[{"hash":"1560918557489610961","title":"Epigenetic transcription regulation","description":"This cluster is enriched for GO terms pointing to chromatin remodeling and transcriptional control, notably histone demethylation (H3-K4/K36), DNA-templated transcription, and regulation of signaling pathways (Notch, hypoxia) that influence gene expression; additional hydroxylation terms may reflect post-translational modifications of transcription-related proteins, supporting a cohesive theme of epigenetic regulation of transcription.","confidence":"High","size":29,"edges":5,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070544","count":10},{"id":"GO:0034720","count":10},{"id":"GO:0036138","count":9},{"id":"GO:0042265","count":9},{"id":"GO:0061428","count":9}]},{"hash":"52017270715995233","title":"Axon growth and cytoskeletal remodeling","description":"The cluster shows multiple GO terms centered on axon biology and cytoskeletal dynamics, including axonal fasciculation, axon extension involved in guidance, and regulation of Rho signaling, which together point to neuronal cytoskeletal remodeling and axon pathfinding. There are also terms related to actin cytoskeleton reorganization and ubiquitin-related deubiquitination that could modulate these signaling pathways, supporting a theme of regulated cytoskeletal dynamics in neuronal development. While a few transport or miscellaneous terms appear, the dominant signal supports axon growth and cytoskeletal regulation.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035523","count":2},{"id":"GO:0070536","count":2},{"id":"GO:1902350","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0007413","count":2}]},{"hash":"315417058765035382","title":"Unknown","description":"The top terms span both eukaryotic cell adhesion processes (cell-matrix adhesion, substrate adhesion-dependent cell spreading) and diverse bacterial/metabolic processes (lipopolysaccharide biosynthetic process, sporulation, fatty acid alpha-oxidation, response to antibiotic, platelet aggregation; plus immune regulation terms). This broad, inconsistent mix provides no clear, single functional theme for the cluster, so an Unknown label with no confidence is appropriate.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0046013","count":4},{"id":"GO:0007160","count":4},{"id":"GO:0070527","count":4},{"id":"GO:0009103","count":4}]},{"hash":"2215007809196133994","title":"Innate Immune Signaling and Transcription Regulation","description":"The terms point to innate immune response and defense against virus, along with regulation of signaling pathways (Ras, NF-kappaB) and transcription, plus ubiquitination. This suggests a cluster of proteins that coordinate immune signaling and transcriptional control, potentially via post-translational regulation, even though a few terms (otolith morphogenesis, chloroquine response) may reflect broader or incidental annotations. Overall, a cohesive theme around immune-related signaling and transcription regulation. ","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046580","count":4},{"id":"GO:0016525","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0045087","count":3}]},{"hash":"1309948807632888570","title":"Cell Cycle and Ribosome Biogenesis Regulation","description":"This cluster is enriched for mitotic cell cycle and cell division, together with ribosome biogenesis and formation of the translation preinitiation complex, indicating a coordinated program of protein synthesis during cell proliferation. Regulatory signals such as positive regulation of GTPase activity and phosphorylation events suggest control of growth signaling, while mRNA transport and hypoxia response reflect broader regulatory layers during division and development.","confidence":"High","size":29,"edges":33,"triangles":7,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":7},{"id":"GO:0000278","count":6},{"id":"GO:0001731","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0051301","count":5}]},{"hash":"2015220052400099688","title":"Telomere maintenance and spindle assembly","description":"The terms converge on telomere maintenance (telomerase regulation, telomere localization) and mitotic spindle/centrosome functions (spindle assembly), implying a cohort coordinating chromosome end protection with chromosome segregation.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0051660","count":5},{"id":"GO:0032212","count":4},{"id":"GO:1904357","count":4},{"id":"GO:0051225","count":4},{"id":"GO:0070198","count":4}]},{"hash":"1671032102231335092","title":"Unknown","description":"The top GO terms are highly diverse (ubiquitin-dependent protein degradation; pericardium morphogenesis; GTPase activation/regulation; mitotic spindle assembly; circadian rhythm regulation; B cell receptor signaling; protein homooligomerization; RNA guanine-N7 methylation; forebrain development), with no single shared function linking them; the cluster also has no edges, suggesting a heterogeneous set rather than a cohesive pathway. None","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0003344","count":4},{"id":"GO:0090630","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0090307","count":4}]},{"hash":"2067845121553798020","title":"Golgi Organization and Retrograde Vesicle Transport","description":"The top GO terms point to Golgi organization and retrograde transport from the Golgi to the ER, as well as cytoplasm-to-vacuole targeting, indicating a central theme of vesicle trafficking and Golgi-ER dynamics. Although other terms (cell division, ephrin signaling, adherens junction organization, development) appear, they are less representative of the core function suggested by the dominant trafficking-related terms. Overall, the cluster appears to group proteins involved in intracellular vesicle trafficking and Golgi-related processes.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032258","count":5},{"id":"GO:0045740","count":4},{"id":"GO:0007030","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0051301","count":4}]},{"hash":"68799482745425502","title":"Neural development and neural progenitor proliferation","description":"The cluster is enriched for terms tied to nervous system development, including neuron projection development and neural precursor proliferation, as well as pituitary gland development and stem cell proliferation, suggesting proteins involved in neural development and progenitor cell growth. Other terms (rDNA heterochromatin formation, apoptotic process, transcription regulation, cAMP response) hint at broader regulatory roles but do not override the neural development theme. ","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0010976","count":6},{"id":"GO:0021983","count":5},{"id":"GO:2000648","count":5},{"id":"GO:0000183","count":5},{"id":"GO:0006915","count":5}]},{"hash":"1084023411267929472","title":"Cytoplasmic translation and ribosome assembly","description":"This cluster is strongly enriched for cytoplasmic translation terms (translation, cytoplasmic translation, cytoplasmic translational termination) and ribosomal large subunit assembly, pointing to proteins involved in the protein-synthesis machinery. The presence of mitochondrial-related GO terms (mitochondrial respiratory chain complex II assembly, mitochondrial electron transport) and Fe-S cluster assembly suggests some paralogs with dual roles or linked cofactors, possibly reflecting mitochondrial biogenesis or shared cofactors with translation factors. The antibiotic and cAMP response terms may reflect stress-related modulation of translation. Overall, the core theme is ribosome function and protein synthesis, with auxiliary mitochondrial-associated processes.","confidence":"Medium","size":28,"edges":318,"triangles":2029,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0051591","count":2},{"id":"GO:0002184","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1093846107082580383","title":"Genome maintenance and chromatin dynamics","description":"This cluster centers on genome maintenance and chromatin dynamics, as shown by GO terms related to DNA replication and repair (G-quadruplex formation, D-loop disassembly, replication-born DSB repair via sister chromatid exchange), heterochromatin formation, and histone modification, all pointing to genome stability and chromatin remodeling. A few terms (cytokinin signaling, pituitary development, vesicle transport) appear peripheral or cross-species, but do not define the core theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007338","count":3},{"id":"GO:0071919","count":3},{"id":"GO:0061820","count":3},{"id":"GO:0009736","count":3},{"id":"GO:0000183","count":3}]},{"hash":"1498453298256457690","title":"Neural-immune development signaling","description":"GO terms cluster around neural development (axon extension, myelination, otolith morphogenesis) and innate immune pathways (TLR7 signaling, type II interferon production, cytokine regulation, diacyl lipoprotein detection), with sialic acid transport tying membrane-associated processes. This suggests a mixed but connected theme of neural development linked to innate immune signaling, rather than a single isolated function.","confidence":"Medium","size":28,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0048846","count":3},{"id":"GO:0015739","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0034154","count":2},{"id":"GO:0045078","count":2}]},{"hash":"149907351679643119","title":"Unknown","description":"The top GO terms include plant-specific processes (chlorophyll biosynthetic process, stamen formation, endodermal cell differentiation) and animal/adherence-related processes (integrin-mediated signaling, cell-matrix adhesion, cellular extravasation), plus ubiquitin-protein degradation (ubiquitin-dependent protein catabolic process, proteasome assembly). The mix spans multiple kingdoms and disparate functions, offering no single unifying theme to tie the proteins together. Therefore there isn't a coherent cluster function to name, so I label it Unknown with None confidence.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006268","count":5},{"id":"GO:0006511","count":4},{"id":"GO:0007229","count":4},{"id":"GO:0045123","count":4},{"id":"GO:0015995","count":4}]},{"hash":"905153284552653760","title":"Mitochondrial Transport and Stress Response","description":"The top GO terms cluster around mitochondrial function: multiple transports across mitochondrial and associated membranes (ornithine, phosphate), regulation of mitochondrial membrane potential, fatty acid and stress responses, and apoptotic mitochondrial changes, suggesting a cohesive mitochondria-centric module involved in transport, energy balance, and stress signaling.","confidence":"High","size":28,"edges":15,"triangles":0,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070542","count":17},{"id":"GO:0008637","count":14},{"id":"GO:1990314","count":14},{"id":"GO:0036233","count":14},{"id":"GO:0090152","count":14}]},{"hash":"1182267620003897932","title":"Endocannabinoid signaling and lipid catabolism","description":"This cluster is driven by lipid-related metabolic terms: regulation of endocannabinoid signaling pathway, triglyceride catabolic process, monoacylglycerol catabolic process, and phosphatidylserine catabolic process, pointing to a cohesive role in lipid metabolism and endocannabinoid signaling. Additional diverse terms (biotin biosynthesis, nitrogen utilization, dephosphorylation) suggest broader metabolism, but the lipid-centric terms are the strongest shared theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":8},{"id":"GO:0019433","count":8},{"id":"GO:0006660","count":7},{"id":"GO:0052651","count":7},{"id":"GO:0009102","count":5}]},{"hash":"1391063197780813544","title":"Unknown","description":"The GO terms cover apoptosis, GTPase activation, lens morphogenesis, responses to growth factors, immune homeostasis, sensory perception, protein tetramerization, and transport regulation, with no single shared function or interaction pattern, so a coherent cluster label isn\u2019t apparent.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0070309","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0097011","count":2}]},{"hash":"114460844599335009","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090502","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0006284","count":4},{"id":"GO:0070301","count":4},{"id":"GO:0042493","count":4}]},{"hash":"682046863447769468","title":"Unknown","description":"The Top terms span ion transport, telomere maintenance, cardiac pacemaker regulation, vasopressin secretion, pain perception, spindle assembly, and telomeric chromosome localization, showing no single cohesive function or pathway linking the proteins. This cluster appears heterogeneous rather than functionally coherent.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0032212","count":2},{"id":"GO:1904357","count":2},{"id":"GO:0098907","count":2},{"id":"GO:2000340","count":2}]},{"hash":"1407135676404388075","title":"Developmental and Immune Signaling","description":"This cluster centers on signaling pathways governing development and immune responses, with terms spanning cell migration, heart development, cytokine signaling (GM-CSF, IL-4, IL-7), T cell receptor signaling, and metabolic cues (insulin signaling and fat differentiation). While diverse, the shared theme is signaling programs that coordinate development and immune/metabolic processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0097011","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0035994","count":4}]},{"hash":"963728706388237307","title":"RNA Processing and Translation with Cytoskeletal Dynamics","description":"The cluster is dominated by RNA metabolism and protein synthesis terms (translation, regulation of translational fidelity, non-stop decay, mRNA processing), indicating a core RNA processing/translation theme. Additional terms point to cytoskeletal and cell-architecture processes (actin bundle assembly, cell migration, epithelial polarity, cell cycle), suggesting these RNA-related proteins may also be linked to cellular structure and division. Overall, the label captures the primary RNA-centric function with a nod to its structural context.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006450","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070481","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0090162","count":2}]},{"hash":"577517541123616954","title":"Cellular signaling and transcription regulation","description":"The set includes GO terms tied to signal transduction (GTPase activity regulation, NOD2 signaling, GPCR-related signaling), transcriptional control (DNA-templated transcription), and a common nexus with post-translational modification (ubiquitination) and cellular responses such as migration and mechanotransduction. The mix suggests a cluster centered on signaling cascades that influence transcription and cell behavior rather than a single precise pathway, hence a broad but coherent label.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2}]},{"hash":"443620496391717255","title":"Microtubule Transport and Centrosome Organization","description":"The cluster is dominated by GO terms describing microtubule-based transport and organization (plus-end-directed vesicle transport along microtubules, cytoplasmic microtubule organization, and microtubule anchoring at the centrosome), as well as related nuclear migration processes. While some entries touch on regulatory aspects like deubiquitination or signaling, the core theme is microtubule dynamics driving vesicle trafficking and centrosome-associated functions.","confidence":"High","size":27,"edges":40,"triangles":14,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0072383","count":4},{"id":"GO:0000743","count":3},{"id":"GO:0031122","count":3},{"id":"GO:0016330","count":3},{"id":"GO:0034454","count":3}]},{"hash":"1604361138007042496","title":"Aminoacyl-tRNA Synthetases and Translation","description":"Dominated by GO terms for methionyl-, leucyl-, and cysteinyl-tRNA aminoacylation, indicating involvement in translation and protein synthesis. Additional terms like actin filament bundle assembly and some developmental or redox/nitrate terms appear as outliers, but the recurring translation-related terms provide a coherent theme.","confidence":"Medium","size":27,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0030579","count":4},{"id":"GO:0008584","count":3},{"id":"GO:0060430","count":3},{"id":"GO:0051017","count":3}]},{"hash":"1417037508403143062","title":"Cell-cycle and nuclear processes","description":"This cluster is enriched for GO terms involving DNA-templated transcription, DNA replication, mitotic cell cycle, centrosome cycle, and regulation of nuclear transport, pointing to proteins that coordinate nuclear activities and cell division. The presence of development-related terms and Golgi transport regulation suggests broader roles, but the dominant theme is nuclear/cell cycle regulation.","confidence":"High","size":27,"edges":45,"triangles":37,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0007118","count":9},{"id":"GO:0046827","count":9},{"id":"GO:0009636","count":9}]},{"hash":"1582258753634263207","title":"RNA Splicing and Translation Regulation","description":"The cluster shows strong signals for post-transcriptional RNA processing and control of translation, with terms like mRNA splicing via spliceosome, regulation of mRNA stability, formation of translation preinitiation complex, translation reinitiation, and maturation of SSU-rRNA. Regulatory ncRNA-mediated gene silencing and related RNA processing terms further support a cohesive role in RNA processing rather than transcription initiation, despite a couple obsolete entries. Overall, these proteins likely participate in RNA maturation, splicing, and regulation of translation.","confidence":"Medium","size":27,"edges":15,"triangles":1,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":12},{"id":"GO:0048026","count":10},{"id":"GO:0031047","count":10},{"id":"GO:0001731","count":7},{"id":"GO:0045292","count":7}]},{"hash":"2078306163653666652","title":"Ephrin signaling and neuronal morphogenesis","description":"The GO terms show a clear theme of neuronal development, with emphasis on ephrin receptor signaling, axon extension, dendrite morphogenesis, and hippocampus development, suggesting roles in neurite outgrowth and synaptic differentiation. Calcium- and actin-dependent exocytosis and cytoskeletal regulation further support synaptic maturation and morphogenesis. Some terms like DNA replication and amino acid starvation response appear as outliers, but they do not negate the dominant neuronal development signal. ","confidence":"High","size":27,"edges":7,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0043552","count":23},{"id":"GO:0021766","count":23},{"id":"GO:0045956","count":23},{"id":"GO:0048013","count":23}]},{"hash":"738493738649059604","title":"Rho/Ras GTPase signaling and actin remodeling","description":"The cluster is enriched for small GTPase\u2013mediated signaling (Ras, Rho), including negative regulation of Ras and regulation of Rho signaling, together with actin-related processes (actin cortical patch assembly) and membrane remodeling (plasma membrane tubulation, membrane invagination). This points to a cohesive theme of cytoskeletal dynamics driven by GTPase signaling, with some developmental and immune-related terms appearing as broader context. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046580","count":3},{"id":"GO:0097320","count":3},{"id":"GO:0060348","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0007264","count":3}]},{"hash":"2102196273862758721","title":"Ubiquitin-Dependent Protein Degradation","description":"Most proteins in this cluster are annotated with ubiquitination-related processes (ubiquitin attachment, ubiquitin-dependent protein catabolic process, autoubiquitination, and specific linkages like K6 and K48) and ERAD, indicating a cohesive function in tagging proteins for degradation. Additional terms such as peroxisomal import and histone catabolic processes are present but less central to the core function. This supports a label centered on ubiquitin-mediated protein turnover.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":10},{"id":"GO:0051865","count":10},{"id":"GO:0042787","count":10},{"id":"GO:0016567","count":8},{"id":"GO:0085020","count":8}]},{"hash":"1060744179305244327","title":"Diverse Metabolic and Pigment Biosynthesis","description":"These proteins are enriched for a variety of biosynthesis and metabolism terms, including retinoid and retinal metabolism, retinol metabolism, melanin biosynthesis, androgen/steroid metabolism, poly-hydroxybutyrate biosynthesis, and antibiotic biosynthesis, with no detected interactions (Edges and Triangles are zero). The common thread is broad metabolic activity across pigment, hormone, and secondary metabolite pathways, rather than a single unifying process, so a label that captures \u201cdiverse metabolic and pigment biosynthesis\u201d is most representative.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0042619","count":8},{"id":"GO:0042574","count":6},{"id":"GO:0008209","count":6},{"id":"GO:0042572","count":6}]},{"hash":"2253164245681564287","title":"Unknown","description":"The top GO terms cover a mix of lipid and sterol metabolism (unsaturated fatty acids, ergosterol regulation), mitochondrial processes (inheritance, genome maintenance), and several unrelated roles (myelin maintenance, sebaceous gland differentiation, nitrate assimilation, response to food). This lack of a cohesive, single theme across the cluster makes it hard to assign a specific, representative function label.","confidence":"","size":27,"edges":37,"triangles":9,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006636","count":3},{"id":"GO:0006675","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0032286","count":2}]},{"hash":"467522016432827434","title":"Vesicle trafficking and cytoskeletal signaling","description":"This cluster centers on GO terms related to intracellular transport (ER-Golgi, general intracellular transport), vesicle exocytosis, and cytoskeletal regulation (Rho signaling, spindle assembly), plus development-related terms (brain development). The shared theme appears to be vesicle trafficking coupled with cytoskeletal dynamics that underpin both cellular division and neuronal development, with some terms touching on broader developmental processes like mating projection growth. ","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010796","count":7},{"id":"GO:0007420","count":7},{"id":"GO:2000300","count":6},{"id":"GO:0031384","count":6},{"id":"GO:0090307","count":5}]},{"hash":"61173315981426232","title":"Mitochondrial metabolism and protein assembly","description":"The cluster\u2019s GO terms point to mitochondrial-focused processes: protein heterooligomerization likely reflects assembly of mitochondrial protein complexes; maintenance of protein location in mitochondrion and tetrapyrrole (heme) metabolism tie to mitochondrial function and energy production; regulation of ATP metabolism and responses to metal ions (manganese) further support a mitochondrial energy/redox theme, with some entries potentially reflecting neuron-related mitochondrial roles. While the terms are diverse, the common thread appears to be mitochondrial metabolism and protein complex assembly.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051291","count":2},{"id":"GO:0072656","count":1},{"id":"GO:1903579","count":1},{"id":"GO:0010042","count":1},{"id":"GO:0032720","count":1}]},{"hash":"2278595125639094542","title":"DNA repair and cell cycle progression","description":"The prominent terms point to DNA damage response mechanisms (base-excision repair, DNA recombination) and signals promoting transition from G1 to S phase, suggesting a core function in maintaining genome integrity while advancing the cell cycle. Additional terms indicate cellular responses to oxidative stress and broader gene expression regulation, which often accompany DNA damage signaling. Some terms are obsolete or peripheral (metabolic regulation, transcription factors), but the central theme is genome maintenance coupled with cell cycle control.","confidence":"Medium","size":27,"edges":25,"triangles":1,"max_degree":16,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:1900087","count":10},{"id":"GO:0006284","count":10},{"id":"GO:0070301","count":10},{"id":"GO:0007568","count":9},{"id":"GO:1903507","count":9}]},{"hash":"429663792962739893","title":"Transcriptional Regulation & Cytoskeletal Dynamics","description":"The cluster is dominated by GO terms for DNA-templated transcription and its regulation, plus processes tied to the cytoskeleton and cell division (mitotic spindle assembly, actin filament depolymerization) and phosphorylation, suggesting a shared function in transcription control coupled to cellular architecture. Peripheral terms like response to antibiotic and amino acid biosynthesis appear less central to the main theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0046677","count":6},{"id":"GO:0007605","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0019284","count":4}]},{"hash":"1652595705069323037","title":"Diverse molecule transport with peroxisomal fatty acid metabolism","description":"The top GO terms are dominated by transport-related processes across a variety of substrates (lipoprotein, thiamine, cobalt, oligopeptides, and even drug transport) and by peroxisomal lipid handling (long-chain fatty acid import into the peroxisome and fatty acid beta-oxidation). This points to a cohesive theme of metabolite/ion transport and peroxisomal lipid metabolism, with a minor apoptosis note. There are no edges, so we rely on GO-term coherence to name the cluster.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001241","count":3},{"id":"GO:0042953","count":2},{"id":"GO:0015888","count":2},{"id":"GO:0060702","count":2},{"id":"GO:0015910","count":2}]},{"hash":"1384525554378116894","title":"Mitochondrial RNA Processing and Respiration","description":"Explanation: The strongest signals are mitochondrial RNA processing, mitochondrial large ribosomal subunit assembly, and cellular respiration, pointing to mitochondrial gene expression and energy production as the core theme; other terms appear as ancillary or broader stress-related processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045333","count":2},{"id":"GO:1902775","count":2},{"id":"GO:0000963","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0042220","count":2}]},{"hash":"1411767839904507137","title":"Mitosis and Cell Cycle Machinery","description":"The top GO terms are dominated by processes tied to cell division and mitosis\u2014cell division, cell cycle, mitotic spindle assembly, and CENP-A\u2013chromatin assembly, plus Okazaki fragment processing in mitotic DNA replication\u2014pointing to a cohesive theme of chromosome maintenance and mitotic progression. Some terms related to ribosome biogenesis and translation initiation appear but do not overwhelm the mitosis-centric pattern. Overall, these proteins co-cluster around mitotic and cell-cycle functions.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0030433","count":5},{"id":"GO:0000747","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0007049","count":4}]},{"hash":"2262216724321994982","title":"Rho GTPase\u2013regulated endosomal trafficking","description":"The top GO terms converge on small GTPase signaling (Rho, GTPase activity) and vesicle/endosome dynamics (intralumenal vesicle formation, Cvt pathway, endosome transport), with phosphatidylinositol signaling reinforcing membrane trafficking. This points to a functional cluster governing cytoskeleton-driven trafficking and endosomal maturation, despite a few outlier terms that may reflect annotation noise.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0070676","count":4},{"id":"GO:0032258","count":3}]},{"hash":"332355195893455836","title":"Secretory Vesicle Trafficking and Exocytosis","description":"Most of the top GO terms cluster around membrane trafficking and secretion: exocytosis, exocyst localization, and regulation of SNARE complex assembly, along with rhabdomere membrane biogenesis and peptide hormone secretion. This points to a cohesive theme of vesicle trafficking and secretory pathway activity, possibly across different cell types. Some terms (pectin catabolic and alginic acid biosynthetic processes) appear unrelated outliers, reducing overall cohesion.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045490","count":2},{"id":"GO:0042121","count":2},{"id":"GO:0035544","count":1},{"id":"GO:0051601","count":1},{"id":"GO:0006887","count":1}]},{"hash":"2101802499905268581","title":"Notch signaling and mitotic transcription regulation","description":"The top GO terms point to DNA-templated transcription, cell cycle and kinetochore localization, and Notch signaling, indicating a group of proteins coordinating transcription with mitotic processes, with some connections to signaling regulation.","confidence":"High","size":26,"edges":51,"triangles":46,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0007219","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0035335","count":4}]},{"hash":"1402397372469421359","title":"MAPK Signaling in Hematopoiesis and Placental Development","description":"The dominant terms point to immune and hematopoietic signaling (GM-CSF response, IL-4 production, hemopoiesis) and MAPK cascades (p38, ERK1/2), with related placental development terms (labyrinthine layer, maternal placenta). Together these suggest a cluster centered on MAPK-mediated immune/hematopoietic signaling and placental development.","confidence":"High","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0097011","count":4},{"id":"GO:0038066","count":3},{"id":"GO:1904628","count":3},{"id":"GO:0070371","count":3},{"id":"GO:0030097","count":3}]},{"hash":"400155725025924868","title":"Fatty acid oxidation and amino acid catabolism","description":"This cluster is dominated by metabolic processes related to energy generation, especially fatty acid beta-oxidation (acyl-CoA oxidase/dehydrogenase) and amino acid catabolism (valine), along with carnitine metabolism. The inclusion of stress responses (cold/starvation) supports a general energy-homeostasis theme. Occasional development terms (liver/heart) may reflect tissue-specific metabolic activity rather than a separate function. Confidence: Medium","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006574","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0033540","count":2},{"id":"GO:0033539","count":2}]},{"hash":"938746508913289071","title":"Endosomal trafficking and Rab/Rap GTPase signaling","description":"The top GO terms cluster around endosome organization and endosome transport between plasma membrane and endosomes, Golgi transport, Rab and Rap signaling, activation of GTPase activity, and microtubule-based movement, indicating a cohesive module of intracellular trafficking and cytoskeletal transport. A few development-related terms may reflect multifunctional proteins, but the dominant signal is endosomal trafficking.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007032","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0021510","count":2},{"id":"GO:1903527","count":2}]},{"hash":"1793288913051996234","title":"Actin-driven cell migration and adhesion signaling","description":"These proteins cluster around cytoskeleton remodeling and cell motility: actin filament bundle assembly, cell migration, Rho-family small GTPase signaling, and adhesion/polarity pathways (podosome assembly, cell spreading, ephrin receptor signaling). The mix of migration, adhesion, and polarity terms points to a common function in actin-driven movement and dynamic cell\u2013substrate interactions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0043552","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0048013","count":3}]},{"hash":"2018513719703314737","title":"Translation Machinery and RNA Metabolism","description":"This cluster is dominated by translation-related GO terms (translation, translational initiation/termination, positive regulation of cytoplasmic translation, selenocysteine incorporation) with supporting RNA processing/mRNA decay terms, suggesting a core function in protein synthesis and mRNA regulation.","confidence":"High","size":26,"edges":316,"triangles":2397,"max_degree":25,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0046677","count":10},{"id":"GO:0006413","count":6},{"id":"GO:0006415","count":5},{"id":"GO:0006353","count":4}]},{"hash":"1325936968919444650","title":"Yeast prospore formation and mitotic control","description":"The top GO terms strongly point to Saccharomyces sporulation and cell-cycle processes: ascospore-type prospore assembly, mitotic cell cycle and spindle assembly, and SCF-dependent ubiquitin-proteasome\u2013mediated protein turnover. Additional terms like maintenance of cell polarity and mRNA transport fit the broader cellular changes occurring during sporulation and mitosis. Altogether, these proteins seem tied to sporulation-associated development and mitotic regulation in yeast.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0031321","count":3},{"id":"GO:0043124","count":3},{"id":"GO:0030011","count":3}]},{"hash":"1405418808651982482","title":"Axon guidance and neural development","description":"GO terms indicate a focus on neuronal connectivity: axon target recognition, spinal cord development, and ephrin receptor signaling point to axon guidance and neural patterning. Microtubule-based movement and ER-to-Golgi vesicle transport support neurite trafficking, while DNA-templated transcription reflects gene regulation in development. Some terms (e.g., negative regulation of Ras signaling, blood vessel remodeling) are broader regulatory processes, but the central theme remains neural development and axon guidance.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007412","count":4},{"id":"GO:0008283","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0007018","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1673522716465975423","title":"Mitotic spindle and cytoskeletal signaling","description":"The top GO terms cluster around microtubule-based movement and mitotic spindle assembly, indicating a focus on cytoskeletal dynamics during cell division, supported by kinase and GTPase regulatory activities. While there are also terms related to development and stress responses, the strongest shared theme is spindle/cytoskeletal regulation, making this label representative of the core function in the group.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0007275","count":2}]},{"hash":"59875086531519110","title":"DNA Repair and Chromatin Assembly","description":"This cluster centers on genome integrity: base-excision repair, DNA recombination, translesion synthesis, and CENP-A\u2013mediated chromatin assembly, with related stress responses to xenobiotics/toxic substances, suggesting a cohesive theme of DNA damage response and chromatin maintenance.","confidence":"High","size":26,"edges":69,"triangles":49,"max_degree":13,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0042493","count":7},{"id":"GO:0006310","count":6},{"id":"GO:0007568","count":6},{"id":"GO:0006284","count":6},{"id":"GO:0051260","count":4}]},{"hash":"413487411572550168","title":"NF-kappaB signaling and ubiquitination","description":"This cluster centers on immune signaling and gene regulation, with several terms linked to NF-kappaB activity regulation, the NOD2 signaling pathway, and protein ubiquitination, plus related post-transcriptional regulation. A few outlier terms (telomere maintenance and muscle-related regulation) exist, but the core theme is immune signaling and ubiquitin-mediated regulation of transcription and stability.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0035994","count":2}]},{"hash":"286637345983449667","title":"Neural development and synaptic signaling","description":"The cluster is enriched for neural-related processes such as axonogenesis, Schwann cell development, visual perception, and long-term potentiation, indicating a core theme of neural development and synaptic signaling. Some terms (e.g., mitotic cell cycle, heart development, abscisic acid signaling) are broader or unrelated noise, but do not override the predominant neural theme.","confidence":"Medium","size":25,"edges":167,"triangles":522,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009738","count":6},{"id":"GO:0000086","count":6},{"id":"GO:0014044","count":6},{"id":"GO:0007409","count":6},{"id":"GO:0043065","count":6}]},{"hash":"617911706223829216","title":"Mitotic progression and ubiquitin-mediated proteolysis","description":"This cluster is marked by GO terms centered on mitosis, cell cycle progression, and APC/C-dependent degradation (anaphase-promoting complex, K11-linked ubiquitination). Although there are a couple of immune-related terms, the recurrent annotations point to regulation of mitotic events and proteolysis as the dominant theme, which justifies the label.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045842","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0051607","count":4}]},{"hash":"2039585177872244258","title":"Ribosome biogenesis and translation (mitochondrial)","description":"The dominant GO terms are translation (GO:0006412), maturation of SSU/LSU rRNA (GO:0000462/GO:0000463), and mitochondrial translation (GO:0032543), pointing to a cluster centered on ribosome assembly and protein synthesis, including mitochondrial ribosomes. Some unrelated terms (transcription, amino acid metabolism, ion transport) are present but less representative. ","confidence":"High","size":25,"edges":68,"triangles":56,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006351","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0006552","count":2},{"id":"GO:0019878","count":2}]},{"hash":"671280918374967408","title":"Calcium-NFAT signaling and translation control","description":"The cluster prominently features GO terms tied to calcineurin-NFAT signaling and its regulation, plus dephosphorylation of serine residues and eIF2\u03b1 dephosphorylation, which together point to calcium-dependent signaling controlling transcription and translation. The inclusion of negative regulation of T cell-mediated cytotoxicity reinforces an immune-regulatory theme driven by NFAT activity. ER-to-Golgi vesicle transport may reflect calcium\u2019s role in secretory pathway dynamics, linking calcium signaling to vesicle trafficking and protein synthesis. Overall, the set suggests a cohesive role in calcium-dependent signaling coordinating translation and immune-related transcription, with some membership anomalies (obsolete terms) but a clear dominant pattern.","confidence":"High","size":25,"edges":52,"triangles":28,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0061587","count":4},{"id":"GO:0007568","count":3},{"id":"GO:0036496","count":3}]},{"hash":"120183789985718944","title":"Neuronal development and signaling","description":"Based on GO terms such as substantia nigra development, excitatory postsynaptic potential, and regulation of calcineurin-NFAT signaling, the cluster appears enriched for neuronal signaling and gene regulation. There are signs of transcriptional activity and trafficking (ER-Golgi transport), supporting a neuronal context with protein processing and trafficking. Some terms (xenobiotic response, lipid A biosynthesis) are less coherent with neurons, suggesting noise or broader cellular stress roles; overall, the core theme centers on neuronal signaling and development with associated transcriptional regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035690","count":5},{"id":"GO:0006888","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0051531","count":4}]},{"hash":"944500040286516067","title":"Ribosome biogenesis and translation initiation","description":"This cluster is dominated by GO terms for ribosome assembly and translation control, including maturation of rRNA, large subunit biogenesis, and formation/reinitiation of translation preinitiation complexes. A single splicing term appears but the core theme centers on ribosome production and initiation of protein synthesis, with some regulatory signals (ubiquitination, nutrient response) accompanying it.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0001731","count":9},{"id":"GO:0002188","count":9},{"id":"GO:0000398","count":9},{"id":"GO:0042273","count":7},{"id":"GO:0000462","count":7}]},{"hash":"249983511450987959","title":"Transcription Regulation and Chromatin Modification","description":"Based on GO terms pointing to transcriptional control by RNA polymerase II and histone modifications (H3K36/H3K4 methylation), the proteins likely participate in regulating gene expression through chromatin state changes. Development-related terms like placental morphogenesis and vasculogenesis suggest roles in developmental gene regulation as well. A few terms related to defense signaling and Rho pathways appear peripheral but do not negate the central transcription/chromatin theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0035441","count":2},{"id":"GO:0097198","count":2}]},{"hash":"974920084993737529","title":"Neuronal Development and Dendrite Morphogenesis","description":"These proteins show strong enrichment for nervous system development, dendrite morphogenesis, hippocampus development, and positive regulation of axon extension, pointing to a module governing neuron differentiation and neurite outgrowth. Signaling components such as JNK cascade regulation and serine phosphorylation/PI3K signaling support neural signal transduction involved in growth and synaptic maturation. The T cell receptor signaling term may reflect shared signaling molecules across pathways rather than a neuronal-specific function; overall the theme centers on neural development and dendritic/axonal growth.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050852","count":12},{"id":"GO:0021766","count":11},{"id":"GO:0045773","count":11},{"id":"GO:0031647","count":11},{"id":"GO:0048813","count":11}]},{"hash":"245279492900320475","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0019068","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0039702","count":1}]},{"hash":"433172809836579583","title":"Developmental signaling and mitotic regulation","description":"Top GO terms point to developmental processes (skin development, multicellular organism development) and signaling control (positive regulation of protein autophosphorylation, serine/threonine kinase activity, GTPase activity) together with cell cycle and mitosis processes (mitotic cell cycle, mitotic spindle assembly) and mRNA transport. This suggests the cluster comprises proteins coordinating development with signaling and cell division, hence the chosen label.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043588","count":12},{"id":"GO:0031954","count":11},{"id":"GO:0007275","count":11},{"id":"GO:0071902","count":11},{"id":"GO:0043547","count":11}]},{"hash":"769591384804646538","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019068","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0039702","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0019076","count":1}]},{"hash":"969650454370488646","title":"Ubiquitination and Proteasome-Mediated Degradation","description":"Most terms point to ubiquitin transfer and proteasomal degradation, including ubiquitin-dependent protein catabolic processes and SCF-dependent ubiquitination, suggesting a cohesive role in protein turnover. The additional terms related to metal stress responses and synapse assembly may reflect context-specific ubiquitin signaling in neurons. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":13},{"id":"GO:0042787","count":12},{"id":"GO:0000209","count":9},{"id":"GO:1903378","count":9},{"id":"GO:0031146","count":9}]},{"hash":"1352167397567925407","title":"TLR-mediated innate immunity and dendritic cell activation","description":"The top GO terms center on innate immune response and Toll-like receptor signaling (TLR4, TLR9, MyD88-independent), with positive regulation of chemokine and cytokine production, IL-18, and type II interferon signaling, which together point to sensing pathogens and activating dendritic cells; ephrin receptor signaling appears, but is less central to the core theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0048013","count":3},{"id":"GO:0032722","count":2},{"id":"GO:0034142","count":2},{"id":"GO:0002756","count":2}]},{"hash":"452561987766129855","title":"Golgi sugar nucleotide transport and fucosylation","description":"The cluster is dominated by GO terms for transport of sugar nucleotides (UDP-glucose, GDP-fucose) into the Golgi lumen and subsequent glycosylation steps (N- and O-linked fucosylation), suggesting a cohesive role in Golgi-based glycosylation. Endosome-to-vacuole trafficking appears as related membrane transport activity, and plant-specific root-development terms are present but secondary to the glycosylation theme.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032511","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0015786","count":1},{"id":"GO:0048527","count":1},{"id":"GO:0036071","count":1}]},{"hash":"1297461687380516598","title":"Mechanotransduction and Stretch Response","description":"The top GO terms center on cellular response to mechanical stimulus and response to muscle stretch, indicating a mechanotransduction-focused cluster. While there are some miscellaneous terms related to signaling and telomere regulation, the strongest and most coherent theme is sensing and responding to mechanical cues, relevant to muscle or cardiac contexts.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":7},{"id":"GO:0032088","count":6},{"id":"GO:0070431","count":6},{"id":"GO:0032212","count":5},{"id":"GO:0035994","count":5}]},{"hash":"1565714696321976379","title":"Reproductive development and prostaglandin signaling with redox balance","description":"The cluster is enriched for gonad development terms (female and male) and prostaglandin biosynthesis, suggesting a focus on reproductive development and prostaglandin-mediated signaling. It also shows redox homeostasis and detoxification terms, indicating concurrent oxidative stress management; platelet aggregation may relate to prostaglandin pathways, reinforcing a reproduction-immune/hemostasis link. Overall, a cohesive theme around gonadal development and prostaglandin biology with redox balance.","confidence":"Medium","size":24,"edges":72,"triangles":82,"max_degree":13,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0008585","count":7},{"id":"GO:0060065","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0045454","count":6}]},{"hash":"436857230211315531","title":"DNA Replication and Repair","description":"This cluster is dominated by GO terms related to DNA replication, DNA unwinding, topological changes, and DNA repair (with additional RNA quality control via nonsense-mediated decay). While a couple terms touch on development, the strongest and most frequent signals point to nuclear DNA metabolism and genome maintenance, justifying a label focused on DNA replication/repair as the core theme.","confidence":"High","size":24,"edges":85,"triangles":64,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0000184","count":6},{"id":"GO:0032508","count":5},{"id":"GO:0090305","count":5}]},{"hash":"813480821690021375","title":"Neural development and transcriptional regulation","description":"This cluster is dominated by terms tied to development and gene regulation, including forebrain development, neural tube closure, multicellular organism development, and DNA-templated transcription, pointing to proteins involved in developmental gene regulation and neural formation. While there are some stress and immune response terms present, the prominent development-related GO terms suggest a coherent theme around developmental transcriptional control.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0006349","count":5},{"id":"GO:0001403","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0007275","count":5}]},{"hash":"1135783562174495085","title":"Genome maintenance and stress response","description":"The cluster is enriched for genome-stability processes (mismatch repair, telomerase holoenzyme assembly) and proteostasis (protein folding), suggesting a core theme of genome maintenance and cellular stress handling. Additional terms point to broader stress signaling (IL-4 response, xenobiotic response, regulation of complement-dependent cytotoxicity) and a developmental annotation (placenta development) that may reflect contextual noise rather than a unifying function. Overall, the strongest signal is genome maintenance with supporting stress-response pathways.","confidence":"Medium","size":24,"edges":29,"triangles":19,"max_degree":10,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006298","count":4},{"id":"GO:0045793","count":4},{"id":"GO:0033160","count":4},{"id":"GO:0071353","count":4},{"id":"GO:1903660","count":4}]},{"hash":"2037859166499500278","title":"RNA processing and nucleotide metabolism","description":"The terms center on RNA processing (mRNA capping, nucleolus organization, tRNA modification) plus nucleotide turnover (various catabolic processes, folic acid, CoA metabolism), hinting at a loose RNA-nucleotide metabolism theme, though no network edges reduce cohesion.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0002943","count":1},{"id":"GO:0007000","count":1},{"id":"GO:2000781","count":1}]},{"hash":"1700078366279590718","title":"ERAD-Linked Translation and Ribosome Biogenesis","description":"This cluster combines ER-associated degradation and retrograde ER-to-cytosol transport with components of ribosome biogenesis and translation regulation (cytoplasmic translation, initiation complex formation, and ribosomal large subunit biogenesis), plus mRNA decay pathways and heat response. The proteins seem to bridge ER protein quality control with cytosolic translation machinery, especially under stress conditions, suggesting a cohesive theme around maintaining proteome quality and controlling translation. ","confidence":"Medium","size":24,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0030970","count":2},{"id":"GO:0070370","count":2},{"id":"GO:0031087","count":2},{"id":"GO:0070651","count":2}]},{"hash":"1573640163357264266","title":"Neuronal development and synaptic vesicle regulation","description":"This cluster's top GO terms cluster around neural development and vesicle trafficking\u2014brain development, regulation of synaptic vesicle exocytosis, and axonogenesis\u2014along with related GTPase activity regulation and endosome-to-Golgi transport. Together they point to proteins involved in neuronal growth, signaling, and vesicle trafficking, rather than housekeeping processes, making a \"neuronal development and synaptic vesicle regulation\" label appropriate. Some outlier terms (e.g., subtelomeric heterochromatin formation) exist, but the dominant theme is neural-related trafficking and signaling.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":4},{"id":"GO:0007420","count":3},{"id":"GO:0031384","count":3},{"id":"GO:0010796","count":3},{"id":"GO:2000300","count":3}]},{"hash":"1534018216733533277","title":"Ribosome biogenesis and translation","description":"The cluster shows strong enrichment for ribosome biogenesis, cytosolic ribosome assembly, large subunit biogenesis/export, LSU rRNA maturation, and translation, indicating a core function in ribosome production and protein synthesis. A few other terms (spliceosome regulation, MAPK-related signaling) are present but appear ancillary to the main ribosome/translation theme.","confidence":"High","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":10},{"id":"GO:0042273","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0048025","count":4},{"id":"GO:0000055","count":3}]},{"hash":"537502221501671394","title":"Neuronal development and signaling","description":"Dominant themes are neuronal development and synaptic signaling, including axonogenesis, excitatory signaling, dopamine response, and Wnt pathway regulation, with potassium transport supporting neural excitability; a few terms like mitotic cell cycle and Gram-positive defense appear as outliers.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":10},{"id":"GO:0006813","count":10},{"id":"GO:0007275","count":9},{"id":"GO:0050830","count":9},{"id":"GO:0006915","count":9}]},{"hash":"1958671567953741312","title":"Multisystem Development and Differentiation","description":"These proteins are enriched for GO terms tied to development of multiple tissues (multicellular organism development, nervous system development, skeletal muscle tissue development, myotube differentiation, and labyrinthine layer blood vessel development) and associated signaling pathways (neurotrophin TRK receptor signaling, integrin-mediated signaling, B cell receptor signaling). The convergence on tissue formation and cell differentiation across muscle, nerve, and vascular contexts explains a single, broad label focused on developmental processes rather than a single pathway or tissue.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0014902","count":2},{"id":"GO:0048011","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0007399","count":2}]},{"hash":"660558760159572904","title":"Muscle and heart development signaling","description":"Based on the top GO terms, the cluster is dominated by muscle-related and heart development processes (heart development, skeletal muscle fiber development, multicellular organism development) and by regulatory signaling activities (positive regulation of protein autophosphorylation, protein kinase activity, GTPase activity, protein homooligomerization). This suggests a cohesive theme around developmental processes in cardiac and skeletal muscle tied to signaling pathways, with some ancillary cellular processes like cilium assembly. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0031954","count":3},{"id":"GO:0071902","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0048741","count":3}]},{"hash":"1118791620866387262","title":"Developmental and Neural Signaling Cluster","description":"This cluster's top GO terms center on development across tissues (Schwann cell, heart, multicellular organism development) and neural/sensory activity (visual perception, excitatory postsynaptic potential). There are also regulatory signaling terms involving phosphorylation and CDK activity, linking development and cell-cycle control. A plant-specific term (abscisic acid signaling) appears but does not dominate; overall, the set points to development- and neural-signaling-related functions.","confidence":"Medium","size":24,"edges":8,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0014044","count":12},{"id":"GO:0034501","count":12},{"id":"GO:0060079","count":11},{"id":"GO:0009738","count":10},{"id":"GO:0007601","count":10}]},{"hash":"853631314965241053","title":"Mitochondrial Translation and Cristae Biogenesis","description":"Top terms indicate a mitochondrial-centric cluster, with positive regulation of mitochondrial translation, cristae formation, and protein insertion into the mitochondrial membrane as core themes. Additional terms related to potassium homeostasis and cardiac muscle contraction align with mitochondrial energy production in muscle, while cellular growth, cell cycle, and xenobiotic response suggest broader metabolic and stress-related roles. Overall, the proteins likely participate in mitochondrial biogenesis and function, justifying a mitochondria-focused label.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0097274","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0007049","count":2}]},{"hash":"960673257874030039","title":"Neurodevelopmental signaling and transcription regulation","description":"The cluster\u2019s top GO terms point to neural development and signaling (corpus callosum development, ephrin receptor signaling, and positive regulation of synapse assembly) together with transcription control (DNA-templated transcription, regulation of transcription), suggesting a theme of developmental signaling linked to gene regulation in neural contexts. Some terms (angiogenesis, defense response to virus, response to antibiotic, sporulation, rRNA maturation) are more general or peripheral, indicating heterogeneity, but the dominant signal appears to be neurodevelopmental signaling coupled with transcription regulation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0001525","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0022038","count":2}]},{"hash":"1571853665832489642","title":"Mitochondrial metabolism and sphingolipid signaling","description":"The top terms point to mitochondrial activity (tricarboxylic acid cycle, autophagy of mitochondrion) and lipid signaling (sphingosine and sphinganine metabolic processes), suggesting a cluster focused on mitochondrial energy metabolism and sphingolipid pathways, with some stress-related terms (photoinhibition) that may reflect cellular condition responses. Despite a few obsolete terms, the core theme is recognizable around mitochondrial metabolism and lipid signaling.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006099","count":1},{"id":"GO:0000422","count":1},{"id":"GO:0046512","count":1},{"id":"GO:0033561","count":1}]},{"hash":"550049385886652872","title":"Neural progenitor proliferation during embryonic development","description":"This cluster centers on embryonic neural development and positive regulation of neural precursor proliferation, with supporting signals for stem cell proliferation, metabolism (glycolytic process), and membrane potential regulation. The combination suggests a program of neural progenitor expansion in early development, aided by energy metabolism and gene-expression regulation (alternative splicing). Confidence: High","confidence":"","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001701","count":6},{"id":"GO:0009409","count":6},{"id":"GO:2000648","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0006096","count":5}]},{"hash":"481475432084925591","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006574","count":5},{"id":"GO:0001889","count":4},{"id":"GO:0005978","count":4},{"id":"GO:0042594","count":4},{"id":"GO:0071357","count":4}]},{"hash":"1456840429335281194","title":"Centrosome, mitosis, and cilium assembly","description":"The cluster is driven by GO terms tying to centrosomal microtubule anchoring, non-motile cilium assembly and its regulation, and mitotic transitions (metaphase/anaphase), plus protein localization to ciliary/photoreceptor structures. Together these point to a core function in centrosome-associated microtubule organization and ciliogenesis, with mitotic regulation as a related aspect. The additional tissue-development terms (prostate, fat pad, leptin signaling) appear more tangential, likely reflecting broader annotation rather than a core shared function, but do not override the central centrosome/cilium/mitosis theme.","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030850","count":6},{"id":"GO:0038108","count":6},{"id":"GO:0060613","count":6},{"id":"GO:0007091","count":6},{"id":"GO:0045842","count":6}]},{"hash":"34051972327356116","title":"Potassium transport and calcium signaling in excitable membranes","description":"The top GO terms emphasize potassium import/export across the plasma membrane, membrane hyperpolarization, and calcium release from the sarcoplasmic reticulum, pointing to a shared theme of ion flux and signaling in excitable cells; other terms present are more peripheral to this core function. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990573","count":6},{"id":"GO:0097623","count":6},{"id":"GO:0060081","count":5},{"id":"GO:0014808","count":4},{"id":"GO:0019373","count":4}]},{"hash":"868450377126695305","title":"Neural development and synaptic signaling","description":"The most represented GO terms are neural-related: long-term synaptic potentiation, excitatory postsynaptic potential, visual perception, Schwann cell development, and heart development, indicating roles in nervous system signaling and organ development. An outlier term (abscisic acid-activated signaling) may reflect annotation noise rather than a true functional theme.","confidence":"Medium","size":23,"edges":44,"triangles":43,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009738","count":7},{"id":"GO:0007601","count":7},{"id":"GO:0010800","count":7},{"id":"GO:0060291","count":7},{"id":"GO:0000086","count":7}]},{"hash":"2024734329993869516","title":"Unknown","description":"The top GO terms are a mix of vertebrate development (brain, blood vessel, heart looping), signaling and apoptosis processes, and diverse metabolic biosynthesis/tRNA modification terms, with no clear single unifying function for the cluster.","confidence":"","size":23,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0001568","count":2},{"id":"GO:0001947","count":2},{"id":"GO:0043065","count":2},{"id":"GO:2001046","count":2}]},{"hash":"1866421255996502404","title":"Unknown","description":"The top GO terms cover telomere maintenance, muscle stretch response, insulin-related glucose import regulation, cell migration, adipocyte differentiation, mRNA processing and stability, and NF-kB regulation, with no single coherent function uniting them. Therefore there isn\u2019t a clear, specific theme to name the cluster, so it\u2019s labeled Unknown. ","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032212","count":5},{"id":"GO:0035994","count":5},{"id":"GO:2001275","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0045736","count":5}]},{"hash":"1531167365625023230","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0010950","count":3},{"id":"GO:0043488","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0090503","count":3}]},{"hash":"2181781083202090639","title":"Ribosome biogenesis and translation machinery","description":"The top GO terms cluster around ribosome biogenesis, formation of translation preinitiation complex, translation reinitiation, and maturation of rRNA, indicating proteins involved in ribosome assembly and the initiation/continuation of translation. A notable signal for positive regulation of GTPase activity aligns with translation factors acting via GTPases. Some secondary terms (transcription regulation, aging) are less central. Overall, these proteins share a common theme of ribosome assembly and protein synthesis.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0035948","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0002188","count":3}]},{"hash":"413432067471257793","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by translation-related terms (translation, cytoplasmic translation, tRNA modification) and ribosome biogenesis (including small subunit biogenesis), with supporting links to cell cycle/division and cell septum assembly, indicating a cohort of proteins involved in ribosome production and protein synthesis that coordinate with cell division.","confidence":"High","size":23,"edges":38,"triangles":12,"max_degree":10,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0006400","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0002181","count":6}]},{"hash":"1069070674879019151","title":"Cerebellar development and neural signaling regulation","description":"This cluster centers on cerebellar development themes (cerebellar cortex formation, Bergmann glial differentiation) and neural signaling (axon regeneration, ERK cascade regulation), with supporting links to cell cycle control. While insulin signaling appears, and there are a few immune signaling terms, the dominant pattern ties to cerebellar neural development and its signaling regulation.","confidence":"Medium","size":23,"edges":251,"triangles":1729,"max_degree":22,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045736","count":12},{"id":"GO:0034501","count":12},{"id":"GO:0008286","count":11},{"id":"GO:0021697","count":11},{"id":"GO:2001275","count":11}]},{"hash":"1881851317061171821","title":"Ribosome Biogenesis and Telomere Maintenance","description":"The cluster is dominated by ribosome biogenesis signals (ribosomal small subunit biogenesis, ribosome biogenesis) and cell cycle processes, with multiple telomere-related terms (positive/negative regulation of telomere maintenance, telomere region localization) and spindle assembly, suggesting a link between nucleolar ribosome production, chromosome dynamics, and telomere maintenance. Poly-ADP-ribosylation and Wnt signaling appear as broader, supportive signals but do not redefine the core theme.","confidence":"Medium","size":23,"edges":22,"triangles":0,"max_degree":22,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0032212","count":2},{"id":"GO:1904357","count":2}]},{"hash":"418215528413389085","title":"Apoptosis and Neural Signaling Pathways","description":"The top GO terms point to apoptosis across different cell types (hepatocyte and myeloid) and neural-related development and signaling (hippocampus development, dendrite regulation, and ephrin receptor signaling). Additional terms about caveolin-mediated endocytosis, PI3K activity, and calcium-dependent exocytosis suggest a broader theme of membrane signaling and trafficking linked to cell death and neural context. Thus, the cluster appears to unify apoptotic processes with neural signaling pathways, with trafficking components also involved. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":3},{"id":"GO:0031532","count":3},{"id":"GO:0043552","count":2},{"id":"GO:0072584","count":2},{"id":"GO:0021766","count":2}]},{"hash":"1238059033865229555","title":"Mitotic cell division and microtubule dynamics","description":"Based on the top GO terms, the cluster is dominated by proteins involved in mitosis: cell cycle, cell division, mitotic spindle assembly, and microtubule-based movement, indicating roles in spindle organization and chromosome segregation. Telomere maintenance aligns with division, while a few outliers like spinal cord development may reflect broader annotation contexts. Overall, the core theme is mitotic machinery and division.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0000920","count":2}]},{"hash":"984644239451776906","title":"Biosynthesis and Catabolic Metabolism","description":"The cluster\u2019s top GO terms span multiple biosynthetic and catabolic processes (biotin biosynthesis, antibiotic biosynthesis, strigolactone biosynthesis, triglyceride and glucuronoside catabolism, 3-phenylpropionate catabolism), alongside regulatory activities (regulation of DNA-templated transcription, regulation of endocannabinoid signaling). This pattern suggests a general grouping around metabolism and its regulation rather than a single specific pathway, justifying a label like \u201cBiosynthesis and Catabolic Metabolism.\u201d Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009102","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0006355","count":5},{"id":"GO:0019391","count":5},{"id":"GO:0019380","count":5}]},{"hash":"2272377389008656331","title":"Neuronal energy metabolism and fatty acid oxidation","description":"This cluster is enriched for fatty acid beta-oxidation, acetyl-CoA and ketone body catabolic processes, and mitochondrial regulation, with a brain development term hinting at neural context. Together, these terms suggest a core function in neuronal energy metabolism through lipid catabolism.","confidence":"High","size":22,"edges":222,"triangles":1396,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019551","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0019518","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0046952","count":5}]},{"hash":"153439223473681014","title":"Neural signaling and synaptic plasticity regulators","description":"This cluster\u2019s top GO terms center on neural signaling and plasticity (regulation of long-term synaptic potentiation, substantia nigra development, myelination in the PNS, cellular response to cAMP, corticosterone response) and cytoskeletal signaling (positive regulation of GTPase activity, regulation of Rho signaling). The mix also includes broader signaling pathways (VEGF signaling) and apoptosis, suggesting proteins involved in neuronal development, signaling, and cell survival rather than a single narrow function. Given the neural emphasis but some non-neural annotations, the label is representative but moderately confident.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900271","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0022011","count":3},{"id":"GO:0009738","count":3}]},{"hash":"2058521018786528105","title":"Pigment and steroid metabolism","description":"The top GO terms point to pigment-related pathways (melanin biosynthesis, retinal metabolism) together with steroid/lipid metabolism (androgen and testosterone biosynthesis/metabolism, sphinganine/lipid metabolism). This suggests a cohesive cluster centered on pigment production and steroid/lipid metabolic processes, with a few more general terms contributing noise. ","confidence":"Medium","size":22,"edges":95,"triangles":197,"max_degree":19,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":20},{"id":"GO:0006355","count":20},{"id":"GO:0042619","count":20},{"id":"GO:0042574","count":19},{"id":"GO:0045150","count":19}]},{"hash":"1052638132829095082","title":"RNA polymerase assembly and transcription regulation","description":"The top GO terms are dominated by RNA polymerase I/II/III assembly and transcription-related processes (e.g., RNA polymerase III transcription, RNA polymerase II core complex assembly, transcription elongation). While a few terms touch on other cellular processes, the shared theme centers on transcription machinery assembly and regulation, making this a coherent label. ","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051531","count":2},{"id":"GO:0010801","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0042797","count":2},{"id":"GO:1990115","count":1}]},{"hash":"1524437207907782246","title":"Chromatin regulation and mitotic processes","description":"The top GO terms cluster around chromatin dynamics (histone modification, nucleosome assembly, transcription regulation), along with transcription and mRNA processing, and mitotic roles (spindle assembly and centrosome separation). This mix points to a cohesive nuclear program linking chromatin regulation with chromosome segregation during cell division, with one outlier term likely representing noise. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0051569","count":2},{"id":"GO:0051299","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1075630132311659042","title":"Developmental Regulation and Cell Cycle","description":"The top GO terms point strongly to organism development (multicellular development, forebrain, skeletal system) and mitosis-related processes (mitotic cell cycle, centrosome separation), with transcriptional control (DNA-templated transcription) also prominent. Additional terms reflect stress and immune signaling (ER-stress\u2013related apoptosis, cadmium response, defense against Gram-positive bacteria), suggesting a cluster of proteins involved in development that are tightly linked to cell-cycle control and stress responses. ","confidence":"Medium","size":22,"edges":17,"triangles":8,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":22},{"id":"GO:0007100","count":22},{"id":"GO:0070059","count":22},{"id":"GO:0006351","count":22},{"id":"GO:0071276","count":22}]},{"hash":"1444229255092705039","title":"Viral replication and protein folding","description":"This cluster shows strong signals for viral processes (uncoating of virus, virion assembly, viral life cycle) alongside protein folding and peptidyl-prolyl isomerization, suggesting a module tied to viral protein synthesis/maturation and assembly with chaperone-like activity. Some terms (cell division, amino acid stimulus) appear more general or noisy, and an outlier plant-related term (sepal formation) likely reflects annotation noise. Overall, the theme centers on viral replication and associated protein-folding machinery.","confidence":"Medium","size":22,"edges":23,"triangles":32,"max_degree":7,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0071230","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0048453","count":4}]},{"hash":"1731469349840129712","title":"Cytoskeletal remodeling and membrane trafficking","description":"The top GO terms center on actin dynamics (cell migration, actin filament bundle assembly), vesicle transport (transcytosis, intracellular transport, Golgi-to-plasma membrane transport), and small GTPase\u2013mediated signaling, with additional links to growth-factor responses and innate immune/oxidative stress responses. Together these suggest a cohesive role in coordinating cytoskeletal remodeling with membrane trafficking during migration, vesicle trafficking, and synapse formation. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0045056","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0007264","count":2}]},{"hash":"2018084721945013992","title":"Diverse Substrate Transport","description":"The cluster\u2019s top GO terms are dominated by transport-related processes across multiple substrates and organelles (lipoprotein transport, thiamine transport, cobalt ion transport, long-chain fatty acid import into peroxisome, doxorubicin transport, oligopeptide export from mitochondrion, and peptide pheromone export). This suggests the proteins share a common role in moving diverse molecules across membranes. Some terms (negative regulation of endoribonuclease activity, stem cell proliferation) may be less central or reflect broader annotations, but the strongest signal is transport activity across cellular compartments. Confidence: High","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":5},{"id":"GO:0042953","count":3},{"id":"GO:0015888","count":3},{"id":"GO:0060702","count":3},{"id":"GO:0015910","count":3}]},{"hash":"1009945237032357124","title":"Cellular Stimulus Response Signaling","description":"The top GO terms point to sensing external cues (mechanical stimulus, muscle stretch, pain perception) and responding via signaling pathways, with additional terms touching on hormonal signaling (vitamin D, salicylic acid) and broader cellular processes like spindle assembly and telomere maintenance. This suggests a broad theme of stimulus detection and downstream signaling rather than a single precise function. Confidence: Medium","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":6},{"id":"GO:0032088","count":5},{"id":"GO:0033280","count":5},{"id":"GO:0032212","count":4},{"id":"GO:0035994","count":4}]},{"hash":"2228405970246928961","title":"Potassium homeostasis and membrane potential","description":"Most of the top GO terms describe potassium ion import/export and intracellular potassium homeostasis, plus membrane repolarization. This suggests the proteins are enriched for roles in maintaining cellular potassium balance and regulating membrane potential, with some additional terms reflecting broader developmental or metabolic annotations.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1990573","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0030007","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0071383","count":3}]},{"hash":"1546142909076789899","title":"DNA replication and mitotic cell cycle","description":"This cluster is strongly enriched for core nuclear processes: DNA replication, mitotic cell cycle, DNA-templated transcription, and DNA repair. Together these GO terms point to a coherent module of chromosomal duplication, genome maintenance, and cell division. The presence of some immune and apoptotic signals may reflect downstream stress response connections to DNA damage or development signals (e.g., retinoic acid response), but the dominant theme remains DNA replication/repair and mitosis.","confidence":"High","size":22,"edges":50,"triangles":27,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006260","count":21},{"id":"GO:0000278","count":21},{"id":"GO:0006351","count":20},{"id":"GO:0006281","count":20},{"id":"GO:0045087","count":19}]},{"hash":"2210435666007841234","title":"GTPase-regulated cytoskeletal dynamics","description":"This cluster centers on small GTPase signaling (Ras, Rho), including regulation of GTPase activity and pathways like filopodium assembly, pointing to control of cytoskeletal remodeling and cell morphology. Developmental terms (heart, blastocyst) appear but do not override the dominant theme of GTPase-driven cytoskeletal regulation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0007264","count":3}]},{"hash":"1944545669479312254","title":"Ubiquitin signaling and cell motility","description":"The top GO terms cluster around ubiquitin-dependent protein catabolic process and deubiquitination, with additional terms on Rho signaling and cell migration, suggesting a theme of ubiquitin-regulated regulation influencing cytoskeletal dynamics and motility. Some terms (heart development, ribosomal export, ethanol response) are peripheral, but the strongest shared signal is ubiquitin-mediated control of processes that affect cell movement.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0007205","count":3}]},{"hash":"2302523105170142286","title":"LPS and metal-ion stress response","description":"GO terms reveal strong signals for response to lipopolysaccharide and to metal ions (selenium and aluminum), plus related stress and metabolic hints (ethanol response, dopamine/serotonin regulation, thiamine biosynthesis). This suggests a cluster centered on environmental/stress signaling with accompanying metabolic adjustments, rather than a single precise pathway. ","confidence":"Medium","size":21,"edges":12,"triangles":4,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032496","count":6},{"id":"GO:0009228","count":5},{"id":"GO:0043046","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0010269","count":4}]},{"hash":"200467780344735595","title":"RNA processing and translation initiation regulation","description":"The cluster is enriched for mRNA processing and splicing (spliceosome-mediated, alternative splicing, 5\u2019/3\u2019 end processing) as well as components involved in forming translation preinitiation complexes and regulating translational initiation, plus mRNA stabilization and small-subunit processome assembly, all pointing to coordinated RNA maturation and control of translation. While a few terms (like blastocyst formation) are less central, the dominant theme ties RNA processing to initiation of translation and ribosome biogenesis.","confidence":"High","size":21,"edges":207,"triangles":1274,"max_degree":20,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001825","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0060211","count":6},{"id":"GO:1901407","count":6},{"id":"GO:0045292","count":6}]},{"hash":"2136173608023038639","title":"Unknown","description":"The GO terms span phosphorylation/dephosphorylation, methylation, various biosynthetic pathways, DNA repair, viral processes, and brain development, with no single cohesive biological theme tying them together. A concise, representative label cannot be reliably inferred from this diverse set.","confidence":"","size":21,"edges":66,"triangles":11,"max_degree":11,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0016310","count":5},{"id":"GO:0016311","count":4},{"id":"GO:0016032","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0032259","count":3}]},{"hash":"114467618697564122","title":"Golgi- and SNARE-mediated vesicle trafficking in neurons","description":"The top GO terms cluster around Golgi-centered vesicle transport (ER-to-Golgi, intra-Golgi, Golgi-to-ER, retrograde transport), Golgi ribbon formation, SNARE complex assembly, and vesicle fusion with the Golgi, plus exocytic delivery of neurotransmitter receptors to the postsynaptic membrane and associated synaptic potentiation. This combination suggests a cohesive module of SNARE-driven vesicle trafficking linked to receptor delivery in neurons.","confidence":"High","size":21,"edges":51,"triangles":9,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":9},{"id":"GO:0090161","count":8},{"id":"GO:0048280","count":7},{"id":"GO:0006891","count":7},{"id":"GO:0090316","count":6}]},{"hash":"1970816637299926846","title":"Diverse Signaling and Development Regulation","description":"The top GO terms span multiple signaling pathways (GTPase activation, IGF receptor signaling, integrin activation, tachykinin signaling, GM-CSF response) and developmental/differentiation processes (hemopoiesis, myelination, placental development). There isn\u2019t a single shared pathway, but a common theme of regulation of signaling and development, justifying a broad regulatory cluster label rather than a specific pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":1},{"id":"GO:0048009","count":1},{"id":"GO:0033623","count":1},{"id":"GO:0030097","count":1},{"id":"GO:0060709","count":1}]},{"hash":"524241667363424795","title":"Neural development and tissue differentiation","description":"GO terms cluster around nervous system development and tissue differentiation (multicellular organism development, pain perception, synaptic plasticity, glial regulation, myoblast fusion, skin development), suggesting neural development and tissue differentiation as the theme; plant ABA signaling and an obsolete oxidative stress term are outliers.","confidence":"Medium","size":21,"edges":34,"triangles":11,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":13},{"id":"GO:0019233","count":12},{"id":"GO:0051260","count":8},{"id":"GO:0043588","count":8},{"id":"GO:0009738","count":8}]},{"hash":"1736133764987718810","title":"Unknown","description":"The GO terms are highly diverse, spanning mRNA splicing, ion transport, ATP synthesis, cell-cycle regulation, endosome-Golgi trafficking, neural development, tissue polarity, Wnt signaling, dopamine signaling, and organ size regulation, with no clear unifying function across the cluster. This prevents a concise, representative label.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0045842","count":1},{"id":"GO:1905279","count":1}]},{"hash":"502052378079918823","title":"Neural development and synaptic signaling","description":"This cluster is dominated by neuronal functions: axonogenesis, regulation of dendrite morphogenesis, excitatory postsynaptic potential, long-term memory, and calcium ion transport, all pointing to neural development, synaptic activity, and plasticity. The presence of negative regulation of protein kinase activity suggests modulation of signaling pathways underlying these processes, while the amphetamine response aligns with neurotransmitter signaling. A plant-related GO term is an outlier but does not obscure the central neural theme.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0007409","count":4},{"id":"GO:0043950","count":3},{"id":"GO:0050774","count":3}]},{"hash":"1288863758095441082","title":"Unknown","description":"GO terms cover a wide and disparate set of processes: positive/negative regulation of GTPase activity, ribosome biogenesis, spinal cord development, regulation of angiogenesis/VEGF signaling, I-kappaB phosphorylation, xenobiotic response, transcription by RNA polymerase II, and tRNA processing. There is no single shared function or pathway linking these proteins, and the network has no edges, so a specific, representative label cannot be confidently assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0021510","count":3},{"id":"GO:0016525","count":3},{"id":"GO:0034260","count":3}]},{"hash":"109198971541014068","title":"NOD2-NF-kappaB innate immune signaling","description":"This cluster centers on innate immune signaling, highlighted by the NOD2 signaling pathway and regulation of NF-kappaB activity, suggesting a cohesive theme of inflammatory signal transduction. While some terms are obsolete and the network edges are absent, the core terms point to NOD2-driven NF-kappaB\u2013related processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0061408","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0032212","count":2}]},{"hash":"1296312444970496133","title":"Cilium/Flagellum Assembly and Motility","description":"Most terms point to ciliary/flagellar function: axoneme assembly, sperm motility, cilium movement; there is also actin filament network formation and microtubule severing, which relate to cytoskeletal dynamics essential for motility. Polyglutamylation is a known post-translational modification affecting microtubule function in flagella; ER protein folding and redox homeostasis may reflect general quality control in secretory/ciliated cells. Taken together, the cluster centers on cilium/flagellum assembly and motility.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0051013","count":1}]},{"hash":"1769170176068718654","title":"Unknown","description":"The GO terms point to a wide mix of functions: innate immune signaling (TLR7 pathway, interferon production, detection of diacyl lipopeptides), neural and inner-ear development (myelination, neuron maturation, otolith morphogenesis), cell cycle regulation, intracellular trafficking, and kidney development via Wnt signaling. There is no clear, unifying biological process connecting these terms, so a cohesive, specific label cannot be assigned with confidence.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034154","count":3},{"id":"GO:0045078","count":3},{"id":"GO:0042496","count":3},{"id":"GO:0042552","count":3},{"id":"GO:0050707","count":3}]},{"hash":"63655966529317351","title":"Cardiac Muscle Signaling and Sarcomere Organization","description":"The top GO terms mix small GTPase/Ras signaling, regulation of cAMP/cGMP pathways, membrane potential, and sarcomere organization, with a note of cardiac muscle proliferation. This pattern points to coordinated signaling and structural regulation in cardiac muscle cells, including sarcomere dynamics and contraction-related signaling, rather than a general, non-specific signaling cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007264","count":9},{"id":"GO:0046580","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0042391","count":7},{"id":"GO:0071321","count":7}]},{"hash":"779270580823458387","title":"Muscle development and signaling cluster","description":"This cluster shows a strong enrichment for skeletal muscle tissue development, response to muscle stretch, and integrin-mediated signaling, along with related signaling and retinoic acid response terms, suggesting a core theme around muscle differentiation and cell\u2013ECM communication. Some terms like visual perception or B cell receptor signaling may reflect shared signaling components or broader cell-cycle roles, but the dominant muscle-related terms drive the label.","confidence":"Medium","size":21,"edges":144,"triangles":460,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":19},{"id":"GO:0007601","count":19},{"id":"GO:0046827","count":18},{"id":"GO:0050853","count":17},{"id":"GO:0007519","count":17}]},{"hash":"250350260193194527","title":"JNK Signaling and Cytoskeletal Remodeling","description":"The cluster shows strong hints of MAPK/JNK pathway regulation (GO:0046328) alongside actin cytoskeleton dynamics (GO:0051017, GO:0016477), cell migration, and responses to mechanical stimuli, heat, and calcium flux, pointing to a stress-responsive signaling program that coordinately governs cytoskeletal remodeling and movement. While there are broader terms such as ubiquitination, cell cycle, apoptosis, and immune responses, the core theme appears to be JNK-associated signaling coupled to cytoskeletal and mechanical sensing.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046328","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0009408","count":3}]},{"hash":"259022148809237586","title":"Metabolic and Developmental Signaling","description":"The cluster shows core metabolic processes (glycolysis, thiamine biosynthesis) alongside developmental and signaling terms (gastrulation, neural precursor proliferation, membrane potential regulation, cellular response to cAMP), suggesting a link between energy metabolism and developmental signaling.","confidence":"Medium","size":20,"edges":28,"triangles":13,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":10},{"id":"GO:0045654","count":9},{"id":"GO:0009228","count":9},{"id":"GO:0006096","count":8},{"id":"GO:0042391","count":8}]},{"hash":"1684174136556382857","title":"Transcriptional Regulation and Heterochromatin Formation","description":"The cluster is enriched for DNA-templated transcription and chromatin-related processes, including heterochromatin formation and gene silencing, with links to nucleosome density and cohesin regulation. Although several terms are obsolete, the prevailing theme is transcription control via chromatin state and epigenetic silencing, reflected also by Hsp90-related transcription factor regulation. This supports a label focusing on transcriptional regulation anchored in chromatin dynamics.","confidence":"Medium","size":20,"edges":25,"triangles":6,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0090050","count":2},{"id":"GO:1902894","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0010978","count":2}]},{"hash":"1857791335768810657","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms describing ubiquitination and proteasome-mediated degradation (ubiquitin-dependent protein catabolic process, polyubiquitination, SCF-dependent ubiquitination, and general protein ubiquitination). These indicate a core function in tagging substrates for proteasomal destruction. Additional terms on circadian rhythm regulation and DNA replication initiation suggest broader regulatory roles of ubiquitin ligases in cell cycle timing and replication control, but the common thread remains ubiquitin-proteasome\u2013driven proteostasis.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000083","count":8},{"id":"GO:0042787","count":8},{"id":"GO:0031146","count":7},{"id":"GO:0000209","count":7},{"id":"GO:0016567","count":7}]},{"hash":"1992472424283984922","title":"Neural synapse organization and glutamate receptor regulation","description":"These proteins cluster around synaptic formation and signaling in neurons, with terms like gephyrin clustering (inhibitory postsynaptic density), postsynaptic membrane assembly, terminal button organization, and regulation of NMDA/AMPA receptor activity. Neurodevelopment terms (retina development, neuroblast differentiation) support a neuronal context. Metabolic or unrelated terms appear incidental. ","confidence":"High","size":20,"edges":158,"triangles":690,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0060041","count":6},{"id":"GO:0002076","count":6},{"id":"GO:0002087","count":6},{"id":"GO:0097116","count":5},{"id":"GO:0016042","count":5}]},{"hash":"1544553604013515817","title":"Chromatin regulation and RNA processing","description":"This cluster is dominated by GO terms related to DNA methylation, DNA repair, nucleosome dynamics, spliceosome activity, and regulatory ncRNA-mediated gene silencing, all pointing to chromatin remodeling and RNA metabolism as core functions. Some outlier terms (retinal development, muscle regulation, xenobiotic response) exist, but the prevailing theme centers on chromatin-based gene regulation and RNA processing. ","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046549","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0086004","count":3},{"id":"GO:0006306","count":2},{"id":"GO:0006281","count":2}]},{"hash":"258212643942322751","title":"LPS biosynthesis and sugar metabolism","description":"The top GO terms are dominated by lipopolysaccharide biosynthetic processes (core region, O antigen, general LPS biosynthesis) and related sugar metabolism (galactose, GDP-mannose, ADP-L-glycero-beta-D-manno-heptose), suggesting proteins involved in LPS assembly and sugar donor pathways. Some plant secondary metabolism terms (anthocyanin-containing compounds, phenylpropanoid biosynthesis) may reflect annotation overlap or multifunctional enzymes, but the strongest signal points to bacterial cell envelope biosynthesis; transcription-related terms appear less central. Medium","confidence":"Medium","size":20,"edges":28,"triangles":4,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0006351","count":6},{"id":"GO:0097171","count":5},{"id":"GO:0009699","count":5},{"id":"GO:0009244","count":5}]},{"hash":"2127493886709011421","title":"Small GTPase signaling and actin remodeling","description":"This cluster centers on GTPase-driven signaling (activation of GTPase activity; small GTPase-mediated signal transduction; Ras signaling) together with actin cytoskeleton organization and filopodium regulation, plus growth factor signaling (IGF receptor pathway) and related processes like cell division. The cohesive theme is intracellular signaling that controls cytoskeletal dynamics, cell movement, and growth-regulating pathways, with some regulatory checks on these signals (e.g., negative regulation of Ras signaling and vascular remodeling). ","confidence":"High","size":20,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060313","count":5},{"id":"GO:0043314","count":5},{"id":"GO:0090630","count":4},{"id":"GO:0048009","count":4},{"id":"GO:0007264","count":4}]},{"hash":"1531473513007891216","title":"Unknown","description":"The GO terms are highly heterogeneous (retinoic acid response, vascular development, pattern specification, innate immunity, interferon signaling, sieve element differentiation, acetylcholine-related processes, ubiquitin-proteasome catabolism, and even a righting reflex), showing no clear common function or pathway that ties the proteins together. This makes it unlikely to assign a specific, cohesive label beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071300","count":2},{"id":"GO:0001568","count":2},{"id":"GO:0009952","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0060335","count":2}]},{"hash":"147491951607994396","title":"Spliceosome-driven RNA processing and transcription regulation","description":"The majority of top terms point to RNA splicing (via spliceosome), mRNA processing, and transcription termination, with regulatory ncRNA-mediated gene silencing and chromatin remodeling indicating gene expression control at multiple levels. This suggests a cohesive cluster centered on RNA processing and transcription regulation.","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":16},{"id":"GO:0048026","count":16},{"id":"GO:0000398","count":15},{"id":"GO:0006369","count":14},{"id":"GO:0042766","count":13}]},{"hash":"1472297686359840371","title":"Neural development and synaptic maturation","description":"The cluster's top GO terms center on nervous system development, axon extension, synaptic plasticity and maturation, and synapse formation, indicating a coherent theme of neuronal differentiation and maturation. Although a couple of terms relate to mitotic cell cycle and ubiquitin-dependent proteolysis, these likely reflect general regulatory processes rather than the cluster's core function. Therefore, the label captures the main functional theme of the proteins.","confidence":"High","size":20,"edges":21,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0009561","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0045773","count":1},{"id":"GO:0031915","count":1}]},{"hash":"104627954230280306","title":"Intracellular trafficking and cell division","description":"The GO terms are dominated by Golgi-to-plasma membrane transport, endocytic recycling, and retrograde transport, plus mitotic spindle assembly and cell cycle processes, indicating a theme of membrane logistics intertwined with cell division. Some terms on cytoskeletal remodeling (filopodium assembly, dendritic spine morphogenesis) also align with trafficking during division.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006893","count":5},{"id":"GO:0090307","count":4},{"id":"GO:0032456","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4}]},{"hash":"1749856510396051183","title":"Ubiquitin-Proteasome Proteolysis and Proteostasis","description":"The top GO terms cluster around protein turnover and degradation, notably SCF-dependent proteasomal ubiquitin-dependent catabolic processes and protein ubiquitination. Other terms connect to broader cellular regulation (translational preinitiation complex formation, autophosphorylation) and degradation pathways (phagolysosome assembly, lysosome-related processes), with additional developmental annotations. Taken together, the cluster appears to represent a proteostasis-focused group with links to cell cycle regulation and development, rather than a single narrow function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0031146","count":8},{"id":"GO:0090307","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0007420","count":7},{"id":"GO:0001845","count":7}]},{"hash":"2036114082733823471","title":"Kinase signaling and transcriptional regulation","description":"These proteins cluster around positive regulation of serine/threonine kinase activity and protein autophosphorylation, paired with transcription-related processes (DNA-templated transcription, mRNA processing/transport). This suggests a theme where kinase signaling intersects with gene expression control, despite some context-specific terms (oligodendrocyte differentiation, hypoxia response). ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007205","count":7},{"id":"GO:0031954","count":6},{"id":"GO:0071902","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0043547","count":6}]},{"hash":"1386611528323200973","title":"Intracellular Signal Transduction Regulators","description":"The strongest shared function across the proteins is intracellular signal transduction, with multiple entries indicating regulation of signaling pathways, plus assorted regulatory roles in gene expression (mRNA stability) and specialized processes such as telomere maintenance regulation and cardiac electrophysiology. This mixture suggests a cluster of regulators of signaling cascades and transcriptional control rather than a single, cohesive pathway, hence the label focusing on intracellular signaling regulators. ","confidence":"Medium","size":20,"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:0035994","count":3},{"id":"GO:1904357","count":3},{"id":"GO:0035508","count":3}]},{"hash":"321585582722535243","title":"Rho GTPase Driven Cytoskeleton Remodeling","description":"These terms cluster around cytoskeletal dynamics and small GTPase signaling: thrombin-activated receptor signaling implicates GPCR pathways; regulation of Rho protein signal transduction and activation of GTPase activity point to Rho-family GTPases driving actin remodeling; terms for filopodium assembly, mitotic contractile ring actin filament bundle assembly, and membrane repair reflect changes in the cytoskeleton and membrane organization. Some terms like glucose homeostasis and vasoconstriction are less directly connected but may reflect broader signaling contexts in vascular or epithelial cells. Overall, the cluster is best described as Rho GTPase\u2013driven cytoskeleton remodeling.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070493","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0042593","count":2},{"id":"GO:0045907","count":2},{"id":"GO:0008542","count":2}]},{"hash":"2157197605417281011","title":"Chromatin remodeling and transcription regulation","description":"The terms cluster around histone modification (histone acetylation), nucleosome dynamics, heterochromatin boundary formation, and transcription/meiotic cycle regulation, which together point to chromatin remodeling and gene expression control. A couple terms (androgen receptor signaling, sarcomere organization) seem peripheral to this core theme but don\u2019t override the dominant chromatin/gene regulation signal.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060765","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0035948","count":1},{"id":"GO:1900051","count":1},{"id":"GO:0042766","count":1}]},{"hash":"1844177709503570205","title":"Secretory signaling and neuronal development","description":"Most terms cluster around vesicle trafficking and exocytosis (secretory granule localization, acetylcholine secretion/biosynthesis) and neural growth (axonogenesis) with PI and Rho signaling modulating cytoskeleton and membrane trafficking. While some terms relate to bone formation, angiogenesis, and membrane repair, the dominant pattern is secretory signaling linked to neuronal development, hence the name.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048015","count":2},{"id":"GO:0060348","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0032252","count":2},{"id":"GO:0007409","count":2}]},{"hash":"8075335999049196","title":"EGFR-PI3K-JNK Developmental Signaling","description":"This cluster centers on signaling pathways (EGFR, PI3K-Akt, JNK) and developmental processes (spinal cord development, myelination, germ cell development). The proteins likely participate in coordinating growth and neural development. A slightly outlying glycosylation term exists but does not define the cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035269","count":2},{"id":"GO:0031641","count":2},{"id":"GO:0045792","count":2},{"id":"GO:0007173","count":2},{"id":"GO:0046329","count":2}]},{"hash":"2090782229496596352","title":"Rho/Ral GTPase signaling in morphogenesis","description":"This cluster is dominated by GO terms linked to regulation and activation of Rho and Ral GTPase signaling, with cellular responses to cAMP/cGMP, pointing to small GTPase\u2013driven signaling pathways. The presence of morphogenesis terms across tissues (midbrain, heart trabecula, lens) suggests these signaling activities contribute to developmental tissue patterning. Immune-related terms appear less central to the core theme, which remains signaling-regulated morphogenesis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0071321","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0071320","count":3},{"id":"GO:1904693","count":3}]},{"hash":"351408416180337315","title":"Developmental and vascular regulation","description":"The top GO terms cluster around embryonic development (inner cell mass proliferation) and vascular processes (negative regulation of angiogenesis, blood vessel remodeling, extravasation), with additional notes on transcriptional control and protein maintenance. This suggests a regulatory program active during development with a focus on vascular development, rather than a single enzymatic function. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001833","count":2},{"id":"GO:0016525","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0030091","count":2},{"id":"GO:0055114","count":2}]},{"hash":"2255365671187201513","title":"Quinone biosynthesis and central metabolism","description":"This cluster is enriched for quinone biosynthesis (menaquinone and phylloquinone) and broad energy metabolism pathways, including glycolysis, the TCA cycle, fatty acid beta-oxidation, and valine catabolism, with supporting signals like xenobiotic response and cAMP. The prominence of quinone-related terms alongside central carbon metabolism points to a cohesive role in cofactor biosynthesis and energy production.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":11},{"id":"GO:0009234","count":10},{"id":"GO:0010124","count":10},{"id":"GO:0042372","count":10},{"id":"GO:0006635","count":10}]},{"hash":"340008672791934128","title":"Rho GTPase signaling and ER stress\u2013induced apoptosis","description":"The top terms cluster around regulation of Rho GTPase activity and Rho signaling, alongside ER stress\u2013related apoptosis (PERK pathway) and neural development cues, suggesting a combined role in cytoskeletal signaling and stress-induced cell death in development.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007568","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0046856","count":2},{"id":"GO:0060134","count":2}]},{"hash":"240389728391035336","title":"Striatal neuron development and synaptic plasticity","description":"The GO terms point to neuronal development focused on striatal neurons (striatal medium spiny neuron differentiation) and synaptic regulation (long-term synaptic depression, AMPA receptor clustering, ephrin receptor signaling, retinoic acid response). This pattern suggests a theme of striatal neuron development and synaptic plasticity. A few terms (e.g., subtelomeric heterochromatin formation, thymus development) appear less related and may reflect background noise. Overall, the cluster seems best described by neuronal differentiation and synaptic signaling in the striatum.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":3},{"id":"GO:0048013","count":2},{"id":"GO:0021773","count":2},{"id":"GO:1904703","count":2},{"id":"GO:1902237","count":2}]},{"hash":"1866999729822033238","title":"Neural and Skeletal Development","description":"Based on the top GO terms, the cluster shows enrichment for neural and skeletal developmental processes, notably forebrain development, neural tube closure, and skeletal system morphogenesis. This points to a shared function in development, particularly neural and skeletal formation. Some other terms reflect broader cellular processes (e.g., translation initiation, RNA methylation, chromatin assembly) that are less specific to development, but do not override the clear developmental theme suggested by the prominent neural-related terms.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0048705","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0031954","count":1},{"id":"GO:0001731","count":1}]},{"hash":"1930637259663460606","title":"Rho/Ras GTPase signaling and cytoskeletal trafficking","description":"This cluster centers on small GTPase regulation (Rho, Ras), GTPase activation, and actin cytoskeleton remodeling (actin crosslinking, cell adhesion), together with intracellular transport and COPII vesicle cargo loading, pointing to a coordinated role in signaling, cytoskeletal dynamics, and secretory trafficking. While there are immune-related terms (IL-2/IL-4 production), the dominant theme supports GTPase-driven cytoskeletal and trafficking processes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0046580","count":3},{"id":"GO:0090630","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0045737","count":2}]},{"hash":"1833863745762226684","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":146,"triangles":625,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0046677","count":6},{"id":"GO:0042254","count":5},{"id":"GO:0000463","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0051301","count":4}]},{"hash":"1286899654837681723","title":"Unknown","description":"The GO terms span innate immune signaling (TLR7 pathway, diacyl lipopeptide detection, interferon and cytokine regulation) as well as cell cycle, apoptosis, splicing, and various developmental processes, with no single cohesive function tying all proteins together. Therefore a single, representative label cannot be confidently assigned.","confidence":"","size":19,"edges":18,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0008637","count":2},{"id":"GO:0034154","count":2},{"id":"GO:0045078","count":2}]},{"hash":"998830641765301781","title":"Ubiquitin-Proteasome Regulation and DNA Damage Response","description":"The cluster is dominated by ubiquitin-related processes (autoubiquitination, K11-linked ubiquitination, SCF-dependent proteasomal degradation, polyubiquitination) indicating coordinated protein turnover via the ubiquitin-proteasome system, and includes DNA damage response elements (nucleotide-excision repair, G1 checkpoint signaling). Some GO terms also point to innate immune signaling (IFN and TNF pathways), which can be connected to ubiquitin-mediated regulation. Overall, the shared theme is ubiquitin-proteasome regulation coupled with DNA damage response and related signaling.","confidence":"High","size":19,"edges":98,"triangles":225,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":9},{"id":"GO:0051865","count":9},{"id":"GO:0070911","count":7},{"id":"GO:0031146","count":7},{"id":"GO:0070979","count":6}]},{"hash":"1180705596168295373","title":"Unknown","description":"The top GO terms span cardiovascular signaling, telomere maintenance, mRNA stability, and membrane localization with no single unifying function, and the graph has no edges, so there is no cohesive functional module to label. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0035994","count":3},{"id":"GO:1904357","count":3}]},{"hash":"1895208969746272313","title":"Phospholipid Biosynthesis and Remodeling","description":"This cluster is dominated by GO terms for lipid production and remodeling, including CDP-diacylglycerol biosynthesis, phosphatidylcholine acyl-chain remodeling, cardiolipin remodeling, and ether lipid biosynthesis, with a supporting link to mitochondrial ATP synthesis. Together they point to a coherent function in constructing and modifying membrane lipids, particularly phospholipids and cardiolipin in mitochondria. Some tissue-related terms appear but do not define the core theme. ","confidence":"High","size":19,"edges":53,"triangles":57,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0016024","count":5},{"id":"GO:2001246","count":4},{"id":"GO:0006663","count":4},{"id":"GO:0035965","count":4},{"id":"GO:0042775","count":4}]},{"hash":"527647234977834954","title":"Actin cytoskeleton remodeling and cell migration","description":"The cluster is dominated by GO terms related to actin filament bundle assembly and cell migration (plus supporting signal transduction), pointing to roles in cytoskeletal dynamics driving cell movement; a few telomere-related terms seem less connected and may reflect annotation noise. Overall, the common theme is actin-driven cytoskeleton remodeling and motility.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":4},{"id":"GO:0032212","count":3},{"id":"GO:0035994","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0016477","count":3}]},{"hash":"708916357933386155","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The cluster is dominated by ubiquitin-related terms (ubiquitination, ubiquitin-dependent protein catabolic processes, SCF-dependent proteasomal degradation, and K48-linked ubiquitination), pointing to a cohesive ubiquitin-proteasome system governing protein turnover; a few terms about peroxisomal import and signaling appear but are secondary. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0016567","count":6},{"id":"GO:0032088","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0031146","count":5}]},{"hash":"1938817581388860510","title":"Embryonic Development and Tissue Remodeling","description":"This cluster centers on developmental processes (placenta and thyroid gland development, multicellular organism development) and on tissue organization (cell-matrix adhesion, tight junction assembly), with accompanying protein turnover regulation (autophagy and proteasomal degradation) and mechanotransduction (response to muscle stretch). While one term is plant-specific (abscisic acid signaling), the overall pattern points to coordinated embryonic differentiation and establishment of tissue architecture, making the label representative and fairly specific.","confidence":"Medium","size":19,"edges":146,"triangles":606,"max_degree":18,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0060709","count":19},{"id":"GO:0035994","count":19},{"id":"GO:0016242","count":19},{"id":"GO:0032092","count":19},{"id":"GO:0009738","count":19}]},{"hash":"60515789818098453","title":"Neuronal signaling and mitochondrial turnover","description":"This cluster is driven by neural-related functions: phototransduction, chemical synaptic transmission, and long-term potentiation point to neuron-specific signaling and plasticity, while autophagy of mitochondrion and regulation of cellular respiration indicate mitochondrial quality control in neurons. The presence of these related terms supports a cohesive theme around neuronal signaling coupled with mitochondrial turnover, though other terms are present as background noise. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007602","count":2},{"id":"GO:0018298","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0060291","count":2}]},{"hash":"2165526605151666568","title":"Golgi-Associated Vesicle Trafficking","description":"Proteins in this cluster are linked to intracellular membrane trafficking centered on the Golgi apparatus. The top terms emphasize maintaining Golgi location, Golgi-to-vacuole transport, endocytic recycling, retrograde transport from endosomes to the Golgi, and lysosomal transport, all pointing to a cohesive Golgi/endosome/lysosome trafficking module. A couple of terms touch on sphingolipid homeostasis and granule (dense core) transport regulation, suggesting membrane composition and regulated secretion contexts as well. Overall, the cluster represents Golgi-associated vesicle trafficking and recycling processes.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051684","count":2},{"id":"GO:1904811","count":1},{"id":"GO:0006896","count":1},{"id":"GO:1904810","count":1},{"id":"GO:0032456","count":1}]},{"hash":"1971729044308445273","title":"Cilium Assembly and Photoreceptor Protein Localization","description":"The top terms strongly point to ciliary biology, with multiple GO terms for non-motile cilium assembly and its regulation, plus protein localization to the photoreceptor outer segment, suggesting a theme of cilium formation and trafficking in photoreceptors. Some unrelated GO terms (prostate development, photosynthesis) appear as noise, but the core cluster signal centers on cilium-related processes and photoreceptor protein localization.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0030850","count":4},{"id":"GO:0038108","count":4},{"id":"GO:0060613","count":4},{"id":"GO:0045842","count":4},{"id":"GO:0015979","count":4}]},{"hash":"1329451793865863566","title":"Neuronal GTPase signaling and synaptic regulation","description":"Dominant enrichment for regulation of Rho/GTPase signaling and synaptic-related processes (synaptic vesicle priming, glutamatergic transmission, and regulation of synaptic plasticity) along with brain development. This points to a cluster of proteins involved in neuronal signaling and synaptic regulation, driven by small GTPase\u2013mediated control of vesicle trafficking and plasticity, with a few peripheral vascular/immune terms. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0043087","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0043314","count":2}]},{"hash":"1668852570290198673","title":"Ubiquitin-dependent proteasomal degradation","description":"This cluster is dominated by GO terms related to ubiquitination and proteasome-mediated protein catabolism (e.g., ubiquitin-dependent protein catabolic process, protein polyubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, histone catabolic process, and autoubiquitination), indicating a core ubiquitin-proteasome system. The presence of K6-linked ubiquitination and stress-related terms like cadmium response and TNF signaling suggests linked regulatory roles, but the primary signal is ubiquitin-mediated proteolysis. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":15},{"id":"GO:1903378","count":11},{"id":"GO:0000083","count":9},{"id":"GO:0000209","count":9},{"id":"GO:0051865","count":8}]},{"hash":"1026853798708976220","title":"Amino acid catabolism and central carbon metabolism","description":"This cluster shows strong enrichment for amino acid catabolic processes (L-alanine and L-lysine), central carbon metabolism (TCA cycle, pyruvate biosynthesis), and cofactors/biosynthesis (biotin, protoporphyrinogen IX), indicating a core metabolic module. The Notch signaling pathway and DNA-templated transcription terms appear peripheral to this metabolic theme, suggesting regulatory proteins are included but not dominant.","confidence":"Medium","size":18,"edges":102,"triangles":292,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":8},{"id":"GO:0033512","count":7},{"id":"GO:0006099","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0019878","count":6}]},{"hash":"542637432850352287","title":"TLR-mediated innate immune response","description":"The cluster shows enrichment for innate immune and interferon signaling terms, including defense against bacteria (Gram-positive/Gram-negative), dsRNA response, LPS signaling, and TLR7 signaling, indicating a Toll-like receptor\u2013driven innate immune program that activates cytokine and interferon production.","confidence":"High","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050830","count":4},{"id":"GO:0045359","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0043330","count":4},{"id":"GO:0031663","count":4}]},{"hash":"314449388559467413","title":"Golgi-directed vesicle transport and cytoskeleton dynamics","description":"This cluster is enriched for plus-end-directed vesicle transport along microtubules, Golgi localization, actin cytoskeleton organization, and multiple transport processes (carbohydrates, nitrates, sialic acid) as well as neurotransmitter loading into synaptic vesicles. These terms point to proteins that coordinate vesicle trafficking with Golgi positioning and cytoskeletal dynamics. Thus the label Golgi-directed vesicle transport and cytoskeleton dynamics is appropriate.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072383","count":3},{"id":"GO:0051683","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0030036","count":2},{"id":"GO:1900754","count":2}]},{"hash":"1129550661126830816","title":"Vesicle trafficking and cytoskeletal regulation","description":"The proteins cluster around membrane dynamics and transport, with GO terms for vesicle exocytosis, transmembrane transport, and tubulin (cytoskeletal) assembly, plus signaling (ephrin pathway) and cell division. Although a few entries are marked obsolete or related to mitochondrial outer membrane permeabilization, the dominant theme ties vesicle trafficking to cytoskeletal regulation and signaling, suggesting a cohesive role in membrane trafficking and cytoskeletal dynamics.","confidence":"Medium","size":18,"edges":22,"triangles":3,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097345","count":7},{"id":"GO:2000300","count":7},{"id":"GO:0000060","count":7},{"id":"GO:0031384","count":7},{"id":"GO:0010796","count":7}]},{"hash":"297141085735564599","title":"Actin remodeling in synaptic potentiation","description":"The top GO terms combine actin filament polymerization/nucleation/capping with neuronal synaptic activity, including long-term potentiation and excitatory postsynaptic potential, suggesting a core function in actin-driven remodeling that underpins synaptic plasticity at excitatory synapses. Some terms (oligodendrocyte development, subtelomeric heterochromatin formation) are less central to this theme, but the strongest signal points to actin dynamics facilitating synaptic strength changes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030041","count":2},{"id":"GO:0045010","count":2},{"id":"GO:0051694","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0006348","count":2}]},{"hash":"183312681862629868","title":"Insulin/IGF signaling with Rho GTPase regulation","description":"The top GO terms highlight insulin receptor signaling and IGF signaling, together with Rho GTPase activation and regulation of signal transduction, pointing to a core theme of insulin/IGF-driven signaling linked to cytoskeletal dynamics and cell adhesion (integrin activation). Additional regulatory processes (ubiquitination, ncRNA-mediated silencing, NF-kB regulation) suggest broader gene expression control in developmental contexts such as hemopoiesis and placental development. Confidence: High","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0031047","count":2},{"id":"GO:0043124","count":2},{"id":"GO:0016567","count":2}]},{"hash":"1063299650425676478","title":"Vascular and inflammatory signaling","description":"This cluster centers on signals involved in vascular remodeling and inflammation (collagen fibril organization, endothelial delamination, NF-kappaB regulation, chemokine production), with supporting inputs from calcium signaling, neuroendocrine (vasopressin) and cardiac (SA node) regulation, and nociception, suggesting a broad vascular\u2013inflammatory signaling theme. Confidence: Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0051592","count":2},{"id":"GO:0030199","count":2},{"id":"GO:0098907","count":2},{"id":"GO:2000340","count":2}]},{"hash":"2266565841008007290","title":"Neuronal development and synaptic function","description":"This cluster shows a consistent enrichment for nervous system\u2013related processes such as multicellular organism development, Schwann cell development, excitatory postsynaptic potentials, long-term potentiation, visual perception, and responses to muscle activity, suggesting a role in neural development and synaptic function. The presence of mitotic cell cycle terms may reflect developmental proliferation, while the abscisic acid signaling term appears as potential annotation noise from cross-kingdom mappings. Overall, the dominant theme is neural development and synaptic activity.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":8},{"id":"GO:0014044","count":8},{"id":"GO:0060079","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0009738","count":7}]},{"hash":"1704921256273370330","title":"Septation and vesicle trafficking regulation","description":"The cluster shows septation after cytokinesis, budding apical growth, and polarity establishment, plus endosome-to-Golgi and other intracellular transport processes, with links to phosphorylation and CDK/GTPase signaling, suggesting coordination of cell division, polarity, and membrane trafficking.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000920","count":2},{"id":"GO:0042327","count":2},{"id":"GO:2000100","count":2},{"id":"GO:0031031","count":2},{"id":"GO:0007118","count":2}]},{"hash":"1644224080187729911","title":"Neuroimmune Signaling and Development","description":"The top GO terms point to neural development processes such as axonogenesis and myelination, together with innate immune/signaling roles including TLR7 signaling, detection of diacyl lipopeptide, regulation of cytokine production, and type II interferon production. This suggests a cluster of proteins involved in neural development that also participate in neuroimmune signaling or cross-talk, with additional signaling regulation terms supporting a coordinated signaling function.","confidence":"Medium","size":18,"edges":15,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0007409","count":3},{"id":"GO:1903215","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0030433","count":2}]},{"hash":"457892599477369186","title":"Calcium-dependent neuronal signaling and synaptic plasticity","description":"This cluster is dominated by terms related to calcium signaling regulation, calcineurin-NFAT signaling, and long-term synaptic potentiation, all central to neuronal signaling and plasticity. The presence of substantia nigra development reinforces a neural context, while autophosphorylation and kinase regulation suggest a broader kinase-mediated control of these pathways. A single cell-cycle term appears as noise rather than the main theme, so the overall label reflects the neural calcium signaling/plasticity core.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0031954","count":2},{"id":"GO:1900271","count":2},{"id":"GO:0051343","count":2}]},{"hash":"875247649792862877","title":"Unknown","description":"The top terms span skin development, kinase regulation, translation initiation, chromatin assembly, and RNA modification, with obsolete entries. They do not point to a single cohesive function, so a specific label is not supported.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0043588","count":12},{"id":"GO:0031954","count":11},{"id":"GO:0071902","count":11},{"id":"GO:0043547","count":11},{"id":"GO:0001731","count":10}]},{"hash":"1757228053008377754","title":"TORC1-regulated transcription and ribosome biogenesis","description":"This cluster is dominated by GO terms for DNA-templated transcription, ribosome biogenesis, and TORC1 signaling, all pointing to a growth and gene-expression program controlled by TORC1. Additional terms related to mRNA transport and regulation of GTPase activity support a broader RNA metabolism and signaling context, with a few metabolic transport terms that are secondary to the core growth/transcription theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0038202","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0070262","count":3}]},{"hash":"449076629870409397","title":"NF-kappaB/NOD2 Immune Signaling Regulators","description":"This cluster is anchored by multiple terms tied to NF-kappaB transcription factor regulation (including cytoplasmic sequestration) and the NOD2 signaling pathway, pointing to immune signaling control. Additional terms reflect broader stress and metabolic responses (fat cell differentiation, thermoception, salicylic acid response, muscle stretch), which can intersect with immune signaling in stress contexts. Overall, the dominant theme is regulation of immune response signaling rather than a single metabolic or structural function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0045444","count":5},{"id":"GO:0071446","count":5},{"id":"GO:0032212","count":5},{"id":"GO:0035994","count":5}]},{"hash":"890508171544230502","title":"Unknown","description":"The top GO terms cover a wide range of distinct processes (metabolism, transport, signaling, development, and cell-cycle regulation) with no single unifying function. This spread suggests the proteins are involved in multiple unrelated roles or that annotations are dispersed, making a concise, representative label difficult. The cluster thus appears to be functionally diverse or noisy.","confidence":"","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042149","count":8},{"id":"GO:0019346","count":8},{"id":"GO:0006183","count":8},{"id":"GO:0060041","count":8},{"id":"GO:0030071","count":8}]},{"hash":"636958594744254396","title":"Blue light signaling and DNA damage response","description":"The top GO terms cluster around blue light phototransduction, photoreactive repair, phototropism, circadian regulation of calcium oscillations, blue light signaling, and processes related to DNA damage response and checkpoint regulation, suggesting a theme of light sensing coupled to DNA damage signaling. Minor terms like lipid storage and glucagon response appear as peripheral functions but do not change the overall photoreceptive/DNA damage emphasis.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000719","count":2},{"id":"GO:0010617","count":2},{"id":"GO:0009588","count":2},{"id":"GO:0019915","count":2},{"id":"GO:0006975","count":2}]},{"hash":"905102648571540298","title":"Nuclear transcription, RNA processing, and DNA repair regulators","description":"The top GO terms point to core nuclear processes: DNA-templated transcription, regulation of transcription by RNA polymerase II, and mRNA processing, alongside DNA repair and related regulatory activities like deubiquitination. The presence of cell migration and heart development hints at developmental regulation and signaling roles tied to these nuclear functions. Overall, this cluster seems enriched for proteins involved in gene expression control and genome maintenance, with broader implications in development and regulatory signaling.","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:0045944","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0006281","count":2},{"id":"GO:2001275","count":2}]},{"hash":"2164484317822203590","title":"Unknown","description":"The top terms cover a broad mix of stress and heat responses, development, spermatogenesis, behavior, translation regulation, and viral processes, with each term represented only once and no evident enrichment or cohesive biological theme. There are no edges or clusters linking these proteins, making a unified function hard to assign.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034605","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0071549","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0048515","count":1}]},{"hash":"1253502494889484634","title":"Transcriptional Regulation and Cytoskeletal Signaling","description":"The cluster shows a mix of GO terms centered on transcriptional regulation and mRNA processing (regulation of DNA-templated transcription, mRNA processing) along with signaling related to the cytoskeleton (regulation of Rho signal transduction) and cell migration. This suggests a shared theme of coordinating gene expression with cytoskeletal dynamics, despite some terms being obsolete or representing niche pathways like deubiquitination or necroptosis. Medium","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0016477","count":2},{"id":"GO:1990108","count":2},{"id":"GO:1901026","count":2},{"id":"GO:0007205","count":2}]},{"hash":"1287832132079568877","title":"Mitochondrial function and apoptotic signaling","description":"The terms cluster around mitochondrial biology: regulation of mitochondrial membrane potential, apoptotic mitochondrial changes, response to superoxide, magnesium export from mitochondrion, and mitochondrial membrane localization related to fission. These point to mitochondrial homeostasis and stress-induced apoptosis as the core theme. A few items reference broader trafficking (ER-Golgi transport) or growth signaling (IGF stimulus) that are less central but not contradictory to the main theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:2000269","count":1},{"id":"GO:0008637","count":1},{"id":"GO:1990314","count":1},{"id":"GO:0036233","count":1}]},{"hash":"1619753829822683883","title":"Membrane Transporters and Exporters","description":"The cluster is dominated by GO terms tied to transport across membranes and between organelles\u2014ions (potassium, cobalt), vitamins (thiamine), lipids (long-chain fatty acids into peroxisomes), peptides, and even drug-related transport (doxorubicin). These patterns point to transporter or export functions, though a few terms (like RNA regulation) are outliers. Overall, a transport/export theme best explains the group.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0071805","count":2},{"id":"GO:0042953","count":2},{"id":"GO:0015888","count":2},{"id":"GO:0060702","count":2}]},{"hash":"500123120310679118","title":"Mitotic cell division and chromatin assembly","description":"This cluster is driven by strong signals for cell division and chromosome/centromere dynamics (cell division, CENP-A chromatin assembly, positive regulation of centriole elongation, mitotic DNA replication checkpoint signaling), indicating a cohesive mitotic/chromatin theme; auxiliary terms related to proteostasis (autophagosome maturation, ubiquitin-dependent ERAD) and transcriptional regulation appear secondary to this core function.","confidence":"High","size":17,"edges":120,"triangles":465,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0030433","count":7},{"id":"GO:0061641","count":7},{"id":"GO:0097352","count":7},{"id":"GO:0001319","count":7}]},{"hash":"47836528191652597","title":"RNA processing and mRNA metabolism","description":"This cluster is dominated by GO terms tied to the RNA life cycle: transcription termination, splicing and spliceosomal assembly, histone mRNA metabolism, nuclear import, translation, and importantly, P-body assembly and deadenylation-dependent decapping, which together point to RNA processing, export/import, and mRNA turnover being the central theme of the group. A few chromatin-related terms appear sparsely, likely as ancillary connections rather than core functions. ","confidence":"Medium","size":17,"edges":119,"triangles":471,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0033962","count":5},{"id":"GO:1990141","count":5},{"id":"GO:0051170","count":5},{"id":"GO:0008334","count":5}]},{"hash":"2133413089471930950","title":"Ubiquitin-Dependent Proteolysis","description":"Dominated by ubiquitin-dependent protein catabolic processes (ERAD), indicating a proteostasis/degradation theme; a few transcription-related terms are present but far less representative and may reflect multifunctional components. Overall, the cluster centers on protein degradation with possible ancillary regulatory connections.","confidence":"Medium","size":17,"edges":19,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0006352","count":1},{"id":"GO:0051123","count":1},{"id":"GO:2000648","count":1}]},{"hash":"1820215893252397091","title":"Neuronal synaptic signaling and plasticity","description":"The top GO terms cluster around neuronal signaling and synaptic modulation: ephrin receptor signaling, regulation of AMPA receptor clustering, long-term synaptic depression, cellular response to retinoic acid, and differentiation of striatal medium spiny neurons. This points to a module focused on synaptic communication and plasticity, especially AMPA receptor regulation and LTD. Some terms (thymus development, brood size) seem incidental and not central to the core function. ","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048013","count":1},{"id":"GO:0021773","count":1},{"id":"GO:1904703","count":1},{"id":"GO:1902237","count":1},{"id":"GO:0060292","count":1}]},{"hash":"353720849237092319","title":"Developmental Differentiation and Membrane Transport","description":"This cluster shows strong signals for developmental processes across tissues (ectoderm development, renal medulla development, midbrain dopaminergic neuron differentiation) and for membrane transport (proton transmembrane transport). The inclusion of anisotropic cell growth and cortical microtubule cytoskeleton localization suggests coordinated regulation of cell shape, growth, and trafficking during development. A few terms may reflect annotation noise, but the dominant theme is development-linked differentiation with membrane transport roles.","confidence":"Medium","size":17,"edges":66,"triangles":123,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":10},{"id":"GO:0007050","count":8},{"id":"GO:0051211","count":8},{"id":"GO:0007398","count":8},{"id":"GO:0072053","count":8}]},{"hash":"1401005811512287869","title":"Membrane-associated transport and cell survival regulation","description":"The cluster centers on membrane-related transport (potassium ion and UDP-glucose transmembrane transport) and membrane protein processing (GPI anchor biosynthesis), coupled with cell fate pathways such as autophagy regulation and DNA-damage\u2013induced apoptotic signaling. While some terms relate to perception and development (photoreceptor maintenance, visual perception, fungal-type cell wall organization, lateral root development), the common thread ties to membrane-associated processes that modulate survival and maintenance of cellular function.","confidence":"Medium","size":17,"edges":27,"triangles":11,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0007601","count":1},{"id":"GO:1902230","count":1},{"id":"GO:0010506","count":1},{"id":"GO:0031505","count":1}]},{"hash":"1814877939663224173","title":"Diverse Molecule Transport","description":"The GO terms are dominated by transport processes across membranes and organelles, including thiamine, cobalt, lipoprotein, and peroxisomal fatty acid transport, as well as peptide export. A lone regulatory term is present but does not outweigh the transport-focused set, so the cluster is best described as diverse molecule transport. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080051","count":2},{"id":"GO:0042953","count":2},{"id":"GO:0015888","count":2},{"id":"GO:0060702","count":2},{"id":"GO:0015910","count":2}]},{"hash":"2260286133610253032","title":"Unknown","description":"The top GO terms span plants and animals and cover diverse processes (hormone signaling, chlorophyll regulation, prostate and sex differentiation, cell cycle, metal stress, and general negative regulation of enzymes), with no clear, single biological theme binding the cluster. Confidence is None.","confidence":"","size":17,"edges":8,"triangles":0,"max_degree":7,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051291","count":10},{"id":"GO:0030850","count":6},{"id":"GO:0007091","count":6},{"id":"GO:0010288","count":6},{"id":"GO:0051348","count":6}]},{"hash":"1971292441049384371","title":"Hormone and xenobiotic metabolism","description":"This cluster centers on metabolic and regulatory processes related to hormones and foreign compounds: estrogen and thyroid hormone metabolism, bile acid and ethanol/xenobiotic catabolism, plus regulatory roles in hormone levels and adipocyte differentiation. The shared theme is metabolic processing and hormonal regulation, despite no direct interaction data within the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010765","count":2},{"id":"GO:0006068","count":1},{"id":"GO:0030573","count":1},{"id":"GO:0002002","count":1},{"id":"GO:0042403","count":1}]},{"hash":"2290378921924085475","title":"Rho-dependent actin remodeling and vesicle trafficking","description":"The cluster prominently features actin cytoskeleton reorganization (lamellipodium assembly) and regulation of Rho/Ras signaling, together with components of endosomal vesicle fusion and endosome-to-lysosome transport, indicating a cohesive program of cytoskeletal dynamics coupled to vesicular trafficking. Some terms are obsolete or developmental, but the core theme centers on actin-driven membrane remodeling and intracellular transport.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031532","count":3},{"id":"GO:0035023","count":2},{"id":"GO:0034058","count":2},{"id":"GO:0008333","count":2},{"id":"GO:0043552","count":2}]},{"hash":"1208986743029645481","title":"Protein and RNA methylation","description":"The top terms are dominated by methylation-related processes: peptidyl-lysine methylation (mono- and dimethylation), peptidyl-glutamine methylation, RNA guanine-N7 methylation, and 7-methylguanosine mRNA capping. This points to a cluster of methyltransferase activities influencing both protein and RNA modifications, with supporting signals from related biosynthetic methylation steps (e.g., cobalamin/antibiotic biosynthesis). While a few terms are broader biosynthetic processes, the recurring motif is methylation, suggesting a cohesive functional theme around methyltransferases and methylation-dependent reactions.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046690","count":2},{"id":"GO:0036068","count":1},{"id":"GO:0018026","count":1},{"id":"GO:0017000","count":1},{"id":"GO:1901052","count":1}]},{"hash":"1276223660271330554","title":"Neural, cardiac, and endocrine development","description":"This cluster contains GO terms spanning nervous system development and myelination, heart development (cardiac atrium formation, cardioblast migration, heart rate regulation), skeletal muscle differentiation, and endocrine lineages (adrenal chromaffin cell differentiation, pancreatic PP cell fate). Together these terms point to coordinated developmental programs across neural, cardiovascular, and neuroendocrine tissues.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006366","count":7},{"id":"GO:0035914","count":6},{"id":"GO:0042552","count":5},{"id":"GO:0003210","count":5},{"id":"GO:0007399","count":5}]},{"hash":"1816594675510240843","title":"Neuronal development and proteostasis regulation","description":"This cluster is driven by terms for neuron development and dendritic spine morphogenesis, pointing to neural differentiation and synaptic structuring. It also includes themes of protein stability regulation and proteasomal degradation, suggesting a focus on proteostasis in neural contexts. While DNA replication/transcription terms appear, they seem general rather than defining the cluster. Overall, the theme aligns best with neural development coupled with proteostasis control.","confidence":"Medium","size":16,"edges":40,"triangles":49,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0000902","count":6},{"id":"GO:0014850","count":5},{"id":"GO:0032435","count":5},{"id":"GO:0006351","count":5}]},{"hash":"325475545606726025","title":"Protein acetylation and amino acid metabolism","description":"Top GO terms indicate enrichment for acetylation-related processes (peptidyl-lysine N6-acetylation, N-terminal acetylation/propionylation) alongside diverse amino-acid metabolic activities (glucosamine, arginine biosynthesis) and related catabolic reactions. This points to a cluster of proteins involved in post-translational acetylation and general amino-acid metabolism, though a few terms (e.g., leaf formation) may be incidental noise.","confidence":"Medium","size":16,"edges":84,"triangles":211,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0018003","count":13},{"id":"GO:0019491","count":12},{"id":"GO:0060358","count":12},{"id":"GO:0045150","count":12},{"id":"GO:0046208","count":12}]},{"hash":"781895848289519305","title":"Neuromuscular and Schwann cell dynamics","description":"This cluster centers on neural and peripheral nerve biology, with terms for musculoskeletal movement, neuromuscular control, Schwann cell migration/proliferation regulation, and neurofilament cytoskeleton organization, complemented by glutamate reuptake indicating glial/neuron signaling. Lipid biosynthesis (ceramide) may relate to myelin membrane biology, while immune/oxidative stress terms are present but less central. Overall, the proteins likely function in neural integrity and neuromuscular signaling with Schwann cell involvement.","confidence":"Medium","size":16,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001306","count":2},{"id":"GO:0050881","count":2},{"id":"GO:0002238","count":2},{"id":"GO:0051935","count":2},{"id":"GO:0046513","count":2}]},{"hash":"1502067993327337989","title":"Mitochondrial transport and stress response","description":"This cluster centers on mitochondrial functions, including membrane potential regulation, various ion transports (ornithine, magnesium, phosphate), and apoptotic changes, alongside oxidative stress response and metabolic signaling (IGF stimulus). While a few terms touch on general transport or plasma membrane processes, the dominant theme is mitochondrial membrane transport and stress-related signaling, suggesting a cohesive mitochondrial-centered network.","confidence":"High","size":16,"edges":66,"triangles":110,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":10},{"id":"GO:0008637","count":9},{"id":"GO:1990314","count":9},{"id":"GO:0036233","count":9},{"id":"GO:0090152","count":9}]},{"hash":"1540911576641229083","title":"Cell Cycle and Centrosome/Telomere Maintenance","description":"This cluster centers on processes tied to cell division, centrosome function, and telomere maintenance, highlighted by GO terms for cell division, pericentriolar material localization, and telomerase holoenzyme assembly. Additional terms referencing plant root meristem growth and hormonal signaling suggest broader growth regulation, but the strongest common theme is cell cycle control with centrosome and telomere maintenance. Confidence: Medium","confidence":"","size":16,"edges":10,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0048642","count":1},{"id":"GO:0045201","count":1},{"id":"GO:0042921","count":1},{"id":"GO:1900037","count":1}]},{"hash":"644992478389267356","title":"Placental Development and Immune Signaling","description":"These proteins show enrichment for placental development processes (glycogen cell differentiation in embryonic placenta, labyrinthine layer blood vessel development, maternal placenta development) alongside immune-related activities (IL-4 production, IL-7 response, GM-CSF stimulus) and apoptosis, suggesting a module tied to placental formation and maternal\u2013fetal immune interactions. A visual perception term appears incidental among the terms.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0060709","count":2},{"id":"GO:0097011","count":2},{"id":"GO:0010765","count":2}]},{"hash":"1681013876796005125","title":"Mitochondrial protein import and respiratory chain assembly","description":"The cluster centers on mitochondrial functions: import of proteins into the mitochondrial matrix, assembly of the respiratory chain (complex II) and electron transport from NADH to ubiquinone, and iron-sulfur cluster assembly, with some related chaperone activity and stress-related signals (heat response, apoptotic signaling). Together these terms imply a cohesive theme around mitochondrial protein handling and oxidative phosphorylation, despite a couple of peripheral terms.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:1990507","count":1}]},{"hash":"1800364612383199527","title":"Membrane signaling and cytoskeletal remodeling","description":"GO terms point to membrane-initiated signaling (ephrin and T cell receptor pathways) intertwined with cytoskeletal and membrane remodeling processes (filopodium assembly, plasma membrane tubulation, cell polarity, and adhesion). This coherent theme across multiple terms supports a label focusing on membrane signaling coordinating cytoskeletal dynamics and cell morphology.","confidence":"High","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":3},{"id":"GO:0046847","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0090503","count":2},{"id":"GO:0048013","count":2}]},{"hash":"1765890062674907139","title":"Chromatin Assembly and Cell Division","description":"Proteins in this cluster are enriched for nuclear and chromatin-related processes (nucleus organization; CENP-A chromatin assembly) and cell division, suggesting a module focused on chromatin maintenance and mitosis. While other terms (brain development, immune defense) appear less related, the strongest signal centers on chromatin and cell-cycle functions.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006997","count":3},{"id":"GO:0046626","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0007420","count":3}]},{"hash":"560873160777849314","title":"ER-Golgi Vesicle Trafficking and Phospholipid Biosynthesis","description":"The top GO terms cluster around ER-to-Golgi vesicle transport and Golgi-associated vesicle fusion, plus multiple phospholipid biosynthesis processes (phosphatidylethanolamine, phosphatidylserine, phosphatidylglycerol) and related lipid regulation. This points to a cohesive role in membrane trafficking and membrane lipid biosynthesis, suggesting a specific functional theme for the cluster.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0048280","count":2},{"id":"GO:1905711","count":1},{"id":"GO:0006663","count":1},{"id":"GO:0006659","count":1}]},{"hash":"1976407981515288981","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001824","count":2},{"id":"GO:0090669","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000495","count":1},{"id":"GO:0006417","count":1}]},{"hash":"268977507991870333","title":"Ribosome biogenesis and rRNA maturation","description":"Dominant GO terms are about assembly of the large-subunit preribosome and maturation of LSU- and 5.8S rRNA, pointing to nucleolar factors involved in ribosome biogenesis. A few terms touch on signaling or splicing, but the core theme across the cluster is ribosome assembly/processing, suggesting these proteins function as ribosome biogenesis components. The lack of edges in this snapshot indicates no detected direct interactions among them.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035640","count":2},{"id":"GO:1902626","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0070371","count":2}]},{"hash":"340041698114756953","title":"Microtubule Cytoskeleton and Spindle Dynamics","description":"Proteins in this cluster are enriched for GO terms about microtubule organization and spindle function\u2014polarity establishment, spindle orientation, spindle pole separation, karyogamy, meiosis/mitosis, cytokinesis, and even dendritic transport\u2014suggesting a cohesive role in microtubule-based architecture and movement across cell division and intracellular transport contexts.","confidence":"High","size":16,"edges":85,"triangles":235,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":16},{"id":"GO:0048364","count":16},{"id":"GO:0000743","count":16},{"id":"GO:0000073","count":16},{"id":"GO:0098971","count":16}]},{"hash":"1665499986329237317","title":"Neural and epidermal development signaling","description":"The top GO terms include cerebral cortex and hippocampus development (neural), keratinocyte differentiation (epidermal), and key signaling pathways (Hippo, Wnt), along with cell spreading and centrosome separation, suggesting a coordinated role in developmental signaling and tissue morphogenesis across neural and skin contexts.","confidence":"Medium","size":16,"edges":115,"triangles":493,"max_degree":15,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0007100","count":15},{"id":"GO:0009190","count":14},{"id":"GO:0021987","count":14},{"id":"GO:0021766","count":14},{"id":"GO:0034446","count":14}]},{"hash":"2305686314588953385","title":"Kinase and GTPase signaling with cell cycle control","description":"The top GO terms cluster around regulation of protein autophosphorylation and serine/threonine kinase activity, plus positive regulation of GTPase activity and the mitotic cell cycle, pointing to a theme of phosphorylation-driven signaling connected to cell-cycle regulation. Additional terms like mRNA transport and hypoxia response appear as broader cellular contexts but are less central to the primary signal transduction motif.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":7},{"id":"GO:0031954","count":6},{"id":"GO:0051028","count":5},{"id":"GO:0071456","count":5},{"id":"GO:0071902","count":5}]},{"hash":"1995617751305400029","title":"Unknown","description":"The top terms span translation initiation, RNA methylation, CENP-A chromatin assembly, mitotic spindle orientation, GPCR signaling, aging, glial apoptosis, and genomic imprinting regulation, which shows no single cohesive function tying the proteins together. The terms are diverse and include obsolete entries, suggesting no clear shared theme for this cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0031954","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0007568","count":5},{"id":"GO:0070208","count":5},{"id":"GO:0036265","count":5}]},{"hash":"230977417893516972","title":"Membrane receptor signaling cluster","description":"Based on the top GO terms, several proteins are linked to signaling pathways initiated by membrane receptors (integrin-mediated signaling, complement receptor\u2013mediated signaling, apolipoprotein A-I\u2013mediated signaling). While other terms like translation or metabolism appear, the recurring theme is cell-surface signaling. This label captures the core shared function across these terms more than any single specific pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006574","count":2},{"id":"GO:0006507","count":1}]},{"hash":"236489513988263210","title":"Mitochondrial membrane potential regulation and transport","description":"The top GO terms cluster around mitochondrial functions, including regulation of mitochondrial membrane potential, various transmembrane transports across mitochondrial membranes (e.g., magnesium, phosphate, ornithine), and apoptotic/oxidative stress-related changes. This suggests the proteins share a mitochondrial-centered role in maintaining membrane potential, membrane transport, and responses to reactive oxygen species, with a few outliers related to general signaling. Overall, the theme is mitochondrial homeostasis and transport.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":3},{"id":"GO:0035023","count":2},{"id":"GO:1990314","count":2},{"id":"GO:0036233","count":2},{"id":"GO:0090152","count":2}]},{"hash":"321846735643818232","title":"Ubiquitin-Proteasome\u2013Mediated Cell Cycle Control","description":"Most of the top terms point to ubiquitin-dependent protein degradation (SCF complex, polyubiquitination) and key cell cycle processes (mitotic G1 checkpoint signaling, regulation of DNA replication initiation, microtubule dynamics). While a couple terms are broader (circadian regulation), the dominant theme is control of cell-cycle progression through targeted proteolysis. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000083","count":11},{"id":"GO:0031146","count":10},{"id":"GO:0071276","count":9},{"id":"GO:1902916","count":9},{"id":"GO:0000209","count":9}]},{"hash":"1188768639810928995","title":"Protein quality control and transcription regulation","description":"The terms cluster around ubiquitin-related turnover (deubiquitination, ERAD), autophagic clearance (aggrephagy), and broader protein homeostasis, with additional links to transcriptional regulation (DNA-templated transcription, RNA Pol II regulation) and some trafficking/cytoskeletal processes (actin bundle assembly, GPCR internalization). This points to a theme of maintaining protein quality and coordinating gene expression in response to cellular states, hence a label focusing on protein quality control and transcription regulation. ","confidence":"Medium","size":15,"edges":39,"triangles":56,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1904021","count":2}]},{"hash":"1564525667733584809","title":"Central carbon metabolism and amino acid catabolism","description":"Top GO terms indicate a focus on core energy production and carbon fuel utilization, including the TCA cycle, glycolytic process, and the glyoxylate cycle, along with several amino-acid catabolic pathways (L-alanine, L-lysine via saccharopine, L-kynurenine). This pattern points to a cluster of proteins involved in breaking down nutrients to feed central metabolism. Some outliers (Notch signaling, [2Fe-2S] cluster assembly, oxalic acid secretion) are likely noise or multifunctional annotations but do not negate the overall metabolic theme.","confidence":"Medium","size":15,"edges":101,"triangles":405,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":5},{"id":"GO:0007219","count":4},{"id":"GO:0033512","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0097053","count":4}]},{"hash":"440046445451376385","title":"Redox-Regulated Neural and Vascular Development","description":"The GO terms show a strong emphasis on redox biology (cellular oxidant detoxification, removal of superoxide radicals, cell redox homeostasis) alongside neural and vascular development signals (cerebral cortex development, angiogenesis) and transcriptional regulation (DNA-templated transcription, negative regulation of protein export from nucleus). This combination suggests a module where redox state modulates gene expression to coordinate brain and blood vessel development. An outlier term like sperm capacitation exists but does not override the dominant redox-development theme.","confidence":"Medium","size":15,"edges":11,"triangles":10,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046826","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0048240","count":5},{"id":"GO:0045793","count":5},{"id":"GO:0098869","count":5}]},{"hash":"1493925894837485954","title":"Calcium-Dependent Ion Transport and Signaling","description":"The cluster centers on calcium-related processes: calcium ion import, calcium-responsive signaling, and calcium-channel\u2013driven membrane depolarization, with supporting roles for magnesium and manganese transport and ion homeostasis. The presence of small GTPase\u2013mediated signaling and Ras pathway regulation suggests broader signaling connections, anchored by calcium-dependent signaling; a few terms reflect broader metabolic or neural context but do not change the core theme.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098703","count":4},{"id":"GO:0006828","count":4},{"id":"GO:0046580","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0086045","count":3}]},{"hash":"89820005329861698","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":12,"triangles":8,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0090084","count":4},{"id":"GO:0051259","count":4},{"id":"GO:0031204","count":4}]},{"hash":"1089471771864859470","title":"Unknown","description":"The top terms span immune signaling, cytoskeletal remodeling, synaptic plasticity, developmental processes, tight junctions, and cellular organization, with no clear single theme tying all proteins together, suggesting a mixed set of roles rather than a cohesive cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060335","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0051764","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0007507","count":3}]},{"hash":"1648831174865678317","title":"Unknown","description":"The proteins span chromatin assembly and mitotic maintenance terms but also diverse developmental and immune-related processes, with no clear, single function uniting the cluster; as a result, a concise, representative label cannot be determined.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0048593","count":2},{"id":"GO:0002227","count":1}]},{"hash":"2297270770761025835","title":"Fatty acid elongation and unsaturated lipid biosynthesis","description":"The top GO terms are dominated by fatty acid elongation and various fatty acid biosynthetic processes (long-chain, very long-chain, monounsaturated, polyunsaturated, unsaturated), pointing to a cluster focused on lipid production and elongation rather than trafficking. The transport terms and swim bladder development are present but much less represented and do not define the core function.","confidence":"High","size":15,"edges":21,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0019367","count":1},{"id":"GO:0042761","count":1},{"id":"GO:0035338","count":1},{"id":"GO:0042759","count":1},{"id":"GO:0034626","count":1}]},{"hash":"2016768778442204324","title":"Multi-tissue signaling and morphogenesis","description":"The top GO terms show a mix of signaling (cGMP/cAMP responses, GTPase activation, NMDA receptor regulation) and tissue morphogenesis (heart trabeculae, lens), plus barrier formation and immune-related processes, suggesting the proteins participate in broad signaling and developmental processes across multiple tissues rather than a single, cohesive pathway. This supports labeling as cross-tissue signaling and morphogenesis rather than a narrow function.","confidence":"Medium","size":15,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071321","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0061384","count":2},{"id":"GO:0043303","count":2},{"id":"GO:0002089","count":2}]},{"hash":"1800826782968562073","title":"Lipid Metabolism and Membrane Biogenesis","description":"The top GO terms cluster around lipid biosynthesis and membrane-related processes: unsaturated fatty acid biosynthesis, ergosterol (sterol) biosynthetic regulation, and sphingolipid metabolism, plus endoplasmic reticulum tubular network maintenance. There are also lipids-rich tissue processes listed (sebaceous gland differentiation, myelin maintenance), and membrane-related mitochondrial inheritance, suggesting a membrane/lipid-centric theme. Some terms (nitric oxide/nitrate assimilation, axonal fasciculation) are less connected, appearing as noise. Overall, the cluster is best described by lipid metabolism and membrane biology.","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":2},{"id":"GO:0006675","count":1},{"id":"GO:0006636","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0032286","count":1}]},{"hash":"2225422534637369958","title":"Diverse membrane transporters","description":"This cluster is dominated by GO terms related to transport processes across membranes and organelles (phospholipid translocation, lipoprotein transport, thiamine transport, peroxisomal fatty acid import, cobalt ion transport, oligopeptide export from mitochondrion, peptide pheromone export, doxorubicin transport), suggesting a cohesive theme of transporting diverse substrates. Some terms (e.g., regulation of endoribonuclease activity, stem cell proliferation) appear as outliers, but the overall signal points to membrane transport functions rather than a single specific substrate. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0045332","count":6},{"id":"GO:0042953","count":4},{"id":"GO:0015888","count":4},{"id":"GO:0060702","count":4},{"id":"GO:0015910","count":4}]},{"hash":"716539206630246293","title":"Unknown","description":"The top terms cover a mix of signaling, translation, RNA processing, chromatin assembly, and cell division (e.g., kinase regulation, translation initiation, RNA methylation, CENP-A chromatin, spindle orientation) with no clear single theme, and there are no edges connecting the proteins, indicating a lack of a cohesive functional module. Therefore a simple unknown label is most appropriate.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0061099","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0031954","count":5},{"id":"GO:0001731","count":5},{"id":"GO:0007568","count":5}]},{"hash":"620270987959658340","title":"Protein acetylation and ER quality control","description":"The top GO terms cluster around post-translational protein acetylation (histone H2B and N-terminal acetylation; regulation of tubulin deacetylation) and ER-associated protein quality control pathways (ubiquitin-dependent ERAD, unfolded protein response). While a few terms are metabolically or developmentally themed, the dominant signal is acetylation and ER protein quality control, suggesting a cohesive group of proteins involved in modifying proteins and maintaining ER homeostasis.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":3},{"id":"GO:0010742","count":3},{"id":"GO:0090043","count":3},{"id":"GO:0008286","count":3},{"id":"GO:0043923","count":3}]},{"hash":"963584364751570278","title":"Vertebrate heart and spinal cord development with lipids","description":"This cluster contains GO terms tied to vertebrate development (heart development, spinal cord development, anterior/posterior axis specification) alongside lipid metabolism processes (lipid storage, lipid catabolic process, reverse cholesterol transport) and signaling/regulatory activities (Rho signaling, protein tetramerization). The dominant themes appear to be developmental processes in vertebrates and associated lipid metabolic pathways, with some supporting regulatory interactions, though there is no single tightly shared function across all terms.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904211","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0051262","count":2}]},{"hash":"203852545905894036","title":"Cardiac development and morphogenesis","description":"The cluster\u2019s top GO terms cluster around heart development and atrial septum morphogenesis, including atrial septum primum/secundum morphogenesis and cardiac muscle hypertrophy in response to stress, suggesting a cardiogenesis-related theme. While some terms (IgA isotype switching, nucleosome assembly, neurotransmitter secretion, mitotic cell cycle) appear, they are less central to the main cardiac-focused terms, likely representing broader or incidental annotations.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048298","count":2},{"id":"GO:0003290","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0003289","count":2},{"id":"GO:0014898","count":2}]},{"hash":"1454649694495304330","title":"Organelle inheritance and endosomal trafficking","description":"The cluster is dominated by GO terms tied to organelle inheritance (mitochondrion and peroxisome) and membrane trafficking processes (endocytic recycling, endosome organization, peroxisome fission), suggesting proteins involved in intracellular trafficking and maintenance of organelles. A couple of outlier terms (ribosomal export, GABAergic transmission) may reflect broad annotations but do not outweigh the central theme.","confidence":"Medium","size":15,"edges":23,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0016559","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0000002","count":3}]},{"hash":"2092147701199940558","title":"Unknown","description":"The GO terms cover antiviral response, hormone signaling and development, and cell cycle processes with no clear, unified function across species, suggesting no single cohesive theme for this cluster.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071357","count":8},{"id":"GO:0009938","count":7},{"id":"GO:0030850","count":6},{"id":"GO:0043278","count":6},{"id":"GO:0046661","count":6}]},{"hash":"2141679568385998720","title":"Developmental signaling and stress-response regulators","description":"Reasoning: The proteins are linked to development (nervous system and skeletal muscle), transcriptional regulation (DNA-templated transcription), signaling (B cell receptor pathway), and stress/apoptosis pathways (ER stress-induced apoptosis, senescence, ripoptosome). This pattern suggests regulatory factors that participate in developmental signaling as well as broader cellular stress responses, rather than a single narrow function.","confidence":"Medium","size":14,"edges":10,"triangles":3,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007399","count":3},{"id":"GO:0006351","count":3},{"id":"GO:1902237","count":2},{"id":"GO:0035729","count":2},{"id":"GO:0090400","count":2}]},{"hash":"210664858371784933","title":"Chromatin assembly and remodeling","description":"This cluster centers on chromatin organization and histone dynamics, including DNA replication-dependent chromatin assembly, nucleosome assembly, heterochromatin formation, transcription initiation-coupled chromatin remodeling, and chromatin localization. The grouping of these related terms strongly suggests a cohesive role in building and regulating chromatin structure and associated histone modifications.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051290","count":4},{"id":"GO:0006335","count":4},{"id":"GO:0000183","count":4},{"id":"GO:0045815","count":4},{"id":"GO:0071169","count":4}]},{"hash":"271922773980599189","title":"Tryptophan catabolism and NAD biosynthesis","description":"This cluster shows several strong signals for tryptophan-derived metabolism: L-kynurenine catabolic process, quinolinate biosynthetic process, and anthranilate metabolic process, which are all steps toward NAD+ production. There are also supportive but looser signals of broader amino acid catabolism and [2Fe-2S] cluster assembly, suggesting a broader metabolic context. The Notch signaling term appears less relevant and likely annotation noise. Overall, the core theme is conversion of tryptophan to NAD via the kynurenine/quinolinate pathway.","confidence":"Medium","size":14,"edges":32,"triangles":16,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007219","count":6},{"id":"GO:0042853","count":6},{"id":"GO:0097053","count":6},{"id":"GO:0019805","count":5},{"id":"GO:0044571","count":4}]},{"hash":"1202691710508367516","title":"Embryonic organogenesis and nervous system development","description":"This cluster shows a clear emphasis on developmental processes across multiple organs, especially neural structures (forebrain, cerebellum, retinal development and axon guidance) and supporting organs (heart, muscle, placenta, thyroid), indicating a cohesive theme of embryonic organogenesis and nervous system formation.","confidence":"High","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030878","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0001890","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0007275","count":2}]},{"hash":"2304457868248960050","title":"Dopaminergic Neuron Differentiation and Dendritic Morphogenesis","description":"The top GO terms are dominated by neuronal development and morphology, including midbrain dopaminergic neuron differentiation, neuron fate determination, and regulation of dendritic spine morphogenesis and filopodium assembly. While there are a few non-neuronal terms (endothelial barrier, immune clustering, trafficking), the strongest and most recurrent theme centers on neural development and synaptic/dendritic architecture, suggesting proteins that function together in neuronal differentiation and dendrite/spine formation.","confidence":"Medium","size":14,"edges":19,"triangles":6,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":2},{"id":"GO:0061001","count":2},{"id":"GO:1905279","count":2},{"id":"GO:0051489","count":2},{"id":"GO:0008283","count":2}]},{"hash":"1530342271726768331","title":"Neuronal development and synaptic regulation","description":"The cluster is enriched for terms tied to brain development, intracellular transport, vesicle fusion, and cortical microtubule cytoskeleton localization, as well as regulation of synaptic plasticity and neuronal signaling. While there are general transcriptional and apoptotic regulation terms, the neuron/brain-focused terms predominate, suggesting a cohesive role in neuronal development and synaptic function.","confidence":"High","size":14,"edges":44,"triangles":82,"max_degree":10,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006886","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0045945","count":3},{"id":"GO:1905433","count":2}]},{"hash":"214361720684505606","title":"Brain development and neuronal stress responses","description":"Top GO terms emphasize brain-related development (synapse assembly, third ventricle development) and neuronal signaling, plus responses to metal-induced stress (cadmium, methylmercury) and apoptotic pathways. The presence of ubiquitination regulation and circadian rhythm control also aligns with neural physiology. Together, these terms suggest a cluster centered on neuronal development with associated stress response and regulatory processes.","confidence":"Medium","size":14,"edges":14,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1903378","count":1},{"id":"GO:0071276","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0060386","count":1},{"id":"GO:0021678","count":1}]},{"hash":"1666639765179913603","title":"Peripheral nerve development and myelination","description":"The top terms converge on neural development, particularly myelination in the peripheral nervous system and axon guidance/fasciculation, suggesting the cluster centers on PNS development and wiring. Some terms about transcription regulation and non-neural processes are broader and lessen the coherence, hence a moderate rather than high confidence.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":2},{"id":"GO:0009268","count":2},{"id":"GO:0006368","count":1},{"id":"GO:0048096","count":1},{"id":"GO:0006355","count":1}]},{"hash":"475389020577548315","title":"Plant photomorphogenesis and jasmonic acid signaling","description":"The cluster shows a cohesive theme around plant development influenced by light and hormone signaling: red/far-red light responses and phototransduction point to photomorphogenesis, while jasmonic acid signaling and flower development indicate hormone-regulated growth. Some cytoskeletal assembly terms may reflect morphogenesis, and a single mRNA decay term is peripheral. Overall, the terms suggest a plant-specific light and hormone signaling cluster.","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0030035","count":2},{"id":"GO:0009911","count":1}]},{"hash":"984183622309789885","title":"Virus-host interaction and replication","description":"The GO terms cluster around the viral life cycle and how viruses manipulate host cells: virion assembly, proviral latency establishment, viral release, and host entry; coupled with nuclear import of viral components and modulation of NF-kappaB signaling. Lipid droplet organization often relates to viral replication and assembly environments, while mitotic cell cycle terms suggest host cell cycle manipulation by viruses. Together these terms point to a cohesive theme of virus\u2013host interaction and replication. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0034389","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0075713","count":2}]},{"hash":"836289472541715848","title":"Antibiotic and xenobiotic catabolism","description":"The cluster includes catabolic processes for various substrates (triglycerides, nylon, beta-lactam antibiotics) and related antibiotic-response and beta-lactamase regulation terms, plus proteolysis and ROS/metabolic regulation. This suggests a cohesive theme of enzymes involved in degrading diverse compounds and managing antibiotic/xenobiotic stress, with ties to energy and glucose homeostasis, making a label centered on antibiotic/xenobiotic catabolism reasonable.","confidence":"Medium","size":14,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:0030655","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0033252","count":1},{"id":"GO:0019876","count":1}]},{"hash":"84667203232993230","title":"DNA Damage Response and Translational Control","description":"The top GO terms point to a coordinated stress response involving both transcriptional regulation (DNA-templated transcription elongation/termination, antitermination) and translational control (translation and regulation of translation), plus cellular responses to gamma radiation and UV. This suggests the proteins participate in DNA damage\u2013related signaling and gene expression tuning under stress, justifying a label centered on DNA damage response and translational regulation.","confidence":"High","size":14,"edges":17,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0045727","count":3},{"id":"GO:0071480","count":3},{"id":"GO:1902164","count":3},{"id":"GO:0006353","count":3}]},{"hash":"1400734531212651396","title":"Neural development and axon guidance signaling","description":"This cluster is enriched for neural development and signaling terms: axon guidance, neural tube patterning, and calcineurin-NFAT signaling, plus cell-matrix adhesion and integrin signaling, consistent with neuronal pathfinding and tissue morphogenesis. While there are broader developmental terms (visual perception, metanephric morphogenesis), the recurring emphasis on neuronal guidance and adhesion supports labeling as neural development/signaling.","confidence":"Medium","size":14,"edges":14,"triangles":1,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0060396","count":2},{"id":"GO:2001046","count":2},{"id":"GO:0072284","count":2}]},{"hash":"1917870726712799154","title":"Neuronal development and synaptic regulation","description":"Top GO terms point to brain development and neural signaling processes (brain development, vesicle fusion, and regulation of synaptic plasticity), suggesting a cluster tied to neuronal growth and communication. Additional terms on protein turnover (SCF-dependent degradation) and transcriptional regulation (ribosomal protein gene transcription) align with synaptic remodeling. Some outliers (obsolete histone acetylation, invasive growth in response to glucose limitation) exist but do not overshadow the neural-focused signals. Overall, the cluster appears to represent neuronal development and modulation of synaptic signaling.","confidence":"Medium","size":14,"edges":34,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0043966","count":2},{"id":"GO:0046777","count":2},{"id":"GO:0031146","count":2}]},{"hash":"94958772551444460","title":"Translation machinery and ribosome biogenesis","description":"This cluster is dominated by GO terms tied to cytoplasmic translation, initiation/termination, and ribosome biogenesis, plus selenocysteine incorporation. The co-occurrence of these translation-related terms suggests proteins are core components of the protein synthesis machinery, with some regulatory links (e.g., positive regulation of cytoplasmic translation, response to amino acid starvation). A single antibiotic-response term is present but does not dominate the set.","confidence":"High","size":14,"edges":41,"triangles":46,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0046677","count":6},{"id":"GO:0042254","count":4},{"id":"GO:1903833","count":4},{"id":"GO:0006415","count":4}]},{"hash":"161779722898450277","title":"Transcription Initiation and RNA Processing","description":"The terms converge on nuclear gene expression machinery: RNA polymerase II preinitiation complex assembly and DNA-templated transcription initiation indicate transcription initiation, while box C/D snoRNP assembly points to RNA processing. A few terms relate to chromatin regulation and Notch-responsive transcription, but overall the cluster centers on transcription and RNA processing functions, justifying the label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007020","count":2},{"id":"GO:0051123","count":1},{"id":"GO:0007221","count":1},{"id":"GO:0030707","count":1},{"id":"GO:0032435","count":1}]},{"hash":"1351852438654247916","title":"Unknown","description":"The top GO terms are highly heterogeneous, including muscle- and nervous-system development, circadian regulation, distal tubule morphogenesis, sarcomere organization, and even a plant-specific flowering term, plus electron transport and ubiquitination. No single cohesive function or pathway ties these proteins together confidently, so a specific, representative label cannot be assigned.","confidence":"","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0022900","count":1},{"id":"GO:0009911","count":1},{"id":"GO:1990390","count":1},{"id":"GO:0007399","count":1},{"id":"GO:0042752","count":1}]},{"hash":"203082677224697292","title":"Chromatin assembly and mitosis","description":"This cluster centers on centromere and chromatin dynamics (CENP-A containing chromatin assembly; establishment of mitotic spindle orientation) and general gene expression control (translation preinitiation complex formation; RNA guanine-N7 methylation). A signaling angle is hinted by positive regulation of protein autophosphorylation. While spermatogenesis and glial apoptosis are more tissue-specific, the core terms suggest a cohesive theme around chromatin organization, chromosome segregation, and regulation of gene expression during cell division. ","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0070208","count":1}]},{"hash":"120186728607112063","title":"Fungal cell wall biosynthesis and glycoprotein assembly","description":"The top GO terms are dominated by fungal-type cell wall biogenesis, cell wall organization, and cell wall mannoprotein biosynthetic processes, along with GDP-mannose biosynthesis, all pointing to a shared role in constructing and glycosylating fungal cell walls. The translation term appears but is less central to this theme, suggesting the core function of the cluster is cell wall assembly/glycoprotein production rather than translation. ","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":4},{"id":"GO:0008360","count":2},{"id":"GO:0009272","count":2},{"id":"GO:0009103","count":2}]},{"hash":"219127919271023823","title":"Mitotic Machinery and ER-Golgi Trafficking","description":"The top GO terms cluster around cell division and mitotic processes (mitotic spindle assembly, mitotic DNA replication, sister chromatid cohesion, cell division) together with vesicle trafficking steps between the ER and Golgi (COPII vesicle budding, ER-to-Golgi transport), suggesting a functional theme of mitosis linked with secretory pathway components; brain development and defense-related terms appear peripheral but do not override the central mitosis/trafficking signal.","confidence":"Medium","size":14,"edges":15,"triangles":2,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0090114","count":3},{"id":"GO:0051301","count":3}]},{"hash":"551580451116650244","title":"Placental development and cytokine signaling","description":"This cluster centers on placental-related processes (glycogen cell differentiation in embryonic placenta development; labyrinthine layer blood vessel development) and a set of immune/hormonal signaling responses (IL-4 production, IL-7 response, GM-CSF stimulus, prostaglandin response), with supporting endocrine/metabolic signaling (insulin receptor signaling). Together, these point to signaling networks active in placental development that integrate immune cues and hormonal regulation.","confidence":"Medium","size":14,"edges":13,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0060709","count":2},{"id":"GO:0032633","count":2},{"id":"GO:0060716","count":2},{"id":"GO:0098761","count":2}]},{"hash":"1537642040384267711","title":"Unknown","description":"The top GO terms are spread across cellular stress response, translation initiation, chromatin and mitotic processes, RNA methylation, and glial apoptosis, with no clear, single shared function tying them together. Several terms are obsolete. This dispersion suggests the cluster does not reflect one cohesive biological role, so a concise, unified label isn\u2019t justified.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0031954","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0070208","count":1}]},{"hash":"82398965839525529","title":"Unknown","description":"The terms span proteostasis (misfolded protein response, proteasome-related localization, deubiquitination) and diverse nuclear processes (RNA decay, tRNA gene clustering, and mitotic chromosome events) with many obsolete GO terms, and there are no network edges to tie them into a single coherent function. This lack of a unifying theme makes a specific, concise label inappropriate.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904379","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0070932","count":1},{"id":"GO:0035520","count":1},{"id":"GO:0071218","count":1}]},{"hash":"1322075754643117797","title":"Antiviral innate immune signaling with cytoskeletal remodeling","description":"These proteins show strong enrichment for innate immune and antiviral functions (innate immune response, defense response to virus, TLR7 signaling, and positive regulation of type II interferon production), suggesting a core role in antiviral defense. Coupled with terms about actin filament organization and cell migration, there appears to be accompanying cytoskeletal remodeling linked to immune signaling. Some terms related to development and polarity may be ancillary. Overall, the prevailing theme is antiviral innate immunity with cytoskeletal dynamics.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0071260","count":7},{"id":"GO:0045087","count":6},{"id":"GO:0090162","count":5},{"id":"GO:0021707","count":5},{"id":"GO:0016477","count":5}]},{"hash":"1004486044298338852","title":"Immune signaling and inflammatory regulation","description":"The cluster is driven by immune-related processes: negative regulation of NF-kappaB, NOD2 signaling, IL-6 production regulation, inflammatory response, and B cell proliferation. PARP-mediated ADP-ribosylation supports DNA damage response linked to immunity, while the other terms (spindle assembly, telomere maintenance) appear less central. Overall, the common theme is immune signaling and inflammation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0070212","count":3},{"id":"GO:0070431","count":2},{"id":"GO:0002322","count":2},{"id":"GO:0030011","count":2}]},{"hash":"534149986843240539","title":"Nutrient Metabolism and Hormonal Stress Responses","description":"This cluster centers on diverse metabolic processes (retinol/retinal metabolism, fructose and arabinose catabolism, cholesterol turnover and digestion) along with kidney-related water homeostasis and cellular responses to hormones and stress (cadmium, thyroid hormone, water deprivation), suggesting a broad metabolic/core nutrient processing theme with environmental signaling rather than a single, tight pathway.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":11},{"id":"GO:0042574","count":9},{"id":"GO:0046370","count":8},{"id":"GO:0007586","count":6},{"id":"GO:0071276","count":6}]},{"hash":"237152644342774044","title":"Cardiac muscle development and contraction","description":"The top GO terms indicate ventricular morphogenesis, myofibril assembly, and contraction, plus calcium-release channel regulation, suggesting proteins involved in heart muscle structure, excitation-contraction coupling, and development. Some non-cardiac terms present, but the core signal is cardiac function.","confidence":"High","size":13,"edges":25,"triangles":12,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0055010","count":3},{"id":"GO:0060315","count":3},{"id":"GO:0055003","count":3},{"id":"GO:0060048","count":3},{"id":"GO:0031848","count":2}]},{"hash":"1835468792043128780","title":"Mitochondrial tRNA charging and translation","description":"This cluster is dominated by GO terms for mitochondrial translation and aminoacylation of multiple mitochondrial tRNAs (seryl, threonyl, prolyl, glycyl), plus regulation of translational fidelity, implying a cohesive set of proteins involved in mitochondrial protein synthesis. A few metabolism-related terms like the TCA cycle are present but do not outweigh the translation-focused signal. ","confidence":"High","size":13,"edges":12,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0070158","count":3},{"id":"GO:0015966","count":3},{"id":"GO:0097056","count":3},{"id":"GO:0070159","count":3}]},{"hash":"1099739877030749532","title":"Oxidative stress response and xenobiotic detoxification","description":"The cluster is dominated by GO terms related to detoxification of oxidants and xenobiotics, redox homeostasis, and catabolic processes for toxins/xenobiotics, with additional signals of antioxidant response. A single term for translation elongation is present but less representative of the overall theme, supporting a focus on oxidative stress defense and detox pathways.","confidence":"High","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":8},{"id":"GO:0045454","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0002182","count":4},{"id":"GO:0043508","count":4}]},{"hash":"1393478993448125548","title":"Drosophila development and oogenesis","description":"Top GO terms point to oogenesis-related processes in Drosophila, such as pole plasm oskar mRNA localization and centripetally migrating follicle cell migration, alongside broader development terms like lens morphogenesis and spermatogenesis. The presence of cell division and RNA processing terms suggests these proteins participate in developmental programs and germline biology. While not perfectly cohesive, the strongest signal is developmental/oogenesis biology in Drosophila, supporting a label around that theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002089","count":2},{"id":"GO:0007283","count":1},{"id":"GO:0007076","count":1},{"id":"GO:0019090","count":1},{"id":"GO:0000335","count":1}]},{"hash":"601790809123047678","title":"Unknown","description":"The top GO terms are highly diverse (memory, skin development, mesodermal differentiation, complement signaling, apoptotic regulation, and membrane proteolysis), with no single coherent function or pathway tying the 13 proteins together. This suggests multi-functional or unrelated roles rather than a specific cluster function.","confidence":"","size":13,"edges":49,"triangles":86,"max_degree":12,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0051044","count":9},{"id":"GO:0032516","count":9},{"id":"GO:0007613","count":9},{"id":"GO:0043588","count":9},{"id":"GO:0006507","count":8}]},{"hash":"872268507687886263","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0071035","count":1},{"id":"GO:1901917","count":1},{"id":"GO:0071033","count":1},{"id":"GO:0034476","count":1}]},{"hash":"2176247675464259383","title":"Translation Initiation Complexes","description":"The top GO terms are dominated by translation, translational initiation, and formation of preinitiation complexes, pointing to a cluster enriched in ribosome initiation factors and initiation assembly. A few other annotations (cellular senescence, methylation, mitochondrial inner membrane insertion) may reflect secondary associations or annotation noise, but the prevailing signal centers on translation initiation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006413","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0009236","count":2}]},{"hash":"169760169797898245","title":"Placental development and embryonic differentiation","description":"These proteins show a pattern centered on placental development (maternal placenta development; glycogen cell differentiation in placental development) with supporting embryonic differentiation signals (IGF receptor signaling, GTPase activation, regulation of integrin activation) and transcriptional regulation. The cluster appears to reflect a developmental program linked to placentation and related embryonic tissue differentiation rather than a single, cohesive pathway, justifying a placenta- and development-focused label.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0001893","count":2},{"id":"GO:1903955","count":1},{"id":"GO:0090630","count":1},{"id":"GO:0048009","count":1}]},{"hash":"1541315446534104242","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0033512","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1374691577175833104","title":"Translational Regulation and Protein Synthesis","description":"Based on the predominance of translation-related GO terms (translation, translational initiation, translational elongation, positive regulation of cytoplasmic translation, and selenocysteine incorporation) and the accompanying mRNA decay term, the cluster appears to center on the machinery and regulation of protein synthesis. The incidental terms for cell cycle, glial proliferation, and antibiotic response may reflect broader cellular states or contexts where translation is modulated. Overall, the core signal is translation control and protein synthesis.","confidence":"High","size":13,"edges":23,"triangles":6,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":5},{"id":"GO:0007049","count":4},{"id":"GO:2000767","count":4},{"id":"GO:0006413","count":3},{"id":"GO:0014009","count":3}]},{"hash":"888880590486309407","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":4},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0009553","count":2},{"id":"GO:0000398","count":2}]},{"hash":"401361895317963276","title":"Unknown","description":"The top GO terms span neural plasticity, glial development, vascular signaling, and broad cell cycle regulators, with no single unifying biological process tying them together. The absence of edges suggests the proteins do not form a cohesive functional module, supporting an Unknown label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035562","count":2},{"id":"GO:1900271","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0071277","count":2}]},{"hash":"824161955081428723","title":"Developmental ECM remodeling and morphogenesis","description":"These proteins cluster around extracellular matrix remodeling activities (collagen catabolic process, basement membrane disassembly, bone resorption) and developmental morphogenesis (lung branching, neural precursor proliferation, thyroid hormone response). An immune term (T cell mediated cytotoxicity) appears but the dominant signal is remodeling of the ECM during organ development and morphogenesis, suggesting roles in tissue shaping rather than immune defense.","confidence":"Medium","size":13,"edges":34,"triangles":49,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0001913","count":8},{"id":"GO:2000179","count":8},{"id":"GO:0030574","count":8},{"id":"GO:0034769","count":8},{"id":"GO:0050790","count":8}]},{"hash":"332668589469802913","title":"Developmental transcription and stress response proteins","description":"The top GO terms span transcription (DNA-templated transcription), development (multicellular organism development, forebrain development) and regulatory signaling (peptidyl-serine dephosphorylation), with additional terms pointing to vesicle transport and cellular stress responses (ER-Golgi transport, response to toxic substances, cadmium). This suggests a cluster of proteins involved in developmental transcriptional programs and their modulation by cellular stress, rather than a single, tightly defined pathway. The mix of terms and a few outdated entries warrant a cautious, mid-level confidence in this label.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009636","count":2},{"id":"GO:0006349","count":2}]},{"hash":"1325753157276467726","title":"Vesicle trafficking and synaptic regulation","description":"The cluster is dominated by GO terms related to intracellular vesicle transport, exocytosis, and synaptic modulation (Golgi vesicle fusion, Golgi-to-endosome transport, vesicle fusion with vacuole, and regulation of synaptic transmission including GABAergic). While telomere-related terms appear, the strongest shared theme is vesicle trafficking and neurotransmission, which justifies the label. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0032212","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0048210","count":1},{"id":"GO:0043524","count":1}]},{"hash":"257306388309112384","title":"Plant Oxidative Stress and Lignin/Cell Wall Remodeling","description":"Based on GO terms dominated by plant-specific oxidative stress responses (hydrogen peroxide catabolic process, response to oxidative stress, cellular oxidant detoxification) together with lignin catabolic process and plant-type cell wall organization, plus regulation of cellular respiration and autophagy of mitochondrion, the cluster likely represents a plant-wide response to oxidative stress that includes remodeling of the cell wall and lignin metabolism.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042744","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0009664","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0046274","count":1}]},{"hash":"1467843933292602710","title":"Mitotic spindle assembly and kinetochore attachment","description":"The dominant GO terms center on mitotic spindle organization, kinetochore-microtubule attachment, chromosome alignment, and the spindle assembly checkpoint, indicating a cohesive mitotic machinery module. A couple terms appear as peripheral noise (e.g., Golgi organization, barrier establishment) but do not override the main theme.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":2},{"id":"GO:0090557","count":2},{"id":"GO:0007030","count":2},{"id":"GO:0051455","count":1},{"id":"GO:0051310","count":1}]},{"hash":"525606899156077136","title":"Plant floral development and fertilization","description":"Top terms highlight plant reproductive biology: floral organ specification, ovule development, abscission, and double fertilization, aligning with a plant floral development/fertilization theme. A heat response term adds stress context, while a few unrelated animal terms reduce confidence. Overall, a Plant floral development and fertilization label with Medium confidence.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048833","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0009408","count":2}]},{"hash":"2193035796205609664","title":"Endosome trafficking and receptor recycling","description":"This cluster is best described by its emphasis on endosomal dynamics and receptor recycling: terms like regulation of endosome size and receptor recycling are core to membrane trafficking. The presence of Rho signaling and glutamatergic synaptic transmission suggests links to cytoskeletal remodeling and neuronal signaling, which often accompany endosomal transport. Some terms appear unrelated (heart development, histone methylation), but the strongest cohesive theme centers on endosome trafficking and receptor recycling.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0051036","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0001881","count":1}]},{"hash":"929527227335405599","title":"Splicing Regulation & RNA Silencing","description":"Most terms point to RNA processing: regulatory ncRNA-mediated gene silencing and positive regulation of mRNA splicing via the spliceosome, with related spliceosome conformational changes. These converge on RNA processing control, implying the cluster centers on splicing regulation and RNA-mediated silencing. Other terms like innate immune response, cell polarity regulation, and Rho signaling appear as contextual roles rather than core functions, so the primary theme remains RNA processing regulation.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0032005","count":2},{"id":"GO:0031139","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1190399770407868999","title":"Unknown","description":"Explanation: The top GO terms are highly diverse and span transcription factor regulation (NF-kappaB), RNA splicing (tri-snRNP assembly), lipid mediator biosynthesis (prostaglandin), hormone response (thyroid hormone), inflammatory regulation (IL-1), stress/secretion (water deprivation, body fluid secretion), muscle development (myoblast migration), gland development (prostate), and ion transport (potassium export). There isn\u2019t a cohesive, single-function theme linking these proteins, so an Unknown label with None confidence is appropriate.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0000244","count":2},{"id":"GO:0031394","count":1},{"id":"GO:0097066","count":1},{"id":"GO:0032652","count":1}]},{"hash":"2130212648363892791","title":"DNA replication and centrosome cycle","description":"The cluster\u2019s strongest signals are DNA replication (GO:0006260), centrosome cycle (GO:0007098), and positive regulation of nuclear cell cycle DNA replication (GO:0010571), which together point to core cell-division machinery. Other terms show diverse developmental and signaling roles, suggesting pleiotropy or broader annotations, but the dominant theme is replication and cell cycle control.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0010800","count":5},{"id":"GO:0045444","count":4},{"id":"GO:0021987","count":4},{"id":"GO:0021766","count":4}]},{"hash":"190283743227081192","title":"Neural development and dendritic spine morphogenesis","description":"This cluster is dominated by neuron-centric terms: neuron fate determination and midbrain dopaminergic neuron differentiation, along with dendritic spine morphogenesis and filopodium/actin-related remodeling. Supporting processes like endosome-to-Golgi transport and PI3K signaling point to coordinated intracellular trafficking and signaling that underpin neural development and synaptic structure. Some terms (endothelial barrier, lymphocyte aggregation, alpha-glucan metabolism) appear less central, but do not outweigh the neural differentiation and synaptic morphogenesis theme.","confidence":"Medium","size":12,"edges":20,"triangles":11,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043552","count":9},{"id":"GO:0061001","count":9},{"id":"GO:1905279","count":9},{"id":"GO:0051489","count":9},{"id":"GO:0008283","count":9}]},{"hash":"8880593398093232","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0019062","count":1},{"id":"GO:0097309","count":1},{"id":"GO:0002128","count":1}]},{"hash":"566193157506959437","title":"Calcineurin-NFAT Signaling and Tissue Remodeling","description":"This cluster centers on the calcineurin-NFAT signaling axis (GO:0033173, GO:0051531) with related immune regulation (e.g., negative regulation of T cell cytotoxicity) and tissue remodeling themes (branching in blood vessel morphogenesis, connective tissue replacement) plus cell\u2013cell adhesion. The presence of substantia nigra development suggests broader developmental roles of NFAT signaling, while a few outlier terms (e.g., meiotic checkpoint signaling) may reflect broad network connections or annotation noise. Overall, the terms cohere around NFAT/calcium signaling coordinating immune activity with tissue morphogenesis and vascular development.","confidence":"High","size":12,"edges":48,"triangles":97,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036496","count":5},{"id":"GO:0051343","count":5},{"id":"GO:0033173","count":5},{"id":"GO:0021762","count":5},{"id":"GO:0051531","count":5}]},{"hash":"776135125512387038","title":"Golgi trafficking and membrane recycling","description":"The cluster\u2019s strongest shared themes are Golgi-related transport and membrane recycling, including Golgi to lysosome transport, regulation of Golgi organization, and endocytic recycling, with protein phosphorylation likely modulating these processes. Other terms (memory, angiogenesis, cardiac contraction) are more peripheral, making a trafficking-focused label the most representative.","confidence":"Medium","size":12,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:0006468","count":2},{"id":"GO:0090160","count":2},{"id":"GO:0007616","count":2},{"id":"GO:1903358","count":2}]},{"hash":"1733272523382663087","title":"Notch receptor processing and proteolysis","description":"The top terms cluster around proteolytic processing of membrane proteins and Notch signaling, including Notch receptor processing, membrane protein ectodomain and intracellular domain proteolysis, and the Notch signaling pathway. Trafficking-related terms (ER to Golgi transport) support receptor maturation, and amyloid-beta formation aligns with gamma-secretase activity shared with Notch processing. While some developmental and spore-wall terms appear, the clearest common theme is Notch receptor proteolysis driving signaling.","confidence":"High","size":12,"edges":13,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060576","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0060628","count":1},{"id":"GO:0034205","count":1},{"id":"GO:0060465","count":1}]},{"hash":"2099139664465863203","title":"Epidermal development and wound healing","description":"This cluster shows strong enrichment for skin-related processes, including skin development, mesodermal differentiation, and wound healing with epidermal cell spreading, indicating a primary role in epidermal formation and repair. Peripheral terms such as complement signaling and lipid-related pathways may reflect skin immune and metabolic context but are secondary to the main epidermal/wound-healing theme. Confidence: High","confidence":"","size":12,"edges":16,"triangles":5,"max_degree":11,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0043588","count":9},{"id":"GO:0006507","count":5},{"id":"GO:2001237","count":5},{"id":"GO:0038027","count":5},{"id":"GO:0045919","count":5}]},{"hash":"935279729517838185","title":"Oxidative stress response and redox homeostasis","description":"This cluster is defined by strong links to redox biology: redox homeostasis, oxidation-reduction processes, and detoxification of oxidants, with deglutathionylation and cellular responses to oxidative stress; a few transcription-related terms are present but secondary, indicating the core theme is redox regulation and oxidative stress defense.","confidence":"High","size":12,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":4},{"id":"GO:0080058","count":3},{"id":"GO:0034599","count":3}]},{"hash":"725485805233471313","title":"TLR4 signaling and cytokine production","description":"The cluster is dominated by GO terms related to Toll-like receptor 4 signaling, including MyD88-independent TLR signaling, NF-kappaB-related regulation, and production of pro-inflammatory cytokines/chemokines (IL-1, IL-8) and chemokines, pointing to innate immune activation via TLR4. A non-immune term (tRNA export) appears as noise, but the overall theme links TLR4-driven signaling to inflammatory mediator production.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071225","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0032088","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0050711","count":1}]},{"hash":"1066309762217947668","title":"Bacterial metabolite and envelope biosynthesis","description":"The top GO terms cluster around biosynthetic processes in bacteria, including antibiotic biosynthesis, biotin biosynthesis, lipopolysaccharide biosynthesis (and LPS core), and UDP-N-acetylglucosamine biosynthesis, pointing to a shared role in producing metabolites and cell envelope components. Some regulatory or RNA modification terms are present, but the strongest signal is biosynthesis-related pathways.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0036265","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0008284","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1204131201023765844","title":"Cell signaling and migration","description":"This cluster centers on GO terms related to cell signaling and membrane-associated processes that influence movement and cytoskeletal dynamics, including Wnt signaling, GPCR pathways, and cell migration, as well as endocytosis (pinocytosis) and protein ubiquitination which regulate signaling cascades. Although some terms are obsolete or variably connected (e.g., telomere maintenance and mechanotransduction), the strongest overarching theme is signaling at the membrane that can drive migration and cytoskeletal rearrangements. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0048549","count":2}]},{"hash":"771615698993536712","title":"Proteostasis\u2013Immune Signaling under Stress","description":"The cluster combines ubiquitin-proteasome\u2013related processes (deubiquitination, proteasome core complex assembly) with immune signaling routes (non-canonical NF-kappaB, C-type lectin receptor signaling) and defense responses (plant-type hypersensitive response), along with stress-related regulation of metabolism and mRNA stability. This points to a cohesive theme around protein turnover and signaling that modulates stress and immunity.","confidence":"Medium","size":12,"edges":63,"triangles":192,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":10},{"id":"GO:0060071","count":7},{"id":"GO:0010950","count":7},{"id":"GO:0006521","count":7},{"id":"GO:0009651","count":7}]},{"hash":"1351939882933189468","title":"Transmembrane Transport of Ions and Metabolites","description":"The Top Terms are dominated by transport-related processes across membranes, including nitrate and nitrite transmembrane transport, phosphate ion transmembrane transport, and transport of sugars and metabolites (fucose, sialic acid, 4-hydroxyphenylacetate). The presence of a neurotransmitter loading into synaptic vesicle term also fits a vesicular transport/trafficking theme. A few obsolete chromatin-related terms appear but with no supporting network connections, suggesting annotation noise. Overall, the cluster appears to group proteins by a shared function in transmembrane transport and related trafficking, justifying the proposed label as the best single-theme summary.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016569","count":1},{"id":"GO:2000270","count":1},{"id":"GO:0043486","count":1},{"id":"GO:1900754","count":1},{"id":"GO:0015706","count":1}]},{"hash":"1027091433342564868","title":"RNA Methylation and Processing Cluster","description":"The dominant GO signals center on RNA modification and mRNA/rRNA processing (7-methylguanosine capping, rRNA modification, N7 methylation, and N-terminal methylation), suggesting a cohesive RNA-processing module. Other terms reflect broader metabolic and stress response roles but are less central to this cluster.","confidence":"Medium","size":12,"edges":10,"triangles":1,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035690","count":8},{"id":"GO:0036265","count":6},{"id":"GO:0000154","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0090398","count":5}]},{"hash":"234169599226962479","title":"Unknown","description":"The top terms are a scattered mix, including obsolete annotations and unrelated processes (DNA repair, mitotic cell cycle, protein targeting to membrane, histone methylation, IgA class switching, heart development). There isn\u2019t a clear, shared function tying these proteins together, so a singular interpretable label isn\u2019t supported.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0033160","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0031532","count":2}]},{"hash":"121600357659993965","title":"Cell division and endosome transport","description":"The top GO terms cluster around proliferative processes (mitotic cell cycle, cell population proliferation, cell division) with supportive endomembrane trafficking terms (endosome organization and transport). Some nutrient-response signals are present, suggesting growth is linked to nutrient status. Overall, the dominant theme is proliferative growth coupled with endosomal dynamics.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0000278","count":2}]},{"hash":"654165045351801719","title":"Unknown","description":"The Top Terms span telomere maintenance, muscle stretch response, cardiac action potential regulation, adipocyte differentiation, cell migration, and RNA processing, with several obsolete terms, showing no coherent single function or pathway tying all proteins together.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0098907","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1680187286031433949","title":"Golgi-ER Vesicle Transport and Exocytosis","description":"The proteins show strong enrichment for ER\u2013Golgi vesicle transport, retrograde Golgi\u2013ER trafficking, general protein transport, and exocytosis/exocyst localization, pointing to a cohesive role in vesicle trafficking and secretion. Some unrelated terms (defense response, gonad development) may reflect multifunctional proteins but do not define the core function.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0006890","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0050830","count":2}]},{"hash":"579634953799296105","title":"Unknown","description":"The top GO terms are a mix of nuclear/chromatin-related processes (deneddylation, desumoylation, regulation of chromatin binding, kinetochore assembly, endoreduplication) and tissue/developmental terms (spongiotrophoblast and labyrinthine layer development, erythrocyte differentiation), with a few unrelated terms. There isn\u2019t a single coherent biological theme linking all terms, so a specific, representative label isn\u2019t identifiable.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010226","count":1},{"id":"GO:0000338","count":1},{"id":"GO:0010724","count":1},{"id":"GO:0016926","count":1},{"id":"GO:0060712","count":1}]},{"hash":"2085373208633391957","title":"Genome maintenance and proteostasis","description":"The top terms include DNA replication, transcription, and cell division, alongside ER stress and proteostasis components (ERAD, unfolded protein response, proteasome assembly). This suggests a cluster tied to genome maintenance and general protein quality control rather than a single pathway.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0030968","count":3}]},{"hash":"854232088888027332","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms are translation, ribosome biogenesis, ribosomal large subunit assembly, and cytoplasmic translation, indicating this cluster centers on ribosome assembly and protein synthesis. Obsolete export term and a few peripheral terms appear, but the main signal is ribosome-related.","confidence":"High","size":11,"edges":46,"triangles":120,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0006407","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000027","count":3},{"id":"GO:0002181","count":2}]},{"hash":"1274162775815970621","title":"Triglyceride metabolism and lipid remodeling","description":"Most of the top GO terms describe triglyceride catabolic processes (triglyceride catabolic process, triglyceride mobilization, positive regulation of triglyceride catabolic process) and related lipid remodeling (triglyceride acyl-chain remodeling), as well as phospholipid catabolic processes (phosphatidylcholine and phosphatidylethanolamine catabolic processes). This points to a cohesive theme centered on triglyceride metabolism and lipid remodeling. A few terms (prostate gland development, axon regeneration, glucose response) are peripheral to this core lipid theme. ","confidence":"High","size":11,"edges":11,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:2000480","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0010898","count":2},{"id":"GO:0036153","count":2},{"id":"GO:0019433","count":2}]},{"hash":"1173052213759662259","title":"MAPK signaling and developmental cues","description":"The top GO terms show strong enrichment for ERK1/2 and p38MAPK cascades, indicating a core MAPK signaling focus. Stimuli such as GM-CSF and PMA suggest activation via surface receptors leading to MAPK signaling, while several development-related terms (nervous system development, skeletal muscle development, cardiac muscle differentiation, cortex layer formation) imply roles in differentiation contexts. The presence of B cell receptor signaling hints at immune signaling linked to MAPK pathways as well. Taken together, the cluster seems centered on MAPK signaling with auxiliary ties to development and immune responses.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070371","count":4},{"id":"GO:0038066","count":3},{"id":"GO:0097011","count":3},{"id":"GO:1904628","count":3},{"id":"GO:0007399","count":3}]},{"hash":"1658116186239922352","title":"Neural development and synaptic exocytosis regulation","description":"This cluster is driven by brain-related development terms (hippocampus and brain development) and synaptic function terms (regulation of synaptic vesicle exocytosis, dendritic spine morphogenesis, calcium-dependent exocytosis), suggesting the proteins work together in neural development and neurotransmitter release. Some terms like kidney development appear but do not override the neural-centric theme.","confidence":"High","size":11,"edges":40,"triangles":67,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021766","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0031384","count":5}]},{"hash":"1610487638131980338","title":"Rho GTPase\u2013mediated cytoskeletal remodeling and ephrin signaling","description":"The cluster is characterized by terms tied to Rho-family GTPase signaling, regulation of filopodium assembly, and small GTPase-driven signal transduction, along with the ephrin receptor pathway and cell spreading. These point to coordinated cytoskeletal remodeling and cell\u2013cell signaling processes governing protrusion formation and adhesion, with some ancillary involvement in apoptosis and cytokine production.","confidence":"High","size":11,"edges":16,"triangles":4,"max_degree":7,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:1900026","count":7},{"id":"GO:0035023","count":7},{"id":"GO:0046847","count":6},{"id":"GO:0007264","count":6},{"id":"GO:0048013","count":5}]},{"hash":"1140493566168768416","title":"RNA Splicing and Translation Initiation Regulation","description":"This cluster is enriched for spliceosome-mediated alternative mRNA splicing, cis splicing, and small-subunit processome assembly, highlighting RNA maturation; it also shows signals for mRNA stabilization and regulation of translational initiation and preinitiation complex formation, pointing to a cohesive theme of RNA processing coupled with control of translation initiation. The blastocyst formation term is less central to the main theme but may reflect developmental contexts of splicing/translation regulation.","confidence":"High","size":11,"edges":19,"triangles":15,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":5},{"id":"GO:0000380","count":5},{"id":"GO:0001825","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0060211","count":4}]},{"hash":"1395566662106995130","title":"Fungal sterol and lipid biosynthesis","description":"The cluster is dominated by GO terms related to sterol and lipid metabolism, including ergosterol biosynthetic process, cholesterol biosynthesis via lathosterol, fatty acid and ether lipid biosynthesis, and MIPC metabolism, which together indicate a cohesive role in fungal membrane lipid production and modification. Some terms like B cell chemotaxis and propylene catabolic process appear incidental, but the core signal points to sterol and lipid biosynthesis in fungi. ","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035754","count":4},{"id":"GO:0042208","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0046485","count":3},{"id":"GO:0080064","count":3}]},{"hash":"2063340571867470083","title":"Mitochondrial autophagy (mitophagy)","description":"The two top GO terms are autophagy of mitochondrion and cytoplasm-to-vacuole targeting by the Cvt pathway, both describing selective autophagy processes. This points to mitophagy/autophagy as the core theme of the cluster, with additional minor metabolic signals. Hence, the label focuses on mitochondrial autophagy as representative.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000422","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0010259","count":1},{"id":"GO:0043457","count":1},{"id":"GO:1903779","count":1}]},{"hash":"987241054173145818","title":"Ion and Substrate Membrane Transporters","description":"The GO terms cluster around membrane transport of ions, sugars, xenobiotics, and related solutes, plus neurotransmitter vesicular loading, pointing to a group of membrane transport proteins with broad substrate specificity.","confidence":"Medium","size":11,"edges":12,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:1900754","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0015751","count":3}]},{"hash":"1359043301763328085","title":"Unknown","description":"The terms span diverse processes\u2014from cytoskeletal dynamics and skin/developmental roles to ER-stress\u2013induced apoptosis, TORC1 signaling, translation initiation, and RNA methylation\u2014without a single cohesive function tying all proteins together, so a specific label isn\u2019t justifiable.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030042","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0070059","count":3},{"id":"GO:1904263","count":3},{"id":"GO:0043588","count":3}]},{"hash":"1140492852210661169","title":"Neural Development and Synaptic Signaling","description":"This cluster is dominated by terms tied to neural development and function, including long-term synaptic potentiation, axonogenesis, Schwann cell development, and visual perception, suggesting proteins involved in neuronal differentiation and synaptic connectivity. While terms like heart development and ABA signaling appear, the core signal centers on neural development and synaptic activity.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060291","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0009738","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0000086","count":6}]},{"hash":"1764467339201768560","title":"ER-Golgi Vesicle Transport","description":"The top GO terms cluster around vesicle trafficking between the endoplasmic reticulum and Golgi, as well as related intracellular transport steps (Golgi to plasma membrane, retrograde Golgi-ER, and general protein transport). Some additional terms touch ER stress (unfolded protein response) and nutrient signaling, but the dominant theme is intracellular vesicle transport along the early secretory pathway, suggesting this label best captures the cluster\u2019s function.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0008283","count":2},{"id":"GO:0006348","count":2},{"id":"GO:0043001","count":2},{"id":"GO:0006623","count":2}]},{"hash":"113556891327362572","title":"Mechanotransduction and Stretch Response","description":"This cluster is best described by terms related to mechanosensing and response to mechanical stimuli, including cellular response to mechanical stimulus and response to muscle stretch, with related processes like cell migration. While there are telomere maintenance and adipogenesis terms present, the strongest signals point to a mechanical-stimulus response program.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":7},{"id":"GO:0032212","count":6},{"id":"GO:0035994","count":6},{"id":"GO:2001275","count":6},{"id":"GO:0016477","count":6}]},{"hash":"813341332393963641","title":"Lipid metabolism and sebaceous gland differentiation","description":"The top GO terms center on lipid and sphingolipid metabolism (sphinganine metabolism, mannosyl-inositol phosphorylceramide metabolism), fatty acid response, and differentiation of skin-related glands (sebaceous gland cells, white fat cells, tarsal gland development). Some terms are unrelated (e.g., CNS myelin maintenance), but the dominant theme links lipid biology with skin/gland differentiation, suggesting a module in cutaneous lipid metabolism and gland development.","confidence":"Medium","size":11,"edges":25,"triangles":23,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0044130","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0006667","count":3},{"id":"GO:0050872","count":3}]},{"hash":"2293718179992840703","title":"Fungal lipid biosynthesis and ER-Golgi transport","description":"The top GO terms cluster around membrane lipid production and trafficking, including unsaturated fatty acid biosynthesis, ergosterol biosynthesis regulation, and sphingolipid (MIPC) metabolism, plus ER-to-Golgi vesicle transport, suggesting a core theme of membrane biogenesis and vesicular trafficking in fungi. Some vertebrate-specific terms appear in the set, likely due to broad GO annotations, but the dominant signal is lipid membrane synthesis and trafficking.","confidence":"Medium","size":11,"edges":14,"triangles":4,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000001","count":3},{"id":"GO:0006675","count":2},{"id":"GO:0006636","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0032286","count":2}]},{"hash":"2242927784006119897","title":"Neuronal dendrite and spine morphogenesis with trafficking","description":"The top GO terms center on neuronal development: dendrite morphogenesis, hippocampus development, and dendritic spine morphogenesis indicate a neuronal morphogenesis theme. Supporting processes include membrane trafficking and endocytosis (Golgi to plasma membrane transport, endocytosis, retrograde transport), suggesting coordinated structural remodeling with membrane dynamics. The ossification term appears as noise; overall, the cluster seems to reflect neuronal structural development coupled with vesicular trafficking.","confidence":"High","size":11,"edges":13,"triangles":4,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043931","count":3},{"id":"GO:0021766","count":3},{"id":"GO:0048813","count":3},{"id":"GO:0034260","count":3},{"id":"GO:0006893","count":3}]},{"hash":"184600145451788319","title":"Actin Cytoskeleton Assembly and Cytokinesis","description":"This cluster is dominated by GO terms related to actin dynamics, including actin filament network formation, formin-nucleated actin cable assembly, and mitotic contractile ring actin bundle formation, along with centrosome maintenance and regulation of GTPase activity. These together point to actin cytoskeleton remodeling during cell division and cytokinesis, with related processes like nuclear migration and neuroblast division supporting the broader theme of division-associated cytoskeletal organization. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051639","count":2},{"id":"GO:0070649","count":2},{"id":"GO:0000743","count":2},{"id":"GO:1903477","count":2},{"id":"GO:0045769","count":2}]},{"hash":"1773047647610132826","title":"Endocannabinoid signaling and glycerolipid metabolism","description":"The proteins show strong representation of endocannabinoid signaling (endocannabinoid signaling pathway, regulation of endocannabinoid signaling) together with lipid metabolism/remodeling processes (arachidonate metabolic process, triglyceride catabolic process, acylglycerol acyl-chain remodeling, phosphatidylserine catabolic process). Although some plant-related terms appear (pectin catabolic process, trehalose stimulus, salicylic acid signaling), the dominant pattern points to lipid-mediated signaling and glycerolipid turnover, suggesting a coherent cluster around lipid signaling/metabolism rather than non-lipid functions.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071926","count":2},{"id":"GO:0045490","count":2},{"id":"GO:0080151","count":2},{"id":"GO:0071327","count":2},{"id":"GO:0006660","count":2}]},{"hash":"294689821834915255","title":"Vertebrate neural and cardiac development","description":"The proteins are enriched for terms tied to nervous system development, retina/eye development, myelination, and heart formation (cardiac atrium), with additional notes on adrenal chromaffin differentiation and transcriptional regulation. Together these point to developmental differentiation programs in vertebrate neural/eye and cardiac tissues, rather than a single metabolic pathway. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032933","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0042552","count":1},{"id":"GO:0003210","count":1}]},{"hash":"663987464979020248","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0042274","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0000469","count":1}]},{"hash":"1177291968735487781","title":"Developmental signaling and metabolic regulation","description":"This cluster shows enrichment in both developmental signaling (Wnt pathway regulation, bone ossification, neural precursor proliferation) and metabolism/redox processes (glycolysis, redox homeostasis, nitrate assimilation), suggesting a coordinated theme of growth/development coupled with metabolic control rather than a single narrow function.","confidence":"Medium","size":10,"edges":25,"triangles":30,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0043931","count":2},{"id":"GO:0006096","count":1}]},{"hash":"675594420196768164","title":"Innate and adaptive immune activation","description":"This cluster\u2019s top GO terms are centered on immune processes, including innate immune response, interferon signaling, and positive regulation of B cell proliferation, indicating a theme of immune activation and signaling. A few terms (tRNA export, actin localization, mitochondrial morphogenesis, reproductive development) are less related, but the dominant signal points to immune-related functions.","confidence":"Medium","size":10,"edges":15,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0006409","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0030890","count":2},{"id":"GO:0006915","count":2}]},{"hash":"795311437109706833","title":"Multispecies development and morphogenesis signaling","description":"The terms cluster around development and morphogenesis across species: vertebrate neuronal development (axonogenesis, dopaminergic neuron differentiation, ventral spinal cord interneuron specification, Purkinje cell signaling), cell migration (lamellipodium assembly), plant development (phloem development, ovule morphogenesis), and related signaling pathways (growth hormone receptor signaling, B cell receptor signaling). This points to a unifying theme of developmental differentiation and tissue morphogenesis mediated by signaling, hence multispecies development and morphogenesis signaling.","confidence":"Medium","size":10,"edges":12,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048936","count":4},{"id":"GO:1904948","count":4},{"id":"GO:0090334","count":4},{"id":"GO:0050859","count":3},{"id":"GO:0060396","count":3}]},{"hash":"1379366423166274347","title":"Neural development and neuroimmune signaling","description":"The cluster centers on neuronal development signals (neuron maturation, SVZ-to-olfactory-bulb migration, dopamine signaling) alongside immune-related terms (innate immune response, interferon signaling, defense against Gram-negative bacteria) and cytoskeletal/trafficking processes (actin bundle assembly, endosome-to-Golgi transport), suggesting a theme of neurodevelopment with neuroimmune regulation.","confidence":"Medium","size":10,"edges":27,"triangles":30,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0060348","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0060335","count":4},{"id":"GO:0045842","count":4}]},{"hash":"1188246575594536228","title":"Mitochondrial respiration and proton transport","description":"The dominant signals in this cluster point to mitochondrial energy metabolism: aerobic respiration, mitochondrial electron transport (ubiquinol to cytochrome c), complex III assembly, and proton transmembrane transport. Together they indicate a role in oxidative phosphorylation and proton motive force generation. A couple of outlier terms (visual perception, chloride transport) and obsolete GO terms are present, but they do not outweigh the core mitochondrial theme, so the label reflects the main function of the cluster.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0043966","count":2},{"id":"GO:1902600","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0034551","count":1}]},{"hash":"1855238012765364420","title":"Mitochondrial replication and inheritance","description":"The cluster shows prominent mitochondrial-related GO terms, including positive regulation of mitochondrial DNA replication, mitochondrion inheritance, and inner mitochondrial membrane organization, indicating a cohesive theme around mitochondrial maintenance and biogenesis, with supporting notes on membrane localization.","confidence":"High","size":10,"edges":11,"triangles":1,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0001302","count":3},{"id":"GO:0090297","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1903905","count":2},{"id":"GO:0045861","count":2}]},{"hash":"1277178921700300518","title":"Rho GTPase and Integrin Signaling","description":"The cluster is dominated by GO terms tied to Rho protein signal transduction regulation and GTPase activation, with another term pointing to regulation of integrin activation. This points to a core theme of cytoskeletal dynamics and cell adhesion signaling, influenced by Rho-family GTPases and integrin pathways. Other terms (vacuolar transport, Cvt autophagy, placental development, etc.) suggest additional, broader roles but do not override the central signaling pattern. Confidence: Medium","confidence":"","size":10,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0090630","count":1},{"id":"GO:0048009","count":1},{"id":"GO:0033623","count":1},{"id":"GO:0032258","count":1}]},{"hash":"2295220534030452904","title":"Neuronal Synaptic Signaling and Plasticity","description":"The cluster is enriched for terms tied to neuronal signaling and synaptic modulation: AMPA receptor clustering, long-term synaptic depression, ephrin receptor signaling, and striatal neuron differentiation, plus retinoic acid response. IGF stimulus response and ER-stress\u2013related apoptotic signaling reflect supportive neuronal survival and growth pathways. Overall, the common theme is modulation of synaptic function in neurons.","confidence":"Medium","size":10,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1990314","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0048013","count":2},{"id":"GO:0021773","count":2},{"id":"GO:1904703","count":2}]},{"hash":"299559063878411801","title":"Splicing and Chromatin Remodeling in Neuronal Gene Regulation","description":"The cluster is dominated by RNA processing and chromatin-related terms (splicing regulation, spliceosome activity, spliceosomal conformational changes, nucleosome mobilization, DNA topology changes, and chromatin remodeling) with an added neuronal context (BDNF response and exploration behavior). This suggests a cohesive theme of how RNA splicing and chromatin dynamics regulate gene expression in neurons. ","confidence":"Medium","size":10,"edges":28,"triangles":56,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:1990416","count":5},{"id":"GO:0006265","count":5},{"id":"GO:1901407","count":4}]},{"hash":"863013290021790445","title":"Neuronal Cytoskeleton and Polarity","description":"Most terms describe cytoskeleton organization and polarity, including mitotic spindle processes and neuronal architecture (dendritic transport, neuron projection maintenance, cerebellar layer structure, microtubule polarity). The common thread is regulation of cytoskeletal dynamics that shape both cell division and neuronal structure, so a label focusing on neuronal cytoskeleton and polarity fits best.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":7},{"id":"GO:0048364","count":7},{"id":"GO:0000073","count":7},{"id":"GO:0098971","count":7},{"id":"GO:0051296","count":7}]},{"hash":"2256535302349801698","title":"Nucleocytoplasmic transport and growth signaling","description":"The top GO terms connect nuclear transport processes (NLS-bearing protein import into nucleus, nuclear pore complex assembly, mRNA transport) with growth and signaling regulation (TORC1 signaling, positive regulation of GTPase activity, meiotic spindle elongation, endothelial proliferation, phospho-regulation of STAT). This suggests a coordinated program linking nuclear trafficking to cellular growth and signaling pathways, rather than a single, narrow function. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":3},{"id":"GO:0097711","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0070262","count":3}]},{"hash":"534469418181840786","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0061158","count":2},{"id":"GO:0090398","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0018012","count":2}]},{"hash":"2098843118801025002","title":"Developmental transcription and cell migration","description":"This cluster centers on developmental processes (forebrain and multicellular organism development), transcriptional control (DNA-templated transcription), and cell movement (cell migration, invasive growth), with supporting ties to mitotic spindle assembly. Although some terms relate to endocytosis and stress (pinocytosis regulation, cadmium response) and two terms are obsolete, the dominant theme ties transcriptional regulation to development and cellular motility. Confidence in this label is Medium.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0048549","count":3},{"id":"GO:0006349","count":2}]},{"hash":"1074063256450227753","title":"Unknown","description":"The GO terms are highly diverse, spanning GTPase regulation, TOR signaling, translation control, lysosome localization, neural development, and even viral replication, with no clear unified theme. The network is also sparsely connected (one edge) and includes obsolete terms, suggesting noise rather than a cohesive functional cluster. Therefore, no specific, representative label can be assigned.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":1},{"id":"GO:0071230","count":1},{"id":"GO:0061462","count":1},{"id":"GO:0019079","count":1},{"id":"GO:0043154","count":1}]},{"hash":"1022487045524454784","title":"Potassium and Sodium Ion Transport and Membrane Potential","description":"The top GO terms cluster around potassium and sodium ion transport, intracellular potassium homeostasis, and regulation of membrane potential (including resting potential maintenance and cardiac repolarization), indicating a cohesive set of ion channels/transporters governing cellular excitability. A few terms related to mechanosensation and calcium signaling appear but are secondary to the dominant ion-transport theme.","confidence":"High","size":10,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":5},{"id":"GO:0030322","count":4},{"id":"GO:0097623","count":3},{"id":"GO:0060075","count":3},{"id":"GO:0071805","count":3}]},{"hash":"1430655981972844139","title":"GTPase-Regulated Vesicle Trafficking","description":"The cluster is enriched for small GTPase\u2013related signals (positive regulation of GTPase activity; Rap signaling) and vesicle trafficking processes (COPII vesicle budding; retrograde Golgi\u2013ER transport), pointing to a cohesive role in GTPase-driven trafficking; other terms about development and mitosis are present but secondary. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0090103","count":2},{"id":"GO:0032486","count":2},{"id":"GO:2000785","count":2},{"id":"GO:0008283","count":2}]},{"hash":"848929608312044892","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"This cluster centers on mitochondrial function, including transport of ions and metabolites across mitochondrial membranes (magnesium and phosphate transport, ornithine transmembrane transport), regulation of mitochondrial membrane potential, and responses related to mitochondrial stress and apoptosis, with a note of adaptive thermogenesis linking to mitochondrial energy metabolism. A few terms (e.g., glycine transport at the plasma membrane) are peripheral, but the dominant pattern is mitochondrial transport and energetic regulation.","confidence":"High","size":10,"edges":12,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0008637","count":8},{"id":"GO:1990314","count":8},{"id":"GO:0036233","count":8},{"id":"GO:0090152","count":8},{"id":"GO:0000066","count":8}]},{"hash":"715292449896782703","title":"Unknown","description":"The terms span protein turnover, metabolism, and signaling (protein transport, proteolysis, vacuolar catabolism, carbon fixation, acetyl-CoA metabolism, methanogenesis, cGMP response, GTPase activation, and immune-related degranulation) with no clear single theme or shared function, and there are no interactions tying the proteins together. ","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0007039","count":1},{"id":"GO:0061077","count":1},{"id":"GO:0015977","count":1}]},{"hash":"1299776498985709683","title":"Unknown","description":"The top GO terms mix neural development (neural tube and metencephalon) with insulin signaling and several metabolism-related processes, including sucrose catabolic process and vitamin D receptor signaling, plus obsolete terms. There is no single, coherent function or pathway that clearly binds these terms for this cluster, and several terms appear unrelated or outdated, suggesting a heterogeneous set rather than a defined module.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008286","count":3},{"id":"GO:0021915","count":3},{"id":"GO:0022037","count":3},{"id":"GO:0035948","count":2},{"id":"GO:1900051","count":2}]},{"hash":"2008774925433926535","title":"Unknown","description":"These proteins have a mix of GO terms spanning telomere maintenance, muscle stretch response, neural and fat cell differentiation, cell migration, RNA processing, and kinase signaling. There isn\u2019t a coherent, single functional theme linking these terms, suggesting a mixed or non-specific cluster. ","confidence":"","size":9,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0021707","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0016477","count":2}]},{"hash":"2083831532970679807","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042274","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0039702","count":1}]},{"hash":"2160835268679128643","title":"Calcium-regulated immune signaling","description":"The cluster combines terms tied to calcium ion transport and calcium-mediated signaling (ER calcium homeostasis, calcium transport, signaling regulation) with immune activation functions (positive regulation of T cell proliferation and migration, IL-6 and TNF production, respiratory burst after phagocytosis). This points to a cohesive theme of calcium-dependent signaling in immune cell activation, supported by a palmitoylation term that often marks signaling proteins. An outlier term like blastoderm segmentation is noted but does not override the core theme.","confidence":"Medium","size":9,"edges":11,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006816","count":2},{"id":"GO:0042102","count":1},{"id":"GO:2000406","count":1},{"id":"GO:0045728","count":1},{"id":"GO:0007350","count":1}]},{"hash":"2141522140323757958","title":"Nuclear transcription regulation and mitotic cell cycle","description":"The terms are dominated by transcription control (negative regulation of RNA Pol II transcription, DNA-templated transcription) and mitosis (mitotic cell cycle), with supporting terms for nuclear export and microtubule-associated localization, suggesting a cluster centered on nuclear regulation of gene expression and cell division. Immune signaling terms appear but seem ancillary to the core theme, pointing to broader regulatory connections rather than a single clean pathway. ","confidence":"Medium","size":9,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0046827","count":2},{"id":"GO:0046007","count":2}]},{"hash":"1728904765138264877","title":"Unknown","description":"The top GO terms span diverse and largely unrelated processes (ER targeting, signal peptide processing, kinase activity regulation, spermatid development, BMP/TGF-\u03b2 and NF-\u03baB signaling, photosystem-related adjustment, germ-line masculinization, and vacuole fusion). There isn\u2019t a single cohesive function or pathway linking these proteins, suggesting the cluster is functionally heterogeneous or noisy. Therefore, I label it Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045047","count":1},{"id":"GO:0006465","count":1},{"id":"GO:0033674","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0030512","count":1}]},{"hash":"287611924131617774","title":"Ubiquitin-mediated regulation of apoptosis and signaling","description":"The top GO terms center on ubiquitination (polyubiquitination, ubiquitin-dependent protein catabolic process, autoubiquitination, K48-linked ubiquitination) and on regulation of cell fate pathways (necroptotic/apoptotic regulation) plus signaling pathways (Wnt, Toll-like receptor). This suggests a cohesive cluster of proteins involved in tagging substrates for degradation and modulating apoptosis and signaling processes.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060544","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0000209","count":3}]},{"hash":"711710213792474665","title":"Membrane receptor signaling and cell polarity","description":"GO terms in this cluster point to receptor-mediated signaling (ephrin, EGFR, TCR) and concurrent processes that shape and organize the cell surface, including polarity, tight junctions, podosome assembly, and centrosome localization. This suggests a cohesive theme of membrane signaling coordinating cell architecture rather than a single pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048013","count":2},{"id":"GO:0060292","count":2},{"id":"GO:0043552","count":2},{"id":"GO:0034260","count":2},{"id":"GO:0050852","count":2}]},{"hash":"1155393692963947113","title":"Cardiac development and small GTPase signaling","description":"This cluster is enriched for GO terms tied to small GTPase\u2013mediated signal transduction, including Ras-regulated pathways, and multiple heart-related processes such as regulation of heart rate, heart development, and cardiac myofibril assembly. Additional annotations for phosphatidylinositol signaling and negative regulation of protein kinase activity suggest a signaling network guiding cardiac muscle formation and cell shape, with some links to general development (bone development, axonogenesis). The combination points to proteins involved in cardiac development and its signaling pathways.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007264","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0002027","count":2},{"id":"GO:0008360","count":2},{"id":"GO:0055003","count":2}]},{"hash":"1704917336695602963","title":"RNA processing and translation initiation","description":"The cluster shows strong enrichment for RNA processing and ribosome-related steps: RNA guanine-N7-methylation and mRNA splicing via spliceosome, plus formation of translation preinitiation complex. While there are some signaling (GTPase activity regulation, autophosphorylation) and chromatin assembly (CENP-A) terms, the dominant themes are RNA processing and translation initiation, justifying a label focused on those processes.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0031954","count":2}]},{"hash":"215387702559934258","title":"Muscle development and tissue remodeling via NFAT signaling","description":"The top GO terms cluster around calcineurin-NFAT signaling and its regulation, plus processes like epithelial-to-mesenchymal transition, branching of connective tissue, vascular morphogenesis, and muscle fiber type transitions. Together these point to developmental differentiation and tissue remodeling guided by NFAT signaling rather than a single metabolic process. Some broader terms (DNA replication, ER-Golgi transport) seem ancillary to the main theme. Confidence in this thematic label is moderate because the signals span multiple related, but distinct, remodeling pathways.","confidence":"Medium","size":9,"edges":18,"triangles":19,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0006888","count":6},{"id":"GO:0051343","count":5},{"id":"GO:0033173","count":5},{"id":"GO:0021762","count":5}]},{"hash":"1936920374159900946","title":"Nuclear RNA Processing and Transport","description":"These proteins show annotations spanning RNA processing (tRNA processing, splicing factor/import, transcription regulation by RNA Pol II, pre-miRNA export) and nuclear export/transport (tRNA, ribosomal subunits, hnRNP-related import), suggesting a cohesive role in RNA metabolism and nuclear trafficking rather than a single specific pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042331","count":1},{"id":"GO:0071528","count":1},{"id":"GO:0042176","count":1},{"id":"GO:0010014","count":1},{"id":"GO:0035048","count":1}]},{"hash":"253795309832132436","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":7,"triangles":4,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006268","count":9},{"id":"GO:0009432","count":9},{"id":"GO:0042766","count":7},{"id":"GO:0035640","count":7},{"id":"GO:0000393","count":7}]},{"hash":"1412943403395001831","title":"RNA Splicing and Post-transcriptional Regulation","description":"This cluster is enriched for RNA processing and post-transcriptional control terms: mRNA splicing via the spliceosome, snoRNA splicing, regulation of mRNA stability, regulatory ncRNA-mediated gene silencing, and factors related to translation initiation and poly(A) tail regulation. These collectively point to coordinated RNA processing and stability control, with only a minor, less representative blastocyst formation term. ","confidence":"High","size":9,"edges":10,"triangles":3,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0010610","count":4},{"id":"GO:0034247","count":3},{"id":"GO:0001825","count":3}]},{"hash":"826963303475578552","title":"Nuclear mRNA Processing & Splicing","description":"Top GO terms cluster around nuclear RNA maturation, including mRNA surveillance, export from the nucleus, and spliceosomal snRNP assembly, suggesting a shared role in RNA processing and splicing within the nucleus. Some terms are unrelated (e.g., certain metabolic processes), but the dominant signal supports a nuclear RNA processing/splicing theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071033","count":1},{"id":"GO:0006406","count":1},{"id":"GO:0000973","count":1},{"id":"GO:0040022","count":1},{"id":"GO:0000387","count":1}]},{"hash":"1302050921823595643","title":"Neuronal synaptic plasticity and calcium signaling","description":"This cluster centers on neuronal signaling and activity-dependent plasticity: regulation of long-term potentiation, calcineurin-NFAT signaling, calcium handling, substantia nigra development, and actin remodeling, all pointing to synaptic function and structural dynamics in neurons. Some terms (e.g., bioluminescence, obsolete PDE activity) may reflect annotation noise, but the core theme is neuronal calcium\u2013dependent signaling and plasticity.","confidence":"Medium","size":9,"edges":27,"triangles":37,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031954","count":6},{"id":"GO:1900271","count":6},{"id":"GO:0051343","count":6},{"id":"GO:2001246","count":6},{"id":"GO:0008218","count":6}]},{"hash":"236249483128068672","title":"Unknown","description":"Top terms mix transcription regulation, telomere maintenance, ubiquitin-dependent proteolysis, differentiation, and stress responses with several obsolete entries, and there are no edges connecting proteins. This lack of a coherent functional theme suggests the cluster cannot be meaningfully named beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0032088","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0071446","count":2}]},{"hash":"1582049966701620886","title":"Ribosome Biogenesis & RNA Processing","description":"Most terms concentrate on ribosome assembly and maturation, including ribosome biogenesis and rRNA processing. The presence of protein folding and peptidyl-prolyl isomerase terms aligns with chaperone activities supporting ribosome assembly. Some viral-related and obsolete terms appear, likely reflecting annotation noise rather than a true viral function. Overall, the cluster centers on components and processes tied to ribosome production and RNA maturation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0048453","count":1},{"id":"GO:1901407","count":1}]},{"hash":"1605758079025403218","title":"Cell Cycle Regulators","description":"Dominant GO terms point to cell cycle control and proliferation (cell cycle, G1/S transition, mitotic M phase, cell population proliferation), suggesting these proteins mainly regulate cell division. Immune signaling terms (interleukin-4 response, NK cell cytotoxicity) appear secondary, and a few tRNA modification terms are present but do not define a cohesive core. Overall, the core theme is cell cycle regulation with some ancillary immune signaling associations.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":2},{"id":"GO:0002143","count":2},{"id":"GO:0032447","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0042267","count":2}]},{"hash":"525205096769736485","title":"GTPase signaling and filopodium assembly","description":"This cluster centers on small GTPase\u2013mediated signaling (GO:0007264) that drives cytoskeletal remodeling, particularly filopodium assembly and its regulation (GO:0046847, GO:0051489), and cell spreading via adhesion-dependent processes (GO:1900026). While there are some terms related to Ras signaling modulation, mitochondrial fission, and cytokine-related responses that are less central, the dominant signal is GTPase-driven actin dynamics and filopodium formation.","confidence":"Medium","size":8,"edges":12,"triangles":3,"max_degree":6,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007264","count":8},{"id":"GO:1900026","count":8},{"id":"GO:0046847","count":8},{"id":"GO:0051489","count":7},{"id":"GO:0000266","count":7}]},{"hash":"1206113282171608723","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3}]},{"hash":"470458889746771810","title":"Neuronal development and morphogenesis","description":"The cluster is enriched for neural development and neurite-related processes, including neuron fate determination, midbrain dopaminergic neuron differentiation, regulation of dendritic spine morphogenesis, and filopodium assembly, pointing to a cohesive theme of neuronal differentiation and morphology; additional terms on trafficking and proliferation may reflect broader cellular contexts but do not override the neural focus.","confidence":"Medium","size":8,"edges":15,"triangles":10,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1903833","count":7},{"id":"GO:0043552","count":7},{"id":"GO:0061001","count":7},{"id":"GO:1905279","count":7},{"id":"GO:0051489","count":7}]},{"hash":"792961810964227848","title":"Unknown","description":"The top GO terms span several unrelated areas, including metabolism (thiamine, glutathione, glycolysis, glutamate), nucleotide turnover (thymidine catabolism), redox/oxidative stress (menadione response), and also chromatin remodeling and development (rDNA heterochromatin formation, gastrulation, aging). Because there is no single cohesive biological function tying the proteins together, there is no meaningful label beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0006096","count":1},{"id":"GO:0042391","count":1}]},{"hash":"1398591759758626429","title":"Mitochondrial Dynamics and Immune Signaling","description":"The top GO terms strongly point to mitochondrial processes\u2014positive regulation of mtDNA replication, mitochondrial inheritance, and inner mitochondrial membrane organization\u2014suggesting a core role in mitochondrial dynamics. The other terms hint at membrane-associated and immune-related functions (protein localization to membrane raft, TLR3 signaling, T cell polarity, cell adhesion molecule production, and ECM disassembly), which together imply a cluster where mitochondrial dynamics interface with membrane signaling and immune pathways, possibly at mitochondria-associated membranes. Confidence: Medium.","confidence":"","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0090297","count":4},{"id":"GO:0030433","count":4},{"id":"GO:1903905","count":4},{"id":"GO:0045861","count":4},{"id":"GO:0060355","count":4}]},{"hash":"1829519338727660502","title":"Proteostasis and Translation Regulation","description":"The cluster centers on ubiquitin-proteasome\u2013driven protein catabolism and the assembly/ regulation of translation initiation complexes, with supporting terms for mRNA surveillance and translation upregulation. While neuron differentiation and proliferation terms appear, the strongest, most frequent signals tie to protein quality control and control of protein synthesis, suggesting a proteostasis/translation-focused cluster.","confidence":"Medium","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0032436","count":5},{"id":"GO:0030182","count":3},{"id":"GO:0070196","count":3},{"id":"GO:0006283","count":3},{"id":"GO:0001732","count":3}]},{"hash":"1465925814388519590","title":"Insulin-regulated actin remodeling in neurons","description":"The cluster is dominated by actin cytoskeleton-related terms (filopodium and ruffle assembly, actin filament polymerization and crosslinking, actin organization), plus insulin receptor signaling pathway terms and a note on excitatory postsynaptic potential regulation. This points to actin dynamics at neuronal synapses that may be modulated by insulin signaling, forming a coherent theme of insulin-regulated actin remodeling in neurons.","confidence":"Medium","size":8,"edges":23,"triangles":33,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":2},{"id":"GO:0046847","count":2},{"id":"GO:2000463","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0008286","count":2}]},{"hash":"2205935532795287239","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0002107","count":1},{"id":"GO:0010606","count":1}]},{"hash":"1774888960414314960","title":"Mitotic cell cycle control","description":"The proteins are enriched for GO terms centered on mitotic progression and cell-cycle transitions (G1/S, G2/M), spindle pole separation, and chromosome condensation, with an additional signal for DNA-templated transcription during division. While there are a few broader growth-related terms (retinoic acid response, mammary gland proliferation), the dominant theme is coordination of mitosis and cell-cycle control.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0046626","count":2},{"id":"GO:2000775","count":2},{"id":"GO:0000082","count":2}]},{"hash":"1534877118626932709","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006613","count":1},{"id":"GO:0000244","count":1},{"id":"GO:0071166","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0000472","count":1}]},{"hash":"1022231278959324002","title":"Diverse regulation of cellular processes","description":"The top GO terms are all regulatory in nature, spanning telomere maintenance, mRNA stability, signaling pathways (salicylic acid signaling), chemokine production, and regulation of electrophysiological properties, suggesting a broad, cross-cutting theme of regulatory control across multiple cellular processes rather than a single cohesive function.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":7},{"id":"GO:0035994","count":7},{"id":"GO:1904357","count":7},{"id":"GO:0035508","count":7},{"id":"GO:0007253","count":7}]},{"hash":"2268614935959569168","title":"Histone acetylation and transcription regulation","description":"This cluster centers on GO terms for DNA-templated transcription and its regulation, along with several histone acetylation terms (H2A/H3/H4). These points together suggest chromatin-modifying proteins that modulate transcription, potentially in response to stress signals like cadmium. While some terms are obsolete, the core theme is histone modification linked to transcription control.","confidence":"Medium","size":8,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0043981","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0043968","count":1},{"id":"GO:0043982","count":1}]},{"hash":"2091447135419425829","title":"Unknown","description":"The terms mix bacterial lipopolysaccharide biosynthesis with a mitochondrial respiratory chain assembly term, providing no single cohesive function. This suggests the cluster may be a mixed or noisy annotation rather than a true functional module.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009244","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0009060","count":1},{"id":"GO:0033617","count":1}]},{"hash":"2260114682778974664","title":"Nucleolar transcription and ribosome biogenesis","description":"This cluster centers on nuclear processes: multiple terms for transcription (RNA polymerase I/II/III) and ribosome biogenesis, suggesting a role in ribosome production and associated transcriptional machinery. Some outlier terms (endosome transport, calcium channel regulation) appear less representative of the main theme. ","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0007032","count":2},{"id":"GO:0006360","count":1},{"id":"GO:0006369","count":1},{"id":"GO:0006366","count":1}]},{"hash":"2305165073112316356","title":"DNA replication and centromere chromatin assembly","description":"The cluster is dominated by GO terms tied to DNA replication, mitotic replication checkpoint signaling, and CENP-A containing chromatin assembly, which together point to chromosome duplication and centromere maintenance during the cell cycle. Additional terms related to centrosome/centriole dynamics and general protein quality control (autophagy, ERAD) appear but do not outweigh the core replication/centromere theme. Overall, this cluster seems best described by processes governing chromosome maintenance during cell division.","confidence":"Medium","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0044209","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0061641","count":4}]},{"hash":"2111540230917927424","title":"Cytoskeleton and spindle dynamics in cell division","description":"The GO terms point to microtubule/cytoskeleton organization (microtubule cytoskeleton polarity, spindle orientation, spindle pole body separation, actomyosin ring assembly) and nuclear movement events (nuclear migration, karyogamy), indicating a shared theme of cytoskeletal control over cell division and nuclear dynamics. Some terms also touch on neuronal transport and brain structure, which can reflect cytoskeletal roles in neurons, supporting a cohesive module of cytoskeleton- and division-related functions.","confidence":"Medium","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":8},{"id":"GO:0048364","count":8},{"id":"GO:0000743","count":8},{"id":"GO:0000073","count":8},{"id":"GO:0098971","count":8}]},{"hash":"2219602499441048327","title":"Developmental Transcriptional Regulation","description":"Most enriched terms point to vertebrate development (forebrain development, neural tube closure, multicellular organism development) and transcriptional control (DNA-templated transcription). A few stress- or defense-related terms are present but appear peripheral, suggesting the core cluster reflects proteins involved in regulating gene expression during development rather than a single stress pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006349","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0071276","count":4}]},{"hash":"920899595966057672","title":"Ubiquitin-Dependent Protein Degradation & Inflammatory Signaling","description":"This cluster is enriched for ubiquitination-related processes (autoubiquitination; ubiquitin-dependent protein catabolic process; K6-linked ubiquitination) and inflammatory signaling pathways (TNF-mediated signaling; JNK cascade), suggesting a theme of protein turnover linked to stress/inflammatory signaling, despite some obsolete or unrelated terms.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0042787","count":4},{"id":"GO:0070512","count":3},{"id":"GO:1903762","count":3},{"id":"GO:0033209","count":3}]},{"hash":"1851320456838823813","title":"Developmental Signaling Regulation","description":"The cluster features terms related to regulation of key signaling pathways (negative regulation of TGF-beta receptor signaling, BMP signaling, and NF-kappaB signaling) and development-centric processes (maintenance of meristem identity, masculinization of hermaphroditic germ-line). While a couple terms (like photosystem stoichiometry adjustment) seem less connected, the dominant theme is modulation of signaling pathways in developmental contexts, especially plant development. This supports a label around developmental signaling regulation.","confidence":"Medium","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":8},{"id":"GO:0030514","count":8},{"id":"GO:0080005","count":8},{"id":"GO:0042006","count":8},{"id":"GO:0042347","count":8}]},{"hash":"1832084979742197696","title":"Vesicle trafficking and ion transport","description":"This cluster is driven by endomembrane trafficking terms (ER-to-Golgi transport; SNARE complex disassembly) pointing to vesicle-mediated cargo movement. The accompanying ion transport and membrane potential terms (zinc, sodium, potassium transport; membrane repolarization) suggest nodes involved in membrane homeostasis alongside trafficking. The dephosphorylation/phosphorelay signals could reflect regulatory layers that tie signaling to trafficking processes.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006470","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0000160","count":2},{"id":"GO:0035494","count":2},{"id":"GO:0051301","count":2}]},{"hash":"825408929466568156","title":"Unknown","description":"The GO terms listed are highly diverse (neural development, lipid digestion, vesicle trafficking, renal/epithelial transport, retinoic acid response, etc.), with no single dominant function or shared biological process linking the proteins. The lack of edges and a cohesive theme makes it impossible to assign a meaningful, specific cluster name. ","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990349","count":1},{"id":"GO:0021670","count":1},{"id":"GO:0044241","count":1},{"id":"GO:0085018","count":1},{"id":"GO:0070295","count":1}]},{"hash":"323503351289800434","title":"Bacterial cell wall and capsule polysaccharide biosynthesis","description":"This cluster\u2019s top GO terms are centered on biosynthesis of cell wall polysaccharides, including capsule polysaccharide, teichoic acid, and mycolate-containing layers, with UDP-D-galactose metabolism and lipid-linked sugar biosynthesis supporting these pathways. The terms collectively point to assembly and modification of the bacterial envelope\u2019s carbohydrate components, spanning capsule and related cell wall structures. Immunoglobulin production appears as an outlier, but the dominant signal is capsule/cell wall polysaccharide synthesis.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070592","count":2},{"id":"GO:0052573","count":2},{"id":"GO:0045227","count":2},{"id":"GO:0071769","count":2},{"id":"GO:0036108","count":1}]},{"hash":"726823881113776156","title":"RNA Processing and Gene Expression Regulation","description":"The cluster centers on RNA-focused processes (splicing via spliceosome; RNA guanine-N7 methylation) and core gene expression steps (DNA-templated transcription; translation preinitiation complex formation), with additional regulatory cues (positive regulation of GTPase activity; protein autophosphorylation). Some terms like aging and male gonad development are less directly tied, but the dominant theme is RNA processing and regulation of gene expression.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0008584","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1493751313652812655","title":"Energy metabolism and redox balance","description":"The cluster is dominated by central carbon metabolism terms: 2-oxoglutarate metabolic process, glycolytic process, and the TCA cycle, along with anaerobic respiration and glutathione metabolic process. These point to core energy production and redox maintenance. The presence of a neuronal development term and membrane potential regulation likely reflects broader cellular energetic and redox-related functions rather than a distinct signaling or developmental pathway. Overall, the theme is energy metabolism with redox homeostasis.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006103","count":2},{"id":"GO:0009061","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0006096","count":1}]},{"hash":"1013097356304648877","title":"Cardiac Calcium Signaling and SR Ca Release","description":"This cluster is dominated by terms tied to heart muscle calcium handling: ventricular cardiac muscle morphogenesis, negative regulation of ryanodine receptor, and release of sequestered Ca2+ from the sarcoplasmic reticulum. While there are some auxiliary terms related to metabolism and stress responses (glucose response, hydrogen peroxide, sumoylation, glucocorticoid signaling), the strongest common theme is calcium signaling in cardiac muscle. ","confidence":"High","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055010","count":3},{"id":"GO:0060315","count":3},{"id":"GO:0014808","count":3},{"id":"GO:0030850","count":2},{"id":"GO:0048680","count":2}]},{"hash":"2265571654480534322","title":"Neural development and brain maturation","description":"This cluster is dominated by terms tied to brain development, notably cerebral cortex development and neuron maturation, suggesting a neural-development theme. Additional terms point to transcriptional regulation and proteasomal protein turnover that often accompany development, while a few outliers (immune response and sperm capacitation) may reflect broader roles of the proteins or annotation artifacts.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0032436","count":2},{"id":"GO:0060716","count":2},{"id":"GO:0045793","count":2}]},{"hash":"571562820557640177","title":"Neuronal signaling, vesicle trafficking, and cytoskeleton regulation","description":"This cluster centers on neuronal synaptic signaling and membrane dynamics, as seen in terms like negative regulation of short-term neuronal synaptic plasticity, retrograde signaling by neuropeptide, and positive regulation of vesicle fusion, along with protein localization to the cortical microtubule cytoskeleton. GTPase regulation and membrane repair further support a role in dynamic trafficking and cytoskeletal control, characteristic of neuronal membrane trafficking and signaling modules.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0001778","count":2},{"id":"GO:0034244","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1905433","count":1}]},{"hash":"535292782933417037","title":"Eye development and retinal metabolism","description":"The cluster is enriched for retinal metabolic process, cellular response to retinoic acid, and Harderian gland development, all pointing to ocular development and retina function. The presence of GABA shunt suggests neural activity linked to the eye/retina, with additional metabolic processes that may be supportive. Together, these terms indicate a cohesive module centered on eye/retinal development and metabolism.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0019544","count":7},{"id":"GO:0042574","count":7},{"id":"GO:0050885","count":7},{"id":"GO:0071300","count":7},{"id":"GO:0006068","count":7}]},{"hash":"2150865928875428201","title":"ER Protein Folding and ER Stress Response","description":"This cluster is centered on endoplasmic reticulum proteostasis: proteins involved in folding in the ER, ER stress/UPR response, chaperone-assisted refolding, and ER-associated degradation, plus redox maintenance. The strong presence of GO terms for protein folding in the ER, ER stress, chaperone activity, and ERAD indicates a cohesive role in secretory protein maturation and quality control, despite a few more general terms (DNA replication/transcription) appearing in the set due to broader cellular processes.","confidence":"High","size":7,"edges":14,"triangles":10,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0034975","count":7},{"id":"GO:0034599","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0018279","count":5},{"id":"GO:0045454","count":4}]},{"hash":"178441975483098485","title":"DNA repair and RNA processing","description":"The top GO terms show strong enrichment for nucleotide-excision repair and SOS response, indicating involvement in DNA damage response. Additional terms relate to RNA metabolism and processing (translation initiation, translation reinitiation, spliceosome-mediated regulation of splicing, rRNA processing), suggesting a link between genome maintenance and RNA maturation/translation control in this cluster. A minor lipoprotein transport term appears once but does not define the main theme. Taken together, this cluster seems to center on DNA repair coupled with RNA processing/translation regulation.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0000464","count":2}]},{"hash":"844467935239871063","title":"Neuronal ERK signaling and synaptic plasticity","description":"The cluster\u2019s top GO terms cluster around neural development and signaling, especially hippocampus development and positive regulation of ERK1/ERK2 cascade, along with processes tied to synaptic function (calcium-dependent exocytosis, regulation of synaptic plasticity) and Rho signaling. This pattern suggests a coherent theme of neuronal signaling pathways that control development and activity-dependent synaptic strength, despite one plant-related term appearing peripherally. Confidence: High.","confidence":"","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":3},{"id":"GO:0070374","count":3},{"id":"GO:0033138","count":3},{"id":"GO:0043552","count":2},{"id":"GO:0032092","count":2}]},{"hash":"605484226124006620","title":"Unknown","description":"The listed GO terms span mechanosensing, plant hormone signaling, multiple cell-cycle stages, Schwann cell development, adipogenesis, axonogenesis, DNA replication, drug response, and telomere maintenance. This broad and diverse mix lacks a single cohesive function or pathway tying the proteins together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035994","count":2},{"id":"GO:0009738","count":2},{"id":"GO:0000086","count":2},{"id":"GO:0051321","count":2},{"id":"GO:0014044","count":2}]},{"hash":"2283688599065755020","title":"Unknown","description":"The proteins map to a broad set of GO terms including ER-Golgi transport, neuron projection development, actin dynamics, translation initiation, RNA methylation, chromatin assembly, and signaling, with no clear single function binding them together. The lack of edges suggests no cohesive pathway, so a specific label isn\u2019t well-supported.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0031175","count":4},{"id":"GO:2000601","count":4},{"id":"GO:0051016","count":4},{"id":"GO:0031954","count":3}]},{"hash":"1054692265096583185","title":"Cytoskeletal Dynamics and Adhesion in Development","description":"This cluster shows recurring GO terms tied to microtubule regulation, focal adhesion assembly, muscle attachment, and developmental morphogenesis, suggesting proteins coordinating cytoskeleton dynamics with cell-matrix adhesion during development.","confidence":"Medium","size":7,"edges":13,"triangles":9,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007026","count":1},{"id":"GO:0009652","count":1},{"id":"GO:0086097","count":1},{"id":"GO:0048734","count":1},{"id":"GO:0048041","count":1}]},{"hash":"1299916863881207413","title":"SSU rRNA maturation and RNA methylation","description":"This cluster centers on RNA processing for ribosome biogenesis, highlighted by the enrichment of SSU rRNA maturation (GO:0000462) and guanine-N7 methylation (GO:0036265). The presence of vacuolar transport and ion-handling terms likely reflects secondary or multifunctional roles or broader cellular context, but the dominant theme remains ribosome RNA maturation. ","confidence":"Medium","size":7,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070317","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0015991","count":1},{"id":"GO:0007033","count":1}]},{"hash":"813525893003810945","title":"Nuclear DNA repair and chromatin maintenance","description":"These proteins cluster around nuclear genome maintenance and chromatin regulation, including ubiquitin-proteasome turnover in the nucleus, heterochromatin maintenance, histone modification, and multiple DNA repair pathways (NER, NHEJ) and meiotic chromosomal events (DSB formation, synaptonemal complex). This suggests a function in protecting genome integrity and chromatin structure in the nucleus.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:1990920","count":7},{"id":"GO:1901044","count":7},{"id":"GO:0006344","count":7},{"id":"GO:0071596","count":7},{"id":"GO:0070911","count":7}]},{"hash":"1719750209424516119","title":"RTK signaling and actin cytoskeleton remodeling","description":"The cluster includes GO terms for small GTPase-mediated signal transduction and multiple receptor tyrosine kinase pathways (ephrin, EGFR, T cell receptor signaling), paired with actin remodeling processes (actin filament branching, podosome and filopodium assembly). This points to a shared theme where RTK-driven signaling governs cytoskeletal rearrangements underlying cell migration, adhesion, and growth in multicellular contexts.","confidence":"High","size":7,"edges":6,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007264","count":7},{"id":"GO:0043552","count":6},{"id":"GO:0048013","count":6},{"id":"GO:0071803","count":6},{"id":"GO:0050852","count":6}]},{"hash":"1170051599720079158","title":"ER-Golgi trafficking and cell cycle regulation","description":"The top GO terms strongly point to ER\u2013Golgi vesicle transport (ER to Golgi, COPII budding, Golgi\u2013ER retrograde transport) as the core activity, with additional signals for cell division and mitotic spindle assembly. This suggests the cluster centers on vesicle trafficking between the ER and Golgi, coupled with cell growth/division processes and related signaling (e.g., TORC1). Brain development and mRNA transport terms may reflect broader roles, but the dominant theme is ER\u2013Golgi trafficking linked to cell cycle regulation.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0008283","count":2},{"id":"GO:0051028","count":2}]},{"hash":"451934946059965818","title":"Neuronal development and epithelial polarity","description":"The top GO terms point to neural development (hippocampus development, dendrite morphogenesis, axon extension) and to cell polarity in epithelial cells (establishment/maintenance of epithelial polarity, tight junction assembly). While other terms touch on metabolism or immunity, the dominant signals cluster around neural growth and epithelial organization, suggesting proteins involved in shaping neurons and epithelial cell architecture. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021766","count":3},{"id":"GO:0045956","count":3},{"id":"GO:0045197","count":3},{"id":"GO:0045773","count":3},{"id":"GO:0070830","count":3}]},{"hash":"1902289009095788224","title":"Bacterial cell wall and envelope biogenesis","description":"This cluster is dominated by GO terms related to peptidoglycan biosynthesis, cell wall organization, and lipopolysaccharide biosynthesis, all pointing to assembly and growth of the bacterial cell envelope and division processes. Additional terms on UDP-N-acetylglucosamine and related biosynthesis support the theme, though a couple are more general metabolic steps. Overall, the core signal is bacterial envelope biogenesis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0009252","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0016049","count":2}]},{"hash":"142762258985761326","title":"Neural development and mitochondrial-cytoskeletal dynamics","description":"The top GO terms point to neural tissue development (retina homeostasis, substantia nigra development) and cytoskeletal processes (actin filament bundle assembly, actomyosin contractile ring contraction), together with mitochondrial processes (mitochondrion inheritance, establishment/localization). This suggests a coherent module coordinating neuronal development with cytoskeletal organization and mitochondrial distribution. Some terms refer to obsolete histone acetylation, which weakens but does not overturn the core neural-cytoskeletal-mitochondrial theme.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":5},{"id":"GO:0042766","count":5},{"id":"GO:0001895","count":5},{"id":"GO:0043982","count":5},{"id":"GO:0021762","count":5}]},{"hash":"1728728537816028295","title":"Unknown","description":"The GO terms span diverse processes, including development, defense, cell cycle, signaling, RNA transport, hypoxia response, and protein oligomerization, with no single dominant function tying the proteins together.","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0031954","count":2},{"id":"GO:0006349","count":2}]},{"hash":"520221329592262290","title":"Brain Development and Stress-Response Signaling","description":"Because the terms prominently point to brain and multicellular development (forebrain development, brain development, multicellular organism development) and also to signaling and stress responses (TORC1 signaling, ER stress\u2013related apoptosis, cadmium response), the cluster seems to reflect developmental programs influenced by cellular stress pathways rather than a single specific function. The mix suggests a developmental theme intertwined with stress signaling.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007568","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0001403","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0007275","count":5}]},{"hash":"2006887717098120510","title":"Diverse Membrane Transporters","description":"The top GO terms cluster around transmembrane transport of ions and metabolites across organelles (K+, Cl\u2212, Co2+, lipoproteins, thiamine, long-chain fatty acids into peroxisomes, carbohydrate derivatives), suggesting a group of membrane transporter proteins; one term on endoribonuclease regulation is likely noise.","confidence":"Medium","size":7,"edges":7,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0042953","count":1},{"id":"GO:1902476","count":1},{"id":"GO:0015888","count":1},{"id":"GO:0060702","count":1}]},{"hash":"733327643288176755","title":"Mitochondrial inner membrane protein import","description":"These proteins cluster around mitochondrial targeting and inner membrane insertion, suggesting a role in transporting or inserting proteins into the mitochondrial inner membrane. Although the GO terms are obsolete, the shared themes point to a mitochondrial import/insertion function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0045039","count":1}]},{"hash":"703235107357020653","title":"Inflammation and leukotriene biosynthesis","description":"The cluster\u2019s top GO terms cluster around inflammatory responses (acute and chronic) and leukotriene biosynthesis, plus related LPS response and calcium signaling\u2014pointing to innate immune/inflammatory processes and lipid mediator production. Some terms (e.g., Leydig cell differentiation, cornification) are less directly tied, but the dominant signal is inflammation and leukotriene synthesis.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0033327","count":1},{"id":"GO:0032526","count":1},{"id":"GO:0070268","count":1},{"id":"GO:0002544","count":1},{"id":"GO:0008285","count":1}]},{"hash":"2247664472807627345","title":"Neurovascular signaling and development","description":"This cluster's top GO terms span neural functions (long-term synaptic potentiation, neurotransmitter secretion, clustering of voltage-gated potassium channels) and vascular/heart development (angiogenesis, heart development, VEGF signaling regulation), along with signaling and cytoskeletal remodeling (phosphatidylinositol signaling, actin crosslink formation). Together they point to proteins involved in coordinating neural activity with vascular development or neurovascular signaling, even though one plant-specific pathway term appears due to cross-annotation.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":4},{"id":"GO:0007507","count":4},{"id":"GO:0051764","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0007269","count":3}]},{"hash":"1375159358925057105","title":"Cell cycle and replication machinery","description":"This cluster's top GO terms are dominated by cell cycle and DNA-related processes (G1/S transition, meiotic cycle, DNA replication, and kinetochore localization) plus DNA-templated transcription, pointing to a core cell-division/dna-processing module. A handful of terms about Schwann cell development, neuronal signaling, cocaine response, and abscisic acid signaling likely reflect annotation noise or multifunctional proteins rather than a single tissue- or pathway-specific function.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000082","count":5},{"id":"GO:0051321","count":5},{"id":"GO:0014044","count":5},{"id":"GO:0034501","count":5},{"id":"GO:0060079","count":5}]},{"hash":"2158182945518405063","title":"RNA cap and methylation enzymes","description":"GO terms cluster around methylation-related processes: 7-methylguanosine mRNA capping, guanine-N7 methylation, and various N-terminal and protein methylations, plus rRNA processing. This points to RNA- and protein-modifying enzymes, especially methyltransferases involved in RNA capping and ribosome biogenesis. Obsolete aging and nodulation terms appear as background noise rather than core features.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001300","count":2},{"id":"GO:0090398","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0018012","count":1},{"id":"GO:0036265","count":1}]},{"hash":"112089415438480561","title":"Ubiquitin-dependent signaling and apoptosis regulation","description":"The top GO terms cluster around ubiquitination pathways (K48- and K6-linked ubiquitination, ubiquitin-dependent ERAD) and their consequences on signaling and cell fate (NF-kappaB activation, cell surface receptor signaling, regulation of apoptotic process, regulation of cell cycle). This points to a cohesive theme of ubiquitin-mediated control of signaling and apoptosis, with a few peripheral terms. ","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0042981","count":1},{"id":"GO:0070936","count":1}]},{"hash":"1799248175267553043","title":"NO/cGMP Signaling and Nitrosative Stress","description":"The top GO terms point to nitric oxide-related signaling (positive regulation of guanylate cyclase activity), nitrosative stress responses, S-nitrosylation, and gasotransmitter biology (including hydrogen sulfide biosynthesis). These create a coherent theme around NO/cGMP signaling and redox biology, with some metabolic terms like nitrate catabolism and copper import that may be accompanying but not defining. Overall, the cluster appears to represent NO/cGMP-mediated signaling and nitrosative stress responses.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031284","count":1},{"id":"GO:0071500","count":1},{"id":"GO:0043602","count":1},{"id":"GO:0018119","count":1},{"id":"GO:0070814","count":1}]},{"hash":"166945955071658955","title":"Plant Growth and Hormone Signaling","description":"The cluster\u2019s terms cluster around plant development: seed growth regulation and responses to major hormones (ethylene, gibberellin, and ABA), with chromatin remodeling and other growth-related processes. While there are telomere-related terms, the dominant signal points to hormonal control of plant development and gene expression. Therefore, a label centered on plant growth and hormone signaling fits best.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080113","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0031627","count":1},{"id":"GO:0009723","count":1},{"id":"GO:1904792","count":1}]},{"hash":"2008469253091431173","title":"Unknown","description":"The Top Terms span hormonal development (prostate gland development, male sex differentiation, steroid hormone receptor complex assembly), immune/interferon responses (type I interferon, interferon-alpha, antiviral defense regulation), cell cycle transitions (mitotic metaphase/anaphase), and even photosynthesis, with no single coherent theme tying the proteins together. This suggests the cluster is heterogeneous or potentially misannotated, so a single representative function is not identifiable.","confidence":"","size":6,"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:0071357","count":2},{"id":"GO:0071276","count":1}]},{"hash":"1319041130477725555","title":"Ubiquitin-Driven Immune Signaling Regulation","description":"Dominant ubiquitination-related terms (ubiquitin-dependent catabolic process, autoubiquitination, K6-linked ubiquitination) along with immune signaling pathways (TNF signaling, RIG-I pathway, JNK cascade regulation) suggest a cohesive role in ubiquitin-mediated control of innate immune responses.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0070512","count":3},{"id":"GO:1903762","count":3},{"id":"GO:0033209","count":3},{"id":"GO:0039536","count":3}]},{"hash":"677018333868042020","title":"Neuronal differentiation and spine morphogenesis regulation","description":"The dominant GO terms point to neuron development and neurite/spine dynamics, including neuron fate determination, midbrain dopaminergic neuron differentiation, and regulation of dendritic spine morphogenesis and filopodium assembly. While a few terms touch on other cell types (endothelial barrier, lymphocyte aggregation), the strongest signal is neuronal differentiation and regulation of neurite/spine morphology.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043552","count":3},{"id":"GO:0061001","count":3},{"id":"GO:1905279","count":3},{"id":"GO:0051489","count":3},{"id":"GO:0008283","count":3}]},{"hash":"788134069157067241","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1890007944849057264","title":"Nucleocytoplasmic export of ribosomal subunits and mRNA","description":"The top GO terms are dominated by export from the nucleus for ribosomal subunits (small and large) and mRNA, pointing to a shared function in nucleocytoplasmic transport. Other terms hint at related cellular contexts (cell division, centrosome processes) but do not redefine the main theme. This makes the proposed label an appropriate reflection of the cluster\u2019s core function.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0034501","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0042176","count":2},{"id":"GO:0010824","count":2}]},{"hash":"227336002945712204","title":"LPS Biosynthesis and Antibiotic Response","description":"The strongest signals are lipopolysaccharide biosynthetic process and lipid A biosynthetic process, pointing to bacterial LPS assembly. The presence of response to antibiotic and response to xenobiotic stimulus supports a connection to antimicrobial exposure or outer-membrane-associated functions. Some terms (aging, liver regeneration, apoptotic process, fungal-type cell wall biogenesis) appear as noise or cross-species annotations, but do not override the core LPS-related signals.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0097421","count":2}]},{"hash":"1353687131445522499","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000472","count":3}]},{"hash":"1917663935562502733","title":"Neuronal Polarity and Spine Morphogenesis","description":"The top GO terms center on cell polarity maintenance and neuronal structure, including dendritic spine morphogenesis, filopodium assembly, and neuron fate determination, with additional signals related to endosome-Golgi transport and barrier establishment. This points to a core theme of polarity-driven neuronal morphogenesis, with some cross-talk to endothelial/transport regulation\u2014consistent with a cluster focused on neuronal polarity and spine formation.","confidence":"Medium","size":6,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030011","count":2},{"id":"GO:0043124","count":2},{"id":"GO:1903833","count":1},{"id":"GO:0043552","count":1},{"id":"GO:0061001","count":1}]},{"hash":"1024293816311828788","title":"Ubiquitin-Dependent Proteolysis","description":"The top GO terms are dominated by ubiquitin-dependent protein catabolic processes, including K48-linked ubiquitination and autoubiquitination, indicating a core function in tagging proteins for degradation. A secondary term about peroxisomal matrix protein import suggests some trafficking-related connections, but the central theme is ubiquitin-mediated turnover. Some obsolete X-chromosome\u2013related terms appear as annotation noise. Overall, the cluster is best described as ubiquitin-dependent proteolysis.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0016558","count":2},{"id":"GO:0060816","count":2},{"id":"GO:0070936","count":2}]},{"hash":"20132411263895759","title":"Chromatin organization and centromere assembly","description":"Based on GO terms such as CENP-A containing chromatin assembly, regulation of chromosome condensation, silent mating-type cassette heterochromatin formation, and nucleosome mobilization, the proteins cluster around chromatin structure and remodeling, including centromere-associated assembly. While several terms are unrelated or obsolete, the strongest signal is chromatin organization. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002227","count":1},{"id":"GO:0007283","count":1},{"id":"GO:0061408","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0061641","count":1}]},{"hash":"1682220929084241161","title":"Fungal mating, morphogenesis, and cell wall synthesis","description":"The cluster is enriched for fungal-specific processes such as karyogamy (nuclear fusion during mating) and fungal-type beta-glucan biosynthesis (cell wall formation), along with cell morphogenesis and DNA replication, suggesting a coordinated fungal mating/morphogenesis program with cell wall biogenesis. Other terms like SRP-dependent targeting and iron-sulfur cluster assembly reflect supporting cellular processes common to these functions. Overall, a fungal mating and morphogenesis focus is most consistent.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":4},{"id":"GO:0000902","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0090084","count":3},{"id":"GO:1903751","count":3}]},{"hash":"2152916998428552170","title":"Unknown","description":"The GO terms span nuclear import, GTPase regulation, TORC1 signaling, ciliary docking, spindle elongation, development, and organ identity; there isn't a single cohesive function tying all proteins together, so a specific label is not warranted.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0048496","count":2},{"id":"GO:0000011","count":2},{"id":"GO:0038202","count":2}]},{"hash":"816239285774475021","title":"RNA Pol II Transcription Initiation Complex","description":"Top GO terms center on RNA polymerase II transcription initiation and preinitiation complex assembly, including Pol II preinitiation complex assembly, initiation at Pol II promoters, and regulation of Pol II-mediated transcription, which together point to proteins that form or regulate the RNA Pol II transcription machinery; the other terms (e.g., viral process, mitochondrial targeting) appear ancillary and do not redefine the core function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051123","count":1},{"id":"GO:0006367","count":1},{"id":"GO:0006357","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0006351","count":1}]},{"hash":"973418926098662560","title":"Adhesion signaling and mechanotransduction","description":"Rationale: Top GO terms highlight integrin-mediated signaling, regulation of tight junction assembly, response to mechanical cues (muscle stretch), and anoikis regulation, all pointing to signaling events at cell-ECM and cell-cell interfaces that control adhesion, survival, and barrier integrity. The ensemble suggests a coherent theme of adhesion-related signal transduction; a few terms (retinoic acid and ABA responses) are less directly related but do not overwhelm the main pattern.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0071300","count":4},{"id":"GO:0043552","count":4},{"id":"GO:0060709","count":4},{"id":"GO:0035994","count":4},{"id":"GO:0007229","count":4}]},{"hash":"1518359515607228328","title":"Wnt-regulated neuronal development and vesicle trafficking","description":"This cluster centers on neuronal development signals (e.g., hippocampus development) and regulation of neuron survival, combined with vesicle trafficking processes (endocytic recycling and calcium-dependent exocytosis) and canonical Wnt signaling. The mix of pro/anti-apoptotic regulation alongside synaptic vesicle cycling suggests a theme of neuronal development paired with synaptic machinery, with Wnt signaling likely modulating these processes.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090263","count":5},{"id":"GO:0043525","count":4},{"id":"GO:0043524","count":4},{"id":"GO:0031384","count":4},{"id":"GO:0010796","count":4}]},{"hash":"571801705133530586","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0000393","count":2},{"id":"GO:0006310","count":2},{"id":"GO:1904574","count":2}]},{"hash":"2098656738698184907","title":"Chromatin modification and transcription regulation","description":"The cluster centers on histone modification (H3-K79 and K4 methylation) and chromatin assembly (CENP-A\u2013containing), with related transcription-related terms such as DNA-templated transcription and RNA methylation. This points to a cohesive theme of epigenetic regulation of gene expression and transcription initiation/modulation.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034729","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0031954","count":1},{"id":"GO:0001731","count":1}]},{"hash":"933651900496723517","title":"Neuronal synaptic plasticity and spine morphogenesis","description":"The cluster is dominated by GO terms related to neuronal signaling and synaptic remodeling, including dendritic spine morphogenesis and positive regulation of long-term synaptic plasticity, along with ephrin receptor signaling and retinoic acid response, which together point to neuronal synaptic plasticity as the core function; other terms reflect general cellular processes that may overlap but do not define the cluster.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048013","count":2},{"id":"GO:0071300","count":2},{"id":"GO:0050798","count":2},{"id":"GO:0034446","count":2},{"id":"GO:0060997","count":2}]},{"hash":"994459612774905640","title":"Seed Growth Hormone Response","description":"The terms point to seed growth regulation and responses to key plant hormones (ethylene, gibberellin, and abscisic acid), suggesting a theme of hormone-regulated seed development. Although there are mentions of broader nuclear processes (chromatin remodeling, telomere loops), the central pattern is seed growth control via hormone signaling. The lack of observed edges among the proteins also makes this a tentative, low-confidence label.","confidence":"Low","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080113","count":1},{"id":"GO:0072362","count":1},{"id":"GO:0031627","count":1},{"id":"GO:0009723","count":1},{"id":"GO:1904792","count":1}]},{"hash":"1665077157340383997","title":"Octopamine signaling and locomotion in invertebrates","description":"The top GO terms point to neurobehavioral signaling, especially octopamine signaling, locomotion and regulation of forward movement, plus behavioral responses to psychoactive substances (amphetamine, ethanol). This suggests a cohesive theme of invertebrate neural signaling governing movement and behavior, with other terms reflecting broader metabolic or stress-related contexts rather than a single enzymatic function. The lack of edges but presence of coherent behavioral terms supports a name centered on neurobehavioral signaling.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0001975","count":2},{"id":"GO:0007626","count":2},{"id":"GO:0043059","count":1},{"id":"GO:0001816","count":1}]},{"hash":"1118917880073910809","title":"Proteostasis and chaperone-mediated folding","description":"This cluster is dominated by GO terms related to protein stability, misfolded protein detection, and chaperone-assisted assembly, plus heat response, pointing to a proteostasis/quality-control role under stress. Some telomere/RNA-related terms and host-cell translocation appear but are less central to the core theme.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1901998","count":5},{"id":"GO:0090666","count":5},{"id":"GO:0044053","count":5},{"id":"GO:1904851","count":5},{"id":"GO:0048291","count":5}]},{"hash":"586436520250357671","title":"Ubiquitin-mediated proteolysis","description":"The top GO terms cluster around ubiquitin-tagging and proteasomal degradation (SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, protein polyubiquitination, positive regulation of ubiquitin ligase activity), indicating a core function in protein turnover and post-translational modification. Other terms such as translation initiation and cadmium response appear more peripheral or context-specific, but do not outweigh the ubiquitin-proteasome theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0032933","count":3},{"id":"GO:0071276","count":3},{"id":"GO:1904668","count":3},{"id":"GO:0031146","count":3}]},{"hash":"598910624548472207","title":"DNA replication and centromere chromatin maintenance","description":"The top GO terms point mainly to genome maintenance processes: DNA replication, CENP-A chromatin assembly at centromeres, and mitotic replication checkpoint signaling, which together suggest a core cluster around DNA replication and centromere/chromatin maintenance during cell cycle. Other terms about autophagosome maturation and inclusion body assembly appear as broader cellular quality-control processes that sometimes accompany stress responses, but do not define the core function. The viral genome replication term likely reflects shared replication machinery usage rather than a primary function of the cluster. Overall, the dominant theme is genome replication and chromatin maintenance in mitosis and cell-cycle regulation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0061641","count":4},{"id":"GO:0097352","count":4}]},{"hash":"226452967688520702","title":"Unknown","description":"The top GO terms span diverse processes (germ-line masculinization, meristem identity maintenance, transcription, vacuole fusion regulation, and multiple signaling pathways like TGF-beta/BMP and NF-kappaB) with no clear shared function or interaction pattern (edges = 0). This lack of a cohesive theme makes it inappropriate to assign a specific functional label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042006","count":2},{"id":"GO:0061191","count":2},{"id":"GO:0010074","count":2},{"id":"GO:0035970","count":2},{"id":"GO:0042347","count":2}]},{"hash":"465426225509941194","title":"Nuclear DNA Repair and Chromatin Regulation","description":"This cluster centers on nuclear processes: ubiquitin-proteasome\u2013dependent protein turnover, heterochromatin maintenance, and multiple DNA repair pathways, including nonhomologous end joining and meiotic double-strand break formation with synaptonemal complex organization. The combination of chromatin maintenance and DNA repair signals a cohesive theme of nuclear genome maintenance and chromatin dynamics, with one outlier immune term likely incidental.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:1990920","count":5},{"id":"GO:1901044","count":5},{"id":"GO:0006344","count":5},{"id":"GO:0071596","count":5},{"id":"GO:0070911","count":5}]},{"hash":"154019764402702821","title":"Histone demethylation in embryonic development","description":"The cluster centers on histone H3K36 and H3K4 demethylation terms, pointing to chromatin modification, with accompanying developmental processes such as blastocyst formation, mesodermal differentiation, and axis specification. This suggests a theme of epigenetic regulation guiding embryonic development, despite some terms being obsolete. ","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070544","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0001825","count":1},{"id":"GO:0048821","count":1},{"id":"GO:2000864","count":1}]},{"hash":"2276024202864322784","title":"Ribosome biogenesis and proteasomal degradation","description":"Top terms show strong ties to both ribosome biogenesis and proteasomal protein degradation, suggesting a cluster focused on the production of ribosomes and the concurrent protein turnover that governs translation readiness. Additional terms related to translation initiation, RNA methylation, and chromatin assembly fit within the broader context of gene-expression regulation linked to ribosome assembly and function. While the set covers related processes rather than a single exclusive function, the convergence on ribosome-related assembly and proteasomal degradation provides a coherent, specific label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0031954","count":1}]},{"hash":"129536607539750782","title":"Mitotic cell division and progression","description":"Based on GO terms, most annotations cluster around cell division and mitosis (cell cycle, metaphase/anaphase transition, and regulation of mitotic progression), suggesting these proteins function together in mitotic regulation. A few terms appear unrelated (cadmium response, photosynthesis), likely noise or cross-annotations.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0071276","count":1},{"id":"GO:0030850","count":1},{"id":"GO:0035457","count":1},{"id":"GO:0050689","count":1}]},{"hash":"444166638726190795","title":"Unknown","description":"The top GO terms are a mix of diverse biosynthetic processes (poly-hydroxybutyrate, lipopolysaccharide core, rhamnose, phenylpropanoid, fatty-acyl-CoA) plus unrelated areas like hair follicle development and B cell chemotaxis, with no connectivity between proteins (edges = 0). This suggests no coherent, shared function for the cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":2},{"id":"GO:1902987","count":1},{"id":"GO:0097171","count":1},{"id":"GO:0001942","count":1}]},{"hash":"1377905796899424663","title":"Unknown","description":"This cluster shows no interactions (Edges 0) and its GO terms are scattered across behavior and many unrelated metabolic/biosynthetic processes with several obsolete terms, giving no unifying function. Therefore there isn\u2019t a coherent label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060756","count":1},{"id":"GO:0019550","count":1},{"id":"GO:0006107","count":1},{"id":"GO:0015908","count":1},{"id":"GO:0033585","count":1}]},{"hash":"2016475053015645519","title":"Unknown","description":"The top terms span translation, development across plants and animals, signaling pathways, and cytoskeletal organization, showing no single coherent function or pathway linking the proteins. This broad mix suggests an Unknown label rather than a specific function cluster.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0050859","count":1},{"id":"GO:0060396","count":1},{"id":"GO:0048482","count":1},{"id":"GO:0021521","count":1}]},{"hash":"1326268501536922507","title":"Embryogenesis and Mesoderm Differentiation","description":"The top GO terms cluster around embryonic development processes\u2014blastocyst formation, mesodermal differentiation, axis specification, and brain development\u2014with additional tissue-specific developmental terms, indicating a broad but development-centric theme centered on embryogenesis and mesoderm patterning. Confidence reflects the apparent developmental-focus, though some terms are more tissue-specific rather than strictly embryonic.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001825","count":2},{"id":"GO:0048821","count":2},{"id":"GO:2000864","count":2},{"id":"GO:0048333","count":2},{"id":"GO:0021678","count":2}]},{"hash":"300503544028291394","title":"Unknown","description":"The terms are a mix of methylation-related processes (RNA methylation, mRNA capping, N-terminal methylation) and diverse biosynthetic pathways, with no clear common function or interactions among the four proteins, so there isn\u2019t a cohesive label to assign.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090398","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0018012","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0018013","count":1}]},{"hash":"127461667513458603","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0090043","count":1},{"id":"GO:0043970","count":1}]},{"hash":"1480067990032360900","title":"Actin Cytoskeleton Remodeling and Cell Migration","description":"The top GO terms are dominated by actin-related processes (actin filament bundle assembly) and cell migration, indicating the proteins mainly participate in actin cytoskeleton dynamics that drive movement. Other terms (telomere maintenance, muscle stretch) are much less frequent and don't define the core function of this cluster. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0032212","count":2},{"id":"GO:0035994","count":2},{"id":"GO:1904357","count":2}]},{"hash":"2054528133438621957","title":"Cytokine-driven antibacterial immune response","description":"The top GO terms cluster around cytokine production, IL-1\u03b2 regulation, bacterial detection, and defense against Gram-negative bacteria, with xenophagy regulation further supporting an antibacterial immune function; a few non-immune terms exist but do not override the dominant immune theme.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042391","count":1},{"id":"GO:0006409","count":1},{"id":"GO:0050718","count":1},{"id":"GO:0045214","count":1},{"id":"GO:1904417","count":1}]},{"hash":"1055798180802773843","title":"Autophagy- and ubiquitin-mediated quality control","description":"A core theme across the terms is protein quality control under stress, including aggrephagy and ubiquitin-dependent ERAD, with cytoskeletal organization supporting autophagosome trafficking and organelle quality control (e.g., mitochondrial fusion regulation) and stress responses such as cadmium exposure. Some transcription-related terms appear ancillary, but the predominant signal is autophagy/ERAD-mediated protein turnover under stress.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0071276","count":3},{"id":"GO:1904021","count":3},{"id":"GO:0006357","count":3},{"id":"GO:0010637","count":3}]},{"hash":"1333985898326313592","title":"Neural development and chromatin remodeling","description":"This cluster shows prominent chromatin modification signals (histone H4 acetylation and nucleosome mobilization) alongside neural-development terms ( retina homeostasis and substantia nigra development ), suggesting epigenetic regulation shaping neural differentiation. Additional cues from cytoskeleton dynamics and mitochondrial localization point to neuronal morphology and energy-demanding processes but do not override the central neural-chromatin theme. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":4},{"id":"GO:0042766","count":4},{"id":"GO:0001895","count":4},{"id":"GO:0043982","count":4},{"id":"GO:0021762","count":4}]},{"hash":"1124595219727204682","title":"Cytokine signaling and hematopoiesis","description":"The top GO terms cluster around immune signaling and cytokine production (interferon-alpha response; IL-2/TH2/IL-4 related cytokines) and hematopoietic differentiation (megakaryocytes), suggesting a function in immune regulation and blood cell development. Some developmental terms appear, but the cytokine/immune themes are most prominent. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061085","count":1},{"id":"GO:2000703","count":1},{"id":"GO:0035457","count":1},{"id":"GO:2000219","count":1},{"id":"GO:0032703","count":1}]},{"hash":"1800463028140471898","title":"Rab-regulated endocytosis and vesicle recycling","description":"The terms cluster around vesicle trafficking and endocytosis, especially endocytic recycling and synaptic vesicle endocytosis, with a focus on Rab GTPase regulation and Rab signaling. This suggests a core theme of Rab-mediated vesicle cycling and membrane trafficking, with a few peripheral terms (insulin response, basal localization, some noise) that do not redefine the main function.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0090305","count":2},{"id":"GO:0003335","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0048488","count":1}]},{"hash":"1477611208514459705","title":"ER protein folding and quality control","description":"The GO terms point to endoplasmic reticulum\u2013associated processes, notably protein folding in the ER, post-translational targeting and translocation to membranes, and ERAD-related maturation. The presence of heat-response and chaperone-related terms supports a role for ER chaperones in folding and preventing aggregation, consistent with ER quality control and maturation of secretory proteins. Despite some obsolete terms, the core pattern is ER folding/quality control.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090084","count":1},{"id":"GO:0030433","count":1},{"id":"GO:0051259","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0009408","count":1}]},{"hash":"677847514859693978","title":"Ubiquitin-Mediated Transcription and Signaling Regulation","description":"The top GO terms are dominated by ubiquitin-related processes (protein autoubiquitination; ubiquitin-dependent proteolysis) and regulation of transcription, along with signaling pathways (JNK cascade, TNF signaling, TLR signaling) and anti-apoptotic and cell cycle regulation. This points to a cluster of proteins involved in ubiquitin-dependent control of transcription and inflammatory/survival signaling rather than a single pathway, justifying a label centered on ubiquitin-mediated regulation of transcription and signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0000122","count":2},{"id":"GO:1903762","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0071157","count":2}]},{"hash":"877546379751940295","title":"Autophagy and Endocytic Trafficking Regulators","description":"These proteins show enrichment in GO terms tied to autophagy/vacuolar targeting (protein targeting to vacuole involved in autophagy), receptor-mediated endocytosis, and ubiquitin-dependent MVB sorting, pointing to a shared role in vesicle trafficking and protein turnover. Some transcriptional or developmental terms may be incidental, but the vesicle trafficking theme is strongest.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0071211","count":2},{"id":"GO:0035441","count":2},{"id":"GO:0072307","count":2}]},{"hash":"1655441350491859708","title":"Sodium/Potassium Ion Transport and Homeostasis","description":"The cluster shows strong enrichment for ion transport terms across the plasma membrane, especially sodium and potassium export/import and proton translocation, along with cell volume homeostasis and salt-stress response. These collectively point to a shared function in maintaining ionic gradients and cellular osmotic balance. Some other terms (BDNF signaling or cardiac conduction) are less central to this core theme but may reflect broader contextual roles. Overall, ion transport and membrane homeostasis best explain the group.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031547","count":2},{"id":"GO:0086092","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0051595","count":2},{"id":"GO:0006884","count":2}]},{"hash":"1913328736375591486","title":"DNA Repair and Chromatin Regulation","description":"The strongest signals are DNA maintenance-related: UV-damage excision repair, single strand break repair, and DNA strand elongation in replication, with supporting roles from K6-linked ubiquitination and PAR-mediated ATP generation that couple DNA damage signaling to chromatin remodeling. Some terms (neuron differentiation, chorion development, cytokinesis) are less representative and likely incidental. Overall, the cluster centers on DNA repair processes and chromatin regulation.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0085020","count":1},{"id":"GO:2001170","count":1},{"id":"GO:0070914","count":1},{"id":"GO:0045666","count":1},{"id":"GO:0000910","count":1}]},{"hash":"838206433553913766","title":"RNA processing and translation regulation","description":"These proteins are linked to RNA processing and control of translation, with terms for spliceosome assembly and catalytic steps, ribosomal subunit biogenesis, and positive regulation of translation. While a few terms touch on other processes, the strongest signal is post-transcriptional gene expression through splicing and translation control. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1990416","count":1},{"id":"GO:0009268","count":1},{"id":"GO:0045727","count":1},{"id":"GO:0000244","count":1}]},{"hash":"2258938100337535059","title":"Proteolysis and peptide maturation","description":"This cluster shows enrichment for proteolysis and peptide-processing activities, including digestion, membrane proteolysis, angiotensin maturation, APP biosynthesis regulation, and antigen processing for MHC II. These terms suggest a common theme around generating or remodeling peptides for functional outcomes, with some related lipid biosynthesis terms as ancillary processes.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007586","count":1},{"id":"GO:0042985","count":1},{"id":"GO:0002803","count":1},{"id":"GO:0002003","count":1},{"id":"GO:0071268","count":1}]},{"hash":"1572342017895109987","title":"NO/cGMP signaling and nitrosative stress","description":"This cluster\u2019s top GO terms cluster around nitric oxide-related signaling and nitrosative stress: cellular response to nitrosative stress; peptidyl-cysteine S-nitrosylation; positive regulation of guanylate cyclase activity (NO/cGMP pathway); hydrogen sulfide biosynthesis; nitrate catabolic process; and related redox/modification processes. Collectively these terms point to gasotransmitter biology and redox signaling as the unifying theme for these proteins.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031284","count":4},{"id":"GO:0071500","count":4},{"id":"GO:0043602","count":4},{"id":"GO:0018119","count":4},{"id":"GO:0070814","count":4}]},{"hash":"1339792805981451604","title":"Amino acid transport across plasma membrane","description":"The proteins cluster around transmembrane transport, especially amino acid movement across the plasma membrane (methionine, D-serine, D-alanine, leucine) and related ion/cosubstrate transport (calcium, carnitine). There is a single outlier term on photosynthesis, which is likely incidental noise; the dominant pattern is amino acid and ion transport across membranes.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019684","count":1},{"id":"GO:0006810","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0032973","count":1},{"id":"GO:1990034","count":1}]},{"hash":"912335257112890751","title":"IGF signaling and cytoskeletal regulation","description":"These four proteins show enrichment for IGF receptor signaling and for processes that govern cytoskeletal dynamics and cell adhesion (activation of GTPase activity, regulation of integrin activation, and regulation of filopodium assembly), with additional hints of developmental contexts like hemopoiesis and myelination. The cluster likely centers on growth-factor\u2013driven signaling that modulates the cytoskeleton and adhesion, rather than a single narrowly defined pathway.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":2},{"id":"GO:0048009","count":2},{"id":"GO:0033623","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0060709","count":2}]},{"hash":"677570874969056433","title":"Golgi\u2013ER Vesicle Trafficking","description":"The cluster\u2019s terms cluster around Golgi localization, ER-to-Golgi transport, Golgi-to-vacuole transport, Golgi inheritance, and vesicle trafficking including synaptic vesicle budding/transport. This points to a cohesive theme of the secretory pathway and vesicle movement through the Golgi/ER, with some neuronal-process terms likely reflecting tissue context. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021691","count":1},{"id":"GO:1901998","count":1},{"id":"GO:0006896","count":1},{"id":"GO:0048313","count":1},{"id":"GO:0008344","count":1}]},{"hash":"991466444479589847","title":"Amino acid and polyamine metabolism with acetylation","description":"The top GO terms point to biosynthesis and catabolism of amino acids (arginine, glucosamine) and polyamines (putrescine, spermine), as well as various acetylation-related modifications (N-terminal acetylation, propionylation, acetylation of metabolites). While one term about leaf formation and some obsolete terms appear, the dominant theme across the cluster is metabolic processing of amino acids and polyamines along with protein/peptide or metabolite acetylation, supporting this label.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019491","count":2},{"id":"GO:0060358","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0046208","count":2},{"id":"GO:0006041","count":2}]},{"hash":"135794027992451378","title":"Translation Initiation and Reinitiation","description":"The top GO terms are dominated by translation-related processes: formation of the translation preinitiation complex and translation reinitiation, suggesting the proteins cluster around initiating or reusing ribosomes for protein synthesis. Other terms (transcription start site regulation, mRNA splicing, chromatin-related processes) are present but far less represented, so the core theme is translation initiation. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001825","count":1},{"id":"GO:0001178","count":1},{"id":"GO:0060211","count":1}]},{"hash":"1328412382718071445","title":"Neural development and myelination","description":"The top GO terms cluster around nervous system development, optic nerve morphogenesis, substantia nigra development, myelination, and paranode axon localization, indicating a core theme of neural development and axonal maturation. A few immune-related terms appear but do not override the dominant neural focus.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904238","count":1},{"id":"GO:0021631","count":1},{"id":"GO:0042552","count":1},{"id":"GO:0021762","count":1},{"id":"GO:0007399","count":1}]},{"hash":"2038852916015752650","title":"Ubiquitin-driven immune signaling and apoptosis","description":"The terms are dominated by ubiquitination-related processes (protein ubiquitination, ubiquitin-dependent protein catabolic process, autoubiquitination, K6-linked ubiquitination) alongside immune signaling activities (adaptive immune response, RIG-I signaling regulation, NF-kappaB activation) and apoptosis regulation. This points to a cluster of proteins involved in tagging substrates with ubiquitin to regulate innate immune pathways and cell fate, with a possible secondary link to histone modification. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0036205","count":1},{"id":"GO:0002250","count":1},{"id":"GO:0039536","count":1}]},{"hash":"671853321552013054","title":"LPS and glycan biosynthesis","description":"The top GO terms cluster around lipopolysaccharide biosynthesis (core region and O-antigen) and related sugar metabolism (galactose, GDP-mannose, ADP-L-glycero-beta-D-manno-heptose), suggesting a cohesive function in producing bacterial cell envelope glycans and glycan precursors. Some terms appear plant-associated or obsolete, but the dominant pattern supports a label focused on LPS/glycan biosynthesis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0009699","count":2},{"id":"GO:0009244","count":2},{"id":"GO:0009243","count":2}]},{"hash":"1911021406236627719","title":"Plant metabolism and vascular development","description":"The top GO terms point to core metabolic processes (oxaloacetate metabolism; alanine/tyrosine biosynthesis; lipid-related processes) combined with plant-specific developmental signals (ethylene response and phloem/xylem histogenesis). Although several terms are obsolete, the combination suggests proteins involved in fundamental plant metabolism with roles in vascular tissue development. Overall, a concise label focusing on plant metabolism intertwined with vascular development fits best.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006107","count":2},{"id":"GO:0019550","count":1},{"id":"GO:0009723","count":1},{"id":"GO:0015908","count":1},{"id":"GO:0033585","count":1}]},{"hash":"129624429343895054","title":"Endosome-to-Golgi Vesicle Transport","description":"Endosome-to-Golgi and recycling endosome-to-Golgi transport terms dominate the cluster, plus general intracellular vesicle transport and regulation of vesicle fusion. The inclusion of GTPase activation aligns with Rab-family regulators driving vesicle trafficking, supporting a cohesive vesicle transport module.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":1},{"id":"GO:0048227","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0034499","count":1},{"id":"GO:0045737","count":1}]},{"hash":"2304063467691029759","title":"Sphingolipid biosynthesis and lipid signaling","description":"This cluster is dominated by terms tied to lipid metabolism and membrane biology: sphingolipid metabolic process, phosphatidylserine metabolic process, L-serine transport, and serine palmitoyltransferase activity (a key enzyme in sphingolipid biosynthesis). Myelination and ER stress\u2013induced apoptotic signaling further point to lipid-based membrane dynamics and related stress responses. Immune terms like defense response to oomycetes and detection of virus are less specific but may reflect membrane/lipid-signaling cross-talk rather than a single immune module.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034635","count":1},{"id":"GO:0002229","count":1},{"id":"GO:1904219","count":1},{"id":"GO:1902237","count":1},{"id":"GO:0042552","count":1}]},{"hash":"135092646165497882","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051259","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0009408","count":3}]},{"hash":"1822681122965228448","title":"Unknown","description":"No shared GO terms or functional signals are provided to tie these proteins together. The cluster has minimal connectivity (1 edge, 0 triangles) and no enriched terms, so a clear common function cannot be inferred; label is Unknown.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[]},{"hash":"938761909434281229","title":"NFAT calcium-calcineurin signaling regulators","description":"The top GO terms center on the calcineurin-NFAT signaling cascade and its regulation, indicating a shared role in calcium-dependent transcriptional signaling. While other terms touch on development and adhesion, the clearest common theme is NFAT/calcineurin pathway regulation, suggesting regulators of this signaling axis as the core function of the cluster.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0036496","count":3},{"id":"GO:0051343","count":3},{"id":"GO:0033173","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0051531","count":3}]},{"hash":"671810876918579489","title":"Cytoskeletal dynamics and neuronal synapse organization","description":"The GO terms converge on microtubule-based transport, centrosome dynamics, integrin regulation, and synapse organization, alongside signals related to neural structure and cell fate. This points to a cohesive theme of cytoskeletal remodeling and cell adhesion driving neural connectivity and remodeling, even though some terms span broader cellular processes. Therefore, a label emphasizing cytoskeletal dynamics shaping neural architecture and synapses seems representative.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":2},{"id":"GO:0021693","count":2},{"id":"GO:0033624","count":2},{"id":"GO:0021685","count":2},{"id":"GO:0007100","count":2}]},{"hash":"1986873232594187291","title":"Glycolysis and Pyruvate Metabolism","description":"The top GO terms center on glycolysis, gluconeogenesis, and pyruvate metabolism, with supporting roles for phosphorylation and carbohydrate-related transport, pointing to a central carbon metabolism theme. A few outlier terms related to autophagy or development appear only once and do not redefine the cluster's main function.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0006094","count":1},{"id":"GO:0006090","count":1},{"id":"GO:0009401","count":1}]},{"hash":"1647883326616269729","title":"Diverse Biosynthesis and Methylation Enzymes","description":"The GO terms point to a mix of biosynthetic and modification processes (antibiotic and nonribosomal peptide biosynthesis, lignin and cobalamin biosynthesis, as well as methylation and protein methylation). There isn\u2019t a single cohesive pathway tying all terms together, suggesting these proteins are involved in varied biosynthetic/metabolic roles rather than one specific function. Therefore this label captures the overarching theme without overclaiming a precise pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":1},{"id":"GO:0043041","count":1},{"id":"GO:0009809","count":1},{"id":"GO:0043642","count":1},{"id":"GO:0042135","count":1}]},{"hash":"21213114885399348","title":"Mitotic spindle assembly and centromere chromatin assembly","description":"The top GO terms are dominated by mitosis-related processes, notably mitotic spindle assembly and establishment of spindle orientation, along with CENP-A containing chromatin assembly, pointing to roles in chromosome segregation and centromere chromatin organization. Other terms are present but do not outweigh the core theme of cell division and chromatin assembly.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0031954","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0007568","count":1}]},{"hash":"1790689559177997042","title":"Plant meristem development and signaling","description":"The cluster centers on plant growth and meristem-related processes, highlighted by GO terms such as leaf development, root meristem growth, and meristem structural organization, along with phosphorylation/dephosphorylation indicating signaling activity. This suggests proteins involved in regulating plant growth via signaling pathways and meristem formation, despite some peripheral terms like DNA repair or tRNA modification being present.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0097056","count":1},{"id":"GO:0048366","count":1}]},{"hash":"866662667084993746","title":"Aminoacyl-tRNA Synthetases in Translation Signaling","description":"The cluster is dominated by GO terms for valyl-, leucyl-, methionyl-, and isoleucyl-tRNA aminoacylation and translation, pointing to a core set of aminoacyl-tRNA synthetases driving protein synthesis. The additional terms for positive regulation of angiogenesis, MAPK cascade, endothelial cell proliferation, and PI3K/AKT signaling reflect known noncanonical roles of tRNA synthetases in signaling pathways that influence angiogenesis and cell proliferation, suggesting these proteins participate in translation-related functions with signaling outputs. Overall, this cluster centers on aminoacyl-tRNA synthetases with translational roles and allied signaling activities.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006438","count":1},{"id":"GO:0006429","count":1},{"id":"GO:0006431","count":1},{"id":"GO:0006428","count":1},{"id":"GO:0006450","count":1}]},{"hash":"647437428669344262","title":"Ubiquitin-mediated innate immune signaling and apoptosis","description":"The GO terms converge on ubiquitination processes (protein ubiquitination, autoubiquitination, K6-linked ubiquitination) alongside immune signaling regulation (adaptive immune response, negative regulation of RIG-I signaling, NF-kappaB activation) and apoptosis control, with some antiviral transport regulation. This suggests a functional module where ubiquitin networks modulate innate immune responses and cell fate decisions, rather than a single physical complex, making a coherent, albeit sparse, immune-apoptosis regulatory cluster.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0002250","count":1},{"id":"GO:0039536","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0042981","count":1}]},{"hash":"589661810422985588","title":"Transmembrane transporters for vitamins and xenobiotics","description":"The terms are dominated by various transmembrane transport processes: vitamin and thiamine transport, xenobiotic transport, lipoprotein transport, and fatty acid import into peroxisomes, pointing to a coherent theme of membrane transport of diverse metabolites.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0042891","count":2},{"id":"GO:0042953","count":2},{"id":"GO:0015888","count":2}]},{"hash":"1925748076041478921","title":"Embryonic Mesodermal Differentiation and Erythropoiesis","description":"This cluster is driven by GO terms tied to embryonic development, including blastocyst formation, mesodermal differentiation, somite axis specification, third ventricle development, and erythrocyte development. Together they point to early lineage specification and mesoderm- and hematopoietic-related processes. Some terms are obsolete or vary in specificity, suggesting annotation noise, but the core theme remains embryogenesis and mesodermal differentiation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001825","count":1},{"id":"GO:0048821","count":1},{"id":"GO:2000864","count":1},{"id":"GO:0048333","count":1},{"id":"GO:0036138","count":1}]},{"hash":"1926385508451588211","title":"Unknown","description":"The terms point to a variety of biosynthetic processes\u2014from bacterial lipid and quinone pathways to plant phenylpropanoids and animal bile acids\u2014plus bioluminescence and seed germination, with several obsolete GO terms. This diversity suggests no single shared function to bind the cluster, so the label Unknown is appropriate.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902987","count":1},{"id":"GO:0008218","count":1},{"id":"GO:0019427","count":1},{"id":"GO:0001676","count":1},{"id":"GO:0070395","count":1}]},{"hash":"15081265481671087","title":"Golgi-ER-Endosome vesicle trafficking","description":"The top GO terms point to vesicle transport within the secretory/endomembrane pathway, including targeting to vacuole, ER-Golgi transport in both directions, and endocytosis, plus retrograde trafficking between endosomes and Golgi. This suggests the cluster comprises proteins involved in intracellular vesicle trafficking rather than other cellular processes; a few terms (chromatin assembly, spine morphogenesis) appear less related and may reflect annotation noise. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0006897","count":2},{"id":"GO:0061641","count":1}]},{"hash":"1256329346757650523","title":"Vacuolar amino acid transport","description":"The top GO terms are all linked to transport of various amino acids across the vacuolar membrane (e.g., L-glutamate, L-arginine, histidine, lysine, alanine, tyrosine, glutamine), including both import into and export from the vacuole, indicating a cohesive function as vacuolar amino acid transporters.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901481","count":1},{"id":"GO:0006867","count":1},{"id":"GO:1990818","count":1},{"id":"GO:0090515","count":1},{"id":"GO:0090513","count":1}]},{"hash":"1087916517796023837","title":"Unknown","description":"The top terms span mitochondrial complex IV assembly, ephrin receptor signaling, ER stress-induced apoptotic signaling, retinoic acid response, integrin signaling, thymus development, and IL-2 production, among others. These terms cover mitochondrial function, multiple signaling pathways, development, and immune-related processes with little clear overlap, suggesting no single cohesive function for the cluster. Therefore, Unknown with no clear representative theme.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":1},{"id":"GO:0048013","count":1},{"id":"GO:1904703","count":1},{"id":"GO:1902237","count":1},{"id":"GO:0071300","count":1}]},{"hash":"2012369805303548381","title":"Mitochondrial aminoacyl-tRNA synthetases","description":"These proteins are annotated with multiple mitochondrial tRNA aminoacylation terms (aspartyl-, asparaginyl-, lysyl-, phenylalanyl-tRNA charging) and a general translation term, pointing to aShared role in the mitochondrial translation machinery. Despite a few unrelated terms, the dominant pattern is mitochondrial tRNA charging enzymes, supporting a cohesive functional cluster. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070146","count":3},{"id":"GO:0070145","count":3},{"id":"GO:0072581","count":3},{"id":"GO:0070154","count":3},{"id":"GO:0071915","count":3}]},{"hash":"1868176758818475843","title":"Muscle mitochondrial dynamics and distribution","description":"The top GO terms center on mitochondria\u2014fusion, inheritance, and intracellular distribution\u2014along with mitochondrial fragmentation in apoptosis and muscle-activity related processes, suggesting a cluster of proteins coordinating mitochondrial remodeling in muscle cells. While some endocytic terms appear, the dominant theme is mitochondrial dynamics, supporting a muscle-specific context.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901998","count":1},{"id":"GO:0008344","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0043653","count":1},{"id":"GO:0014873","count":1}]},{"hash":"63941122393921269","title":"Unknown","description":"The GO terms are highly diverse (phototaxis, digestion, APP biosynthesis regulation, synaptic depression, antibacterial peptide production, transport, angiotensin maturation, sensory perception of touch/pain, amphetamine response), with only single annotations and no interactions among the proteins. There is no cohesive theme or shared pathway linking them, so a meaningful, specific label cannot be assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042331","count":1},{"id":"GO:0007586","count":1},{"id":"GO:0042985","count":1},{"id":"GO:0060292","count":1},{"id":"GO:0002803","count":1}]},{"hash":"2219316290826318156","title":"Lipid A/LPS biosynthesis","description":"The top GO terms cluster around lipid A and lipopolysaccharide biosynthesis (Kdo2-lipid A biosynthetic process, lipid A biosynthetic process, lipopolysaccharide biosynthetic process), indicating these proteins are likely enzymes involved in constructing the LPS outer-m membrane component. Some immune-regulatory terms (T cell apoptotic processes, IL-10/IL-12 production) appear but likely reflect cross-annotation or host-interaction context rather than core cluster function. Overall, the dominant signal is LPS biosynthesis.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036104","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0009409","count":1},{"id":"GO:0070233","count":1}]},{"hash":"789531924344129790","title":"TLR7-IFN innate immune signaling","description":"The proteins appear linked to innate immune pathways, with GO terms for toll-like receptor 7 signaling, positive regulation of type II interferon production, detection of diacyl bacterial lipopeptide, and regulation of cytokine production, suggesting a coherent theme of innate immune sensing and cytokine responses. Some developmental terms are present but seem less central to the cluster\u2019s core function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034154","count":2},{"id":"GO:0045078","count":2},{"id":"GO:0042496","count":2},{"id":"GO:0042552","count":2},{"id":"GO:0050707","count":2}]}]