Tone","description":"Dominant terms focus on heart muscle action potential generation and membrane repolarization, ventricular electrical activity, and vasoconstriction, complemented by aldosterone biosynthesis which influences blood pressure and autonomic signaling via GPCR pathways. While a few terms touch on mechanosensation and metabolism (diet-induced thermogenesis), the overarching theme centers on cardiac excitability and vascular regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050976","count":3},{"id":"GO:0098914","count":3},{"id":"GO:0007216","count":2},{"id":"GO:0002024","count":2},{"id":"GO:0032342","count":2}]},{"hash":"708318261371897517","title":"Cardiac signaling and electrophysiology","description":"This cluster centers on cardiac muscle function and blood pressure regulation: ventricular action potentials, membrane repolarization, vasoconstriction, vasopressin secretion, and aldosterone biosynthesis, plus hypertrophy in response to stress. A neuronal GPCR term appears but the dominant theme is heart-related signaling and electrophysiology, suggesting a cohesive cardiovascular cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007216","count":3},{"id":"GO:0002024","count":3},{"id":"GO:0032342","count":3},{"id":"GO:0086002","count":3},{"id":"GO:0071651","count":3}]},{"hash":"359455616218791371","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042774","count":1},{"id":"GO:0033617","count":1},{"id":"GO:1902600","count":1},{"id":"GO:2000344","count":1},{"id":"GO:0007283","count":1}]},{"hash":"552113461459128954","title":"Cardiac Electrophysiology and Vascular Regulation","description":"This cluster centers on terms describing cardiac muscle cell action potentials, membrane repolarization, vasoconstriction, and hormonal influences on vascular tone (vasopressin and aldosterone biosynthesis). These together point to cardiovascular electrical activity and regulation of blood pressure and flow. While there are a few less central terms (protein homooligomerization, GPCR signaling, diet-induced thermogenesis), the dominant theme is heart electrophysiology coupled with vascular/hormonal regulation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0007216","count":1},{"id":"GO:0002024","count":1},{"id":"GO:0032342","count":1},{"id":"GO:0086002","count":1}]},{"hash":"1582903012544615171","title":"Unknown","description":"The GO terms span a mix of catabolic metabolism for sugars and acids, lipid biosynthesis, basic central carbon metabolism, and even a GPCR signaling pathway, with no single clear function tying all eight proteins together. Because there is no coherent, shared biological process dominating the cluster, I label it Unknown with no confidence in a representative function.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042838","count":1},{"id":"GO:0043427","count":1},{"id":"GO:0046392","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0006107","count":1}]},{"hash":"678968846515701215","title":"DNA Repair and Damage Response","description":"These eight proteins are linked by terms in nucleotide-excision repair, DNA damage recognition, base-excision repair, UV-damage excision, and DNA damage\u2013triggered apoptotic signaling, indicating a cohesive DNA repair and damage-response module. An outlier term for organism growth is present but does not alter the main theme.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000715","count":1},{"id":"GO:1901255","count":1},{"id":"GO:0008630","count":1},{"id":"GO:0006284","count":1},{"id":"GO:0035264","count":1}]},{"hash":"527864415465761999","title":"DNA-Templated Transcription Regulation","description":"The top GO terms are dominated by DNA-templated transcription and its regulation, indicating the cluster centers on transcriptional control. While there are some secondary plant-specific and stress/viral process terms present, the core signal remains transcription regulation.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:1901348","count":2},{"id":"GO:1905778","count":2},{"id":"GO:0035066","count":2}]},{"hash":"1575438157512724634","title":"Brain development and autophagy regulation","description":"The top GO terms show a tilt toward brain development, with additional signals for autophagy and mitophagy regulation, plus stress-responsive processes (DNA damage signaling and xenobiotic response). This pattern points to neural-development-related proteins that are also involved in cellular quality control and stress responses. The metabolism-related terms are less cohesive but may reflect broader cellular state. Overall, the most representative theme is neural development coupled with autophagy/mitophagy regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0010666","count":1},{"id":"GO:0043456","count":1}]},{"hash":"1426689884587055711","title":"ECM Organization and Skin/Basement Membrane Development","description":"This cluster centers on extracellular matrix organization and tissue development (skin, basement membranes, collagen fibril organization, cuticle development, and related ECM remodeling through ossification and catabolic processes), with kidney ECM context as additional support.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043588","count":2},{"id":"GO:0001957","count":1},{"id":"GO:0045650","count":1},{"id":"GO:2000860","count":1},{"id":"GO:0032836","count":1}]},{"hash":"2187566751377728184","title":"Cell Cycle Regulation & DNA Replication","description":"The top terms cluster around DNA replication and cell cycle control (DNA replication, G1 arrest in response to pheromone, spindle attachment in meiosis I), with telomere maintenance also linked to genome integrity. Although there are a few immune or trafficking terms present, the strongest and most coherent signal is coordination of genome duplication and cell cycle progression, justifying a cell cycle\u2013focused label.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0071469","count":2},{"id":"GO:0046641","count":2},{"id":"GO:0000751","count":2}]},{"hash":"2077728621819287170","title":"Retroviral life cycle","description":"Top GO terms point to stages of retroviral replication and assembly: virion assembly, fusion of viral membrane with the host, and establishment of proviral latency, as well as RNA-templated DNA biosynthesis (reverse transcription) and genome activation within the host. While some terms (protein folding, isomerization) reflect general cellular processes, the collection overall suggests a retroviral lifecycle theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0006278","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0075713","count":1}]},{"hash":"910078193978353397","title":"DNA Damage Response and Gene Expression Regulation","description":"These proteins co-represent a network centered on responding to DNA damage (SOS response), coordinating DNA-templated transcription, replication, and recombination, and coupling transcription with RNA processing steps such as mRNA export and splicing. The presence of ncRNA-mediated silencing and spliceosome-related regulation suggests additional post-transcriptional control, all consistent with a cluster that links DNA damage response to transcriptional and RNA-processing regulation. Autophagosome maturation and viral genome replication appear as peripheral terms, indicating broader stress-related roles but not dominant drivers of the core function.","confidence":"High","size":7,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0006260","count":2}]},{"hash":"673921301665022465","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000627","count":2},{"id":"GO:0097222","count":2},{"id":"GO:0010323","count":2},{"id":"GO:0016120","count":2},{"id":"GO:0045716","count":1}]},{"hash":"179568148892436791","title":"Translation initiation and tRNA charging","description":"The terms cluster around tRNA aminoacylation (arginyl and glycyl), translation initiation and preinitiation complex formation, and related ribosome biogenesis processes (small-subunit processome assembly). This suggests a cohesive theme centered on assembling and regulating the protein synthesis machinery, with a few outliers likely representing noise. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006420","count":2},{"id":"GO:0006426","count":2},{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1}]},{"hash":"323967411149240367","title":"Glutathione Detoxification and Ubiquitination-Driven Proteostasis","description":"The cluster centers on detox pathways (oxidant detoxification, glutathione metabolism, xenobiotic catabolism) and protein-quality-control processes (ubiquitination, sumoylation, autoubiquitination, and ERAD), suggesting a coordinated module for detoxification coupled with proteostasis via ubiquitin-related modifications. Minor terms like placenta morphogenesis and viral replication regulation are less central to the core theme.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0042178","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0016925","count":2}]},{"hash":"1586528485055639080","title":"Unknown","description":"The terms span telomere maintenance, pH response, immune cell proliferation/differentiation, cell cycle arrest, axon guidance, endocytosis, genomic imprinting, meiosis spindle attachment, and development (vagina), with no clear shared pathway or function linking them, so a cohesive label isn\u2019t interpretable.","confidence":"","size":7,"edges":16,"triangles":17,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":7},{"id":"GO:0071469","count":7},{"id":"GO:0046641","count":7},{"id":"GO:0000751","count":7},{"id":"GO:0030517","count":7}]},{"hash":"2033908012885649214","title":"Ribosome biogenesis and translation quality control","description":"This cluster is dominated by GO terms for translation (initiation, termination, general translation) and RNA surveillance pathways (no-go decay, nonstop decay), plus maturation of rRNA for ribosome assembly, suggesting a cohesive function in ribosome biogenesis and translation quality control.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":2},{"id":"GO:0071025","count":1},{"id":"GO:0070966","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0006415","count":1}]},{"hash":"2218275561599150060","title":"Bacterial ribosome biogenesis and SRP targeting","description":"This cluster is dominated by terms tied to protein synthesis and ribosome assembly (GO:0042254 ribosome biogenesis; GO:0051301 cell division) and to SRP-dependent cotranslational targeting to membranes (GO:0006614 and GO:0006616), suggesting a core theme of ribosome-associated translation and protein targeting to the membrane. Additional terms like lipopolysaccharide biosynthesis and flagellum organization point to bacterial envelope and motility components, but the strongest, recurrent signals center on translation machinery and membrane-associated targeting, supporting a label focused on ribosome biogenesis and SRP-mediated targeting in bacteria.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0044781","count":1},{"id":"GO:0007165","count":1}]},{"hash":"1223560225786749402","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006306","count":5},{"id":"GO:0070417","count":5},{"id":"GO:1903241","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0000378","count":5}]},{"hash":"819615655720775589","title":"Large subunit ribosome biogenesis and export","description":"The key terms converge on ribosome biogenesis, specifically the large subunit: LSU assembly, rRNA maturation, preribosome formation, and export of the LSU from the nucleus. A couple of unrelated terms (lipopolysaccharide biosynthesis, ER targeting) seem incidental noise. Overall, the cluster likely comprises proteins involved in large subunit ribosome biogenesis and export.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000027","count":1},{"id":"GO:0000463","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000466","count":1}]},{"hash":"1583790810271837545","title":"Post-transcriptional Regulation of Gene Expression","description":"The proteins cluster shows enrichment for translation initiation control (formation of translation preinitiation complex, regulation of translational initiation), RNA processing/spliceosome activity (small-subunit processome assembly, regulation of alternative splicing, spliceosome-related terms), and post-transcriptional mechanisms (miRNA-mediated translation inhibition, mRNA stabilization). This points to a cohesive theme of post-transcriptional gene expression regulation, despite a couple of unrelated terms appearing in the set.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0001825","count":2}]},{"hash":"774752327849985045","title":"Unknown","description":"These GO terms span telomere maintenance, pH response, T cell proliferation, cell cycle arrest, axon extension regulation, endocytosis, imprinting regulation, meiosis kinetochore attachment, NK T cell differentiation, and vaginal development. The set lacks a clear, dominant shared function or pathway across most proteins, so a specific, informative label cannot be assigned.","confidence":"","size":7,"edges":7,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":6},{"id":"GO:0071469","count":6},{"id":"GO:0046641","count":6},{"id":"GO:0000751","count":6},{"id":"GO:0030517","count":6}]},{"hash":"1714125933446179807","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0000028","count":1},{"id":"GO:0006407","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0042254","count":1}]},{"hash":"2037205645684508235","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":15,"triangles":13,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006306","count":4},{"id":"GO:0070417","count":4},{"id":"GO:1903241","count":4},{"id":"GO:0006268","count":4},{"id":"GO:0000378","count":4}]},{"hash":"1210539357966039163","title":"Developmental morphogenesis and ECM signaling","description":"The top GO terms cluster around developmental processes: positive regulation of osteoblast differentiation, central nervous system development, branching morphogenesis of epithelial tubes, and cellular response to cell-matrix adhesion, pointing to tissue formation and ECM interactions. Additional terms like regulation of calcium-release channel activity, response to ethanol, and platelet aggregation suggest broader signaling contexts, but the developmental and ECM-morphogenesis theme remains central.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045669","count":3},{"id":"GO:0007417","count":2},{"id":"GO:0071638","count":2},{"id":"GO:0071460","count":2},{"id":"GO:0048754","count":2}]},{"hash":"2290124289039069824","title":"Plant cell cycle and DNA replication machinery","description":"The top GO terms cluster around MCM complex assembly, pre-replicative complex assembly, and DNA replication initiation, along with cell cycle-related terms, pointing to core replication machinery and cell-cycle control in plants. Some terms about root meristem growth and photosynthesis reflect plant context, but the dominant theme is replication initiation and cell-cycle progression in a plant setting.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0072689","count":6},{"id":"GO:0010082","count":6},{"id":"GO:1902450","count":6},{"id":"GO:1902975","count":6},{"id":"GO:0015979","count":6}]},{"hash":"164802452041138477","title":"DNA replication and damage response","description":"The cluster centers on genome maintenance during replication and stress, highlighted by DNA unwinding, primer synthesis, topological changes, and DNA damage tolerance, with SOS-like signaling and transcriptional regulation by RNA Pol II. Additional RNA processing terms (mRNA decay, snoRNA release) suggest broader RNA quality control linked to genome integrity.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000184","count":6},{"id":"GO:0006306","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0045944","count":5}]},{"hash":"1192487569883746054","title":"Ribosome Biogenesis and Translation","description":"Dominant terms are translation and ribosome-related processes (translation, cytoplasmic translation, ribosome biogenesis, ribosomal large subunit export). This suggests the cluster mainly comprises proteins involved in ribosome assembly and protein synthesis; a few unrelated terms appear as minor associations.","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006400","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0055072","count":1}]},{"hash":"2201283273583582659","title":"Nuclear gene expression regulation","description":"The top GO terms together point to regulation of transcription (DNA-templated transcription, transcription-coupled repair, negative regulation of RNA Pol II) and regulation of translation initiation (formation of translation preinitiation complex, translational termination-reinitiation), with additional hints at chromatin regulation and protein turnover/deneddylation. This suggests the proteins function as regulators of gene expression in the nucleus, spanning transcription, chromatin context, and post-translational control, rather than a single linear pathway. Given the diverse but related roles, the label captures a cohesive theme without overfitting to a single process.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071033","count":1},{"id":"GO:0090052","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0032436","count":1}]},{"hash":"1000387506484370460","title":"Proteostasis and translation regulation","description":"The cluster centers on protein homeostasis and quality control: regulation of translation initiation and preinitiation complex formation, proteasome-mediated degradation, unfolded protein response regulation, and related post-translational processing and storage of proteasomes. Additional terms about oxidative stress and mitochondrial fission align with general stress responses, reinforcing a proteostasis-focused theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032364","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0043161","count":1}]},{"hash":"591130090353096239","title":"Transcription by RNA Pol I-III and Ribosome Biogenesis","description":"This cluster centers on core transcriptional machinery across RNA polymerases I, II, and III (including Pol III transcription elongation and termination, tRNA transcription, and RNA-templated transcription) and on ribosome biogenesis, suggesting a common role in RNA synthesis and ribosome assembly. A few unrelated terms appear at low frequency, but the dominant theme is transcription and ribosome production, justifying this label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006385","count":1},{"id":"GO:0006386","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0006366","count":1}]},{"hash":"1251637684500810845","title":"Translational Initiation Regulation","description":"This cluster is best described by a central theme of regulation of protein synthesis initiation, as evidenced by GO:0006446 (regulation of translational initiation) and GO:0002183 (cytoplasmic translational initiation) among the top terms. Additional terms hint at linked signaling and stress responses (positive regulation of GTPase activity, cellular response to nitric oxide, and amino acid starvation), which often accompany translation control. Some obsolete terms are present, but the core theme points to modulation of translation initiation and related cellular responses.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060358","count":2},{"id":"GO:0043547","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0071732","count":1},{"id":"GO:0006446","count":1}]},{"hash":"327568714506188535","title":"RNA processing and translation regulation","description":"This cluster is dominated by terms related to translation initiation and ribosome biogenesis (regulation of translational initiation, formation of translation preinitiation complex, small-subunit processome assembly) plus RNA processing and silencing (negative regulation of mRNA splicing via spliceosome, miRNA-mediated gene silencing by inhibition of translation). Some outlier terms reference development (brown fat cell differentiation, blastocyst formation) and DNA replication, but the core pattern points to post-transcriptional control of gene expression.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050873","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1}]},{"hash":"439737353026079533","title":"RNA processing and ribosome biogenesis","description":"The top GO terms are dominated by RNA processing activities (mRNA polyadenylation, mRNA splicing via spliceosome, snoRNA splicing, pre-mRNA cleavage for polyadenylation) and components related to translation initiation and preinitiation complex formation, plus small-subunit processome assembly, indicating a cluster of proteins involved in RNA processing and ribosome biogenesis. A few unrelated terms (blastocyst formation, viral translation events) are present but don\u2019t outweigh the core theme.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":2},{"id":"GO:0034247","count":2},{"id":"GO:0098789","count":2},{"id":"GO:1902625","count":1}]},{"hash":"1292335770302010836","title":"Unknown","description":"The top GO terms span neural development (axon extension, nervous system development) and broad RNA biology/translation processes (translation initiation, preinitiation complex formation, small-subunit processome assembly), plus some developmental and viral translation-related terms. There isn\u2019t a single cohesive function tying these terms together, and the small edge count suggests a noisy, mixed set rather than a distinct, unified cluster.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045773","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0000278","count":2},{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2}]},{"hash":"623043355479709368","title":"DNA replication & chromosome maintenance","description":"The terms cluster around DNA-templated replication, telomere maintenance, recombination, chromosome separation, and chromatin-related processes (including rDNA maintenance and meiotic recombination resolution), pointing to a module focused on genome duplication and chromosome stability.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":2},{"id":"GO:0007004","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0000712","count":2},{"id":"GO:0051304","count":2}]},{"hash":"839846394614706450","title":"Bacterial Biosynthesis and Stress-Response Metabolism","description":"The top GO terms span diverse biosynthetic processes (lipopolysaccharide, pyridoxine, L-serine, thiamine, gluconeogenesis, chlorophyll) and a stress/response angle (hyperosmotic salinity, sporulation). This points to a broad bacterial metabolic cluster rather than a single specific pathway, so a label emphasizing biosynthesis and stress-related metabolism is most representative.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0008615","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0030435","count":2}]},{"hash":"1717353205029748898","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2}]},{"hash":"513812201994816493","title":"Translation machinery and antibiotic stress response","description":"This cluster centers on translation (GO:0006412) and stress responses to translation inhibitors (cycloheximide) and antibiotics, indicating a cohesive group of translation-related proteins involved in stress adaptation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046898","count":1},{"id":"GO:0046677","count":1}]},{"hash":"645880948190516058","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms for ribosome biogenesis, translation, and rRNA processing, pointing to core protein synthesis machinery and assembly. Supporting terms like cell division and microtubule movement fit with growth and mitotic processes, reinforcing a growth/translation\u2013related cluster, while a few peripheral/obsolete terms likely reflect annotation noise.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000747","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070306","count":1}]},{"hash":"223959434836880339","title":"DNA Repair and Replication","description":"The dominant GO terms describe DNA repair, DNA replication, and DNA damage response (including nucleotide-excision repair, translesion synthesis, and UV-C response). These processes collectively reflect maintenance of genome integrity during replication and in response to DNA damage. The inclusion of both error-free and error-prone TLS terms suggests a cluster of proteins involved in DNA damage tolerance, not just repair. Therefore, 'DNA Repair and Replication' best captures the shared function.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0071897","count":1},{"id":"GO:0070987","count":1},{"id":"GO:0006297","count":1}]},{"hash":"2246722464088818359","title":"Protein quality control and unfolded protein response","description":"The top terms center on proteostasis: response to unfolded protein, misfolded protein transport, chaperone-dependent refolding, and protein complex oligomerization, suggesting a proteostasis/quality-control cluster. Redox homeostasis and translation-related terms may reflect linked stress responses.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0035719","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0051259","count":2}]},{"hash":"1495625273747232223","title":"Lysine Methylation","description":"The cluster is dominated by GO terms for peptidyl-lysine methylation (mono-, di-, and trimethylation) and includes histone H3-K36 methylation, pointing to lysine methyltransferase enzymes that modify histones and other proteins, i.e., chromatin/modification activity. Some other terms (plastid transcription, ribosomal assembly, differentiation) may reflect annotation noise rather than a shared function, but the lysine methylation signal is strong and representative.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018026","count":1},{"id":"GO:0032088","count":1},{"id":"GO:0048863","count":1},{"id":"GO:0051149","count":1},{"id":"GO:0042793","count":1}]},{"hash":"1026623788444735899","title":"Ubiquitin-Proteasome Regulation and Transcription Control","description":"This cluster is driven by ubiquitination-related processes (autoubiquitination, K48/K63-linked ubiquitination, ubiquitin-dependent protein catabolic process, and polyubiquitination) and proteasomal degradation, indicating a core role in targeted protein turnover. Additional terms point to transcriptional regulation (RNA polymerase II\u2013mediated transcription) and histone catabolic processes, suggesting a link between ubiquitin signaling, chromatin dynamics, and transcription control.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0070534","count":2}]},{"hash":"1073966416120315228","title":"Neural development and synaptic morphogenesis","description":"The top GO terms point to brain development and neural connectivity, including retinal axon guidance, corpus callosum development, dendritic spine morphogenesis, and trans-synaptic signaling, with supportive hints from retinoic acid response and Hedgehog pathway regulation. While there are a few non-neural morphogenesis terms, the dominant theme centers on neural development and synaptic formation and modulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":3},{"id":"GO:0050798","count":2},{"id":"GO:0099557","count":2},{"id":"GO:0060021","count":2},{"id":"GO:0060997","count":2}]},{"hash":"1573720837593952447","title":"Glutamatergic Synaptic Transmission and AMPA Receptor Regulation","description":"This cluster is dominated by terms related to glutamatergic signaling, including neurotransmitter secretion, trans-synaptic signaling, dendritic spine morphogenesis, and AMPA receptor clustering regulation, all central to synaptic transmission and plasticity. Some development-related terms may reflect broader roles of shared proteins, but the core theme centers on synaptic communication at glutamatergic synapses.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1903895","count":1},{"id":"GO:0051968","count":1},{"id":"GO:0099557","count":1},{"id":"GO:0007269","count":1},{"id":"GO:0060292","count":1}]},{"hash":"156715414581527573","title":"Nuclear envelope and nuclear migration dynamics","description":"This cluster centers on nuclear envelope organization/anchoring and nucleokinesis/nuclear migration along microfilaments, with centrosome localization also implicated, suggesting a shared theme of nuclear-cytoskeletal coupling and cell migration; the other terms (mitochondrial translation, spermatogenesis, collagen biosynthesis) appear less directly related and may be incidental.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0090292","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0021817","count":1}]},{"hash":"1552691942167479975","title":"Ubiquitin-Dependent ERAD and Proteostasis","description":"The top GO terms are dominated by ubiquitination-related processes (K63-linked ubiquitination, autoubiquitination) and the ubiquitin-dependent ERAD pathway, plus a note on chaperone-mediated protein complex assembly. This points to a protein quality-control cluster centered on tagging misfolded proteins for degradation and managing proteostasis, with a few stress-response terms that may reflect broader context but are less central. ","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0070534","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0090035","count":4},{"id":"GO:0030579","count":4}]},{"hash":"1335201801229631619","title":"Unknown","description":"The GO terms are a mixed bag spanning innate immune response and virus defense, plant developmental processes (root meristem growth, cytokinin signaling), general cellular regulation (sumoylation, chromatin remodeling, rRNA processing), and even muscle differentiation, with no single unifying function evident across the cluster. This breadth suggests no cohesive theme to anchor a specific, concise label.","confidence":"","size":7,"edges":9,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0010082","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0042098","count":2},{"id":"GO:0045842","count":2}]},{"hash":"893216011996517182","title":"Mitotic Cytoskeleton and Cell Cycle Regulation","description":"The cluster is driven by strong signals for actin cytoskeleton organization and re-entry into the mitotic cell cycle, with multiple terms referencing mitotic cycles in development. This suggests a cohesive theme around how the cytoskeleton interfaces with cell division, even though some other terms (autophagy, transcription regulation) are more peripheral. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":2},{"id":"GO:2000775","count":1},{"id":"GO:0000320","count":1},{"id":"GO:0019085","count":1},{"id":"GO:1905866","count":1}]},{"hash":"1201015564450967057","title":"Unknown","description":"The top GO terms span transcriptional regulation, bacterial biosynthetic pathways (LPS, mannosylglycerate), metal ion homeostasis, transport, signaling regulation, and even muscle-related processes; there is no clear single function or pathway tying these terms together, suggesting the cluster is heterogeneous or noisy rather than functionally cohesive.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0009103","count":1},{"id":"GO:0031448","count":1},{"id":"GO:0051001","count":1},{"id":"GO:0016311","count":1}]},{"hash":"1414040116210436110","title":"Unknown","description":"The Top Terms include a disparate mix of processes (morphine response, brain development, photosynthesis, prostate and striatum development) and several obsolete annotations, with no coherent shared function tying the proteins together. Given this heterogeneity, there isn't a clear, specific biological theme to name the cluster, so Unknown is appropriate.","confidence":"","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0043278","count":3},{"id":"GO:0007091","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0021756","count":3},{"id":"GO:0016576","count":3}]},{"hash":"837650678293618334","title":"Plant metabolism with SA-mediated defense","description":"The top terms point to diverse metabolic pathways (amino acid and lipid biosynthesis) alongside plant-specific processes (fruit ripening, SA-mediated systemic acquired resistance) and DNA-templated transcription, suggesting a cluster of proteins involved in coordinating metabolism with defense signaling in plants.","confidence":"Medium","size":7,"edges":14,"triangles":13,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034276","count":5},{"id":"GO:0055089","count":5},{"id":"GO:0042218","count":5},{"id":"GO:0019518","count":5},{"id":"GO:0042853","count":5}]},{"hash":"448830540269774359","title":"Notch signaling and amino acid metabolism","description":"The Top Terms include Notch signaling and several amino acid\u2013related processes (serine biosynthesis, alanine catabolism, kynurenine catabolism, transsulfuration, glycine betaine biosynthesis) along with a cAMP response. There are also development-related terms (heart morphogenesis, hindbrain development, pituitary gland development), which suggests a unit where signaling pathways interface with amino acid metabolism during development. Confidence: Medium","confidence":"","size":7,"edges":14,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051591","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0042853","count":2},{"id":"GO:0097053","count":2},{"id":"GO:0007219","count":2}]},{"hash":"757104192520790214","title":"Chromatin-associated transcription regulation","description":"Based on the top GO terms, the cluster is enriched for regulation of DNA-templated transcription and establishment of protein localization to chromatin, which points to nuclear/chromatin regulatory functions. The other terms (androgen metabolism, retinol/melanin metabolism, antibiotic-related processes) are diverse and may reflect annotation noise, but the strongest signal centers on chromatin-related transcriptional control.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0071169","count":2},{"id":"GO:0008209","count":1},{"id":"GO:0042376","count":1}]},{"hash":"1260216990901586091","title":"Neural Development and Axon Guidance","description":"This cluster shows strong enrichment for nervous system development and connectivity: retinal ganglion cell axon guidance, optic nerve morphogenesis, corpus callosum development, dendritic spine morphogenesis, trans-synaptic signaling, and retinoic acid response, with hedgehog pathway regulation contributing to neural patterning. While a couple terms touch other morphogenesis areas, the dominant theme is CNS development and axon guidance.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050798","count":2},{"id":"GO:0099557","count":2},{"id":"GO:0060021","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0048546","count":2}]},{"hash":"1636345766108353218","title":"Ubiquitin-Mediated Protein Quality Control","description":"This cluster centers on ubiquitination and proteostasis, with GO terms for K63-linked ubiquitination, autoubiquitination, and ubiquitin-dependent ERAD and chaperone-mediated protein assembly regulation, indicating a module of proteins involved in tagging and processing misfolded or regulatory proteins for degradation or refolding. Some peripheral terms (granzyme signaling, stress responses) are present but do not override the core theme. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":2},{"id":"GO:0090035","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030579","count":2},{"id":"GO:0008626","count":2}]},{"hash":"2081866222614968779","title":"Diverse regulatory and signaling proteins","description":"The terms indicate involvement in regulation of protein function (sumoylation), signaling (cAMP and peptide hormone responses), and gene expression control (RNA stability, DNA metabolism), plus redox homeostasis; no single pathway dominates, suggesting a broad regulatory/signal-processing cluster.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0045454","count":1},{"id":"GO:2001153","count":1},{"id":"GO:0046856","count":1},{"id":"GO:0006308","count":1}]},{"hash":"1136287848080320882","title":"Neuronal synaptic signaling and exocytosis","description":"Neuronal communication terms dominate the cluster: excitatory postsynaptic potential, GABAergic synaptic transmission, calcium-dependent exocytosis, axon extension, and related phosphorylation and protein stability regulation. This points to a module centered on synaptic signaling and regulated vesicle release, with some outlier terms (kidney development, mast cell degranulation, mitochondrial fission) likely reflecting shared exocytosis or signaling pathways rather than a kidney- or mast cell-specific role.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0001822","count":2},{"id":"GO:0000266","count":2},{"id":"GO:0043304","count":2}]},{"hash":"644360284898751264","title":"Proteostasis via Ubiquitination and Autophagy","description":"This cluster centers on ubiquitin-related processes (sumoylation, autoubiquitination, deubiquitination, ERAD) and autophagic pathways (aggresome assembly, mitophagy), with additional links to membrane trafficking and stress responses. Together, these GO terms reflect cellular protein quality control and degradation pathways that maintain proteome homeostasis.","confidence":"High","size":7,"edges":12,"triangles":10,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":5},{"id":"GO:0051865","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0030433","count":5},{"id":"GO:1904021","count":4}]},{"hash":"811225330820210114","title":"Oxidative Stress and DNA Repair","description":"This cluster is driven by GO terms related to redox balance and detoxification (cell redox homeostasis, cellular oxidant detoxification, oxidation-reduction process) together with nucleotide-excision repair, indicating a bacterial stress-response module that links oxidative damage protection to DNA repair. Some outlier terms (e.g., lipopolysaccharide biosynthesis, estradiol response) likely reflect annotation noise rather than a coherent function, but the core theme centers on managing oxidative stress and maintaining genome integrity.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1532623184157136025","title":"Central carbon metabolism and quinone biosynthesis","description":"This cluster shows GO terms tied to gluconeogenesis, organic-acid catabolism (e.g., mandelate, galactonate, glucarate), and quinone biosynthesis (menaquinone and phylloquinone), pointing to a metabolism-focused group. Some annotations like cell wall organization or apoptotic signaling are infrequent or ancillary, suggesting the main theme is metabolic pathways rather than a single coherent function.","confidence":"Medium","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0071555","count":1},{"id":"GO:1903298","count":1}]},{"hash":"1757785807067866189","title":"Mitosis and Centriole Regulation","description":"This cluster centers on mitotic and centrosomal processes: centriole replication, chromosome alignment during metaphase, and mitotic cytokinesis\u2014plus supporting roles like chromosome attachment to the nuclear envelope and sumoylation that modulate these events. A few terms touch on EGFR signaling and spermatogenesis, but the dominant theme remains cell division and centrosome/chromosome dynamics.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097240","count":1},{"id":"GO:0097064","count":1},{"id":"GO:0046601","count":1},{"id":"GO:0016925","count":1},{"id":"GO:0045742","count":1}]},{"hash":"1059828590656158143","title":"Protein quality control and signaling regulation","description":"The cluster centers on protein homeostasis and signaling: references to ubiquitin-dependent ERAD indicate protein quality control, while TORC1 signaling, regulation of kinase activity and GTPase activity point to cellular signaling modulation; additional terms on mRNA/tRNA transport and redox balance support a broader maintenance role rather than a single pathway. This combination supports naming as protein quality control coupled with signaling regulation.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0070262","count":2}]},{"hash":"1458112968113495863","title":"ER protein folding and redox homeostasis","description":"This cluster centers on endoplasmic reticulum\u2013associated processes: protein folding in the ER, ER stress response, and redox regulation (oxidative stress, deglutathionylation). These terms together suggest a theme of maintaining protein maturation and redox balance within the ER, despite a few noisy/obsolete terms like viral process. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0006662","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1263357681695713248","title":"Endosomal-Vacuolar Trafficking","description":"The terms point to vesicle trafficking among Golgi, endosomes, and vacuoles, including endocytosis, Golgi\u2013endosome transport, early/late endosome-to-Golgi/vacuole sorting, and multivesicular body sorting\u2014hallmarks of the endosomal-vacuolar/MVB pathway. Some unrelated terms appear but do not dominate the cluster.","confidence":"High","size":7,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":1},{"id":"GO:0000147","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0071985","count":1},{"id":"GO:0034498","count":1}]},{"hash":"129111861387504412","title":"Mitochondrial Respiration and Mitophagy","description":"The top GO terms cluster around mitochondrial energy metabolism and turnover, notably regulation of cellular respiration and autophagy of mitochondrion (mitophagy). Some outlier terms exist, but the strongest signal points to mitochondrial function and quality control, justifying a label focused on mitochondrial respiration and mitophagy.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007289","count":2},{"id":"GO:0010259","count":2},{"id":"GO:0043457","count":2},{"id":"GO:0000422","count":2},{"id":"GO:0007124","count":1}]},{"hash":"1400605524687451185","title":"Unknown","description":"The top GO terms span diverse biological processes: ion transport and homeostasis (copper, zinc, calcium), lipid and phospholipid metabolism, amino acid biosynthesis, and even pathways like lipopolysaccharide biosynthesis and epoxygenase P450 activity. This broad mix of metabolic, transport, and specialized biosynthetic terms suggests no single coherent function links all proteins in this cluster, so a specific, representative label cannot be established.","confidence":"","size":7,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006874","count":2},{"id":"GO:0046272","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0046839","count":2},{"id":"GO:0006825","count":2}]},{"hash":"119467591991011482","title":"Quinone and pigment biosynthesis","description":"The top terms are dominated by biosynthetic processes for chlorophyll and various quinones/vitamins (chlorophyll biosynthesis, phylloquinone/menaquinone/ubiquinone/plastoquinone biosynthesis, vitamin K biosynthesis, and related heme O biosynthesis), indicating a cohesive theme of pigment and redox-cofactor production. A few unrelated terms appear at very low counts, but they do not detract from the main connectivity. Confidence: High","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015995","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0048034","count":1},{"id":"GO:0042372","count":1},{"id":"GO:0032194","count":1}]},{"hash":"1417493526305046510","title":"Proteasome-driven antigen presentation and immune signaling","description":"The GO terms point to a cluster centered on antigen processing and presentation via MHC class I (including TAP-dependent transport), coupled to proteasome-related proteolysis (proteasome core assembly, ubiquitin-dependent degradation, and deubiquitination) and immune receptor signaling (TCR and Fc-epsilon pathways). This suggests a functional theme where proteasome- and ubiquitin-mediated processing feeds antigen presentation and downstream immune signaling. The presence of a viral process term further supports a host immune response context.","confidence":"High","size":7,"edges":19,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":5},{"id":"GO:0002479","count":5},{"id":"GO:0016579","count":5},{"id":"GO:0080129","count":5},{"id":"GO:0038095","count":5}]},{"hash":"1662617824978756813","title":"Unknown","description":"The top terms span diverse processes (eye lens differentiation, rRNA processing, imprinting, fungal cell wall regulation, microtubule movement, chromatin modification, neural tube closure, DNA repair, and TGF-beta response) with several marked obsolete, and there are no connecting edges. There is no clear shared function tying these proteins together, so Unknown with no confidence is appropriate.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1},{"id":"GO:0007018","count":1}]},{"hash":"23480405056112742","title":"Mitochondrial Protein Synthesis","description":"The cluster is dominated by GO terms for mitochondrial tRNA aminoacylation (tryptophan, tyrosyl, valyl) and translation, pointing to mitochondrial protein synthesis machinery. The other terms present (vascular development, LPS biosynthesis, etc.) are low-frequency or likely incidental, so the core theme that ties the cluster together is mitochondrial translation and aminoacylation activities.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070183","count":1},{"id":"GO:0070184","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006438","count":1},{"id":"GO:0001525","count":1}]},{"hash":"2164139014060567595","title":"Unknown","description":"The GO terms are highly diverse (lens fiber differentiation, rRNA processing, imprinting regulation, fungal cell wall regulation, microtubule movement, chromatin modification, neural tube closure, homologous recombination repair, TGF-beta response) with no obvious shared function. The cluster has only a single edge and several obsolete terms, suggesting weak or noisy connectivity rather than a cohesive biological module. Therefore no sensible, specific label can be assigned.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0070306","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0032995","count":3},{"id":"GO:0007018","count":3}]},{"hash":"212060680546974468","title":"Photoreception and cGMP signaling","description":"This cluster is best characterized by light-detection terms (visible light, far-red light responses) and cGMP-related processes (cGMP catabolism/metabolism), pointing to phototransduction pathways. The other terms (cardiac/oocyte-related) appear singletons and may be noise rather than core features. ","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036006","count":1},{"id":"GO:0071321","count":1},{"id":"GO:0055118","count":1},{"id":"GO:0046069","count":1},{"id":"GO:0060282","count":1}]},{"hash":"1771982808254264315","title":"Wnt-Driven Embryonic Morphogenesis","description":"These proteins cluster around developmental signaling and organogenesis, highlighted by canonical Wnt signaling involved in apoptosis regulation, cranial skeletal development, dorsal identity, renal vesicle formation/metanephros morphogenesis, and adherens junction assembly, all pointing to embryonic tissue morphogenesis rather than a single biochemical activity.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044336","count":2},{"id":"GO:1904888","count":2},{"id":"GO:2000017","count":2},{"id":"GO:0034333","count":2},{"id":"GO:0072033","count":2}]},{"hash":"866822598829210894","title":"Unknown","description":"The cluster's top GO terms span many unrelated processes, including TORC1 signaling regulation, lens development, rRNA processing, imprinting regulation, fungal cell wall biogenesis, microtubule movement, histone modification, neural tube development, and DNA repair, with no clear shared functional theme and zero edges connecting members. This lack of a cohesive signal prevents assigning a confident, specific function label.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:1904263","count":4},{"id":"GO:0070306","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0032995","count":3}]},{"hash":"2046799047071307540","title":"Unknown","description":"The top GO terms are highly diverse, spanning toxin response, miRNA-mediated gene silencing regulation, dephosphorylation, stem cell proliferation, fluoride response, lipoprotein oxidation regulation, mechanosensory behavior, chemokine production, and various metabolic processes (coumarin catabolism, cholesterol metabolism). There is no clear shared molecular function, pathway, or biological process unifying these proteins, so a coherent functional label is not supported.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:2000637","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0072089","count":2},{"id":"GO:1902617","count":2}]},{"hash":"1505076678937070801","title":"DNA Repair and Chromatin Regulation","description":"The dominant terms point to nuclear genome maintenance via homologous recombination repair and chromatin modification (histone methylation), with supporting links to transcription and ubiquitin-mediated protein turnover. A couple of entries appear unrelated (lens differentiation, rRNA processing), indicating some annotation noise but an overall chromatin/repair theme.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000724","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070306","count":1}]},{"hash":"1237571461772649396","title":"Embryonic proteoglycan biosynthesis and skeletal development","description":"These proteins appear to be involved in the biosynthesis of proteoglycans (heparin and chondroitin sulfate) and related glycosylation pathways, with flux through UDP-N-acetylgalactosamine metabolism. The presence of terms tied to ossification, mesoderm development, embryonic skeletal joint formation, BMP signaling, and embryonic fin morphogenesis suggests a role in extracellular matrix composition and skeletal development during embryogenesis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030210","count":1},{"id":"GO:0010401","count":1},{"id":"GO:0019276","count":1},{"id":"GO:0001503","count":1},{"id":"GO:0006486","count":1}]},{"hash":"2038153297160624603","title":"Ubiquitin-Dependent Protein Degradation and Signaling","description":"The top GO terms cluster around ubiquitination processes (autoubiquitination, ERAD, K63-linked ubiquitination) and ubiquitin-driven protein turnover, with peroxisomal import also tied to ubiquitin pathways. The inclusion of TNF signaling and adaptive immune response supports a broader role for ubiquitination in signaling. This functionally ties the proteins to ubiquitin-mediated proteostasis and immune signaling.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0070534","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0016558","count":4}]},{"hash":"2205069976116206757","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031292","count":1},{"id":"GO:0006295","count":1},{"id":"GO:1903469","count":1},{"id":"GO:0045190","count":1},{"id":"GO:0000734","count":1}]},{"hash":"1527321721451091472","title":"Unknown","description":"The top terms show a mix of lipid signaling (endocannabinoid signaling, GPCR glutamate signaling, diacylglycerol metabolism) and carbohydrate catabolic processes (pectin, cellulose) plus trafficking, with no single dominant function linking the members. Given the lack of a cohesive theme and no interaction edges, there isn\u2019t a reliable unifying label to assign.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007216","count":1},{"id":"GO:0045490","count":1},{"id":"GO:0036155","count":1},{"id":"GO:0071327","count":1},{"id":"GO:0019369","count":1}]},{"hash":"922115781417734551","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:1903265","count":1},{"id":"GO:1903883","count":1},{"id":"GO:0001519","count":1}]},{"hash":"2140162227485870972","title":"RNA processing and ribosome biogenesis","description":"The GO terms cluster around RNA metabolism and ribosome production: transcription regulation, RNA editing, tRNA modification, cytoplasmic translation, ribosome biogenesis, and export of the large ribosomal subunit. These point to involvement in RNA processing and assembly of the protein synthesis machinery, with a few cell-division terms that may reflect multi-function proteins.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0016554","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0002181","count":1}]},{"hash":"774135308846005737","title":"Nuclear RNA processing and chromatin regulation","description":"This cluster centers on nuclear processes: splicing (mRNA cis splicing via spliceosome; spliceosomal complex assembly), transcription termination, histone mRNA metabolism, and pericentric heterochromatin formation, plus nuclear import and cell-cycle related regulation. These together point to coordinated control of gene expression and chromatin state in the nucleus, despite a few plant stress-related terms that are less central. ","confidence":"High","size":6,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":3},{"id":"GO:1990141","count":3},{"id":"GO:0042633","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0009737","count":3}]},{"hash":"423546591722790013","title":"MVB sorting and autophagy regulation","description":"Top GO terms cluster around multivesicular body sorting/assembly and autophagosome regulation, with Rab signaling and phagophore assembly site localization supporting a vesicle-trafficking/autophagy module; a few cell cycle terms may reflect context rather than core function. Therefore, the label captures the primary theme of the cluster.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0071985","count":2},{"id":"GO:0010458","count":2},{"id":"GO:0036258","count":2},{"id":"GO:0007049","count":2}]},{"hash":"1557773516801184910","title":"RNA Modification and Transcription Regulation","description":"These proteins cluster around RNA processing/modification and chromatin-based transcription control: tRNA wobble uridine modification, tRNA methylation, and 7-methylguanosine mRNA capping point to RNA processing; histone methylation and peptidyl-lysine dimethylation link to chromatin regulation; and the negative regulation of transcription by RNA polymerase II ties these processes to transcriptional control. Some terms (antibiotic biosynthesis, tellurium ion response, cobalamin biosynthesis) seem peripheral, but the core signals suggest a shared role in RNA/chromatin\u2013mediated regulation.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0046690","count":2},{"id":"GO:0030488","count":2}]},{"hash":"1762402248855493344","title":"Ubiquitin-dependent proteolysis and meiotic cell cycle control","description":"The GO terms are dominated by ubiquitin-mediated protein degradation (SCF-dependent and K63-linked ubiquitination) and meiotic cell-cycle regulation, with additional but weaker hints of immune/viral processes. This points to a cohesive theme of proteostasis linked to meiosis rather than unrelated functions.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0042787","count":2},{"id":"GO:1902104","count":2},{"id":"GO:0051759","count":2},{"id":"GO:0061470","count":1}]},{"hash":"918647176197194004","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0046621","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0038018","count":2},{"id":"GO:1900095","count":2}]},{"hash":"2262753317509627366","title":"Unknown","description":"The GO terms are highly diverse (bacterial biosynthesis, metal and ion transport, dephosphorylation, and even a muscle contraction term), with no clear shared pathway or function among the six proteins and no network edges to link them, so there is no coherent theme to name a specific cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0031448","count":3},{"id":"GO:0051001","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0030026","count":3}]},{"hash":"1809917720456296088","title":"RNA processing and ribosome biogenesis","description":"This cluster is dominated by GO terms for RNA processing (mRNA splicing and pre-mRNA cleavage) and ribosome biogenesis, with additional signals for cell growth/division and protein turnover. Despite a couple of outliers (e.g., lens differentiation), the common theme points to nuclear RNA maturation and ribosome assembly as the core function of these proteins.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000747","count":2}]},{"hash":"656195494374513592","title":"Meiotic Chromosome Cohesion and Orientation","description":"Top GO terms point to meiosis-specific chromosome dynamics, including centromeric cohesion and homolog orientation in metaphase I, plus linear element assembly. Other terms like ribosome biogenesis and actin cytoskeleton organization are present but less central, so the meiosis-focused label best represents the cluster.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0007089","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0000055","count":1}]},{"hash":"2146147423582956885","title":"Methylation-driven transcription regulation","description":"This cluster's GO terms cluster around various methylation reactions (peptidyl-lysine dimethylation/trimethylation, rRNA and tRNA methylation, N-terminal peptidyl-glycine methylation) and also include DNA-templated transcription, regulation of transcription, and rDNA heterochromatin formation, suggesting a cohesive role in methylation-modulated transcription and chromatin state.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0000183","count":1}]},{"hash":"622707900500095754","title":"Unknown","description":"The top GO terms are highly diverse, including protein methylation, RNA processing, various biosynthetic pathways, and stress responses, with no single unifying function, suggesting the cluster is functionally heterogeneous rather than representing a coherent theme.","confidence":"","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006479","count":1},{"id":"GO:0006396","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0019853","count":1},{"id":"GO:0008209","count":1}]},{"hash":"2061838872857037274","title":"Quinone and cobalamin biosynthesis cluster","description":"The top GO terms strongly point to cofactor biosynthesis, with multiple entries for ubiquinone, menaquinone, phylloquinone, and cobalamin biosynthesis, suggesting a cohesive function in producing essential cofactors/quinones. A few RNA modification and transcription-related terms are present but appear less central, so the main theme is cofactor biosynthesis rather than RNA processing. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":4},{"id":"GO:0006744","count":3},{"id":"GO:0018012","count":3},{"id":"GO:0002098","count":3},{"id":"GO:0009234","count":2}]},{"hash":"993122427118800585","title":"Membrane Transport and Ion Channels","description":"The top GO terms are dominated by transport and channel-related processes (oligopeptide export from mitochondrion, doxorubicin transport, potassium ion transmembrane transport, phytochelatin import into vacuole, and regulation of voltage-gated chloride channels), suggesting a shared theme around membrane transport and ion channel activity. A couple of cell-cycle terms (stem cell proliferation, cell division) appear but are less represented, indicating these are not the primary drivers of the cluster. Overall, the data point to a transport/ion-channel-focused cluster with moderate coherence.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072089","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090374","count":1},{"id":"GO:1902161","count":1},{"id":"GO:1900753","count":1}]},{"hash":"1362777426966222418","title":"Mitochondrial gene expression and import","description":"The top terms point to gene expression processes (DNA-templated transcription, regulation of transcription, translation) and mitochondrial-specific activities (protein import into the mitochondrial matrix, regulation of mitochondrial membrane permeability). This suggests a theme of coordinating gene expression with mitochondrial function, even though some terms (like cell cycle regulation) are less directly aligned. Overall, a label focused on mitochondrial-associated gene expression and import captures the common thread.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006412","count":1},{"id":"GO:1903740","count":1},{"id":"GO:2000134","count":1}]},{"hash":"2109851862542676280","title":"Neuronal vesicle trafficking and mitochondrial fission","description":"This cluster centers on neuronal synaptic vesicle dynamics\u2014budding, endocytosis, recycling, and GABAergic transmission\u2014alongside mitochondrial fission (dynamin-related processes). The co-occurrence of vesicle trafficking/endosome-related GO terms with mitochondrial fission terms suggests a coordinated module governing synaptic function and neuronal signaling.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000266","count":2},{"id":"GO:0008344","count":2},{"id":"GO:0016185","count":2},{"id":"GO:0007032","count":2},{"id":"GO:1903423","count":2}]},{"hash":"58716717380919567","title":"Ubiquitin-Dependent Proteolysis and NF-\u03baB/JNK Signaling","description":"This cluster centers on ubiquitin-related processes (autoubiquitination, K48-linked ubiquitination, ubiquitin-dependent protein catabolic process, ERAD) and regulatory signaling pathways (I\u03baB phosphorylation leading to NF-\u03baB activation, TNF-mediated signaling, JNK cascade, apoptosis). The shared theme is how ubiquitination controls protein fate and modulates NF-\u03baB, JNK signaling, and cell survival decisions.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0046621","count":3},{"id":"GO:1903721","count":3}]},{"hash":"10960804050867015","title":"Ubiquitin-Proteasome\u2013Mitophagy Regulation","description":"This cluster centers on ubiquitin-dependent protein turnover: deubiquitination, sumoylation, proteasomal degradation, and mitophagy; it also includes cellular stress responses and regulation of trafficking processes like endocytosis and immune signaling. The combination points to a coherent module of proteostasis and mitochondrial quality control, with broader regulatory roles in protein turnover and cellular stress responses.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":6},{"id":"GO:1900186","count":6},{"id":"GO:0016925","count":6},{"id":"GO:0032436","count":6},{"id":"GO:0000423","count":6}]},{"hash":"1641553558300589274","title":"Antiviral Innate Immunity","description":"The strongest signals are innate immune response and defense response to virus, indicating these proteins may function in antiviral innate immunity. Several other terms appear unrelated or noisy (e.g., photosynthesis, morphine response, cell cycle transitions), so the label is representative but not exhaustive.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0045842","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0050689","count":1},{"id":"GO:0006478","count":1}]},{"hash":"1265572920489463997","title":"Unknown","description":"The terms span protein quality control (aggresome assembly, ERAD), transcription, signaling (TOR, GTPase), cilium-related transport, development, and metabolic responses, with no single cohesive function linking the proteins, and the lack of edges suggests no module-level grouping. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070842","count":3},{"id":"GO:0061188","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0043547","count":1}]},{"hash":"670071234819747810","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0035329","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0060044","count":4},{"id":"GO:0006915","count":4},{"id":"GO:0030216","count":4}]},{"hash":"941133758044335437","title":"DNA-Templated Transcription Regulators","description":"Top GO terms indicate DNA-templated transcription and regulation of DNA-templated transcription, pointing to transcription factors or regulators as the core function of this cluster. The consistent emphasis on transcription and its regulation across the six proteins supports labeling this group as transcription regulators, even in the absence of observed edges.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006355","count":5}]},{"hash":"410280494003764075","title":"Fungal Cell Wall Biosynthesis","description":"This cluster centers on fungal cell wall formation and related glycan biosynthesis: terms like fungal-type cell wall biogenesis, cell wall biogenesis/organization, cell morphogenesis, regulation of cell shape, and GDP-mannose/mannoprotein biosynthesis point to fungal cell wall construction and morphology. Some bacterial-related terms (lipopolysaccharide and lipid A biosynthesis) may reflect annotation noise or shared glycan pathways, but the dominant signal supports a fungal cell wall biosynthesis theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0071555","count":1},{"id":"GO:0009298","count":1},{"id":"GO:0009103","count":1}]},{"hash":"2020251714680133238","title":"Retroviral life cycle and host interactions","description":"The top GO terms predominantly describe steps of the retroviral life cycle: reverse transcription (RNA-templated DNA biosynthesis), virion assembly, fusion of the viral envelope with the host membrane, and establishment of integrated proviral latency. Additional terms indicate host\u2013virus interactions such as host-mediated activation of viral replication and immune-related host processes (leukocyte migration, protein secretion). Collectively, these terms point to a cluster of proteins involved in retroviral replication and viral entry/latency with host interactions.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006278","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1404800555652471629","title":"Endocytosis and RTK signaling regulation","description":"Several GO terms cluster around receptor-mediated endocytosis and clathrin-related regulation (positive regulation of clathrin coat assembly, endocytosis regulation, clathrin-dependent endocytosis) and signaling pathways of receptor tyrosine kinases (EGFR, PDGFR). While a couple of terms like ribosome biogenesis and gastric acid secretion are less connected, the dominant theme is endocytic trafficking coupled with RTK signaling, supporting this label.","confidence":"Medium","size":6,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1},{"id":"GO:2000588","count":1},{"id":"GO:0016188","count":1},{"id":"GO:0045742","count":1}]},{"hash":"1727790650466095935","title":"Osmotic Stress Response and Sugar Metabolism","description":"This cluster centers on osmotic stress responses and sugar metabolism: multiple GO terms reference responses to water deprivation and to osmolytes like sorbitol, mannitol, sucrose, and glucose, indicating adaptation to osmotic stress via carbohydrate management. The presence of bacillithiol and mycothiol biosynthetic processes suggests production of thiol-based compatible solutes used in Gram-positive bacteria to cope with osmotic and redox stress. An outlier term related to feeding behavior and an obsolete term are present but do not alter the main theme.","confidence":"High","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009414","count":1},{"id":"GO:0072708","count":1},{"id":"GO:0010555","count":1},{"id":"GO:0009744","count":1},{"id":"GO:0005985","count":1}]},{"hash":"1400915990059570301","title":"Cellular Stress and Innate Immunity with Cell Cycle Links","description":"The terms show oxidative and metal stress responses (hydrogen peroxide, cadmium), innate immune signaling, and mitotic cell-cycle regulation, suggesting a cohesive theme of stress-activated defense signaling impacting cell division. Some terms (ureter development, morphine response) are less connected, likely annotation noise.","confidence":"Low","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070301","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0045087","count":3},{"id":"GO:0050689","count":3},{"id":"GO:0006478","count":3}]},{"hash":"634659622876289256","title":"Proteostasis and Stress-Response Regulation","description":"The cluster's terms cluster around protein turnover and modification (proteolysis, regulation of kinase activity, deubiquitination), alongside metabolic and oxidative stress processes (glutamine metabolism, hydrogen peroxide catabolic process, inflammatory response). Some terms appear as outliers (e.g., single fertilization, L-dopa biosynthesis), but the overarching theme suggests regulation of protein homeostasis and stress signaling rather than a single specific pathway.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":3},{"id":"GO:0006508","count":3},{"id":"GO:0006469","count":2},{"id":"GO:1903178","count":2},{"id":"GO:0007338","count":2}]},{"hash":"539942831649558262","title":"Oxidative detoxification and redox signaling","description":"Most top GO terms emphasize detoxification of oxidants and nitrogen compounds and regulation of reactive oxygen species, pointing to a core theme of cellular defense against oxidative stress. While there are also signals related to neural development, immune modulation, and hormone/ion responses, these likely reflect interconnected stress and signaling pathways accompanying detoxification. Overall, the cluster seems best captured by oxidative detoxification and redox signaling.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":5},{"id":"GO:0032355","count":4},{"id":"GO:0070458","count":4},{"id":"GO:0007417","count":4},{"id":"GO:0071638","count":4}]},{"hash":"1347384007424745252","title":"RNA Splicing and Processing","description":"The top terms are dominated by RNA splicing and processing functions (splicing, mRNA processing, regulation of alternative splicing via the spliceosome), suggesting a cluster of proteins involved in spliceosome-mediated RNA maturation. Transcription-related terms appear but are less central, and a few terms are obsolete; overall the theme centers on post-transcriptional RNA processing. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016575","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0000381","count":1},{"id":"GO:0008380","count":1},{"id":"GO:1903507","count":1}]},{"hash":"579760008475110340","title":"Unknown","description":"The terms are highly diverse (extracellular matrix organization, multiple biosynthetic pathways, development and differentiation) with no clear, single shared function tying the proteins together, making a specific label inappropriate.","confidence":"","size":6,"edges":6,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030198","count":2},{"id":"GO:0006099","count":1},{"id":"GO:0010510","count":1},{"id":"GO:0045654","count":1},{"id":"GO:0009851","count":1}]},{"hash":"1407834214543760263","title":"Plant light-response and development","description":"These proteins appear linked to plant growth and light-related processes: visual perception (GO:0007601) and maintenance of meristem identity (GO:0010074) point to photomorphogenesis and developmental patterning, while photosystem stoichiometry adjustment (GO:0080005) and mitotic cell cycle (GO:0000278) suggest coordination of cell division with photosynthetic capacity. The set also includes various signaling-related terms (e.g., BMP/TGF-beta pathways) that may reflect annotation cross-talk or non-plant analogies, but the dominant theme is plant light sensing guiding growth and meristem maintenance.","confidence":"Medium","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":3},{"id":"GO:0007601","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0030514","count":2},{"id":"GO:0030512","count":2}]},{"hash":"714467228095175861","title":"Mitochondrial Membrane Transporters","description":"These GO terms cluster around transport across the mitochondrial membranes and related regulation: malate-aspartate shuttle, mitochondrial ATP export/import, transmembrane transport of CoA, phosphate, and deoxynucleotides, as well as L-ornithine and thiamine pyrophosphate transport. The inclusion of regulation of mitochondrial membrane permeability and a response to superoxide suggests the proteins may participate in redox-linked transport regulation, integrating metabolite flux with mitochondrial membrane integrity.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043490","count":2},{"id":"GO:1990616","count":2},{"id":"GO:1990544","count":2},{"id":"GO:0035349","count":2},{"id":"GO:0035435","count":2}]},{"hash":"654000365546901195","title":"Cell cycle and telomere maintenance","description":"Most of the top GO terms cluster around cell cycle control (cell cycle; negative regulation of CDK activity) and telomere maintenance (telomere maintenance via telomerase, telomere capping). This suggests a functional group of proteins involved in regulating cell proliferation and genome stability. While there are some neuronal differentiation and immune signaling terms, they appear less central to the core theme, making 'cell cycle and telomere maintenance' the best unifying label.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0035556","count":4},{"id":"GO:0045736","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0032212","count":3}]},{"hash":"229778263222108102","title":"Neuronal Signaling and Sensory Perception","description":"The GO terms strongly cluster around neural signaling and sensory processes: GPCR signaling, ion transmembrane transport (sodium and potassium), cGMP biosynthesis, and sensory perceptions (vision and pain). While a few terms relate to development (lateral line, pons maturation), the dominant theme is neuronal signaling and sensory perception, suggesting a cohesive functional group related to neural communication and sensory processing.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048169","count":1},{"id":"GO:0038042","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0006182","count":1},{"id":"GO:0048899","count":1}]},{"hash":"6053723937925498","title":"Cytoplasmic Translation Regulation and mRNA Decay","description":"The top GO terms are dominated by translation processes (initiation, elongation, termination, and selenocysteine incorporation) with explicit mentions of positive regulation of cytoplasmic translation and translational regulation. Additional terms point to mRNA decay via deadenylation, as well as responses to xenobiotics/antibiotics that can affect translation. This combination suggests a core theme around control of protein synthesis and RNA stability, making this label descriptive and representative of the cluster\u2019s function.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0035690","count":3},{"id":"GO:2000767","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000288","count":2}]},{"hash":"2078766684138191519","title":"Cell Cycle and Mitosis Regulation","description":"The cluster is dominated by cell cycle and mitosis-related terms (cell cycle, regulation of cell cycle, mitotic actomyosin contractile ring maturation, attachment of spindle microtubules to kinetochore), suggesting a cohesive focus on mitotic progression and chromosome segregation. Additional terms like osmotic stress response and autophagy are present but appear ancillary to the main theme.","confidence":"High","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0071470","count":3},{"id":"GO:0016239","count":3},{"id":"GO:1902406","count":3},{"id":"GO:0001701","count":3}]},{"hash":"962677682662283513","title":"Organelle protein targeting and turnover","description":"The GO terms point to organelle-associated protein handling, including import into chloroplasts, insertion into the mitochondrial inner membrane, and mitochondrial autophagy, along with prenylation/CAAX-box processing. Although some terms are older or less specific, the common theme is organelle protein trafficking and quality control, particularly for mitochondria and chloroplasts.","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000422","count":1},{"id":"GO:0071586","count":1},{"id":"GO:0061077","count":1},{"id":"GO:0071432","count":1},{"id":"GO:0006998","count":1}]},{"hash":"48518431088793180","title":"DNA replication, repair, and cell cycle cluster","description":"This cluster is dominated by nuclear genome maintenance and cell-cycle related terms: DNA replication, DNA repair, DNA-templated transcription, telomere maintenance, and mitotic centrosome separation. While a few terms relate to dendrite morphogenesis, potassium ion transport, or T cell proliferation, the core signal points to genome integrity and cell division.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007100","count":4},{"id":"GO:0006281","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0006813","count":4}]},{"hash":"206487812635198847","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071847","count":1},{"id":"GO:0016188","count":1},{"id":"GO:0048541","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0072578","count":1}]},{"hash":"628071507352355425","title":"Membrane trafficking regulation","description":"This cluster is dominated by GO terms pointing to vesicle trafficking, including endosome-to-plasma membrane transport, very-low-density lipoprotein particle assembly, exocytosis, and lysosomal membrane organization, suggesting a shared role in membrane dynamics and trafficking. A couple of terms (chromosome organization, mammary gland proliferation) are less directly related, so the overall signal favors membrane trafficking regulation rather than a single, tightly defined process. Confidence: Medium.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006193","count":1},{"id":"GO:0009213","count":1},{"id":"GO:0051276","count":1},{"id":"GO:0034379","count":1},{"id":"GO:1905751","count":1}]},{"hash":"687398443296732374","title":"RNA Processing and Translation Regulation","description":"The GO terms cluster around RNA metabolism and control of translation: regulation of translational initiation, formation of translation preinitiation complex, small-subunit processome assembly, splicing regulation via the spliceosome, miRNA-mediated translational silencing, and mRNA stabilization. Together these suggest a shared function in RNA processing and translation regulation, despite some noisy terms. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0001825","count":1}]},{"hash":"84334261575278075","title":"Nuclear RNA Processing and Gene Regulation","description":"The cluster centers on nuclear processes tied to gene expression: mRNA splicing via spliceosome, ribosomal large subunit export from the nucleus, regulation of transcription via RNA polymerase II, and negative regulation of protein kinase activity, pointing to control of gene expression at the nuclear level. Some terms (visual perception, phototransduction, platelet degranulation, development-related) appear peripheral, possibly reflecting multifunctional proteins; however, the dominant theme is nuclear RNA processing and transcriptional regulation.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0032298","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0000398","count":1},{"id":"GO:1903026","count":1}]},{"hash":"3723666932282037","title":"DNA Replication & Centrosome Cycle","description":"The cluster is enriched for GO terms around DNA replication, nuclear cell cycle regulation, and the centrosome cycle, with supporting terms on telomere maintenance and mitotic control. This points to a core theme of cell division and genome maintenance, though a few other terms (developmental morphogenesis, endocytosis, axon guidance) are less directly related, suggesting the main signal is cell-cycle related.","confidence":"Medium","size":6,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0007098","count":6},{"id":"GO:0032212","count":5}]},{"hash":"1360302277414834127","title":"Transcription Regulation and Biosynthesis","description":"The cluster prominently features GO terms tied to transcription (DNA-templated transcription and negative regulation of transcription by RNA polymerase II), suggesting a shared regulatory function. It also includes several biosynthetic/metabolic processes (ubiquinone biosynthesis, vitamin E biosynthesis, antibiotic biosynthesis) and a few miscellaneous metabolic/modification terms, indicating a broader but loosely connected set of metabolic pathways rather than a single, tight function. Given this mix, the group appears to be only loosely cohesive around transcription and metabolism, so the label reflects a general theme rather than a precise function.","confidence":"Low","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006744","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0035573","count":1},{"id":"GO:0010189","count":1}]},{"hash":"1716149431378477902","title":"Cardiac morphogenesis and conduction","description":"The top GO terms are dominated by heart morphogenesis, ventricular cardiac muscle tissue morphogenesis, regulation of cardiac conduction, and cell communication by electrical coupling in cardiac conduction, indicating a cluster of proteins involved in heart development and electrical signaling. While terms like protein refolding, sumoylation, and redox response appear as well, they seem ancillary to the central cardiac development/conduction theme. Hence, the label focuses on cardiac morphogenesis and conduction.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003007","count":2},{"id":"GO:0055010","count":2},{"id":"GO:1903779","count":2},{"id":"GO:0042026","count":2},{"id":"GO:0086064","count":2}]},{"hash":"403928674205486164","title":"Redox Homeostasis and Oxidative Stress Response","description":"This cluster shows multiple GO terms tied to redox biology, including cellular redox homeostasis, hydrogen peroxide catabolic and oxidant detoxification processes, and cellular response to hydrogen peroxide, pointing to a shared function in managing oxidative stress. Some terms relate to reproduction or extracellular matrix, but the dominant signal is redox regulation, justifying a label focused on redox balance and oxidative stress. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045454","count":1},{"id":"GO:0042744","count":1},{"id":"GO:0018171","count":1},{"id":"GO:0007252","count":1}]},{"hash":"786153189152157777","title":"Sugar metabolism and carbohydrate catabolism","description":"The prominent GO terms point to various sugar- and carbohydrate-related metabolic and catabolic processes (D-gluconate, D-xylose, D-glucuronate, rhamnose, glycerol catabolism and phosphorylation). This suggests the cluster is centered on carbohydrate metabolism. A few terms (quorum sensing, cellular response to interleukin-13) appear peripheral and may reflect annotation noise rather than core function. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0019521","count":1},{"id":"GO:0005998","count":1},{"id":"GO:0009372","count":1},{"id":"GO:0035963","count":1}]},{"hash":"2215721874512866251","title":"Nuclear and ciliary protein transport","description":"This cluster centers on intracellular trafficking and localization, with several GO terms pointing to import of proteins and RNAs into the nucleus (NLS-bearing and ribosomal protein import) and to intraflagellar transport involved in cilium assembly, suggesting a shared function in transporting macromolecules to the nucleus or into cilia. Some terms like viral process, visual perception, phototransduction, and platelet degranulation appear less directly related and may reflect broader or off-target associations in the dataset. Overall, the dominant theme is protein/RNA transport and localization to nucleus and cilia.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0006610","count":2}]},{"hash":"1948034494645279836","title":"Unknown","description":"The top GO terms are highly diverse (glycolytic regulation, innate immune response, photosynthesis, mitotic transition, brain development, morphine response, histone methylation), with no clear shared function or pathway linking the proteins, so no coherent cluster theme can be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006110","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0045087","count":1},{"id":"GO:0006478","count":1},{"id":"GO:0035020","count":1}]},{"hash":"230404937372319254","title":"Nuclear transcription and RNA processing","description":"The GO terms point to transcription initiation and promoter clearance by RNA polymerase II, plus RNA processing activities such as splicing, exon ligation, and rRNA maturation in the nucleus. Despite some obsolete terms, the cluster centers on core nuclear RNA synthesis and processing functions.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006306","count":1},{"id":"GO:0001111","count":1},{"id":"GO:0070417","count":1},{"id":"GO:1903241","count":1},{"id":"GO:0006268","count":1}]},{"hash":"2045050841253210985","title":"Unknown","description":"The top GO terms span ubiquitination, telomere maintenance, neuronal differentiation, immune signaling, and vitamin D response, with no single dominant biological process linking all six proteins. This suggests the cluster does not reflect one cohesive function, making an Unknown label appropriate.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0021707","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071651","count":3}]},{"hash":"1191883308304864508","title":"Plant light response and photosynthesis","description":"This cluster centers on plant responses to various light conditions and photosynthetic light harvesting, as reflected by GO terms for red/blue light responses, nonphotochemical quenching, photosynthesis in photosystems I and II, and chlorophyll-related processes such as phytol biosynthesis.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010114","count":1},{"id":"GO:0071486","count":1},{"id":"GO:0010196","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0009769","count":1}]},{"hash":"135261954707332851","title":"Cell Cycle and Genome Maintenance","description":"The top GO terms cluster around core cellular processes: mitosis (mitotic spindle assembly, microtubule-based movement) and genome maintenance (double-strand break repair via homologous recombination, histone modification, ubiquitin-dependent protein catabolic process). A few terms relate to development, which may reflect annotation noise or pleiotropic roles, but overall the set points to conserved cell-division and chromatin-regulation functions. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:2000060","count":1},{"id":"GO:0006349","count":1}]},{"hash":"1105758177781909121","title":"Mitotic spindle assembly and microtubule nucleation","description":"This cluster is dominated by GO terms tied to microtubule nucleation and spindle assembly, including mitotic spindle assembly, gamma-tubulin complex localization, and microtubule nucleation by spindle pole body and other MTOCs. While a few signaling-related terms appear, the strongest and most frequent terms point to microtubule organization during cell division, suggesting the proteins function together in spindle formation and gamma-tubulin\u2013mediated nucleation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":1},{"id":"GO:0051417","count":1},{"id":"GO:0033566","count":1},{"id":"GO:0051415","count":1},{"id":"GO:0009785","count":1}]},{"hash":"116661747177145654","title":"ER Stress Ubiquitin-Proteasome and Autophagy Regulators","description":"The terms point to ER stress-triggered apoptosis, ubiquitin-dependent degradation (ERAD), autophagy regulation, and related trafficking processes, suggesting a cohesive role in ER stress\u2013linked protein quality control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0051260","count":2},{"id":"GO:1904021","count":1},{"id":"GO:1900186","count":1},{"id":"GO:1903094","count":1}]},{"hash":"1224187559880444485","title":"Unknown","description":"The top GO terms are diverse and span hormone metabolism (thyroid hormone), immune and metabolic responses (response to insulin, leukocyte tethering/rolling, immunoglobulin production in mucosal tissue), development (kidney morphogenesis, lens transparency maintenance), extracellular matrix/adhesion (heparan sulfate and heparin proteoglycan biosynthesis, cell\u2013cell adhesion), and even behavior (inter-male aggressive behavior). There isn\u2019t a single coherent function or pathway tying these terms together, so a concise, representative label is not evident.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042403","count":2},{"id":"GO:0032868","count":1},{"id":"GO:0050901","count":1},{"id":"GO:0002426","count":1},{"id":"GO:0036438","count":1}]},{"hash":"1031887879568387874","title":"Unknown","description":"The cluster shows a mix of GO terms from ubiquitin-dependent protein degradation (protein polyubiquitination and ERAD) but also many unrelated terms (lens fiber differentiation, rRNA processing, genomic imprinting regulation, fungal cell wall biogenesis, microtubule movement, histone acetylation, neural tube closure, and DNA repair). With no edges connecting proteins and several obsolete terms, there is no coherent biological theme tying the proteins together, so a reliable, intuitive label cannot be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070306","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006349","count":2}]},{"hash":"1460449266924139344","title":"Ribosome biogenesis: LSU/5.8S rRNA maturation","description":"Mainly driven by maturation of LSU rRNA and 5.8S rRNA, which are core steps in ribosome biogenesis; the other terms seem unrelated to this cluster and may reflect broader or incidental annotations.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0050901","count":1},{"id":"GO:0072177","count":1},{"id":"GO:0072218","count":1}]},{"hash":"1549367365431493644","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms for ribosome assembly and function: tRNA modification, cytoplasmic translation, ribosome biogenesis (small and large subunits), and nuclear export of ribosomal subunits, indicating a coherent role in making and using ribosomes; a few cell-cycle terms appear ancillary rather than core.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0000747","count":1}]},{"hash":"313708608723300556","title":"Unknown","description":"The top GO terms are a mix of skeletal muscle development, immune signaling, circadian rhythm, kidney function, and ubiquitination, with no single unifying biological theme across the proteins. Because the terms do not converge on a clear common function, a precise label for the cluster cannot be confidently assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036268","count":1},{"id":"GO:0002467","count":1},{"id":"GO:0042748","count":1},{"id":"GO:0060693","count":1},{"id":"GO:0035914","count":1}]},{"hash":"1430568768957488071","title":"Chromatin remodeling & DNA repair","description":"These proteins show enrichment for histone modification (acetylation, exchange) and DNA repair, plus spindle organization, suggesting a common role in nuclear chromatin dynamics and cell-cycle\u2013associated maintenance. Some terms are labeled obsolete, which may reflect historical annotations, but the core theme points to chromatin remodeling and genome maintenance rather than a specific signaling pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043967","count":1},{"id":"GO:0042993","count":1},{"id":"GO:0045892","count":1},{"id":"GO:0043968","count":1},{"id":"GO:0006281","count":1}]},{"hash":"1352610157942815924","title":"Glutamatergic signaling and receptor trafficking","description":"Based on the prominent GO terms, the cluster centers on glutamatergic signaling, including synaptic transmission and GPCR-mediated glutamate signaling, with additional support from receptor recycling and regulation of endosome size, suggesting a link to glutamatergic receptor trafficking at the synapse. Some terms are less related (e.g., transcription regulation), but the glutamate signaling and trafficking theme is the strongest common thread.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0051036","count":2}]},{"hash":"1284959760771832775","title":"Unknown","description":"The GO terms are extremely diverse, including telomere maintenance, cellular response to alkaline pH, T cell proliferation, mitotic arrest in response to pheromone, axon/neurite development, caveolin-mediated endocytosis, imprinting regulation (obsolete), spindle\u2013kinetochore regulation in meiosis, NK T cell differentiation, and vagina development. There is no clear common pathway, function, or cellular context linking these terms, and the network has no edges to suggest a cohesive cluster. Therefore the cluster cannot be meaningfully named beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0071469","count":1},{"id":"GO:0046641","count":1},{"id":"GO:0000751","count":1},{"id":"GO:0030517","count":1}]},{"hash":"2074573961213408819","title":"Potassium ion transport and homeostasis","description":"This cluster is dominated by GO terms for moving potassium ions across membranes and maintaining intracellular potassium levels (GO:0097623, GO:1990573, GO:0030007), suggesting a core role in potassium transport and homeostasis. While a few other terms appear (e.g., lipopolysaccharide biosynthesis, dephosphorylation), the clear enrichment for K+ transport/homeostasis supports a cohesive functional theme for these proteins.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097623","count":2},{"id":"GO:0030007","count":2},{"id":"GO:1990573","count":2},{"id":"GO:0009103","count":1},{"id":"GO:0031448","count":1}]},{"hash":"627627526122912798","title":"Membrane transport and ion channels","description":"The most represented GO terms point to transport across membranes and ion channel activity, including oligopeptide export from mitochondrion, doxorubicin transport, lipoprotein transport, phytochelatin import into vacuole, potassium ion transmembrane transport, and voltage-gated chloride channel activity. Some terms (antigen processing via MHC I, stem cell proliferation) are less directly related, but do not negate the overall transport-focused theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090374","count":2},{"id":"GO:0072089","count":2},{"id":"GO:1902161","count":2},{"id":"GO:1900753","count":2},{"id":"GO:0019885","count":2}]},{"hash":"293720073671186682","title":"Plant hormone biosynthesis and fruit ripening","description":"Top GO terms center on biosynthesis of plant hormones (ethylene, gibberellin, auxin, salicylic acid), a secondary metabolite pathway (proanthocyanidin), and fruit ripening, with a ROS-related stress cue (hydrogen peroxide\u2013mediated programmed cell death). This suggests a theme of hormone-regulated development and maturation in plants, with associated defense signaling; the penicillin biosynthetic term appears as annotation noise, and the lack of edges indicates a broad, metabolite-centric grouping rather than a tight complex.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010023","count":1},{"id":"GO:0042318","count":1},{"id":"GO:0010421","count":1},{"id":"GO:0009693","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1390667509282113208","title":"DNA Replication and Transcription","description":"The cluster is dominated by GO terms for DNA-templated transcription and DNA replication, pointing to nuclear genome information processing. While there are outliers related to telomere maintenance, cell cycle, and development, the strongest signals describe transcription and replication functions, suggesting a genome expression/maintenance theme for this cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0071469","count":1}]},{"hash":"1741672825773377107","title":"Chromatin regulation and transcription control","description":"The cluster is driven by terms for DNA-templated transcription and its regulation, plus methylation-related modifications (peptidyl-lysine, N-terminal methylation) and rDNA heterochromatin formation, which together suggest a chromatin-state\u2013mediated control of transcription. Some viral-related terms appear but likely represent noise relative to the core chromatin/transcription theme.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0000183","count":1},{"id":"GO:0018027","count":1},{"id":"GO:0018013","count":1}]},{"hash":"1042743118997279590","title":"Cardiac morphogenesis and conduction signaling","description":"The top GO terms point to heart development and electrical communication in the heart (heart morphogenesis, ventricular cardiac muscle tissue morphogenesis, regulation of cardiac conduction, and cell communication by electrical coupling involved in cardiac conduction), indicating a cohesive theme around cardiac formation and rhythm signaling, despite some generic terms in the list.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035551","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0003007","count":1}]},{"hash":"530339141863456677","title":"Inflammation and Protein Homeostasis","description":"The GO terms converge on inflammatory signaling (positive regulation of TNF production; positive regulation of inflammatory response) and protein quality control (protein refolding, stabilization, chaperone-dependent refolding), with additional ties to mitochondrial import and pore complex assembly, and virion assembly. This suggests a cluster of proteins involved in stress-induced immune responses together with protein maintenance processes, possibly reflecting host-virus interaction dynamics rather than a single, cohesive biological function.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1904469","count":5},{"id":"GO:0046931","count":5},{"id":"GO:0032212","count":5},{"id":"GO:0051085","count":5},{"id":"GO:0050821","count":5}]},{"hash":"1575598408540057663","title":"Unknown","description":"Top terms span exocytosis, kinetochore localization, telomere maintenance, pH response, T cell proliferation, pheromone-induced cell cycle arrest, axon guidance, caveolin-mediated endocytosis, imprinting regulation, and meiotic kinetochore dynamics. This broad spread suggests no single cohesive function for the cluster, indicating Unknown with no clear confidence in a shared theme.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0071469","count":1},{"id":"GO:0046641","count":1}]},{"hash":"2068954680201427696","title":"Regulation of Translation Initiation and RNA Processing","description":"The top GO terms are dominated by processes governing translation initiation and RNA metabolism, including regulation of translational initiation, formation of the translation preinitiation complex, and small-subunit processome assembly, with supporting terms for mRNA splicing and translation silencing. This points to a cluster of proteins involved in controlling protein synthesis at the initiation phase and related RNA processing steps, rather than core metabolic functions. A few outlier terms (e.g., blastocyst formation) may reflect broader developmental annotations but do not override the central theme of translation regulation and RNA processing.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1902625","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0034462","count":3},{"id":"GO:0001825","count":3}]},{"hash":"1764662026433373453","title":"Cardiac contraction regulation via cGMP signaling","description":"The terms are dominated by modulation of cardiac muscle contraction and cGMP pathways, including negative regulation of contraction and relaxation, cellular response to cGMP, and cGMP catabolism, suggesting proteins that influence cardiac contractility through the cGMP signaling axis. An outlier term (GPI anchor biosynthesis) appears but does not define the cluster's theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:1901898","count":1},{"id":"GO:0010753","count":1},{"id":"GO:0036006","count":1},{"id":"GO:0055118","count":1}]},{"hash":"1621196339188442465","title":"Unknown","description":"The cluster has five proteins with no reported interactions (0 edges) and no GO terms to guide interpretation, so no common functional signal is detectable to name the group reliably.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2003878713264296008","title":"Fungal sterol and sphingolipid metabolism","description":"The top terms strongly point to lipid biosynthesis in fungi: ergosterol biosynthesis regulation and mannose-inositol phosphorylceramide (a fungal sphingolipid) metabolism, plus unsaturated fatty acid biosynthesis. Mitochondrial processes (heme A biosynthesis and electron transport) support a broader metabolic context tied to lipid and energy metabolism. Some terms (nitrate assimilation, nitric oxide biosynthesis) are more general and less directly linked, but the lipid/sphingolipid/sterol theme remains the core. ","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0042128","count":2}]},{"hash":"282893576151256999","title":"Nuclear RNA Processing and Chromatin Regulation","description":"The top GO terms cluster around RNA processing and maturation (transcription termination by RNApol II, tRNA processing, mRNA splicing and spliceosome assembly, histone mRNA metabolism) and chromatin organization (pericentric heterochromatin formation). While a few terms reflect broader regulatory or stress responses, the core signature is nuclear RNA processing coupled with chromatin maintenance, justifying a label focused on these functions.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0070317","count":2},{"id":"GO:1990141","count":2},{"id":"GO:0042633","count":2}]},{"hash":"784507628898175960","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006744","count":1},{"id":"GO:0010189","count":1},{"id":"GO:0035690","count":1}]},{"hash":"2165698956391402678","title":"Ribosome Biogenesis (Small Subunit)","description":"The top GO terms are dominated by ribosome biogenesis and ribosomal small subunit biogenesis, indicating a shared function in assembling ribosomes. The other terms are diverse and less representative of the cluster\u2019s main theme, so the ribosome-related terms best define the cluster.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0034220","count":1},{"id":"GO:0071470","count":1},{"id":"GO:0009992","count":1}]},{"hash":"1830589311797312192","title":"Ribosome Biogenesis and Translation","description":"GO terms emphasize cytoplasmic translation, ribosomal large subunit assembly, ribosome biogenesis, and SRP-dependent cotranslational targeting to membranes, defining a protein-synthesis/ribosome assembly cluster. Other terms (interleukin-4 response, NADPH regeneration, cobalamin biosynthesis) are peripheral.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0000027","count":1},{"id":"GO:0042254","count":1}]},{"hash":"1222877833928897154","title":"DNA Replication and Cell Cycle Regulation","description":"The strongest GO signals are DNA replication and positive regulation of nuclear cell cycle DNA replication, plus the centrosome cycle, indicating the cluster centers on replication-associated and centrosome dynamics. Other terms like RNA polymerase II promoter clearance and prespliceosome assembly reflect broader nuclear processes, while embryonic cranial skeleton morphogenesis and obsolete methylation terms may be background annotations. Overall, the group appears best explained by core DNA replication and cell cycle control functions.","confidence":"Medium","size":5,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0010571","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0006306","count":3}]},{"hash":"1377552617111279059","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is dominated by GO terms for ribosome biogenesis, preribosome and cytosolic ribosome assembly, and rRNA maturation, with supporting signals for mRNA export and translation-related processes, pointing to proteins that coordinate ribosome production and RNA maturation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0000463","count":1}]},{"hash":"590436488521017352","title":"Unknown","description":"The top terms are scattered across ribosome biogenesis (rRNA processing and ribosomal subunit export), ER organization, transport, and differentiation with no single dominant process. Because there is no clear shared function tying the proteins together, the cluster is best labeled Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007029","count":1},{"id":"GO:1904751","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0015768","count":1},{"id":"GO:0070306","count":1}]},{"hash":"2056991484351652535","title":"Fungal mating and cell wall biosynthesis","description":"Based on the GO terms, the cluster is enriched for fungal-specific processes: karyogamy involved in conjugation with cellular fusion (mating) and fungal-type cell wall beta-glucan biosynthesis (cell wall synthesis). Other terms point to proteostasis and stress responses (unfolded protein response, response to heat), which often accompany mating and cell wall remodeling in fungi. Together, these suggest proteins involved in fungal mating and cell wall biosynthesis, with supportive roles in stress adaptation.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":2},{"id":"GO:0031204","count":1},{"id":"GO:0070880","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0016226","count":1}]},{"hash":"512850621000518417","title":"Endocytic and secretory membrane dynamics","description":"These terms cluster around membrane remodeling and trafficking: plasma membrane tubulation and pinocytosis point to endocytosis, endosome transport links to vesicular trafficking, and dense core granule maturation reflects secretory pathway activity. Developmental terms (eye and cranial skeletal system development) may reflect context-specific roles rather than a core shared function, but overall the set suggests membrane trafficking and remodeling in cellular processes.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097320","count":2},{"id":"GO:0006907","count":2},{"id":"GO:0001654","count":1},{"id":"GO:0022617","count":1},{"id":"GO:1904888","count":1}]},{"hash":"1159157018284727245","title":"Transmembrane Transporters (ion and metabolite)","description":"The proteins cluster around diverse transmembrane transport GO terms, including ion (sodium, potassium) and metabolite (malate, succinate, citrate, arsenite) transport, and regulation of phosphate transmembrane transport, indicating a shared role in membrane transport. The autophagosome maturation term appears only once and does not define the cluster\u2019s main function.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098656","count":1},{"id":"GO:0015743","count":1},{"id":"GO:0015744","count":1},{"id":"GO:0006813","count":1},{"id":"GO:0015746","count":1}]},{"hash":"1418533161969948376","title":"Ribosome biogenesis and translation","description":"Most top GO terms refer to ribosome production and function: tRNA modification, cytoplasmic translation, ribosome biogenesis, ribosomal subunit biogenesis and export. This indicates the proteins are involved in assembling and operating ribosomes. A few terms related to cell cycle or septum assembly appear, but they are less representative of the cluster\u2019s primary function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0000747","count":1}]},{"hash":"1697356129918272860","title":"Translation Initiation and Ribosome Biogenesis","description":"The proteins in this cluster are linked by GO terms centered on translation initiation (formation of translation preinitiation complex; regulation of translational initiation) and ribosome biogenesis (small-subunit processome assembly). Additional terms point to post-transcriptional regulation of gene expression, including miRNA-mediated translational silencing and splicing-related regulation. Overall, the cluster appears to group factors involved in initiating translation, assembling ribosomes, and coordinating downstream RNA processing and silencing, with some background noise from unrelated terms.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":1},{"id":"GO:0019236","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1590259733768120541","title":"RNA processing and translation regulation","description":"Most terms point to RNA metabolism and protein synthesis (translation, ribosome biogenesis, snoRNP assembly, spliceosome regulation, and nonsense-mediated decay), with a few related to signaling pathways (MAPK cascades) that can influence gene expression. This suggests a cluster centered on RNA processing and control of translation rather than a single receptor or enzyme activity. ","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904571","count":1},{"id":"GO:0000185","count":1},{"id":"GO:0007338","count":1},{"id":"GO:0000492","count":1},{"id":"GO:1900745","count":1}]},{"hash":"516612094175361568","title":"RNA processing and ribosome biogenesis","description":"The cluster is dominated by RNA metabolism and ribosome-related processes: 90S preribosome assembly, rRNA and tRNA processing, RNA-templated transcription, transcription termination, and deadenylation regulation, all pointing to RNA maturation and ribosome biogenesis as the cohesive theme. A few outliers (e.g., DMAPP biosynthesis, pancreatic cell apoptotic regulation) appear incidental noise rather than core features.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:2000676","count":1},{"id":"GO:0050992","count":1},{"id":"GO:0045948","count":1},{"id":"GO:0006353","count":1}]},{"hash":"1271070984224748425","title":"RNA processing and translation regulation","description":"This cluster centers on post-transcriptional control of gene expression, with terms focused on translational initiation regulation, preinitiation complex formation, small-subunit processome assembly, miRNA-mediated translational silencing, mRNA stabilization, and splicing regulation via the spliceosome. These collectively suggest a module tied to RNA processing and control of translation, with a couple of outliers likely representing noise. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0001825","count":2}]},{"hash":"1509585656115006807","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000715","count":2},{"id":"GO:0031365","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0043686","count":1},{"id":"GO:0016032","count":1}]},{"hash":"2083623115575485187","title":"NF-kB pathway regulation and ubiquitination","description":"The cluster's top GO terms converge on stress-related signaling and protein turnover, including positive regulation of I-kappaB phosphorylation (NF-kB activation), regulation of the JNK cascade, apoptotic process regulation, and ubiquitin-related processes (ubiquitin-dependent proteolysis and K6-linked ubiquitination). This suggests proteins acting in NF-kB signaling and ubiquitin-mediated regulation rather than a single, narrow function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903721","count":2},{"id":"GO:0090073","count":2},{"id":"GO:1901253","count":2},{"id":"GO:0070512","count":2},{"id":"GO:0070535","count":2}]},{"hash":"1104996253565486419","title":"Unknown","description":"The top GO terms are a diverse mix\u2014from transcription regulation (initiation and elongation), DNA replication initiation, and miRNA processing to signal transduction and unrelated terms like cerebellar Purkinje cell layer organization and abscisic acid biosynthesis\u2014offering no single coherent biological theme for the cluster. This makes it difficult to assign a specific, representative label, so Unknown is appropriate.","confidence":"","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903468","count":3},{"id":"GO:0090055","count":3},{"id":"GO:0090419","count":3},{"id":"GO:0021693","count":3},{"id":"GO:0032487","count":3}]},{"hash":"1216783784801788656","title":"Transmembrane Ion and Sugar Transporters","description":"The cluster is characterized by multiple transmembrane transport GO terms across a range of substrates (nitrite, D-xylose, trehalose, sodium, potassium, phosphate, nitrate assimilation). This points to a cohesive group of membrane transport proteins dedicated to ion and nutrient uptake and homeostasis. Some osmotic stress and metabolic terms are present but do not outweigh the transporter signal.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":2},{"id":"GO:0006970","count":1},{"id":"GO:0015753","count":1},{"id":"GO:0035725","count":1},{"id":"GO:0035435","count":1}]},{"hash":"935707628107841876","title":"Methylation-Related Modifications","description":"The cluster is dominated by methylation-related GO terms (protein methylation, peptidyl-lysine dimethylation, N-terminal peptidyl-glycine methylation, and rRNA methylation) with supporting cobalamin biosynthesis chemistry, suggesting a cohesive theme around methyl transfer and protein/nucleic acid modification. A few terms related to amine and dopamine metabolism appear but are less central to the core theme.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0032259","count":2},{"id":"GO:0014075","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0018013","count":2}]},{"hash":"1352277948474189802","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006385","count":1},{"id":"GO:0006386","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0006366","count":1}]},{"hash":"1380232874214703785","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031848","count":2},{"id":"GO:0071919","count":2},{"id":"GO:0035390","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0000467","count":1}]},{"hash":"1402603524208130554","title":"ECM Organization and Connective Tissue Morphogenesis","description":"Several terms point to extracellular matrix (ECM) structure and turnover (collagen fibril organization, collagen catabolic process, glomerular basement membrane development, cuticle/collagen-related development, aorta smooth muscle morphogenesis, intramembranous ossification). These together suggest a cluster of proteins involved in ECM arrangement and tissue morphogenesis across tissues. A few terms (complement activation, regulation of macrophage differentiation, aldosterone secretion) are less central but may reflect broader signaling context; overall the dominant theme is ECM organization and connective tissue development.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001957","count":1},{"id":"GO:0045650","count":1},{"id":"GO:2000860","count":1},{"id":"GO:0032836","count":1},{"id":"GO:0001867","count":1}]},{"hash":"150072194336361866","title":"Actin Cytoskeleton Assembly and Cell Division","description":"The terms cluster around actin polymerization, actin bundle assembly, Arp2/3-mediated nucleation, and cortical actin localization, indicating the proteins function together in actin dynamics critical for cell division (with a few outlier terms related to other processes).","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0051666","count":2}]},{"hash":"1742163878701507189","title":"Redox Homeostasis and Oxidative Stress","description":"The strongest shared functions among the proteins are redox-related: cell redox homeostasis, oxidation-reduction process, hydrogen peroxide catabolic process, and peptidyl-cysteine oxidation, pointing to a role in managing cellular redox state. Although there are outliers like NK cell cytotoxicity and spermatogenesis, the redox signals provide the most coherent theme for this cluster.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042267","count":2},{"id":"GO:0022417","count":2},{"id":"GO:0045454","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0042744","count":1}]},{"hash":"1188817603138867520","title":"Stem cell maintenance and differentiation","description":"The prominent GO terms point to regulation of stem cell population maintenance (GO:2000036) and regulation of stem cell differentiation (GO:2000736), suggesting the cluster centers on stem cell regulation during development. Other terms reference broad developmental processes (uterus morphogenesis, third ventricle development) and cellular interactions (recognition of apoptotic cell), which may reflect broader developmental roles or annotation noise, but the stem cell-related terms provide the core theme.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051574","count":1},{"id":"GO:0060275","count":1},{"id":"GO:2000036","count":1},{"id":"GO:0061038","count":1},{"id":"GO:1904388","count":1}]},{"hash":"1875596455618824168","title":"Ubiquitin-Proteostasis and Autophagy","description":"The top GO terms center on ubiquitination processes (autoubiquitination, deubiquitination, ubiquitin-dependent ERAD, sumoylation) and protein degradation pathways, including mitophagy and aggresome assembly, as well as regulation of endocytosis. This combination points to a protein cluster involved in maintaining protein quality through ubiquitin- and autophagy-mediated degradation and trafficking control under cellular stress.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:1903265","count":4},{"id":"GO:0030433","count":4},{"id":"GO:1904021","count":3},{"id":"GO:0016579","count":3}]},{"hash":"2083156565748920496","title":"Unknown","description":"The top terms span energy metabolism (ATP synthesis coupled electron transport, ferredoxin and xanthine catabolic processes), nitrogen fixation, lactation, and regulatory processes in vascular development. This mix shows no cohesive functional theme connecting the proteins, suggesting they represent diverse, unrelated roles. None","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042773","count":1},{"id":"GO:0006124","count":1},{"id":"GO:0007595","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0009399","count":1}]},{"hash":"177484698100309277","title":"Unknown","description":"The listed terms cover both development (male gonad development, multicellular development, osteoblast differentiation) and chromatin regulation (histone acetylation, subtelomeric heterochromatin formation, telomere-related processes) with no clear single function tying the proteins together. Several terms are obsolete or only weakly connected, so a cohesive label is not justifiable.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":3},{"id":"GO:0043966","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0031509","count":2},{"id":"GO:0050830","count":2}]},{"hash":"1878093408918604053","title":"Unknown","description":"The GO terms span membrane proteolysis in ER-to-cytosol transport, spermatid and wing cell fate specification, EGFR ligand maturation, NK cell activation regulation, unfolded protein response, and various metabolic processes, reflecting a highly heterogeneous set with no clear shared function or pathway; with no edges connecting proteins, there is no coherent theme to assign.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904211","count":1},{"id":"GO:0048515","count":1},{"id":"GO:0042676","count":1},{"id":"GO:0038005","count":1},{"id":"GO:0032815","count":1}]},{"hash":"1009644871604500274","title":"UV-induced DNA damage response and translation control","description":"These proteins cluster around cellular responses to UV and gamma radiation and include components involved in translating regulation and ribosome assembly during DNA damage/UV stress, including p53-mediated signaling and translation initiation, suggesting a coordinated response coupling genome integrity sensing with protein synthesis control.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071480","count":1},{"id":"GO:0045727","count":1},{"id":"GO:1902167","count":1},{"id":"GO:0006977","count":1},{"id":"GO:1904803","count":1}]},{"hash":"1584580960126998450","title":"RNA processing and translational regulation","description":"The top GO terms point to RNA processing and control of translation\u2014examples include regulation of translational initiation, formation of the translation preinitiation complex, small-subunit processome assembly, miRNA-mediated translational inhibition, and spliceosome-related mRNA splicing regulation\u2014suggesting a cluster of proteins involved in RNA processing and translation control. Some terms (mismatch repair, blastocyst formation) are unrelated noise, but the dominant signal is RNA processing/translation regulation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006298","count":1},{"id":"GO:0006457","count":1},{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1911399750809330293","title":"Ubiquitin- and Endocytosis Regulation","description":"The cluster\u2019s top GO terms center on ubiquitination-related processes (protein autoubiquitination, protein deubiquitination) and endocytosis regulation (negative regulation of clathrin-dependent endocytosis, aggresome assembly related to protein quality control). This points to a shared theme of protein turnover and trafficking regulation, with a few broader regulatory terms as less directly connected outliers. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0086004","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0032465","count":2},{"id":"GO:0043547","count":2}]},{"hash":"991221966731965533","title":"Synaptic vesicle trafficking and neurotransmission","description":"The shared GO terms center on presynaptic vesicle maturation, vesicle fusion regulation, and synaptic transmission, with supporting signals from intracellular transport and presynaptic signaling. This suggests a cohesive theme of vesicle handling and neurotransmitter release at synapses, despite a few outliers related to tRNA processing and other signaling pathways. Confidence in this being representative and specific to the cluster is High.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016188","count":2},{"id":"GO:0099526","count":2},{"id":"GO:0031340","count":2},{"id":"GO:2000235","count":2},{"id":"GO:0050861","count":2}]},{"hash":"1871203970567218554","title":"Cochlear hair cell synapse and morphogenesis","description":"The terms point to auditory system development and synaptic function in hair cells, notably cochlear morphogenesis, stereocilium organization, glutamate secretion, and synaptic plasticity (long-term depression, retrograde NO signaling, dendritic spine morphogenesis). This suggests a cluster governed by cochlear hair cell synapse formation and signaling rather than general cellular processes.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0035234","count":1}]},{"hash":"748236632227827022","title":"Proteostasis and unfolded protein response","description":"These proteins cluster around protein quality control under stress, highlighted by unfolded protein response, chaperone-assisted refolding, misfolded protein transport, and redox homeostasis. While a couple of terms are unrelated (development, ABA signaling), the dominant theme is proteostasis and stress-related protein handling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0045454","count":1},{"id":"GO:0035719","count":1}]},{"hash":"1836235286859422989","title":"Regulation of gene expression and protein homeostasis","description":"These proteins show a pattern of regulatory activities: transcriptional repression, RNA splicing control, circadian-related regulation, and deubiquitination/protein turnover, with some links to metabolism and stress response. This suggests a broad regulatory cluster centered on controlling cellular state via gene expression and protein homeostasis rather than a single pathway. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090526","count":2},{"id":"GO:1990168","count":1},{"id":"GO:0006977","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0033132","count":1}]},{"hash":"101080461307026877","title":"Mitotic spindle assembly and nuclear migration","description":"This cluster is dominated by GO terms describing microtubule-mediated spindle dynamics and chromosome movements, including lateral attachment of spindle microtubules to kinetochores, initial spindle pole body separation, metaphase chromosome alignment, and nuclear migration along microtubules. The presence of karyogamy-related term also fits, as it involves microtubule-driven nuclear movements during mating. A few terms about neural structure or epidermal homeostasis appear ancillary or broader annotations and do not define the core function. Overall, the set points to mitotic spindle assembly and nuclear movement as the shared theme.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0099607","count":2},{"id":"GO:1990535","count":2},{"id":"GO:0001560","count":2},{"id":"GO:0000073","count":2}]},{"hash":"1385646520717229309","title":"Mitophagy","description":"The cluster is defined by a GO term for autophagy of mitochondrion, pointing to mitophagy (mitochondrial autophagy) as the shared function among these proteins, making \"Mitophagy\" an intuitive label for this group.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000422","count":1}]},{"hash":"11235746071861717","title":"Auditory cochlear development and synaptic signaling","description":"The cluster mixes inner-ear development signals (cochlea morphogenesis, stereocilium organization) with synaptic activity terms (glutamate secretion, dendritic spine morphogenesis, long-term synaptic depression, nitric oxide\u2013mediated retrograde signaling), suggesting a theme around auditory neuron synapse formation and function in the cochlea.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0060292","count":1}]},{"hash":"2255564333922936498","title":"Developmental Signaling and Growth Control","description":"This cluster is enriched for GO terms tied to signaling pathways that regulate organismal development and tissue growth, especially Hippo and Wnt signaling, along with angiogenesis, myoblast fusion, and apoptosis regulation; despite some outliers (neural terms and a plant hormone pathway), the dominant theme is developmental signaling and growth control.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035329","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0007275","count":2}]},{"hash":"603872284212877260","title":"Organelle protein import and insertion","description":"This cluster centers on GO terms for targeting and delivering proteins into organelles\u2014chloroplast stroma import and mitochondrial matrix import, as well as inner membrane insertion\u2014pointing to a shared role in organelle protein localization and integration. The terms collectively indicate a mitochondria/chloroplast protein import/insertion module, with one peripheral term that is less characteristic. ","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032094","count":1},{"id":"GO:0045037","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0000002","count":1}]},{"hash":"289889952216963513","title":"Nucleotide Biosynthesis and Salvage","description":"The cluster is dominated by GO terms for nucleotide metabolism and interconversion (AMP salvage, ADP, CDP biosynthesis, ITP metabolic process, NAD+ biosynthesis, purine ribonucleotide interconversion), indicating a shared function in nucleotide biosynthesis and turnover. Brain and liver development terms appear but are likely incidental or broader annotations; the core theme centers on nucleotide metabolism. ","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0015937","count":4},{"id":"GO:0044209","count":4},{"id":"GO:0006172","count":4},{"id":"GO:0009435","count":4}]},{"hash":"2107218098660277443","title":"ECM remodeling and innate immune defense","description":"GO terms point to extracellular matrix remodeling (tissue remodeling, extracellular matrix disassembly, fibrinolysis, smooth muscle cell\u2013matrix adhesion, smooth muscle cell migration) together with innate immune responses (defense against fungus and Gram-positive bacteria, neutrophil-mediated killing), suggesting a program of ECM turnover coordinated with inflammatory defense.","confidence":"High","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048771","count":1},{"id":"GO:0022617","count":1},{"id":"GO:0050832","count":1},{"id":"GO:0050830","count":1},{"id":"GO:0042730","count":1}]},{"hash":"1936709075617735755","title":"Translational Regulation and Ribosome Biogenesis","description":"This cluster is dominated by GO terms related to translation (GO:0006412), regulation of translation (GO:0045727; GO:0045903; GO:0045947), tyrosyl-tRNA aminoacylation (GO:0006437), ribosome biogenesis (GO:0002254), and maintenance of translational fidelity (GO:1990145). Together they strongly suggest involvement in the protein synthesis machinery and its regulation, including accurate tRNA charging and control of translation initiation, with potential support roles under stress (heat) or antibiotic exposure. A transcription termination term appears less central to the main theme.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045727","count":1},{"id":"GO:0006437","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0045903","count":1}]},{"hash":"1506716360153776522","title":"Secretory Pathway and ER-Golgi Trafficking","description":"The GO terms cluster around proteins involved in processing and transporting through the secretory pathway: ER-Golgi vesicle transport, Golgi ribbon formation, and ER lumen retention, plus positive regulation of Wnt secretion. Proteasome assembly and endopeptidase regulation also point to broader protein processing/quality control linked to the secretory pathway. A few terms are organismal phenotypes, but the molecular functions suggest a cohesive secretory pathway theme. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":1},{"id":"GO:0010950","count":1},{"id":"GO:0061357","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0002121","count":1}]},{"hash":"370903897867701818","title":"DNA Damage Response and Chromatin Regulation","description":"The GO terms cluster around DNA damage response, DSB repair (NHEJ), mitotic G2 checkpoint signaling, and ionizing radiation response, with supporting roles for ubiquitination and chromatin localization. Also transcriptional regulation by RNA Pol II and cell-cycle control, all pointing to a DDR-centered functional theme rather than general metabolism.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060544","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0000209","count":1}]},{"hash":"933193681080111898","title":"Neural Development and Stem Cell Regulation","description":"The top GO terms indicate neural development (cerebral cortex development; pituitary gland development) and cell fate control (apoptotic process; positive regulation of stem cell proliferation), with additional neural metabolism signaling (dopamine catabolic process). Together, these point to a neurodevelopmental and stem cell regulation theme.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0042420","count":1}]},{"hash":"173249055757947553","title":"Neuronal signaling and axon growth","description":"The top GO terms point to neural signaling and development: regulation of Wnt and Hedgehog (Smoothened) pathways, excitatory synaptic activity, axon extension, and calcium-dependent exocytosis. While a couple terms reflect broader or developmental processes, the dominant theme ties to neuronal communication and axon guidance, suggesting proteins involved in neural signaling and connectivity. ","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0043366","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0000186","count":2},{"id":"GO:0007224","count":2}]},{"hash":"1867305696569646922","title":"TGF-\u03b2/BMP signaling inhibition","description":"The top GO terms cluster around negative regulation of BMP signaling and TGF-\u03b2 receptor signaling, with SMAD-related regulation and peptidyl-threonine dephosphorylation, indicating proteins that suppress TGF-\u03b2/BMP pathway activity. Some plant-specific terms appear as outliers, but the dominant pattern supports inhibition of TGF-\u03b2/BMP signaling.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035970","count":4},{"id":"GO:0030514","count":3},{"id":"GO:0030512","count":3},{"id":"GO:0080005","count":3},{"id":"GO:0071560","count":3}]},{"hash":"537170879728742110","title":"T Cell Signaling and Immune Response","description":"Top GO terms indicate immune activation, with prominent signals for GM-CSF and LPS responses, T cell receptor signaling, and T cell proliferation; other terms are more miscellaneous, but the dominant theme is immune signaling in lymphocytes. Confidence arises from the convergence on T cell\u2013related pathways and innate immune responses.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097011","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0071222","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0032212","count":4}]},{"hash":"2169568417016317174","title":"Actin-driven morphogenesis and vesicle transport","description":"These proteins show a strong signal for actin cytoskeleton dynamics (positive regulation of actin nucleation, actin cortical patch assembly, cell migration) and vesicle/particle transport (pigment granule transport), along with developmental morphogenesis processes like dorsal closure and apical bud growth. While a couple of terms touch on other processes, the actin-centric theme is the most consistent across the GO terms, justifying a label centered on actin-driven morphogenesis and transport.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090164","count":2},{"id":"GO:0051904","count":2},{"id":"GO:0051127","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0046663","count":2}]},{"hash":"1845759396235900755","title":"Unknown","description":"The GO terms span visual perception, muscle/embryo development, plant hormone signaling, and core cell cycle phosphorylation, with no single dominant function linking all proteins and no network connectivity. Hence there is no clear shared theme to name the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0000086","count":2}]},{"hash":"716077229922197227","title":"Negative regulation of endocytosis and autophagy","description":"The top GO terms point to suppression of clathrin-dependent endocytosis, GPCR internalization, autophagosome maturation, and aggrephagy, with additional notes on ERAD-related degradation pathways. While a few terms reference unrelated DNA repair, the prevailing pattern is the downregulation of trafficking and protein quality control pathways, especially autophagy and endocytosis. This makes the label a concise reflection of the cluster\u2019s core function.","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1900186","count":3},{"id":"GO:1903071","count":3},{"id":"GO:0034140","count":3},{"id":"GO:1901340","count":3},{"id":"GO:0035973","count":3}]},{"hash":"2221440908420992517","title":"Hippo-Wnt Signaling and Differentiation","description":"This cluster centers on developmental signaling (Hippo and canonical Wnt) and differentiation/morphogenesis processes, including keratinocyte differentiation and dendrite morphogenesis, plus apoptosis and regulation of cardiac proliferation, suggesting a module coordinating growth control with cell fate decisions. Some terms like potassium ion transport appear ancillary, but the core enrichment points to signaling pathways governing development and differentiation.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":3},{"id":"GO:0035329","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0060044","count":2}]},{"hash":"2178748701215515895","title":"Neural Development and Signaling","description":"Based on the GO terms, these proteins are tied to brain development and neuronal signaling (substantia nigra development, hippocampus development, regulation of synaptic plasticity, Rho-mediated signal transduction), with supporting roles in stress-responsive pathways (glucocorticoid signaling) and cell-cycle/apoptosis regulation (p53-related DNA damage response, CDK activity regulation). This pattern suggests a cluster centered on neural development and synaptic signaling, with nearby involvement in cellular stress responses.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007266","count":2},{"id":"GO:0021762","count":1},{"id":"GO:0006977","count":1},{"id":"GO:0000079","count":1},{"id":"GO:0048167","count":1}]},{"hash":"744484632907840077","title":"Unknown","description":"The GO terms are scattered across very different processes (nitric oxide biosynthesis/transport, oxidative stress, blood coagulation, oxygen/bicarbonate transport, muscle contraction, nitrogen fixation, and signaling regulation). There isn\u2019t a single coherent function or pathway that ties all five proteins together, suggesting either multi-functional annotations or noise. Therefore, a precise, representative label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:2000490","count":1},{"id":"GO:0042744","count":1},{"id":"GO:0045429","count":1},{"id":"GO:0007596","count":1}]},{"hash":"2014591978392376863","title":"Mitochondrial protein quality control and turnover","description":"The cluster is dominated by terms tied to mitochondrial machinery (complex III assembly, inner membrane insertion, mtDNA replication) and protein quality control/degradation pathways (protein unfolding, ERAD, proteasome assembly, autophagosome maturation, aggresome formation). Together these terms suggest a cohesive role in maintaining mitochondrial protein homeostasis through synthesis, folding, processing, and timely degradation/clearance. The single transcription initiation term likely reflects incidental annotation rather than a core function of the cluster.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034551","count":2},{"id":"GO:0097352","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0045899","count":2},{"id":"GO:0032979","count":2}]},{"hash":"895645956783988661","title":"Ribosomal RNA maturation and ribosome biogenesis","description":"The dominant GO terms point to maturation of LSU-rRNA and 5.8S rRNA from the tricistronic rRNA transcript, core steps in ribosome biogenesis. Additional terms for RNA (guanine-N7)-methylation and transcription support a broader RNA-processing/regulatory role in the nucleus. The absence of interaction edges suggests these proteins may participate in related RNA-processing activities rather than forming a tightly connected network. Some older/obsolete annotations appear, but the central theme remains rRNA maturation and ribosome assembly.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0016575","count":3}]},{"hash":"1938634120787487530","title":"Unknown","description":"The GO terms are heterogeneous, spanning transcription (DNA-templated transcription) and multiple metabolic processes (amino acid biosynthesis, peptide/ proteolysis, purine metabolism, allantoin assimilation). There is no clear, single shared function tying these proteins together, so a specific label isn\u2019t confidently representative. ","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0010136","count":1},{"id":"GO:0043171","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0006508","count":1}]},{"hash":"1335258900065581192","title":"Cardiac Electrophysiology and Hormonal Regulation","description":"The top GO terms center on cardiac function (cardiac muscle action potential, ventricular regulation, membrane repolarization), vascular tone (vasoconstriction), and endocrine signaling (vasopressin secretion, aldosterone biosynthesis), suggesting a cluster linked to heart electrophysiology with hormonal control of vascular and endocrine processes. Some terms like ossification and diet-induced thermogenesis are less directly connected and may reflect pleiotropy or annotation noise.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":5},{"id":"GO:0007216","count":4},{"id":"GO:0002024","count":4},{"id":"GO:0032342","count":4},{"id":"GO:0086002","count":4}]},{"hash":"2055913173843646992","title":"Unknown","description":"The top GO terms span sensory perception, phototransduction, insect cuticle development, nuclear import, cell cycle processes, hormone metabolism, and cardiac muscle functions, with no single unifying biological theme across the proteins. This suggests the cluster lacks a coherent shared function, warranting an Unknown label.","confidence":"","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0007602","count":3},{"id":"GO:0008365","count":3},{"id":"GO:0060316","count":3}]},{"hash":"1636442673047014996","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster\u2019s GO terms cluster around ubiquitin-mediated processes: ubiquitin-dependent protein catabolic process, monoubiquitinated protein deubiquitination, K11-linked ubiquitination, aggresome assembly, and related regulatory terms such as NF-kappaB inhibition and cell cycle transitions. These indicate a cohesive function in tagging proteins for degradation, managing protein quality control, and modulating signaling and mitosis through ubiquitin ligases and deubiquitinases.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0070842","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0035520","count":1},{"id":"GO:0036353","count":1}]},{"hash":"2158338223752729657","title":"Unknown","description":"The top terms are highly diverse and only weakly related, spanning vision/phototransduction, development, nuclear transport, and cell division, with no interactions among proteins. There isn\u2019t a single coherent function tying the cluster together, so a specific label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0007601","count":1},{"id":"GO:0007602","count":1},{"id":"GO:0072205","count":1},{"id":"GO:0008365","count":1}]},{"hash":"697059939728563485","title":"Endosome\u2013Golgi\u2013Lysosome Trafficking","description":"The proteins show strong enrichment for vesicle trafficking terms spanning endosome transport to lysosome, endosome-to-Golgi routes, Golgi-to-plasma membrane traffic, and Rab-mediated signal transduction, plus Cvt pathway transport; together this points to a cohesive intracellular transport role.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045022","count":2},{"id":"GO:0008333","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0043931","count":2}]},{"hash":"1932016734100537220","title":"Ubiquitin-Mediated Proteostasis","description":"Top terms are dominated by ubiquitination and degradation pathways (K63-linked ubiquitination, autoubiquitination, ubiquitin-dependent ERAD), suggesting a core function in tagging proteins for turnover and maintaining proteostasis, with some stress-response associations like chaperone assembly and apoptotic signaling as downstream effects.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":2},{"id":"GO:0090035","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030579","count":2},{"id":"GO:0008626","count":2}]},{"hash":"1718377073024822910","title":"Hormone signaling and RNA regulation","description":"The top GO terms point to signaling pathways (peptide hormone response, cAMP response, phosphatidylinositol dephosphorylation) along with post-transcriptional control (regulation of mRNA stability). While a few terms are peripheral (redox, corneocyte development), the dominant theme is cellular signaling linked to gene expression regulation, justifying this label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:2001153","count":3},{"id":"GO:0046856","count":3},{"id":"GO:0006308","count":3},{"id":"GO:0080111","count":3}]},{"hash":"1556812264824894130","title":"TLR signaling and inflammatory response","description":"The top GO terms converge on Toll-like receptor signaling (including TLR8) and downstream inflammatory and antiviral responses (interferon production, antibacterial peptides) along with autophagy and inflammatory regulation. A miRNA silencing term is present but likely represents an ancillary regulatory layer rather than the core function of the cluster.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035278","count":2},{"id":"GO:0006469","count":1},{"id":"GO:0032741","count":1},{"id":"GO:0034158","count":1},{"id":"GO:0050729","count":1}]},{"hash":"1753895224224915383","title":"Unknown","description":"The GO terms span ion transport, immune adhesion, hormone secretion, organ development, ECM remodeling, and macrophage differentiation, with no single shared function evident for this small cluster, so a cohesive label can't be assigned.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":2},{"id":"GO:0050901","count":1},{"id":"GO:2000860","count":1},{"id":"GO:0072177","count":1},{"id":"GO:0000501","count":1}]},{"hash":"1669031877315172438","title":"Endomembrane trafficking and cell polarity regulation","description":"These GO terms cluster around vesicle trafficking and membrane organization (ARF signaling regulation, endomembrane system organization, receptor recycling, CAAX-box protein processing) and also include polarity-related localization (pole plasm protein localization, regulation of establishment of cell polarity). Together, they suggest a theme of membrane trafficking coupled with spatial cell-polarity control rather than a single enzymatic activity. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032012","count":1},{"id":"GO:0007318","count":1},{"id":"GO:0010256","count":1},{"id":"GO:0090303","count":1},{"id":"GO:0001881","count":1}]},{"hash":"816060824209211893","title":"Glutamatergic Synaptic Trafficking and Regulation","description":"The cluster shows enrichment in GO terms for glutamatergic synaptic transmission, receptor recycling, and endosome size regulation, pointing to trafficking and signaling at glutamatergic synapses. Rho signaling regulation further supports cytoskeletal dynamics important for synapse function, making this a coherent theme despite some obsolete or nuclear terms present.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":5},{"id":"GO:0035023","count":5},{"id":"GO:0006355","count":5},{"id":"GO:0001881","count":5},{"id":"GO:0051036","count":5}]},{"hash":"333219433896437910","title":"Vacuolar amino acid transport","description":"The GO terms mainly describe transmembrane import and export of various amino acids (lysine, arginine, serine, proline, asparagine) across the vacuolar membrane, indicating a cohesive role as vacuolar amino acid transporters. A non-core term about potassium starvation is present but does not define the cluster\u2019s main function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090517","count":1},{"id":"GO:0006867","count":1},{"id":"GO:0051365","count":1},{"id":"GO:0090516","count":1},{"id":"GO:0015824","count":1}]},{"hash":"2110600870469708166","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019062","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0002128","count":2}]},{"hash":"2257772651369533590","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034475","count":3},{"id":"GO:0034476","count":3},{"id":"GO:0006367","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0071042","count":3}]},{"hash":"185960037629998508","title":"Unknown","description":"The GO terms across these proteins span innate immunity, defense regulation, metabolism, signaling, cell cycle, photosynthesis, neural development, and chromatin modification, with no clear, shared function tying the cluster together. This makes a cohesive label unlikely.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0050689","count":2},{"id":"GO:0006110","count":2},{"id":"GO:0006478","count":2},{"id":"GO:0035020","count":2}]},{"hash":"2163654876062910741","title":"Calcium and metal ion transport","description":"The cluster is dominated by GO terms tied to ion transport and calcium handling (e.g., proton transmembrane transport, intracellular calcium ion homeostasis, negative regulation of cytosolic calcium ion concentration) and metal ion homeostasis (manganese ion, cadmium ion transport). This suggests a common theme of calcium signaling and metal ion transport, with a couple of outlier terms (lipopolysaccharide biosynthetic process and regulation of muscle contraction) that are less coherent with the main theme.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0031448","count":2},{"id":"GO:0030026","count":2},{"id":"GO:0015991","count":2},{"id":"GO:1900082","count":2}]},{"hash":"1710974052778145021","title":"Translation Initiation & Ribosome Assembly Regulation","description":"These terms cluster around initiation of translation and assembly of the translation preinitiation complex, plus components involved in ribosome biogenesis (small-subunit processome). The presence of GO terms for regulation of translational initiation, formation of the translation preinitiation complex, miRNA-mediated translational inhibition, and mRNA stabilization supports a shared theme of controlling translation and ribosome readiness. Some spliceosome-related terms appear ancillary, but the core signal points to translation regulation machinery.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0034462","count":1},{"id":"GO:0001825","count":1}]},{"hash":"1582597449825412242","title":"Chromatin Regulation and Genome Maintenance","description":"This cluster's terms center on chromatin modifications (histone acetylation, histone methylation) and genome-preserving processes like imprinting regulation and homologous recombination repair, suggesting a common theme of chromatin state control and DNA maintenance, with some developmental terms as secondary associations.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0032995","count":2},{"id":"GO:0007018","count":2}]},{"hash":"2024471069501968234","title":"Plant-Type Cell Wall Organization","description":"Based on GO:0009664 (plant-type cell wall organization) being the top term with two instances, the cluster appears centered on plant cell wall organization, suggesting a shared role in plant-type cell wall processes among these proteins.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009664","count":2}]},{"hash":"2037613981943127051","title":"RNA silencing and translation regulation","description":"The top GO terms are dominated by RNA interference and post-transcriptional gene silencing (ncRNA-mediated silencing, primary miRNA processing) and regulatory steps in translation (regulation of translation, IRES-dependent initiation), suggesting a shared theme around RNA-based gene expression control. While a few terms relate to development or defense, the strongest signal centers on RNA processing and translational control, justifying this label for the small cluster.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045071","count":1},{"id":"GO:0033168","count":1},{"id":"GO:0016246","count":1},{"id":"GO:0050829","count":1},{"id":"GO:0031053","count":1}]},{"hash":"411965721885506904","title":"Histone modification and chromatin remodeling","description":"The cluster\u2019s top GO terms are dominated by chromatin-related processes, notably N-terminal peptidyl-lysine acetylation (histone acetylation) and nucleosome disassembly, pointing to chromatin modification/remodeling as the shared function. While a few terms touch broader transcriptional regulation, the strongest signals support a chromatin-focused theme for these four proteins.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0018076","count":1},{"id":"GO:0001207","count":1},{"id":"GO:0031496","count":1},{"id":"GO:0061038","count":1},{"id":"GO:0006337","count":1}]},{"hash":"1566527732721181055","title":"Mitotic cell division and RNA export","description":"The top GO terms point to mitosis and cell division (mitotic metaphase chromosome alignment, mitotic cell cycle, cell division) alongside nucleocytoplasmic transport (mRNA export from nucleus, ribosomal small subunit export from nucleus). This suggests the cluster centers on proteins involved in cell division with supporting roles in RNA/protein trafficking between nucleus and cytoplasm, with additional signals of intracellular transport and organelle-related processes. Confidence: Medium","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007080","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000056","count":2}]},{"hash":"475617441137151144","title":"Unknown","description":"The GO terms are a broad mix of biosynthetic, modification, and stress-response processes (e.g., ubiquinone and vitamin E biosynthesis, tRNA wobble modification, N-terminal serine trimethylation, juvenile hormone biosynthesis, and xenobiotic/tellurium responses). There is no single cohesive function or pathway uniting these terms, and the cluster has no observed edges, making a specific biological label inappropriate.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0006744","count":1},{"id":"GO:0035573","count":1},{"id":"GO:0010189","count":1},{"id":"GO:0035690","count":1}]},{"hash":"1760436089325039620","title":"Unknown","description":"The GO terms are scattered across unrelated functions (obsolete DNA methylation, Asp hydroxylation, obsolete protease activation, and face morphogenesis); there is no clear shared function or pathway linking the proteins, so a meaningful label cannot be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090116","count":1},{"id":"GO:0042264","count":1},{"id":"GO:0097202","count":1},{"id":"GO:0060325","count":1}]},{"hash":"851594773382756760","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms tied to ribosome assembly and translation initiation, including small-subunit processome assembly, formation of translation preinitiation complex, and regulation of translational initiation, suggesting a shared role in ribosome biogenesis and the starting steps of protein synthesis. While there are a few immune-related terms (defense response to protozoan, macrophage differentiation), they appear less central to the core function indicated by the translation-related terms, and may reflect broader cellular context. Overall, the strongest signal points to ribosome-related processes, justifying this label.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903206","count":2},{"id":"GO:0042832","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0030225","count":2}]},{"hash":"968669255581924500","title":"DNA Repair and Ubiquitination","description":"The top GO terms cluster around DNA damage response and ubiquitin-related regulation: DSB processing, homologous recombination repair, meiotic DSB formation, nucleotide-excision repair, and ubiquitination processes (protein and histone). While some terms are obsolete, the dominant theme points to ubiquitin-mediated control of DNA repair pathways. Some outliers (peroxisome import, embryonic development) may reflect broader cellular context or annotation noise, but overall this cluster best fits DNA repair with ubiquitin signaling components.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0070911","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0043951","count":3},{"id":"GO:0010390","count":3}]},{"hash":"1803556526934167798","title":"Ribosome biogenesis and translation","description":"The top terms are dominated by translation (GO:0006412) and 90S preribosome assembly (GO:0034463), pointing to a cluster of ribosome biogenesis and protein synthesis proteins. A few immune-related or miscellaneous annotations appear but with low counts, suggesting minor or noisy associations. Overall, the cluster is best characterized by components of the translation machinery and ribosome assembly.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0045087","count":1},{"id":"GO:0050689","count":1},{"id":"GO:1903220","count":1},{"id":"GO:0006478","count":1}]},{"hash":"2174582421480312021","title":"Mitochondrial tRNA aminoacylation and translation","description":"The GO terms are dominated by mitochondrial tRNA aminoacylation (glycyl-, seryl-, prolyl-, threonyl-, and selenocysteinyl-tRNA) and the broader translation process, including regulation of translational fidelity. This points to a cluster enriched for mitochondrial tRNA synthetases and translation machinery, justifying a label centered on mitochondrial tRNA charging and protein synthesis.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015966","count":1},{"id":"GO:0097056","count":1},{"id":"GO:0070150","count":1},{"id":"GO:0016260","count":1},{"id":"GO:0006412","count":1}]},{"hash":"434616266457578471","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0000466","count":2}]},{"hash":"354826558596634330","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0042273","count":1},{"id":"GO:0000495","count":1},{"id":"GO:0002192","count":1},{"id":"GO:1902626","count":1}]},{"hash":"1854600485390264413","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006306","count":2},{"id":"GO:0070417","count":2},{"id":"GO:1903241","count":2},{"id":"GO:0006268","count":2},{"id":"GO:0000378","count":2}]},{"hash":"758954158235556198","title":"ER-stress\u2013induced apoptosis and stress signaling","description":"The top GO terms emphasize intrinsic apoptotic signaling in response to ER stress, apoptotic processes, and JNK/NF-\u03baB\u2013related signaling, pointing to a core function in stress-activated cell death pathways. Additional terms related to transcription and cell-cycle regulation (DNA-templated transcription, mitotic checkpoints) plus hippo signaling suggest broader stress response and proliferative control. This combination supports labeling the cluster as ER-stress\u2013induced apoptosis and stress signaling.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070059","count":3},{"id":"GO:0035329","count":2},{"id":"GO:0007254","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051092","count":2}]},{"hash":"768244142264427311","title":"Unknown","description":"The top GO terms are mixed: cell cycle/division alongside antibiotic/drug response and various transport and immune-related processes. There isn\u2019t a single cohesive function tying these four proteins together, so a clear, representative label isn\u2019t identifiable.","confidence":"","size":4,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0090374","count":1},{"id":"GO:0072089","count":1}]},{"hash":"2016595882492195338","title":"Sulfur metabolism and redox-related modifications","description":"Several terms point to sulfur-containing pathways and redox chemistry (transsulfuration, Mo-molybdopterin cofactor biosynthetic process, tRNA wobble uridine thiolation, cysteine persulfide formation), suggesting a unifying theme of sulfur metabolism and redox regulation. A few terms (spinal cord development, mitotic M phase) appear unrelated and may reflect annotation noise. Overall, the cluster seems best described by sulfur metabolism and redox-related processes, with some noise from other cellular roles.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":1},{"id":"GO:0021510","count":1},{"id":"GO:2000220","count":1},{"id":"GO:0006071","count":1},{"id":"GO:0035335","count":1}]},{"hash":"2242482166166989087","title":"Unknown","description":"The proteins show no internal interactions (Edges: 0, Triangles: 0) and the top GO terms span a highly diverse set of processes (lens development, rRNA processing, imprinting regulation, fungal cell wall biogenesis, microtubule movement, histone modification, neural tube closure, DNA repair, and TGF-beta signaling) with several obsolete terms. This lack of a cohesive function or pathway suggests no single representative theme for the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1},{"id":"GO:0007018","count":1}]},{"hash":"610644390987203133","title":"Unknown","description":"The top GO terms for this cluster are highly diverse and include lens development, rRNA processing, imprinting regulation, fungal cell wall biosynthesis, microtubule movement, various histone modification terms (some obsolete), neural tube closure, DNA repair, and TGF-beta response. With no edges or shared functional signal among the four proteins, there is no clear common theme to name a coherent function; thus the cluster is Unknown with no confidence.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1},{"id":"GO:0007018","count":1}]},{"hash":"1779943436686782113","title":"Unknown","description":"The GO terms are highly diverse, including telomere maintenance, pH response, T cell proliferation, pheromone-induced cell cycle arrest, axon extension regulation, caveolin endocytosis, meiosis spindle regulation, NK T cell differentiation, and vaginal development. There is no clear, single biological function or pathway tying these together, so a cohesive label cannot be assigned with confidence.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:0071469","count":4},{"id":"GO:0046641","count":4},{"id":"GO:0000751","count":4},{"id":"GO:0030517","count":4}]},{"hash":"400487320535346540","title":"Diverse membrane transporters","description":"This cluster features GO terms centered on transporting various substrates across membranes (peptides, lipids, fatty acids, ions) and drug-related transport, suggesting membrane transporter functions with diverse substrates; a few outliers exist, but the dominant theme is transport.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090374","count":2},{"id":"GO:0072089","count":2},{"id":"GO:1900753","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0019885","count":2}]},{"hash":"823805976885635779","title":"Transmembrane Transport of Metabolites","description":"The top GO terms are dominated by various transport processes across membranes (e.g., oligopeptide export from mitochondrion, cobalt ion transport, carbohydrate transport, vitamin transmembrane transport, branched-chain amino acid transport, xenobiotic export, cysteine transport, teichoic acid transport), indicating the cluster represents membrane transporters or related components handling diverse substrates. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090374","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0000733","count":3},{"id":"GO:0006824","count":3},{"id":"GO:0008643","count":3}]},{"hash":"1707949462058686428","title":"Adhesion-mediated neural signaling","description":"The cluster shows strong representation of cell-ECM adhesion and integrin signaling (collagen fibril organization, hemidesmosome assembly, integrin-mediated signaling) together with neural connectivity and regeneration terms (positive regulation of glutamatergic synaptic transmission, axon regeneration). This pattern suggests a set of proteins that link adhesion and extracellular cues to neural development and repair processes.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"wound healing","top_go_terms":[{"id":"GO:0051968","count":3},{"id":"GO:0030199","count":3},{"id":"GO:0031581","count":3},{"id":"GO:0035001","count":3},{"id":"GO:0046718","count":3}]},{"hash":"739716497488416936","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045716","count":2},{"id":"GO:2000637","count":2},{"id":"GO:0048024","count":2},{"id":"GO:2000627","count":2},{"id":"GO:0022013","count":2}]},{"hash":"286587725150240113","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034354","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0009052","count":1}]},{"hash":"1666894884908022403","title":"Unknown","description":"The GO terms are highly heterogeneous, including DNA replication, viral genome replication, RNA and tRNA methylation, rRNA processing, and various metabolic processes, with no single unifying function apparent for these proteins. Because there is no clear shared pathway or process tying them together, a concise functional label is not supported.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0019079","count":2},{"id":"GO:0009236","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0070901","count":1}]},{"hash":"1898703879396766751","title":"Transmembrane Transporters","description":"The GO terms cluster around transport across membranes, including ion transport (sodium, potassium, nitrite, nitrate), sugars and vitamins, xenobiotics, and neurotransmitter loading into synaptic vesicles. This suggests the proteins function primarily as membrane transporters for ions and small molecules, with a note on vesicular neurotransmitter handling.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0035725","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0035461","count":3}]},{"hash":"371938319480641939","title":"Unknown","description":"The top GO terms span very diverse cellular processes (nuclear transcription and chromatin assembly, centromere assembly, microtubule severing, ER-Golgi transport, cell division, rRNA processing, and even lens differentiation), with no clear single function linking the proteins. Without a cohesive theme or interaction pattern, a specific, representative label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0051013","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0061641","count":3}]},{"hash":"1194834651635136001","title":"Unknown","description":"The top GO terms cover diverse, unrelated processes (segment specification, CNS and muscle development, cytokine production, cell polarity, p38 signaling). There is no single biological function common to all four proteins, so a meaningful, cohesive label cannot be inferred.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007379","count":1},{"id":"GO:0090180","count":1},{"id":"GO:0021556","count":1},{"id":"GO:0031139","count":1},{"id":"GO:1900745","count":1}]},{"hash":"1388551184309604630","title":"Vasculogenesis and myoblast differentiation regulation","description":"Based on GO terms, this cluster shows enrichment for developmental differentiation events, notably positive regulation of vasculogenesis and positive regulation of myoblast differentiation, with another term indicating Notch signaling modulation. This points to a functional theme around lineage specification during development, particularly vascular and muscle lineages, rather than a single metabolic pathway. Some terms are obsolete or generic (DNA-templated transcription, hydroxylation), but the central pattern is differentiation regulation in a developmental context.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001214","count":1},{"id":"GO:0045663","count":1},{"id":"GO:0061428","count":1},{"id":"GO:0045746","count":1},{"id":"GO:0042264","count":1}]},{"hash":"113118173425702923","title":"Vertebrate embryonic organogenesis","description":"The terms are dominated by embryonic development across multiple organs (heart, hindbrain, optic cup, pituitary, digestive tract, and cardiac tissue), suggesting a cluster tied to vertebrate organogenesis rather than a single pathway. Some metabolic terms appear, but the core theme is multi-organ embryonic development. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019285","count":4},{"id":"GO:0003007","count":4},{"id":"GO:0030902","count":4},{"id":"GO:0021983","count":4},{"id":"GO:0002072","count":4}]},{"hash":"189951613605749267","title":"Arp2/3-driven actin polymerization","description":"The top GO terms show clear emphasis on actin cytoskeleton dynamics: actin filament polymerization, actin filament bundle assembly, Arp2/3 complex-mediated actin nucleation, and actin cortical patch localization. Although there are a couple of unrelated terms (retinol/retinal metabolism and brain development), the strongest and most consistent signal is actin filament assembly and nucleation via the Arp2/3 complex, suggesting the cluster represents actin remodeling machinery. ","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":2},{"id":"GO:0042574","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0021762","count":2}]},{"hash":"123315842441272159","title":"Fatty acid biosynthesis and metabolism","description":"This cluster is dominated by GO terms related to fatty acid metabolic processes and biosynthesis across multiple chain lengths (long-, medium-, very long-chain) and related acyl-CoA metabolism, suggesting a lipid metabolism-focused protein group. Some outliers (siderophore biosynthesis, seed coat development) are present but do not redefine the main theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019290","count":2},{"id":"GO:0019654","count":2},{"id":"GO:1902987","count":2},{"id":"GO:0000038","count":2},{"id":"GO:0001676","count":2}]},{"hash":"747591043506545684","title":"Embryonic organogenesis","description":"The top GO terms cluster around embryonic development across multiple organs (heart morphogenesis, hindbrain development, optic cup morphogenesis, pituitary gland development, embryonic digestive tract development), suggesting a shared role in early organ formation. A couple of metabolic terms (e.g., TCA cycle) appear, but they are less representative of the cluster's main theme.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0019285","count":1},{"id":"GO:0003007","count":1},{"id":"GO:0030902","count":1},{"id":"GO:0021983","count":1}]},{"hash":"380128820521548621","title":"Unknown","description":"The top GO terms point to neural development (axonogenesis, visual perception, excitatory postsynaptic potential) but also cell cycle and unrelated processes (cytosine metabolism, plant hormone signaling), so there is no clear, coherent function tying the four proteins together. ","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019858","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0007520","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0000086","count":3}]},{"hash":"1806919575317655064","title":"Unknown","description":"The top terms span metabolism (methionine biosynthesis and dihydroxybenzoate catabolism), RNA processing (tRNA processing and mitochondrial tRNA aminoacylation), cell-cycle signaling (mitotic checkpoint) and telomere localization, plus obsolete annotations like iron sequestration and nitrogen fixation. This broad and scattered set provides no single cohesive function to bind the proteins, so a specific label cannot be confidently assigned.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019281","count":1},{"id":"GO:0019619","count":1},{"id":"GO:0060702","count":1},{"id":"GO:0070154","count":1},{"id":"GO:0070146","count":1}]},{"hash":"1659971595751711157","title":"Unknown","description":"The GO terms span plant defense (systemic acquired resistance) and development (fruit ripening) as well as general metabolism (amino acid and fatty acid biosynthesis/catabolism, sphingomyelin synthesis) and transcription, with several entries labeled obsolete. There is no clear, shared function uniting these proteins, making a precise, high-level label unreliable.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034276","count":1},{"id":"GO:0055089","count":1},{"id":"GO:0042218","count":1},{"id":"GO:0019518","count":1},{"id":"GO:0042853","count":1}]},{"hash":"1497786896925187058","title":"Unknown","description":"The top GO terms are very diverse (metabolic processes like glycogen and mevalonate pathways, stress and signaling responses such as glucocorticoid signaling and morphine/lead ion responses, plus locomotion and vascular morphogenesis), giving no single cohesive function for all four proteins. Unknown","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1900486","count":4},{"id":"GO:0043278","count":4},{"id":"GO:0060316","count":4},{"id":"GO:0010288","count":4},{"id":"GO:0031987","count":4}]},{"hash":"1425230455211195232","title":"Hormone signaling and second-messenger regulation","description":"The top GO terms point to hormone-triggered signaling (cellular response to peptide hormone stimulus) and second-messenger pathways (cellular response to cAMP, phosphatidylinositol dephosphorylation). While other terms are more diverse (redox homeostasis, RNA stability, corneocyte development), the strongest shared theme appears to be activation and modulation of signaling cascades in response to hormonal cues.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":1},{"id":"GO:2001153","count":1},{"id":"GO:0046856","count":1},{"id":"GO:0006308","count":1},{"id":"GO:0080111","count":1}]},{"hash":"1209940892737073261","title":"Fatty Acid and Cofactor Biosynthesis","description":"This cluster centers on biosynthetic processes for lipids and cofactors: fatty acid biosynthesis (short-, medium-, and saturated forms), ubiquinone and vitamin E biosynthesis, and even antibiotic biosynthetic activity, suggesting a core theme of lipid/cofactor production and related secondary metabolism. The presence of RNA modification and xenobiotic-response terms is less cohesive but can reflect broader cellular metabolism and stress responses accompanying biosynthetic activity. Overall, the dominant pattern is biosynthesis of fatty acids and key cofactors.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0051790","count":1},{"id":"GO:0019367","count":1},{"id":"GO:0051792","count":1},{"id":"GO:0006744","count":1}]},{"hash":"1192384766972918808","title":"Rab-Mediated Vesicle Trafficking and Autophagy","description":"Top terms point to Rab signaling, phagophore assembly site localization, phagosome-lysosome fusion, and regulation of synaptic vesicle exocytosis, all emblematic of vesicle trafficking and autophagy processes. While some terms touch on neuronal development and polarity, the shared theme is membrane trafficking and autophagic processes, which justifies this label. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032482","count":2},{"id":"GO:0018125","count":2},{"id":"GO:0034497","count":2},{"id":"GO:0002093","count":2},{"id":"GO:0043497","count":2}]},{"hash":"820383659356118600","title":"Transmembrane nutrient transporters","description":"This cluster is best described by the presence of multiple transmembrane transport GO terms in the Top Terms, including D-glucose transmembrane transport, myo-inositol transport, biotin transport, pantothenate transport, and sodium ion export across the plasma membrane. These points suggest a shared functional theme around membrane transport of nutrients. While there are a couple of outliers (e.g., acetylcholine biosynthetic process and general protein regulation terms), the dominant signal is transport across membranes, making this a coherent, concise label for the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015798","count":1},{"id":"GO:0008292","count":1},{"id":"GO:0071436","count":1},{"id":"GO:0015878","count":1},{"id":"GO:1904659","count":1}]},{"hash":"759772762453216874","title":"Unknown","description":"The terms span diverse developmental processes across multiple species (inner ear, anther tapetum, sex-determination, heart valve formation, stomatal development, Malpighian tubule morphogenesis) and a regulatory metabolic term, giving no single common function. As a result, a specific, representative label cannot be inferred with confidence.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042491","count":1},{"id":"GO:0048658","count":1},{"id":"GO:0007540","count":1},{"id":"GO:0003195","count":1},{"id":"GO:2000323","count":1}]},{"hash":"1999145344426621117","title":"Mitochondrial import and autophagy in neurons","description":"The GO terms show a strong mitochondrial signature\u2014protein import into the mitochondrial matrix, calcium import into mitochondrion, regulation of autophagy of mitochondrion, and ROS metabolism regulation\u2014pointing to mitochondrial function within neurons. Additional terms on neuron signaling and other developmental processes may broaden the context, but the core theme appears to be mitochondria-related functions in neuronal cells.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007270","count":1},{"id":"GO:2000378","count":1},{"id":"GO:1903959","count":1},{"id":"GO:1903146","count":1},{"id":"GO:0036444","count":1}]},{"hash":"852341211811408373","title":"Unknown","description":"The top GO terms are highly diverse, spanning telomere maintenance, cerebellar neuron differentiation, immune signaling regulation, kinase activity regulation, vitamin D response, and protein ADP-ribosylation, with no clear unified function. There isn\u2019t a cohesive theme to label this cluster with a specific, concise function.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0007253","count":1}]},{"hash":"340661094112716782","title":"Unknown","description":"No GO terms or interactions tie these four proteins together, and the network has no edges or significant connectivity. Without functional signals, a specific label cannot be assigned; Unknown is the appropriate, cautious choice.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"15017822984396727","title":"Vascular smooth muscle development","description":"The top GO terms cluster around vascular and smooth muscle biology, including vascular-associated smooth muscle cell differentiation, negative regulation of vascular smooth muscle cell proliferation, ductus arteriosus closure, and urinary bladder development, with PDGFR-beta signaling regulation linking to vascular remodeling. While there are a few more general terms (e.g., sumoylation, response to X-ray), the recurring theme centers on smooth muscle differentiation and cardiovascular development, suggesting these proteins function in vascular/SMM development pathways.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000587","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0016925","count":1},{"id":"GO:0071481","count":1},{"id":"GO:0010735","count":1}]},{"hash":"1524929621515981274","title":"Autophagy and Selective Organelle Turnover","description":"The top GO terms cluster around autophagy processes: autophagosome assembly/maturation, reticulophagy, and glycophagy, along with amino acid starvation response, which collectively point to autophagy-related functions and selective degradation of organelles like ER and glycogen. Some non-specific stress terms are present but do not override the autophagy signal.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097352","count":1},{"id":"GO:0000045","count":1},{"id":"GO:0070257","count":1},{"id":"GO:0061709","count":1},{"id":"GO:0071280","count":1}]},{"hash":"1259022112366745495","title":"Proteostasis and Unfolded Protein Response","description":"The GO terms prominently point to protein folding and quality control, including response to unfolded protein, misfolded protein transport, and chaperone-related refolding. Redox homeostasis supports stress context; while some terms (tRNA import, Smoothened signaling) seem tangential or obsolete, the core cluster centers on proteostasis under cellular stress.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0035719","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0051259","count":1}]},{"hash":"1568150518384960711","title":"Immunoregulation and apoptotic signaling","description":"This cluster centers on immune system regulation and cell death pathways, with GO terms pointing to regulation of T and B cell responses, immunoglobulin production, and various apoptotic/necroptotic signaling processes (TRAIL-mediated and motor neuron apoptosis), suggesting proteins involved in immune signaling intertwined with apoptosis mechanisms.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046642","count":1},{"id":"GO:0071285","count":1},{"id":"GO:0036462","count":1},{"id":"GO:0019724","count":1},{"id":"GO:1902895","count":1}]},{"hash":"1475343569546464454","title":"Unknown","description":"Top GO terms are scattered across transcription regulation, telomere maintenance, immune differentiation, cell cycle, axon guidance, and membrane trafficking, with only a single edge linking four proteins and no coherent single theme. This lack of a unifying function makes a concise, specific label inappropriate.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0071469","count":2},{"id":"GO:0046641","count":2},{"id":"GO:0000751","count":2}]},{"hash":"1458931473653745364","title":"Unknown","description":"The top GO terms are extremely diverse (translation, kinase regulation, cell polarity/bud site selection, sensory perception/phototransduction, development, muscle fusion, cuticle formation, actin patch assembly), with no clear shared pathway or function tying the proteins together. This prevents a confident, specific label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006469","count":1},{"id":"GO:0007121","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0002576","count":1}]},{"hash":"452219109715009810","title":"Nuclear transcription and DNA replication components","description":"The top GO terms cluster around nuclear processes: transcription regulation by RNA polymerase II, promoter clearance, DNA replication and related cell cycle events, and RNA processing (prespliceosome assembly). A few terms like visual perception and cold response are less informative or incidental, but the dominant themes indicate a shared nuclear gene expression and DNA maintenance function.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043547","count":2}]},{"hash":"2193077927569684786","title":"Oxidative Stress Response Signaling","description":"The terms cluster around redox biology and stress responses, including removal of reactive oxygen species, oxidation-reduction processes, aging-related responses, and selenium ion handling, plus accompanying signaling pathways (TGF-beta receptor signaling and TLR3 signaling) and pH response, suggesting a set of proteins involved in cellular redox stress management and stress signaling rather than a single specialized function.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001320","count":1},{"id":"GO:0048773","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0071291","count":1},{"id":"GO:0010447","count":1}]},{"hash":"1186660848158228095","title":"Innate inflammatory signaling and cytokine production","description":"This cluster centers on innate immune activation, with terms for TLR2 signaling, response to dsRNA, and positive regulation of cytokines such as IL-1, IL-18, IL-1\u03b2, and IFN-\u03b1, alongside general inflammatory responses. A single unrelated term (abscisic acid biosynthesis) appears as noise. Overall, the proteins likely participate in innate inflammatory signaling and cytokine production.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":1},{"id":"GO:0032741","count":1},{"id":"GO:0050701","count":1},{"id":"GO:0050729","count":1},{"id":"GO:0045356","count":1}]},{"hash":"2064146166235082347","title":"Fungal ergosterol and sphingolipid biosynthesis","description":"The strongest GO signals are for ergosterol biosynthesis regulation and mannosyl-inositol phosphorylceramide (MIPC) metabolism, both hallmark lipid pathways in fungi. Other terms appear less connected (e.g., mammalian tissue differentiation), suggesting the core theme is fungal lipid biosynthesis. Confidence in this label is Medium.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032443","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0032286","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0042128","count":2}]},{"hash":"1621617901457846028","title":"Purine nucleotide metabolism","description":"This cluster shows GO terms centered on AMP salvage, ADP biosynthesis, purine ribonucleotide interconversion, and ITP metabolism, indicating a shared role in purine nucleotide metabolism and salvage. The other development-related terms appear only once and may reflect incidental annotations; the nucleotide metabolism signal is the strongest trend.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":2},{"id":"GO:0007420","count":1},{"id":"GO:1904158","count":1},{"id":"GO:0006172","count":1},{"id":"GO:0015951","count":1}]},{"hash":"885800193565642026","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006306","count":3},{"id":"GO:0070417","count":3},{"id":"GO:1903241","count":3},{"id":"GO:0006268","count":3},{"id":"GO:0000378","count":3}]},{"hash":"630496293336359274","title":"Membrane Transport and Ion Channels","description":"The GO terms are dominated by transport and ion channel related processes (bile acid secretion; oligopeptide export from mitochondrion; doxorubicin transport; potassium ion transmembrane transport; voltage-gated chloride channel activity; phytochelatin import into vacuole), indicating a cohesive theme of membrane transport and ion channel function. A couple of terms (antigen processing via MHC I and stem cell proliferation) appear less related and may reflect broader or peripheral annotations. Overall, the cluster best fits membrane transport with ion channel activity, despite a few outliers.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032782","count":3},{"id":"GO:0090374","count":2},{"id":"GO:0072089","count":2},{"id":"GO:1902161","count":2},{"id":"GO:1900753","count":2}]},{"hash":"1790604155679857145","title":"Intracellular Transport and Trafficking","description":"These proteins appear linked to the movement of diverse molecules across cellular and organelle membranes: oligopeptides exported from mitochondria, lipoproteins, long-chain fatty acids into peroxisomes, cobalt ions, ceramides, and even transport-related steps in antigen processing for MHC class I, as well as drug/antibiotic transport. Although one term (stem cell proliferation) is unrelated noise, the shared theme is intracellular transport/trafficking.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090374","count":1},{"id":"GO:0072089","count":1},{"id":"GO:1900753","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0019885","count":1}]},{"hash":"1958315505223747090","title":"Auditory hair cell development and synaptic signaling","description":"The GO terms cluster around cochlear/auditory system roles (cochlea morphogenesis; auditory receptor cell stereocilium organization) and synaptic function (dendritic spine morphogenesis; long-term synaptic depression; glutamate secretion; retrograde signaling by nitric oxide), indicating a focus on hair cell development and synaptic signaling in the auditory system. A single term about opsonization seems unrelated noise, but does not override the main theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060088","count":1},{"id":"GO:0098924","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0060292","count":1}]},{"hash":"1206136917744011057","title":"Actin filament assembly and nucleation","description":"The cluster is dominated by GO terms related to actin dynamics: actin filament polymerization, actin filament bundle assembly, actin cortical patch localization, and Arp2/3 complex\u2013mediated actin nucleation. Although a couple of terms pertain to broader developmental processes, they often rely on actin remodeling, supporting a cohesive theme of actin cytoskeleton organization. Confidence: High","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030041","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0021762","count":1},{"id":"GO:0051666","count":1},{"id":"GO:0030476","count":1}]},{"hash":"1670224474531066255","title":"RNA transcription and ribosome biogenesis","description":"The proteins share GO terms across all three RNA polymerases (initiation and termination), transcription fidelity, and transcription-coupled repair, plus nucleolar rRNA transcription and ribosome biogenesis, indicating a cohesive link between transcription machinery and ribosome production.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006386","count":1},{"id":"GO:0001193","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0006283","count":1},{"id":"GO:0006379","count":1}]},{"hash":"377762959897193232","title":"Cell cycle regulation and cytokinesis control","description":"This cluster centers on terms like regulation of cytokinesis and cell cycle, with supporting signals for transcription and GTPase activity regulation, and ERK cascade modulation. While a few terms relate to differentiation or migration in specific tissues, the dominant theme is control of cell division and associated signaling pathways.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032465","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0060487","count":3},{"id":"GO:0070373","count":3}]},{"hash":"1821592457055717467","title":"Proteostasis and mitochondrial maintenance","description":"The GO terms cluster around protein quality control and mitochondrial handling: proteasome regulatory particle assembly, aggresome assembly, autophagosome maturation, ERAD, and general protein processing, plus mitochondrial-centric terms such as protein insertion into the inner membrane, regulation of mtDNA replication, and complex III assembly. This points to a cohesive theme of proteostasis intertwined with mitochondrial protein import/assembly and maintenance, despite one outlier term (blastocyst development). Overall, the data suggest a proteostasis-plus-mitochondrial maintenance function for these proteins.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":3},{"id":"GO:0001824","count":3},{"id":"GO:0034551","count":2},{"id":"GO:0097352","count":2},{"id":"GO:0070842","count":2}]},{"hash":"906952413847586771","title":"Unknown","description":"The Top Terms show a mix of developmental processes (lens fiber differentiation, neural tube closure) with chromatin modification, RNA processing, ubiquitin-mediated proteolysis, microtubule movement, and DNA repair, with no single clear function linking the four proteins. This lack of a cohesive theme suggests there isn\u2019t a straightforward, shared biological role for this cluster. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":2},{"id":"GO:0000447","count":2},{"id":"GO:2000060","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0032995","count":2}]},{"hash":"650571296823315495","title":"Neural differentiation and immune signaling regulators","description":"This cluster shows neural differentiation related terms (cerebellar granule cell differentiation, negative regulation of dendrite development) alongside immune signaling and regulation terms (IL-12 production, chemokine production, NF-kappaB-related regulation) and broader regulatory processes (telomere maintenance regulation, kinase activity). Taken together, it points to proteins that regulate signaling pathways affecting neural development and immune responses, rather than a single specific pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":4},{"id":"GO:0021707","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0071651","count":4},{"id":"GO:0007253","count":4}]},{"hash":"2303443355037956402","title":"Unknown","description":"The GO terms for this cluster are highly diverse and disparate (transcription, immune signaling, cGMP signaling, cardiac regulation, oocyte development, light detection, etc.), with no clear shared function or pathway. With zero edges and only scattered single-term associations, there isn\u2019t a coherent theme to name the cluster beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0036006","count":1},{"id":"GO:0071321","count":1},{"id":"GO:0055118","count":1},{"id":"GO:0046069","count":1}]},{"hash":"2192399795575017320","title":"Blue light-driven cyclic nucleotide signaling","description":"Proteins in this cluster appear tied to photoreception and downstream second-messenger signaling, with GO terms covering blue light signaling, receptor guanylyl cyclase signaling, and biosynthesis of cGMP and cAMP. This points to a shared function in light-induced cyclic nucleotide signaling and subsequent intracellular signal transduction, occasionally linking to transcriptional regulation as a downstream effect.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009785","count":1},{"id":"GO:0035556","count":1},{"id":"GO:0071880","count":1},{"id":"GO:0052565","count":1},{"id":"GO:0007168","count":1}]},{"hash":"2273395502685779968","title":"Unknown","description":"The GO terms are a mix of central metabolism (TCA cycle, glucose and glyoxylate metabolism, pyruvate decarboxylation to acetyl-CoA regulation), antibiotic response, terpenoid biosynthesis, and vertebrate brain development, with no clear overlapping theme. This scattered set suggests no coherent functional motif for the cluster, likely annotation noise or multi-function proteins.","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0072747","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0010510","count":2},{"id":"GO:0016114","count":2}]},{"hash":"2098257075341319652","title":"Cardiac Stress Hormone Signaling","description":"The top GO terms cluster around cardiovascular function and hormonal regulation: regulation of ventricular/arterial cardiac electrical activity, vasoconstriction, and aldosterone biosynthesis point to hormonal control of heart and blood pressure. Hypoxia and osmotic-stress responses fit into systemic stress adaptation that impacts the cardiovascular axis. Some terms (GPCR glutamate signaling, T cell homeostasis) are broader or peripheral, but the dominant signal is cardio-hormonal stress signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":4},{"id":"GO:0008627","count":4},{"id":"GO:0043029","count":4},{"id":"GO:0007216","count":3},{"id":"GO:0002024","count":3}]},{"hash":"259794113873693431","title":"Inositol/PI Biosynthesis","description":"Top GO terms center on inositol biosynthesis and phosphatidylinositol biosynthetic processes, suggesting the core function is inositol/PI lipid metabolism and related signaling. The presence of ABA-activated signaling and hyperosmotic salinity response hints at plant stress signaling connections downstream of PI pathways, though several other metabolic terms (gluconeogenesis, sulfate assimilation, cellulose catabolic) appear more peripheral. Overall, the strongest common theme is inositol/PI biosynthesis, justifying this label.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006661","count":1},{"id":"GO:0006021","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0046855","count":1},{"id":"GO:0009738","count":1}]},{"hash":"2304255185185798069","title":"Protein acetylation and related metabolism","description":"The Top Terms show multiple acetylation-related GO terms (spermidine acetylation, N-terminal peptidyl-glutamic acid acetylation, peptidyl-lysine N6-acetylation, histone H4 acetylation, and acetoin/putrescine acetylation) implying these proteins participate in acetylation reactions. Other terms such as mycothiol biosynthesis, glucosamine metabolism, and arginine biosynthesis may reflect linked acetyl-CoA\u2013dependent metabolic pathways, supporting a cohesive acetylation-centered cluster.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":4},{"id":"GO:0009447","count":4},{"id":"GO:0006526","count":4},{"id":"GO:0018002","count":4},{"id":"GO:0006041","count":4}]},{"hash":"258510562313872353","title":"Unknown","description":"These proteins show a scattered mix of developmental (brain, lung), cell cycle regulation, metabolism, and RNA processing terms, with no common biological process linking all four members and no interactions in the cluster. Because there is no cohesive theme or shared function, I label the cluster Unknown with confidence None. ","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":1},{"id":"GO:1902074","count":1},{"id":"GO:0070314","count":1},{"id":"GO:0019740","count":1},{"id":"GO:0090502","count":1}]},{"hash":"805716809678814905","title":"Zinc Ion Homeostasis and Detoxification","description":"The proteins are linked mainly to zinc-related processes: detoxification of zinc and cadmium ions, zinc ion transport, and intracellular zinc ion homeostasis; while some terms reference other metals, the strongest shared theme is zinc handling and detoxification. This label captures the cluster's likely function with high representativeness.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098849","count":1},{"id":"GO:0032119","count":1},{"id":"GO:0006876","count":1},{"id":"GO:0071584","count":1},{"id":"GO:0055072","count":1}]},{"hash":"1896005825086865912","title":"Meiosis, germ cell development, and DNA repair","description":"This cluster is dominated by germ cell and meiosis-related terms (germ cell development, meiotic mismatch repair, gene conversion at mating-type locus) and DNA repair/DDR terms (interstrand cross-link repair, p53-mediated apoptotic signaling), with additional signals of cell-cycle regulation and embryonic development. The common theme is meiosis and genome maintenance in germ cells; some terms like somatic hypermutation and IgA isotype switching are immune-related diversification but are less central to the core pattern.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007281","count":1},{"id":"GO:0016446","count":1},{"id":"GO:0061500","count":1},{"id":"GO:0007050","count":1},{"id":"GO:0006119","count":1}]},{"hash":"1526768662514375419","title":"Cardiac signaling and vascular regulation","description":"The top GO terms cluster around heart function and blood pressure control: regulation of ventricular cardiac muscle cell action potential, membrane repolarization, and vasoconstriction, as well as vasopressin secretion. Additional terms point to endocrine/metabolic modulation of cardiovascular function (aldosterone biosynthesis, diet-induced thermogenesis, cardiac hypertrophy under stress). A GPCR glutamate signaling term is broader but can feed into signaling networks influencing the heart. Overall, the cluster is best described as cardiovascular signaling and vascular control.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007216","count":1},{"id":"GO:0002024","count":1},{"id":"GO:0032342","count":1},{"id":"GO:0086002","count":1},{"id":"GO:0071651","count":1}]},{"hash":"284539371458905176","title":"Axon guidance and neural development","description":"This cluster is dominated by terms describing neuronal projection and axon guidance (axon extension involved in axon guidance; sympathetic neuron projection extension; branchiomotor neuron axon guidance; trigeminal nerve structural organization), indicating a core theme of neural development. Related terms also touch on broader morphogenesis in eye and organs (retina layer formation, salivary gland branching, renal artery morphogenesis) and a note on intracellular trafficking (protein localization to early endosome), but the strongest signal is neural development and axon guidance.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048846","count":1},{"id":"GO:1902946","count":1},{"id":"GO:0021637","count":1},{"id":"GO:0060666","count":1},{"id":"GO:0061441","count":1}]},{"hash":"1825756330780988345","title":"Unknown","description":"The GO terms span plant hormone signaling (gibberellin and cytokinin pathways), chromatin modification, innate immune and viral defense responses, development, and miscellaneous processes like drug response, with no single unifying function across the proteins; the cluster appears functionally heterogeneous, so there isn\u2019t a coherent label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":3},{"id":"GO:0009938","count":3},{"id":"GO:0090526","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0045087","count":2}]},{"hash":"803034460729667071","title":"Unknown","description":"The top GO terms are highly diverse, spanning telomere maintenance, pH response, T cell proliferation, cell cycle arrest, axon extension, endocytosis, imprinting regulation, meiosis kinetochore attachment, NK T cell differentiation, and vagina development. There is no single cohesive biological theme or process uniting these terms, so a specific functional label cannot be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0071469","count":3},{"id":"GO:0046641","count":3},{"id":"GO:0000751","count":3},{"id":"GO:0030517","count":3}]},{"hash":"734095701683341475","title":"Cardiac Morphogenesis and Electrical Conduction","description":"The top GO terms cluster around heart development and cardiac electrophysiology: heart morphogenesis, ventricular cardiac muscle tissue morphogenesis, regulation of cardiac conduction, and cell communication by electrical coupling involved in cardiac conduction. There are a few general processes listed (protein refolding, protein sumoylation) and a couple of unrelated terms (prostate gland development, male sex differentiation) that may reflect broader cellular contexts, but the dominant theme is cardiac development and electrical conduction, making this a coherent label for the cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0003007","count":1}]},{"hash":"174014012646202984","title":"Unknown","description":"The top GO terms are broad and diverse, spanning immune signaling (interleukin-4), nitric oxide production, telomerase assembly, xenobiotic response, protein folding, ATP response, and growth factor signaling. There isn\u2019t a single cohesive function or pathway tying all three proteins together, suggesting a heterogeneous set of roles rather than a shared molecular theme.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":2},{"id":"GO:0033160","count":2},{"id":"GO:0045429","count":2},{"id":"GO:1905323","count":2},{"id":"GO:0071902","count":2}]},{"hash":"1303288874248056743","title":"Telomere maintenance and neural development regulators","description":"The top GO terms point to regulatory roles in telomere maintenance and capping, alongside neural differentiation and dendrite development, with accompanying modulation of signaling pathways (NF-\u03baB, IL-12, kinase activity), vitamin D response, chemokine production, and post-translational modification. This suggests a cluster of proteins that broadly regulate genomic stability and neural/immune signaling, rather than a single, cohesive pathway. Confidence: Medium","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0021707","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0071651","count":2},{"id":"GO:0007253","count":2}]},{"hash":"320585033436835885","title":"RNA processing and translation regulation","description":"The top GO terms cluster around RNA processing and translation control: spliceosome-mediated mRNA splicing regulation (positive and negative), small-subunit processome assembly, translation preinitiation complex formation, and translational initiation regulation, plus ncRNA/miRNA-mediated gene silencing. This points to a functional cluster of proteins involved in RNA maturation and regulation of protein synthesis.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2}]},{"hash":"648878650123082593","title":"Craniofacial development and Wnt signaling","description":"The GO terms point to cranial development, cranial skeletal system development, and ectoderm development, with a Tendency toward dorsal identity regulation and Wnt signaling, suggesting a craniofacial development theme. A few terms (adherens junction, cytokinesis, Cvt vesicle assembly) reflect broader cellular processes that can accompany development, but the strongest signal relates to craniofacial patterning and its regulatory signaling pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061550","count":1},{"id":"GO:0044336","count":1},{"id":"GO:1904888","count":1},{"id":"GO:2000017","count":1},{"id":"GO:0071255","count":1}]},{"hash":"628219114564065648","title":"Nucleolar Organization","description":"This cluster is best labeled by the single GO term present, nucleolus organization, which suggests a role in organizing nucleolar processes (likely ribosome biogenesis). The lack of additional terms and zero edges make the connection tentative, but the term provides a coherent theme for the cluster.","confidence":"Low","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007000","count":1}]},{"hash":"1315921969480974012","title":"Unknown","description":"The top GO terms are a mix of development (lens fiber differentiation, neural tube closure), RNA processing (rRNA cleavage), chromatin modification (histone acetylation/methylation, imprinting regulation), cell wall biogenesis (fungal), microtubule-based movement, DNA repair, and signaling (TGF-beta). This broad and compartmentalized set provides no single cohesive function tying the proteins together, so a meaningful concise label cannot be assigned beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0032995","count":2},{"id":"GO:0007018","count":2}]},{"hash":"1553762359757680068","title":"DNA Replication Core Machinery","description":"This cluster is anchored by GO terms for DNA biosynthetic process and DNA replication (each seen twice), suggesting the proteins are involved in DNA synthesis or replication. The presence of protein homooligomerization supports assembly of multi-subunit replication complexes, while the other one-off terms (mitochondrial insertion, autophagy, proteostasis) may reflect ancillary interactions or annotation noise. Overall, the core theme appears to be DNA replication-related functions.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071897","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0034551","count":1},{"id":"GO:0097352","count":1}]},{"hash":"1287255079346344964","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0006203","count":1},{"id":"GO:0050992","count":1},{"id":"GO:1901907","count":1},{"id":"GO:0016077","count":1}]},{"hash":"435677599034526637","title":"Transcription Regulation and Oxidative Stress","description":"The top GO terms cluster around regulation of RNA polymerase II\u2013mediated transcription (negative regulation, DNA-templated transcription) and oxidative stress/redox homeostasis (cellular redox homeostasis, oxidant detoxification, cellular response to oxidative stress), suggesting a functional theme that combines transcriptional control with redox response. Some terms are odd or obsolete (viral process, glycerol ether metabolism), and the small size with no edges implies annotation noise or broad/dual annotations rather than a tightly connected protein complex.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0045454","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0006662","count":1},{"id":"GO:0055114","count":1}]},{"hash":"456820953622066087","title":"Osmoregulation and Ion Transport","description":"Based on GO terms, these proteins are linked to transmembrane transport of monoatomic ions, cellular response to osmotic stress, and intracellular water homeostasis. The shared theme is maintaining cellular osmotic balance through ion movement across membranes.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034220","count":1},{"id":"GO:0071470","count":1},{"id":"GO:0009992","count":1}]},{"hash":"322111479296076144","title":"RNA processing and translation initiation regulation","description":"This cluster is enriched for post-transcriptional gene expression control: regulation of translation initiation, preinitiation complex formation, and small-subunit processome assembly, plus splicing regulation and mRNA stability. Although a few terms (blastocyst formation, viral translation termination-reinitiation) seem noisy, the dominant signal centers on RNA processing and translation regulation.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0034462","count":2},{"id":"GO:0001825","count":2}]},{"hash":"254437064367055660","title":"Chromatin remodeling and transcription regulation","description":"The cluster\u2019s strongest signals are around chromatin dynamics and transcription control: DNA-templated transcription, nucleosome disassembly, histone displacement, and N-terminal histone acetylation. These converge on chromatin remodeling as a key regulator of gene expression. A few outlier terms (e.g., uterus morphogenesis, foam cell differentiation) may reflect broader, context-dependent transcription roles, but the core theme remains chromatin-mediated transcription regulation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0018076","count":1},{"id":"GO:0001207","count":1},{"id":"GO:0031496","count":1},{"id":"GO:0061038","count":1}]},{"hash":"1983847423393257370","title":"Chromatin modification and transcription regulation","description":"This cluster\u2019s terms cluster around chromatin remodeling (histone acetylation, nucleosome disassembly) and transcription control (regulation of transcription from RNA Pol II promoter), suggesting a shared role in chromatin-based gene regulation. Other terms present (mating-type switching, uterus morphogenesis, foam cell differentiation) appear unrelated and likely reflect background noise in a small, sparsely connected set. With limited data and some discordant terms, a Medium confidence is appropriate.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018076","count":1},{"id":"GO:0001207","count":1},{"id":"GO:0031496","count":1},{"id":"GO:0061038","count":1},{"id":"GO:0006337","count":1}]},{"hash":"2168348785081522377","title":"Unknown","description":"The GO terms cover a mix of biosynthetic processes, RNA and histone modifications, transcription regulation, and stress responses, with no single dominant function tying them together for this small cluster. This lack of a cohesive theme makes it inappropriate to assign a specific, reliable label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":1},{"id":"GO:0010189","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0017000","count":1}]},{"hash":"1525171748229148569","title":"Redox Homeostasis and Hydrogen Peroxide Response","description":"Based on the top GO terms, the cluster is dominated by redox-related processes (cellular redox homeostasis, hydrogen peroxide catabolic process, cellular oxidant detoxification, and cellular response to hydrogen peroxide), suggesting proteins that cooperate in oxidative stress management. Other terms like I-kappaB phosphorylation and spermatogenesis appear as secondary annotations but do not define the main function of the cluster.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0042744","count":2},{"id":"GO:0018171","count":2},{"id":"GO:0007252","count":2}]},{"hash":"2242674244141286279","title":"ER-Golgi vesicle trafficking and TORC1 signaling","description":"The top GO terms show multiple vesicle transport processes between the ER and Golgi and retrograde transport between Golgi and ER, along with TORC1 signaling and GTPase regulation, pointing to a cluster centered on secretory-pathway trafficking with related signaling. While mRNA transport and cell division terms appear, they are less central to the core theme. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006888","count":2}]},{"hash":"16296537627144212","title":"Spliceosome-mediated mRNA splicing and translation initiation","description":"The top GO terms strongly point to spliceosome-driven mRNA processing (regulation of alternative splicing, cis-splicing) and related steps, plus components of translation initiation (preinitiation complex formation, small-subunit processome assembly). Despite some obsolete terms, the core signal ties RNA splicing to the early stages of translation, justifying a combined label that reflects both processes.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0045292","count":2},{"id":"GO:1902625","count":1},{"id":"GO:0006446","count":1}]},{"hash":"1446817243088711391","title":"Nuclear gene expression regulators","description":"These proteins show GO terms centered on nuclear gene regulation: transcription by RNA polymerase II, transcription-coupled nucleotide-excision repair, nuclear mRNA surveillance, and chromatin-related regulation, plus protein turnover controls (deneddylation/proteasome) that influence expression. Although one term touches translation initiation, the prominent theme is nuclear control of gene expression and genome maintenance, justifying a label around Nuclear gene expression regulators.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071033","count":1},{"id":"GO:0090052","count":1},{"id":"GO:0032436","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0000122","count":1}]},{"hash":"15379016460776679","title":"RNA processing and ribosome biogenesis","description":"The dominant terms point to RNA metabolism and ribosome assembly: tRNA processing, rRNA processing, 90S preribosome assembly, and RNA-templated transcription/termination. There are related but secondary signals about translational initiation and mRNA poly(A) tail regulation, supporting a broader theme of gene expression control at the RNA level. A couple of terms (e.g., stress response and isoprenoid biosynthesis) are less connected. Overall, the cluster appears to consolidate RNA processing and ribosome biogenesis functions.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000676","count":1},{"id":"GO:0050992","count":1},{"id":"GO:0045948","count":1},{"id":"GO:0006353","count":1},{"id":"GO:0034463","count":1}]},{"hash":"1964267336004195938","title":"Small Molecule Catabolism","description":"The proteins appear linked to degradation/metabolism of diverse small molecules, as reflected by GO terms for sorbitol, furaldehyde, retinol, and amino acid catabolic pathways (with some obsolete terms). The terms point to a broad metabolic focus rather than a single, cohesive pathway, so a general \u201csmall molecule catabolism\u201d label fits best.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006062","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0033859","count":1},{"id":"GO:0000947","count":1},{"id":"GO:0018119","count":1}]},{"hash":"957878327713686982","title":"Neural development and axon guidance","description":"The set includes terms about retinal ganglion cell axon guidance, optic nerve morphogenesis, corpus callosum development, dendritic spine morphogenesis, trans-synaptic signaling, and cellular response to retinoic acid, as well as hedgehog pathway regulation, all pointing to neural development and neural connectivity. Although a couple terms relate to other tissues (roof of mouth and digestive tract morphogenesis), those appear less central. This coherence supports a label of Neural development and axon guidance. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050798","count":2},{"id":"GO:0099557","count":2},{"id":"GO:0060021","count":2},{"id":"GO:0060997","count":2},{"id":"GO:0048546","count":2}]},{"hash":"507601135137036504","title":"PLP-dependent amino acid metabolism","description":"GO terms center on PLP-dependent enzymes and amino acid catabolism (e.g., protein-pyridoxal-5-phosphate linkage; alanine, threonine, cysteine pathways; kynurenic acid biosynthesis). This suggests a cluster of PLP-dependent enzymes involved in amino acid metabolism. Some terms related to fatty acid homeostasis and plant defense may be pleiotropic noise, but the PLP\u2013aa metabolism signal is the strongest unifying theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034276","count":2},{"id":"GO:0018272","count":2},{"id":"GO:0055089","count":2},{"id":"GO:0042218","count":2},{"id":"GO:0070814","count":2}]},{"hash":"2073040368952991781","title":"Gram-negative cell wall biosynthesis and division","description":"The top GO terms point to Gram-negative bacterium-type cell wall biogenesis, peptidoglycan biosynthesis, cell wall organization, and cell division, indicating proteins involved in bacterial cell envelope synthesis and division. Some obsolete terms and unrelated annotations appear, but the core signal centers on Gram-negative cell wall biosynthesis and division.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0043164","count":1},{"id":"GO:0051301","count":1}]},{"hash":"2219841742122710332","title":"Cardiac metabolism and vascular signaling","description":"These proteins appear to coordinate pathways relevant to cardiac energy metabolism and vascular development, including glycogen metabolism and its regulation, the mevalonate/isoprenoid biosynthetic pathway, and processes linked to cardiac hypertrophy and blood vessel branching. While some terms reflect general stress or toxin responses, the strongest shared themes point to heart-related metabolic signaling and vascular remodeling.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900486","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0060316","count":2},{"id":"GO:0010288","count":2},{"id":"GO:0031987","count":2}]},{"hash":"1150652819432036866","title":"Organelle Protein Import and Turnover","description":"The GO terms indicate intracellular trafficking (ER-Golgi transport, mitochondrial inner membrane insertion, peroxisome import) plus turnover/quality control (autophagosome maturation, ubiquitin-specific protease regulation, oxidation-dependent protein catabolism), with supporting basic processes like ribosome assembly and microtubule severing. This points to a theme of organelle protein handling and maintenance, hence the label.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0097352","count":2},{"id":"GO:0032979","count":2},{"id":"GO:2000158","count":2}]},{"hash":"988580778827837007","title":"Hypoxia-Driven Vascular Remodeling","description":"The top GO terms center on cellular responses to low oxygen, angiogenesis regulation, and vascular wound healing, with supporting links to metabolism and inflammatory signaling. This suggests proteins coordinating vascular adaptation and tissue remodeling under hypoxic stress, rather than a single enzymatic function.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":1},{"id":"GO:0016525","count":1},{"id":"GO:0006096","count":1},{"id":"GO:0031639","count":1},{"id":"GO:0030855","count":1}]},{"hash":"348754048484976152","title":"Developmental signaling and morphogenesis","description":"The GO terms center on development (CNS development, branching morphogenesis), and cellular responses to stimuli (insulin, ethanol) with associated adhesion and calcium signaling terms, suggesting the proteins participate in signaling pathways guiding tissue morphogenesis and response to cues.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0007417","count":1},{"id":"GO:0071638","count":1},{"id":"GO:0071460","count":1},{"id":"GO:0048754","count":1}]},{"hash":"2283585928193709461","title":"RNA Stability and Translational Regulation","description":"The GO terms center on post-transcriptional control, including mRNA stability (especially under stress), regulation of translational initiation and preinitiation complex formation, and RNA processing/miRNA-mediated inhibition of translation. This suggests the proteins in the cluster function together to regulate RNA stability and the initiation of translation.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":3},{"id":"GO:1902625","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0034462","count":2}]},{"hash":"1700119180228569777","title":"Regulation of Skeletal Muscle Differentiation and Regeneration","description":"The cluster\u2019s terms include negative regulation of striated muscle cell differentiation and skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration, suggesting a theme of modulating muscle development and repair. A few kinase and chromatin-related terms appear, but the dominant signal points to muscle differentiation/regeneration regulation, making this a plausible high-level label for the cluster.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":1},{"id":"GO:0051154","count":1},{"id":"GO:0014834","count":1},{"id":"GO:1904772","count":1},{"id":"GO:0071440","count":1}]},{"hash":"1847382181468835158","title":"Neural development and mitochondrial energy metabolism","description":"The top GO terms point to brain development (brain development, substantia nigra development, cerebellum development) alongside energy-related processes (phosphocreatine biosynthetic process, creatine metabolic process) and mitochondrial complex I/IV assembly, suggesting a cluster of proteins involved in neuronal development with a focus on energy production/handling. The presence of neuronal stress response and phosphorylation terms further supports a neural context where energy regulation is crucial. This combination is plausibly connected, though based on a small set of proteins, so the label is best described as moderately confident.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":1},{"id":"GO:0030644","count":1},{"id":"GO:0021762","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0016310","count":1}]},{"hash":"1109175934526548405","title":"Chaperone-assisted protein folding","description":"This cluster is best described by a core signal of protein folding and chaperone activity, as evidenced by GO:0042026 (protein refolding) and GO:0070389 (chaperone cofactor-dependent protein refolding). While other GO terms present (redox homeostasis, tRNA import, nuclear membrane processes) are diverse, they appear less central to the cluster\u2019s primary function. Therefore, the label foregrounds proteostasis and chaperone-mediated folding.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0035719","count":2},{"id":"GO:0042026","count":2},{"id":"GO:0010198","count":2}]},{"hash":"2231402518181251247","title":"Metabolic Regulation and Insulin Signaling","description":"This cluster shows enrichment for several metabolic processes (D-gluconate metabolism, fatty acid beta-oxidation, carnitine catabolic process) along with redox homeostasis and insulin-related responses (response to insulin, negative regulation of insulin secretion). While a couple of terms relate to tRNA modification, the strong metabolic and insulin-related signals suggest a core theme around energy metabolism and insulin signaling. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0101030","count":1},{"id":"GO:0008616","count":1},{"id":"GO:0032868","count":1},{"id":"GO:0019521","count":1},{"id":"GO:0045454","count":1}]},{"hash":"2403998359449805","title":"Unknown","description":"The top GO terms are highly diverse, including kinase activity regulation, redox homeostasis, tRNA import, protein refolding, developmental signaling, oligomerization, nuclear membrane fusion, and axonemal assembly. With only three proteins and a single edge, there is no cohesive shared function or process linking them, so a single representative label cannot be derived.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0035719","count":1},{"id":"GO:0042026","count":1},{"id":"GO:0010198","count":1}]},{"hash":"985320999370901545","title":"MAPK signaling regulation and cell cycle","description":"The top GO terms cluster around regulation of signaling and division, notably negative regulation of the ERK/MAPK cascade and cell cycle/cytokinesis control, along with related kinase activity, transcription, and GTPase regulation. This suggests a cohesive module of signaling pathway regulation linked to cell cycle progression, with some auxiliary stress and differentiation connections.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070373","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0032465","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1681568074777570769","title":"Unknown","description":"There are no shared GO terms or connections among the proteins (no edges, no triangles, empty Top Terms), so there is no clear common function to label the cluster. The lack of functional signals makes it appropriate to assign Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1085623850985368559","title":"Spindle assembly and microtubule dynamics","description":"The top GO terms are dominated by mitosis and microtubule-related processes (mitotic spindle attachment to kinetochores, spindle pole separation, metaphase chromosome alignment, and nuclear migration along microtubules), indicating a cluster centered on spindle organization and microtubule dynamics. Some terms about neural structure or stem cell homeostasis likely reflect shared cytoskeletal components rather than core cluster function, but the strongest signal is spindle/microtubule regulation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0099607","count":3},{"id":"GO:1990535","count":3},{"id":"GO:0001560","count":3},{"id":"GO:0000073","count":3},{"id":"GO:0007080","count":3}]},{"hash":"129758878030721543","title":"Protein quality control via ubiquitin and autophagy","description":"The cluster shows enrichment for ubiquitin-related processes (sumoylation, deubiquitination, ER-associated ubiquitin-dependent degradation), autophagy/mitophagy, and aggresome formation, plus regulation of endocytosis. Together these terms point to a cohesive role in identifying, sequestering, and degrading damaged or misfolded proteins and organelles via ubiquitin-proteasome and autophagy pathways.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":3},{"id":"GO:1904021","count":2},{"id":"GO:0016579","count":2},{"id":"GO:0070842","count":2},{"id":"GO:1900186","count":2}]},{"hash":"103409317979937328","title":"Mitochondrial dynamics and cytoskeleton","description":"This cluster centers on processes linked to mitochondria, including fission, fragmentation during apoptosis, and mitochondrion localization that is microtubule-dependent, suggesting a core theme of mitochondrial dynamics and cytoskeletal transport. Several terms also touch on cytoskeletal/cell division-related processes (e.g., septum and lipid tube assembly) and energy-demanding functions like muscle development and locomotion, which are connected to mitochondrial activity. Taken together, the data imply a cohesive theme around mitochondrial dynamics intertwined with cytoskeletal organization, hence the label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090529","count":1},{"id":"GO:1901741","count":1},{"id":"GO:0034643","count":1},{"id":"GO:0000266","count":1},{"id":"GO:0008344","count":1}]},{"hash":"2110308649882722955","title":"Cell Cycle and Ribosome Biogenesis","description":"The cluster is dominated by cell division and cell cycle terms, plus ribosome biogenesis and translation-related activities, suggesting proteins tied to growth and protein synthesis; a few RNA processing and stress-response terms appear as incidental or multi-functional signals.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:2000767","count":1},{"id":"GO:0090529","count":1},{"id":"GO:0042254","count":1}]},{"hash":"2224495833793379726","title":"Unknown","description":"The top terms cover a mix of apoptosis, telomere maintenance, piRNA processing, smooth muscle development, synaptic function, spine morphogenesis, learning, and ubiquitination regulation. There isn\u2019t a single coherent biological function tying these terms together, though some terms hint at neuronal processes while others are unrelated (germline and genome stability). Therefore no representative theme emerges for this cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0032212","count":1},{"id":"GO:0034587","count":1},{"id":"GO:0048745","count":1},{"id":"GO:0051968","count":1}]},{"hash":"368176584588676070","title":"Unknown","description":"Top GO terms are highly diverse, spanning cell cycle, development, vision, muscle fusion, hypoxia response, ABA signaling, protein autophosphorylation, neuronal signaling, and apoptosis, with no clear unifying function. This lack of cohesive theme suggests no obvious common biological role for the cluster.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0007601","count":2},{"id":"GO:0007520","count":2},{"id":"GO:0071456","count":2}]},{"hash":"1228489221882443298","title":"Unknown","description":"The three proteins show GO terms spanning several unrelated processes: SRP-dependent protein targeting to membranes and cell division (bacterial/membrane biogenesis), bacterial flagellum organization, and immune/viral response plus RNA processing and kinase regulation. This mixture suggests no single, cohesive function tying the cluster together, so a unique, specific label isn\u2019t supported.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006617","count":1},{"id":"GO:0044781","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1}]},{"hash":"529510537249799338","title":"Membrane Biogenesis and LPS Synthesis","description":"The cluster shows GO terms centered on membrane- and envelope-associated processes, notably lipopolysaccharide biosynthesis and protein insertion/targeting to membranes, with ancillary hints from extracellular polysaccharide biosynthesis. While other terms (cell cycle, metabolism) are less connected, the membrane-related functions provide the most coherent theme for the cluster. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0045226","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0045048","count":1},{"id":"GO:0006620","count":1}]},{"hash":"572800972318456089","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":2},{"id":"GO:0045716","count":1},{"id":"GO:2000637","count":1},{"id":"GO:0048024","count":1},{"id":"GO:2000627","count":1}]},{"hash":"2077656782694169493","title":"Axon guidance and neuronal projection extension","description":"This cluster is dominated by GO terms tied to axon extension and neuron projection guidance (axon extension involved in axon guidance; sympathetic neuron projection extension; branchiomotor neuron axon guidance; trigeminal nerve structural organization), indicating a neural development theme focused on axon pathfinding and neural connectivity. A few terms about endosome localization and morphogenesis appear as supporting processes often linked to development, but the primary signal is axon guidance and neuronal projection.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048846","count":1},{"id":"GO:1902946","count":1},{"id":"GO:0021637","count":1},{"id":"GO:0060666","count":1},{"id":"GO:0061441","count":1}]},{"hash":"815809706702360795","title":"Telomere and Mating-Type Heterochromatin Silencing","description":"The cluster\u2019s GO terms are dominated by heterochromatin maintenance and silencing at telomeres, subtelomeres, and the silent mating-type cassette, indicating a chromatin-silencing module centered on telomere/subtelomere and mating-type loci.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006344","count":3},{"id":"GO:0061186","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0031939","count":3},{"id":"GO:0030466","count":3}]},{"hash":"1290418699159952532","title":"Unknown","description":"The top GO terms are scattered across redox/homeostasis, signaling, various catabolic processes, and a few development-related terms, with no clear, single functional theme tying the proteins together.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0006103","count":1},{"id":"GO:0006214","count":1}]},{"hash":"213464636249134542","title":"ER and Mitochondrial Proteostasis","description":"The top GO terms cluster around protein quality control and turnover across the ER and mitochondria, including ER unfolded protein response, ERAD, aggresome formation, autophagosome maturation, and protein processing, as well as mitochondrial-related processes like complex III assembly, inner membrane insertion, and regulation of mtDNA replication. This suggests a cohesive theme of proteostasis and organelle stress management spanning ER and mitochondria, with some generic terms (e.g., cell division) likely reflecting broader cellular housekeeping. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0034551","count":1},{"id":"GO:0097352","count":1},{"id":"GO:0070842","count":1}]},{"hash":"74250762575387770","title":"Beta-lactam Antibiotic Response","description":"This cluster centers on beta-lactamrelated processes: regulation of beta-lactamase activity, beta-lactam antibiotic catabolic processes, and general response to antibiotics, with nylon catabolic activity as a related metabolic note. A few terms are unrelated or incidental (e.g., visual perception, platelet degranulation), but the dominant theme is antibiotic/\u03b2-lactam metabolism, suggesting a module involved in processing or responding to beta-lactam antibiotics.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033252","count":2},{"id":"GO:0030655","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0019876","count":2},{"id":"GO:0006469","count":1}]},{"hash":"1366341767617581876","title":"Developmental signaling and apoptosis regulation","description":"The top GO terms cluster around regulation of apoptosis (positive regulation and Wnt-mediated negative regulation) and developmental processes (cranial skeletal development, dorsal identity), with additional hints of cell adhesion and intracellular transport. This suggests a set of proteins involved in coordinating developmental signaling with cell survival decisions, rather than a single, narrow function. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":3},{"id":"GO:0051561","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0042144","count":3}]},{"hash":"1151878971856048420","title":"Cofactor and Metabolite Biosynthesis","description":"The GO terms center on biosynthetic processes for cofactors and small molecules (ubiquinone, vitamin E, antibiotic and juvenile hormone biosynthesis) and related metabolite processing, with additional entries for RNA and protein modification, suggesting a broad cluster linked to biosynthesis and modification of diverse metabolites and cofactors.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":2},{"id":"GO:0035573","count":2},{"id":"GO:0010189","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0017000","count":2}]},{"hash":"2037485021834248591","title":"Unknown","description":"The GO terms span disparate processes (limb development, meiotic segregation, embryonic axis specification, transcription, glycosylation, cellulose biosynthesis, cell wall organization) with no clear shared function or coherent biological theme. No edges present, so there is insufficient signal to define a meaningful cluster label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060173","count":1},{"id":"GO:0045144","count":1},{"id":"GO:0006311","count":1},{"id":"GO:0008595","count":1},{"id":"GO:0007406","count":1}]},{"hash":"2265366402169359859","title":"Blue-light phototransduction and cyclic nucleotide signaling","description":"The top GO terms cluster around blue light signaling and signaling via cyclic nucleotides (cGMP and cAMP). Terms include blue light signaling pathway, receptor guanylyl cyclase signaling pathway, cGMP and cAMP biosynthesis, and related adenylyl cyclase pathways, pointing to a phototransduction/second-messenger signaling module. A few terms about transcription regulation seem incidental rather than core to this theme. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009785","count":1},{"id":"GO:0035556","count":1},{"id":"GO:0071880","count":1},{"id":"GO:0052565","count":1},{"id":"GO:0007168","count":1}]},{"hash":"1583802751009289286","title":"Wnt Signaling in Embryonic Development","description":"The top GO terms cluster around canonical Wnt signaling and developmental processes: Wnt pathway involvement in apoptosis regulation, cranial skeletal development, dorsal axis patterning, kidney (renal vesicle) formation, and cell adhesion (adherens junction) with EMT regulation. This combination points to a developmental/morphogenetic program in embryogenesis guided by Wnt signaling, rather than a single narrow function, suggesting a cohesive theme of embryonic development and organogenesis influenced by Wnt signaling.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0044336","count":2},{"id":"GO:1904888","count":2},{"id":"GO:2000017","count":2},{"id":"GO:0034333","count":2},{"id":"GO:0072033","count":2}]},{"hash":"2235150870134819672","title":"Xenobiotic and hormone metabolism","description":"The top GO terms are dominated by xenobiotic, estrogen, ethanol, and flavonoid metabolic processes, pointing to detoxification and hormone-related metabolism. Additional terms like sulfation and glycosaminoglycan biosynthesis align with broader small-molecule processing and post-translational modification, but the core signal is xenobiotic/hormone metabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006711","count":1},{"id":"GO:0006805","count":1},{"id":"GO:0030210","count":1},{"id":"GO:0006478","count":1},{"id":"GO:0030573","count":1}]},{"hash":"1280092426072786061","title":"Unknown","description":"The top GO terms are diverse (development, neural signaling, transcription, apoptosis, lipid biosynthesis regulation, muscle development) with an outlier plant hormone signaling term, showing no single cohesive function for this cluster. Unknown function label is therefore most appropriate.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0035249","count":2},{"id":"GO:0090153","count":2},{"id":"GO:0034351","count":2}]},{"hash":"1340235979818393054","title":"Unknown","description":"Top terms are diverse: telomere maintenance/capping, cerebellar neuron differentiation, immune signaling (chemokine, IL-12, NF-kappaB), kinase activity regulation, vitamin D response, and protein ADP-ribosylation. There is no single coherent function linking all proteins, so a specific label cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":1},{"id":"GO:0021707","count":1},{"id":"GO:1904355","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0007253","count":1}]},{"hash":"632258002996472500","title":"Unknown","description":"The top GO terms are diverse, spanning telomere maintenance and capping, neural differentiation, immune signaling, kinase regulation, vitamin D response, and post-translational modifications, with no single cohesive function tying the proteins together in this small cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0021707","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071651","count":3},{"id":"GO:0007253","count":3}]},{"hash":"629692843417436139","title":"Unknown","description":"The top GO terms are very diverse, covering telomere maintenance/capping, neural differentiation, immune signaling, NF-kappaB regulation, cytokine production, dendrite development, kinase activity regulation, vitamin D response, and protein ADP-ribosylation. There is no evident shared pathway or function linking these proteins, and the cluster has no interactions, so a cohesive biological theme cannot be established.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0021707","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0071651","count":3},{"id":"GO:0007253","count":3}]},{"hash":"943058923705317297","title":"Neural development and behavior","description":"The GO terms are dominated by neural development and neuromuscular function, including lateral ventricle development, axon target recognition, neuromuscular process, adult walking behavior, and eating behavior. These indicate a common theme around nervous system development and behavioral outputs. Some terms about MAP kinase regulation and macrophage homeostasis suggest additional signaling or immune-related roles but do not override the overarching neural focus, so the label reflects the primary function of the cluster as neural development and behavior.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021670","count":1},{"id":"GO:0007385","count":1},{"id":"GO:0002931","count":1},{"id":"GO:0043407","count":1},{"id":"GO:0007628","count":1}]},{"hash":"1102430895919012493","title":"Unknown","description":"The top GO terms cover diverse, mostly unrelated processes: membrane targeting, fungal cell wall beta-glucan biosynthesis, unfolded protein response, iron-sulfur cluster assembly, DNA replication, and various \"negative regulation\" terms including heat response and apoptotic signaling, plus karyogamy. The set lacks a single coherent biological function or pathway tying the proteins together, and with no edges, it\u2019s unclear if these proteins share a common role.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031204","count":1},{"id":"GO:0070880","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0016226","count":1},{"id":"GO:1900035","count":1}]},{"hash":"640844483668087713","title":"Glutamatergic Synapse Regulation and Plasticity","description":"The cluster is driven by GO terms focused on glutamatergic synaptic transmission, GPCR signaling, trans-synaptic signaling, and dendritic spine morphogenesis, pointing to neuronal communication and long-term synaptic plasticity. While some terms touch on development or immune processes, the strongest, recurring themes relate to synaptic regulation and plasticity.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050798","count":2},{"id":"GO:0051966","count":2},{"id":"GO:0048169","count":2},{"id":"GO:0038042","count":2},{"id":"GO:0007626","count":2}]},{"hash":"2021298789781086580","title":"TLR-mediated inflammatory cytokine signaling","description":"The GO terms cluster around Toll-like receptor signaling (including TLR8) and cytokine production (IL-1, IL-18, interferon-alpha) with positive regulation of inflammatory responses, suggesting a core function in innate immune signaling and inflammation; some terms like ER stress and ufmylation may reflect secondary or contextual associations.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034976","count":1},{"id":"GO:1990592","count":1},{"id":"GO:0031987","count":1},{"id":"GO:0046331","count":1},{"id":"GO:0032741","count":1}]},{"hash":"1275293629342351020","title":"NF-kB\u2013driven innate antiviral signaling","description":"These three proteins cluster around innate immune activation and NF-\u03baB signaling, with strong terms for innate immune response, defense against virus, and regulation of canonical and non-canonical NF-kappaB pathways, plus ubiquitination. The combination suggests a shared role in antiviral signaling and inflammatory regulation rather than a general metabolic function, despite a few tangential terms related to T cell differentiation. Overall, the theme is innate antiviral signaling mediated by NF-kB and related ubiquitin controls.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0061470","count":1},{"id":"GO:0000185","count":1}]},{"hash":"537825131335599397","title":"Unknown","description":"No common GO terms are given and the three proteins form only a single edge with no triangles, offering no shared biological meaning to group them. Consequently, a precise functional label cannot be inferred.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"2272216865857431261","title":"Plant seed development and vernalization regulation","description":"This cluster centers on plant-specific developmental processes, notably seed development and vernalization, with associated histone modification terms implying epigenetic regulation of these programs.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048316","count":1},{"id":"GO:0016574","count":1},{"id":"GO:0016571","count":1},{"id":"GO:2001229","count":1},{"id":"GO:0010048","count":1}]},{"hash":"845577287393558889","title":"Acetylation and polyamine metabolism","description":"Most GO terms cluster around acetylation events across diverse substrates (N-terminal, peptidyl-lysine, spermidine, histone-like) and polyamine metabolism (spermidine acetylation, putrescine catabolic process). Additional metabolic pathways (arginine biosynthesis, glucosamine, mycothiol) and sporulation enrichment suggest these proteins participate in broad acetylation-linked metabolic processes, including polyamine handling, with some sporulation-related signaling.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032918","count":2},{"id":"GO:0009447","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0006526","count":2},{"id":"GO:0018002","count":2}]},{"hash":"389482657282371637","title":"Synaptic signaling and plasticity","description":"The GO terms cluster around neuronal communication and synaptic modulation, including regulation of synaptic transmission (glutamatergic), trans-synaptic signaling, dendritic spine morphogenesis, and long-term synaptic plasticity, along with GPCR signaling and behavior. The presence of a few developmental and morphogenesis terms appears incidental; overall the dominant signal points to synaptic signaling and neuronal plasticity.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050798","count":1},{"id":"GO:0051966","count":1},{"id":"GO:0048169","count":1},{"id":"GO:0038042","count":1},{"id":"GO:0007626","count":1}]},{"hash":"519105931964866908","title":"Unknown","description":"The GO terms are highly diverse, spanning RNA processing (tRNA editing), ion transporter regulation, various developmental processes (mesoderm and heart/coronary development), and growth signaling (Hippo). With only three proteins and no consistent shared function, there is no clear single theme to name the cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000235","count":1},{"id":"GO:2000650","count":1},{"id":"GO:2000146","count":1},{"id":"GO:1901165","count":1},{"id":"GO:0031384","count":1}]},{"hash":"1080009423075361599","title":"Unknown","description":"The top terms span disparate processes (eye lens differentiation, rRNA processing, ubiquitin-dependent protein degradation, neural tube development, chromatin modification, DNA repair, and fungal cell wall biogenesis) with no clear shared function. The cluster has 3 proteins but no edges, so there is no coherent functional theme to assign a specific label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:2000060","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1}]},{"hash":"83551493546253276","title":"Regulation of Signaling and Metabolic Processes","description":"The top GO terms point to diverse regulatory roles across cellular processes (kinase activity, transcription, protein catabolism, apoptosis, membrane signaling like MAPK), rather than a single shared pathway. This suggests the cluster represents multifunctional regulators involved in various signaling and metabolic regulation rather than a specific function. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903538","count":1},{"id":"GO:0000188","count":1},{"id":"GO:0000060","count":1},{"id":"GO:0006672","count":1},{"id":"GO:0045945","count":1}]},{"hash":"1183632867805627079","title":"Unknown","description":"This cluster's GO terms are highly heterogeneous with no single unifying function. They touch on development processes (lens fiber differentiation, neural tube closure), RNA processing and rRNA cleavage, DNA repair, ubiquitin-mediated proteolysis, histone modification, microtubule-based movement, and gene regulation, with each term represented by only one protein. Because there is no coherent theme linking all proteins, a confident, specific label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070306","count":1},{"id":"GO:0000447","count":1},{"id":"GO:2000060","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0032995","count":1}]}]