[{"hash":"1681713387952794136","title":"Spliceosome-driven mRNA processing and translation initiation","description":"The terms are dominated by mRNA splicing and regulation via the spliceosome (positive/negative regulation, alternative splicing, spliceosome-mediated processing) along with elements of translation initiation (formation of the preinitiation complex, IRES-dependent initiation) and stress-related mRNA stability/miRNA-mediated silencing, indicating a cluster specialized in RNA processing and early stages of translation control.","confidence":"High","size":29,"edges":293,"triangles":1532,"max_degree":28,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":24},{"id":"GO:0010610","count":22},{"id":"GO:0045292","count":22},{"id":"GO:0048026","count":21},{"id":"GO:0035278","count":21}]},{"hash":"2121109400633720441","title":"Glycine Cleavage and Fe-S Cluster Biogenesis","description":"The top GO terms cluster around glycine decarboxylation (glycine cleavage system), protein lipoylation (a cofactor modification required by the glycine cleavage complex), and iron-sulfur cluster assembly, suggesting a cohesive module for glycine metabolism that depends on Fe-S biogenesis and lipoylation. Translation is a broad housekeeping process that may reflect background activity or co-occurring expression, but the central theme is cofactor maturation and Fe-S\u2013dependent enzyme function.","confidence":"High","size":29,"edges":19,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0009249","count":2},{"id":"GO:0030091","count":2},{"id":"GO:0016226","count":2}]},{"hash":"141740967095148717","title":"Endocrine and reproductive organ development","description":"The cluster\u2019s GO terms cluster around development and differentiation of reproductive and endocrine tissues (male gonad development, uterus development, parathyroid gland development) and related organogenesis processes (ureteric bud formation, pancreatic islet differentiation) with hormonal responses (estrogen). While there are outliers related to immune signaling and neural specification, the predominant theme is organ development and endocrine regulation. ","confidence":"Medium","size":29,"edges":235,"triangles":996,"max_degree":27,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071353","count":7},{"id":"GO:0045064","count":7},{"id":"GO:0008584","count":6},{"id":"GO:0060065","count":6},{"id":"GO:0072107","count":5}]},{"hash":"688145427023818014","title":"RNA processing and ribosome biogenesis","description":"The cluster is enriched for mRNA splicing and spliceosome-associated terms, preribosome large subunit assembly and ribosomal biogenesis, and translation initiation/preinitiation complex formation, with supporting hints from stress granule localization and ncRNA-mediated silencing. This points to a cohesive theme around RNA metabolism and ribosome production, with translational control as a related facet. DNA replication terms appear peripheral to the main signal.","confidence":"High","size":29,"edges":208,"triangles":654,"max_degree":25,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:1902626","count":3},{"id":"GO:0000398","count":3},{"id":"GO:1903608","count":3}]},{"hash":"1841859255554682963","title":"Cell differentiation and signaling regulation","description":"The proteins cluster around processes that regulate differentiation (fat cell differentiation; thymus development) and key signaling pathways (calcineurin-NFAT, NF-kB), with accompanying roles in ubiquitination, cell cycle regulation, and vascular/immune responses, suggesting a broad theme of modulation of development and signaling rather than a single specific function.","confidence":"Medium","size":29,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":3},{"id":"GO:0051534","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0045737","count":3},{"id":"GO:0016567","count":3}]},{"hash":"1665938155203462235","title":"Innate Immunity and Cell Cycle Regulation","description":"The cluster shows strong signals for innate immune response and defense against virus, alongside mitotic cell cycle processes, ubiquitination (K11-linked), APC-dependent degradation, and transcription/chromatin modifications. This suggests proteins that intersect antiviral signaling with cell cycle and chromatin regulation, rather than a single narrowly defined function. ","confidence":"Medium","size":28,"edges":89,"triangles":90,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0070979","count":4},{"id":"GO:2001162","count":4}]},{"hash":"577241181727245968","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":367,"triangles":3014,"max_degree":27,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":7},{"id":"GO:0000480","count":7},{"id":"GO:0000472","count":7},{"id":"GO:0000447","count":7},{"id":"GO:0000462","count":6}]},{"hash":"795472269679356552","title":"Viral entry, fusion, and release processes","description":"The cluster shows multiple GO terms tied to virus\u2013host interactions: viral release from host cell, fusion of virus membrane with host plasma membrane, and symbiont entry into host, plus lipid droplet organization which can be co-opted by viruses. These together point to a coherent theme of viral lifecycle steps and host-entry mechanisms, making the label representative. ","confidence":"High","size":28,"edges":45,"triangles":41,"max_degree":11,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":6},{"id":"GO:0034389","count":5},{"id":"GO:0000413","count":5},{"id":"GO:0048453","count":4},{"id":"GO:0006278","count":4}]},{"hash":"1824034250349904298","title":"Innate immune transcriptional regulators","description":"This cluster is dominated by GO terms for DNA-templated transcription and innate immune processes (innate immune response; defense response to Gram-positive bacteria), pointing to transcriptional regulators that control immune gene expression. Additional terms related to cellular stress responses and development suggest pleiotropy, but the primary signal is transcriptional regulation of innate immunity.","confidence":"Medium","size":28,"edges":41,"triangles":11,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0032436","count":4},{"id":"GO:0071276","count":4}]},{"hash":"2247006448580278289","title":"Translation initiation and ubiquitin-mediated proteostasis in proliferating cells","description":"This cluster is enriched for translation initiation and reinitiation terms, plus ubiquitin-related degradation pathways (K48- and K11-linked ubiquitination, ERAD), and proliferation signals (cell division, cell population proliferation). The combination suggests coordinated control of protein synthesis and proteostasis during cell proliferation, with some transcriptional activity also present.","confidence":"Medium","size":28,"edges":148,"triangles":455,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0051301","count":4}]},{"hash":"972781154648626909","title":"Retroviral integration and latency","description":"The cluster is enriched with terms about DNA-templated transcription, DNA replication, and DNA recombination, but crucially includes explicit retroviral-related processes such as establishment of integrated proviral latency, viral penetration into the host nucleus, and symbiont entry, indicating a cohesion around retroviral genome integration and latency within the host, with some host RNAi regulation involvement.","confidence":"High","size":28,"edges":89,"triangles":79,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0075713","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1}]},{"hash":"2217096585474106604","title":"Estradiol-responsive transcription and differentiation","description":"The top GO terms point to estradiol response, transcriptional control, stem cell differentiation, and regulation of mitotic progression, implying a hormone-driven transcription program that governs differentiation and cell cycle decisions. Additional terms on adhesion regulation and lymphocyte proliferation support a broader proliferative/developmental context, but the central theme is hormone-responsive transcription linked to differentiation.","confidence":"Medium","size":28,"edges":15,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032355","count":4},{"id":"GO:0033629","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0048863","count":2},{"id":"GO:0030071","count":2}]},{"hash":"1496574252424058530","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":79,"triangles":113,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":3},{"id":"GO:0032049","count":2},{"id":"GO:0006120","count":2},{"id":"GO:0016311","count":1},{"id":"GO:0009244","count":1}]},{"hash":"370891824719527044","title":"Cytoskeleton dynamics and apoptotic signaling","description":"The top GO terms center on actin cytoskeleton reorganization, regulation of GTPase activity, and ephrin signaling, accompanied by apoptosis-related terms (intrinsic apoptotic signaling and execution phase). This suggests a coherent theme where cytoskeletal dynamics are tightly linked to signaling pathways that govern cell fate during development and growth, justifying a label focused on cytoskeleton dynamics and apoptotic signaling.","confidence":"Medium","size":28,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031532","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0070059","count":3},{"id":"GO:0048666","count":3},{"id":"GO:0032435","count":3}]},{"hash":"1342149277267102399","title":"Chromatin Remodeling and Transcription Regulation","description":"The top GO terms cluster around chromatin dynamics (histone acetylation, histone exchange, nucleosome mobilization, heterochromatin formation) and transcription initiation, with a tie to regulatory ncRNA\u2013mediated post-transcriptional silencing. Although a few terms touch development and signaling, the dominant theme is chromatin remodeling and transcriptional control, suggesting the proteins work together in gene expression regulation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":1},{"id":"GO:0006348","count":1},{"id":"GO:0007379","count":1},{"id":"GO:0016246","count":1},{"id":"GO:0043486","count":1}]},{"hash":"1598819853158962245","title":"Mitotic spindle and cell cycle regulation","description":"Top terms are dominated by mitosis and cell cycle processes (mitotic spindle assembly/orientation, mitotic cell cycle, centrosome maintenance, CDK activity). This indicates a cluster of proteins involved in division machinery and its regulation; other terms like actin remodeling and pinocytosis suggest cytoskeletal dynamics, with some broader signaling (Wnt, transcription) appearing less central.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045737","count":4},{"id":"GO:0031578","count":3},{"id":"GO:0060733","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0030042","count":2}]},{"hash":"1562202996825986195","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":375,"triangles":3199,"max_degree":27,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0042254","count":7},{"id":"GO:0000470","count":4},{"id":"GO:0000028","count":4},{"id":"GO:0000027","count":4}]},{"hash":"467830485846837863","title":"Developmental signaling and cytoskeletal regulation","description":"The cluster centers on signaling pathways (Rho and ARF regulation, GPCR signaling) and cytoskeletal dynamics (filopodium assembly), with links to morphogenesis in developing tissues (midbrain, heart). While some terms like sensory perception and hematopoiesis are broader, the dominant theme is developmental signaling guiding cell shape and organogenesis, justifying this label. ","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0007605","count":4},{"id":"GO:0007205","count":4},{"id":"GO:1904693","count":4},{"id":"GO:0051262","count":4}]},{"hash":"1260290083797686157","title":"GTPase-Driven Migration and Morphogenesis","description":"The cluster features GO terms tied to regulation of GTPase activity, cell migration (fibroblast migration, chemotaxis), and various forms of morphogenesis (endothelial, vagus nerve) along with signals like receptor tyrosine kinase pathways and sarcomere organization, all pointing to cytoskeletal remodeling and coordinated movement during tissue development. While some terms are less directly related (chromatin binding regulation, osteoblast proliferation), the dominant themes emphasize signaling that controls cytoskeleton dynamics and cell movement in morphogenetic contexts.","confidence":"Medium","size":28,"edges":4,"triangles":0,"max_degree":1,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0043087","count":9},{"id":"GO:0045214","count":7},{"id":"GO:0010763","count":7},{"id":"GO:0007169","count":7},{"id":"GO:0035563","count":7}]},{"hash":"1394774905710618509","title":"RNA processing and translational control","description":"The cluster shows strong enrichment for mRNA processing steps (polyadenylation, spliceosome-regulated splicing, preinitiation complex formation) and for translation initiation/translation control (IRES-dependent initiation, ncRNA-mediated silencing). This combination suggests proteins coordinating RNA maturation with translational regulation, plus miRNA/ncRNA pathways.","confidence":"High","size":28,"edges":62,"triangles":71,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:1901407","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0075522","count":2}]},{"hash":"454138783154639005","title":"RNA and Histone Methylation","description":"The top GO terms cluster around methylation: arginine methylation, RNA guanine-N7 methylation, mRNA capping, and histone methylation, pointing to methyltransferases involved in RNA maturation and chromatin modification, with some peripheral terms (antibiotic biosynthesis, metal response) not contradicting the core theme.","confidence":"High","size":28,"edges":302,"triangles":1874,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0046690","count":22},{"id":"GO:0019919","count":22},{"id":"GO:0043985","count":21},{"id":"GO:0016049","count":21},{"id":"GO:0009236","count":21}]},{"hash":"674031822755938820","title":"DNA-templated Transcription Regulation","description":"The top GO terms are centered on DNA-templated transcription and its regulation, suggesting the proteins in this cluster are primarily involved in transcription control. A couple of biosynthesis terms (antibiotic/phosphinothricin) appear but are minimal and do not outweigh the transcription-focused theme. The lack of network edges further implies a collection of transcription-related proteins rather than a single cohesive biosynthetic pathway.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0031342","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0017000","count":1},{"id":"GO:1901766","count":1}]},{"hash":"1876166252461214906","title":"Actin Cytoskeleton Dynamics in Immune and Neural Development","description":"The cluster centers on actin-related processes (actin cytoskeleton organization, actin filament-based movement, barbed-end capping, parallel filament bundle assembly) and intersects development themes across immune and neural lineages (megakaryocyte and oligodendrocyte development, myelination, brain-derived neurotrophic factor response, T cell antigen processing/presentation). This points to a shared function in regulating actin remodeling to support cell movement and differentiation in both immune and neural contexts, rather than a single, narrow pathway.  ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035855","count":1},{"id":"GO:0002625","count":1},{"id":"GO:0051016","count":1},{"id":"GO:0030048","count":1},{"id":"GO:0030046","count":1}]},{"hash":"1167896678811499735","title":"Cardiac development signaling and actin remodeling","description":"The top GO terms point to heart development and signaling (e.g., cellular response to peptide hormones, activation of GTPase activity) together with cytoskeletal processes (filopodium assembly, cell spreading) and transcriptional regulation, suggesting a cluster of proteins involved in cardiac morphogenesis and related actin remodeling pathways. The mix of signaling, cytoskeletal dynamics, and transcriptional control supports a cardiac development\u2013oriented theme rather than a single isolated function. Edges are absent, indicating potential indirect or context-specific associations in the dataset.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071375","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0033138","count":3}]},{"hash":"887315038769410366","title":"mRNA Localization and Axis Specification","description":"The GO terms cluster around localization of maternal mRNAs (bicoid/oskar) and pole plasm, axis specification in oocytes, and related polarized transport processes (vesicle transport, receptor localization), suggesting a common theme of intracellular mRNA localization and polarized transport guiding development and synaptic function across species.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:1902684","count":1},{"id":"GO:0045450","count":1},{"id":"GO:1903743","count":1},{"id":"GO:0030722","count":1}]},{"hash":"1162192911834981485","title":"Carbohydrate and lipid catabolism (includes chitin)","description":"The top GO terms are dominated by catabolic processes for lipids, carbohydrates, polysaccharides, and specifically chitin, suggesting a metabolic-catabolism theme. Some immune signaling and development terms are present but do not cohesively redefine the cluster, so the metabolism-focused label is most representative.","confidence":"Medium","size":28,"edges":30,"triangles":38,"max_degree":10,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0016042","count":3},{"id":"GO:0005975","count":3},{"id":"GO:0018990","count":3},{"id":"GO:0000272","count":3},{"id":"GO:0070741","count":3}]},{"hash":"2173233973685244295","title":"Bacterial cell wall remodeling","description":"The top GO terms are dominated by peptidoglycan catabolic process and cell wall organization, indicating a cohesive theme of bacterial cell wall metabolism. Other terms present appear sporadic and less represented, so the strong signal is cell wall turnover rather than unrelated processes.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009253","count":2},{"id":"GO:0016998","count":2},{"id":"GO:0071555","count":2},{"id":"GO:1903955","count":1},{"id":"GO:0010813","count":1}]},{"hash":"1484050318865370027","title":"Centromere/Kinetochore Assembly","description":"The top GO terms point to kinetochore assembly (and centromere complex assembly), indicating a group of proteins associated with chromosome segregation machinery. Although only a couple of terms are annotated, their specificity to centromere/kinetochore assembly suggests the cluster functions in the assembly or maintenance of the kinetochore.","confidence":"Medium","size":27,"edges":264,"triangles":1502,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0051382","count":1},{"id":"GO:0034508","count":1}]},{"hash":"1387967890856142711","title":"Ribosome Biogenesis and Translation","description":"Dominant GO terms center on maturation and assembly of ribosomal RNA and ribosomal subunits, as well as translation and RNA processing (RNA capping and transcription by Pol I/III). This indicates a cluster of proteins involved in ribosome biogenesis and translation. Mitochondrial electron transport terms are present but appear ancillary relative to the ribosome-related terms, possibly reflecting dual roles or annotation noise.","confidence":"High","size":27,"edges":217,"triangles":854,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0034553","count":3},{"id":"GO:0006120","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0000466","count":2}]},{"hash":"1193663204175247831","title":"Rho/Rac GTPase signaling and actin cytoskeleton regulation","description":"The cluster centers on regulation of Rho and Rac signaling and GTPase activity, with many terms tied to actin dynamics\u2014microvillus assembly, actin cytoskeleton reorganization, and processes like acrosome assembly and spermatid elongation that depend on actin structure. Additional terms about osteoclast differentiation and intracellular transport further support cytoskeletal remodeling themes, while an apoptotic signaling term appears as a less central outlier. Overall, the data point to coordinated regulation of cytoskeleton via Rho/Rac pathways. ","confidence":"High","size":27,"edges":17,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":4},{"id":"GO:0030033","count":3},{"id":"GO:0035021","count":3},{"id":"GO:0045671","count":3},{"id":"GO:0043547","count":3}]},{"hash":"536866217305260123","title":"Golgi-ER and endosome trafficking with signaling","description":"This cluster centers on vesicle trafficking across the secretory pathway: retrograde Golgi-to-ER transport, Golgi-to-plasma membrane transport, plasma membrane-to-endosome routing, and Golgi vesicle budding. It also includes proteins involved in major signaling pathways (T cell receptor, TNF, Wnt), suggesting regulatory functions that coordinate trafficking with signaling events. A minority of terms touch cell cycle processes (APC-dependent catabolic process), which might reflect shared regulatory roles. Overall, the common theme is membrane trafficking with concurrent signaling regulation, making this label representative.","confidence":"Medium","size":27,"edges":64,"triangles":32,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006890","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0090263","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0048227","count":3}]},{"hash":"928881652883320563","title":"GTPase-driven signaling, endosomal transport, and proteostasis","description":"The terms point to regulation of small GTPases (GTPase activity, Rho signaling) and vesicle trafficking (early to late endosome transport), with supportive signals for proteostasis (proteasome assembly, protein stabilization). Although there are some nuclear/chromatin and neuronal terms present, the strongest and most coherent theme is GTPase-mediated signaling linked to endosomal transport, with proteostasis as a complementary process.","confidence":"Medium","size":27,"edges":182,"triangles":522,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0007049","count":3},{"id":"GO:0043248","count":3},{"id":"GO:0050821","count":3},{"id":"GO:0046294","count":3}]},{"hash":"1916663571011427932","title":"Polyamine Biosynthesis and Transport","description":"This cluster is dominated by GO terms related to polyamine metabolism, including putrescine biosynthesis from arginine via ornithine, spermidine biosynthesis, nor-spermidine biosynthesis, and L-arginine catabolic process, as well as positive regulation of polyamine transmembrane transport. These collectively point to a coherent polyamine production and transport module; other terms like cell wall organization or trans-Golgi network organization may reflect broader growth-related processes but do not override the core polyamine theme.","confidence":"High","size":27,"edges":47,"triangles":27,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0071555","count":4},{"id":"GO:0098629","count":3},{"id":"GO:0001822","count":3},{"id":"GO:0033387","count":3}]},{"hash":"1005623868802937598","title":"Developmental growth signaling and differentiation","description":"The top GO terms cluster around growth-related signaling pathways (cyclic nucleotide biosynthesis, PI3K/AKT, insulin receptor signaling, GPCR desensitization) and development/differentiation processes (heart development, placental glycogen cell differentiation, hemopoiesis, IL-7 response). This suggests a cohesive theme of coordinating growth signaling with proliferative capacity and tissue differentiation across multiple lineages. Therefore, this label captures the shared functional theme of the cluster.","confidence":"Medium","size":27,"edges":28,"triangles":19,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009190","count":24},{"id":"GO:0006260","count":23},{"id":"GO:0043491","count":23},{"id":"GO:0060709","count":23},{"id":"GO:0018107","count":23}]},{"hash":"1654490848341837241","title":"Neuronal actin remodeling and synaptic vesicle regulation","description":"The top GO terms cluster around actin cytoskeleton dynamics\u2014positive regulation of stress fiber assembly, actin filament polymerization, and formin-nucleated actin assembly\u2014along with regulation of synaptic vesicle exocytosis. Brain development terms (hippocampus and substantia nigra) further support a neuronal context, though there are additional non-neuronal associations (keratinocyte development, endothelin signaling). This combination points to actin-mediated remodeling linked to presynaptic vesicle trafficking in neurons as the core theme.","confidence":"Medium","size":27,"edges":121,"triangles":293,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051496","count":18},{"id":"GO:0030838","count":18},{"id":"GO:2000300","count":18},{"id":"GO:0090338","count":18},{"id":"GO:0003100","count":15}]},{"hash":"1097424957451371638","title":"Neuronal cytoskeleton and synaptic morphogenesis","description":"This cluster is dominated by terms related to cytoskeletal organization and signaling (actin cortical patch assembly, sarcomere organization, Rho protein signal transduction, regulation of dendritic spine morphogenesis), pointing to actin dynamics driving neuronal development and synapse formation. The presence of brain-region development terms (hippocampus and substantia nigra) suggests brain-specific roles, while transport and cell size regulation add supporting context for cellular remodeling and trafficking in neurons. Overall, a cohesive theme around cytoskeletal control and neuronal connectivity.","confidence":"Medium","size":27,"edges":127,"triangles":278,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000147","count":7},{"id":"GO:0045214","count":6},{"id":"GO:0021766","count":6},{"id":"GO:0007266","count":5},{"id":"GO:0021762","count":5}]},{"hash":"902599608397381223","title":"Unknown","description":"The cluster shows a heterogeneous set of GO terms, including cellulose catabolic process, flocculation, protein homooligomerization, programmed necrotic cell death, endothelial barrier regulation, and even several obsolete or immune-related terms. There isn\u2019t a single cohesive function or theme linking these terms, making it inappropriate to assign a specific, representative label.","confidence":"","size":27,"edges":17,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0044533","count":4},{"id":"GO:0030245","count":4},{"id":"GO:0000501","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0035897","count":4}]},{"hash":"1808330730581721642","title":"Cell Cycle Regulation and Transcription","description":"The dominant GO terms cluster around DNA-templated transcription and cell cycle transitions (G1/S, G2/M) plus chromosomal condensation markers, indicating proteins that coordinate transcriptional programs with cell division. Developmental terms like cerebral cortex and sperm capacitation may reflect broader regulatory roles, but the shared theme appears to be cell cycle\u2013linked transcriptional control during growth or development.","confidence":"High","size":27,"edges":15,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0048240","count":4},{"id":"GO:0021987","count":4},{"id":"GO:0045793","count":4},{"id":"GO:0043433","count":3}]},{"hash":"2277683557806726243","title":"Dictyostelium sorocarp aggregation","description":"Top GO term indicates aggregation involved in sorocarp development, a hallmark of Dictyostelium social development. The other signals reflect developmental regulation and basic metabolism, but the strongest and most specific clue is sorocarp aggregation, suggesting the cluster centers on Dictyostelium-like developmental processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031152","count":3},{"id":"GO:1903669","count":3},{"id":"GO:1903665","count":3},{"id":"GO:0099132","count":1},{"id":"GO:0015986","count":1}]},{"hash":"95048678873389330","title":"Neural development and chromatin regulation","description":"The top terms point to neural development (cerebral cortex development, neuron projection extension, stem cell proliferation) coupled with chromatin/epigenetic regulation (histone methylation regulation, chromatin binding). Despite some obsolete entries, the prevailing theme is neural differentiation controlled by chromatin state, with supporting metabolism-related terms like guanine metabolism. ","confidence":"Medium","size":27,"edges":60,"triangles":55,"max_degree":12,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0043046","count":21},{"id":"GO:0051573","count":21},{"id":"GO:0046098","count":20},{"id":"GO:0035563","count":20},{"id":"GO:0045648","count":20}]},{"hash":"1309509738221295449","title":"Neural, cardiac, and vascular development signaling","description":"The top GO terms cluster around heart development, Schwann cell development, and angiogenesis, complemented by neural activity and synaptic plasticity terms (long-term potentiation and excitatory postsynaptic potential) and signaling processes. This points to a module involved in the development and signaling of nervous and cardiovascular tissues, with activity-dependent regulation. Some annotations (e.g., abscisic acid-activated signaling) may be cross-species noise, but the dominant theme is neural and cardiovascular development and signaling.","confidence":"Medium","size":27,"edges":17,"triangles":7,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010800","count":5},{"id":"GO:0007507","count":5},{"id":"GO:0014044","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0001525","count":4}]},{"hash":"522367279763696434","title":"Antiviral innate immunity and chromatin regulation","description":"The dominant GO terms point to antiviral innate immune responses (innate immune response, defense response to virus, RIG-I signaling) indicating a link to antiviral sensing and signaling. The presence of PML body organization, histone H2A ubiquitination, and ubiquitin-dependent protein catabolic process regulation suggests involvement of chromatin remodeling and ubiquitin-mediated regulation in these immune processes. Some terms like myelination and vitamin D receptor signaling are less central but can relate to broader immune or nuclear functions, so the overall theme centers on antiviral signaling intertwined with chromatin/ubiquitin regulation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0042552","count":2},{"id":"GO:1900246","count":2},{"id":"GO:2000059","count":2}]},{"hash":"760824468091676742","title":"PNS Signaling and Membrane Remodeling","description":"The terms converge on peripheral nervous system function\u2014myelin maintenance and sensory perception of sound\u2014along with G protein-coupled receptor signaling (notably acetylcholine signaling) and membrane/cytoskeletal dynamics (filopodium assembly, membrane tubulation, and cell spreading). This combination points to a module of neural signaling coupled with membrane remodeling in PNS contexts, such as hair cells or neurons. A few terms (e.g., hemopoiesis) are less related and present at low counts, but do not obscure the dominant theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032287","count":2},{"id":"GO:0007605","count":2},{"id":"GO:0071493","count":2},{"id":"GO:0007213","count":1},{"id":"GO:0032012","count":1}]},{"hash":"390294792034918429","title":"Serotonin metabolism and neural development","description":"The cluster centers on serotonin/tryptophan metabolism (L-tryptophan catabolic process; negative regulation of serotonin secretion) and neural development (substantia nigra development; multicellular organism development), suggesting a neural context for serotonin signaling. Additional terms indicate xenobiotic/toxin and immune-related responses (response to toxic substance; response to xenobiotic stimulus; lipopolysaccharide), implying the genes may also participate in stress-related modulation of neural function. ","confidence":"Medium","size":27,"edges":12,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":5},{"id":"GO:0009636","count":5},{"id":"GO:0042493","count":5},{"id":"GO:0014063","count":4},{"id":"GO:0010269","count":4}]},{"hash":"1523949061473403787","title":"Unknown","description":"The terms point to various tissue-specific development and morphogenesis processes (muscle, nerve, retina, kidney) plus signaling and regulatory processes, with no single shared function. Because the cluster spans multiple lineages rather than a focused pathway, a concise, intuitive label is not evident.","confidence":"","size":27,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0048741","count":13},{"id":"GO:0008360","count":13},{"id":"GO:0035502","count":12},{"id":"GO:0033234","count":12},{"id":"GO:0036444","count":12}]},{"hash":"2179259222442489171","title":"Unknown","description":"The Top Terms span very diverse processes (cellulose and oligosaccharide catabolism, necroptosis, cholesterol metabolism, learning/memory, LPS signaling, innate immune response, hydrolase regulation, and neuromuscular balance), with no clear shared function or pathway linking the proteins. This makes it difficult to assign a specific, coherent label beyond Unknown.","confidence":"","size":27,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":8},{"id":"GO:0070266","count":1},{"id":"GO:0008203","count":1},{"id":"GO:0007611","count":1},{"id":"GO:0009313","count":1}]},{"hash":"696419234422913019","title":"DNA Damage Response and Transcription Regulation","description":"Chosen name reflects the strongest shared theme among the top GO terms: several entries relate to nuclear processes\u2014DNA double-strand break processing (repair), intra-S phase checkpoint signaling, and transcription termination via exosome. A few terms touch on calcium signaling, cell adhesion, and Schwann cell development, indicating broader cellular context, but the core cluster function appears to center on DNA damage response and transcriptional regulation.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051531","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0031573","count":1},{"id":"GO:0014044","count":1},{"id":"GO:1905205","count":1}]},{"hash":"1311418244032119198","title":"Transmembrane ion and small-molecule transporters","description":"The Top Terms cluster is dominated by transmembrane transport across ions (K+, Na+, phosphate) and various small molecules (arabinose, 4-hydroxyphenylacetate, sialic acid, vitamins), plus a neuronal role in neurotransmitter loading into synaptic vesicles. This pattern strongly suggests a group of membrane transporter proteins with diverse substrates, rather than enzymes or signaling molecules, so the label reflects the shared function of the cluster.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0035725","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0015739","count":3}]},{"hash":"1476101898900452843","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is heavily enriched for rRNA maturation (5.8S and LSU rRNA), ribosomal large subunit biogenesis, and mRNA splicing, all core activities in the nucleolus that assemble and process ribosomes and RNA. While there are a few DNA/metabolism terms present, the dominant signal points to nucleolar functions related to ribosome production and RNA processing.","confidence":"High","size":26,"edges":277,"triangles":1699,"max_degree":25,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0006289","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1871047032717336180","title":"Regulation of vesicle trafficking and signaling","description":"The top GO terms cluster around regulation of vesicle-related processes (synaptic vesicle exocytosis, intracellular transport, multivesicular body-related regulation) and broader signaling regulation (Rho signaling, vascular remodeling, extravasation, development, and even cross-species growth processes). This points to a shared theme of controlling vesicle trafficking and signal transduction across cell types and developmental contexts.","confidence":"Medium","size":26,"edges":114,"triangles":227,"max_degree":20,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:2000300","count":8},{"id":"GO:0035023","count":8},{"id":"GO:0043314","count":8},{"id":"GO:0009738","count":8},{"id":"GO:0060313","count":8}]},{"hash":"469479708861648201","title":"RNA methylation and ribosome biogenesis during cell cycle","description":"This cluster is enriched for RNA modification and ribosome biogenesis terms (rRNA methylation, RNA guanine-N7 methylation, ribosomal small subunit export), along with cell division processes (mitotic cell cycle, mitotic spindle assembly). The combination suggests a core theme around RNA processing and ribosome assembly coordinated with mitosis, with some incidental stress-response terms (xenobiotic stimulus, cocaine) paired with trafficking (endosome to lysosome transport). ","confidence":"High","size":26,"edges":118,"triangles":184,"max_degree":17,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035690","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0006972","count":4},{"id":"GO:0000056","count":4},{"id":"GO:0036265","count":4}]},{"hash":"1231556752164289371","title":"Epigenetic and Translational Regulation","description":"The enriched GO terms center on regulation of gene expression, including transcriptional control and translation, and are complemented by multiple methylation-related processes (peptidyl-glutamine methylation, arginine methylation, histone methylation). While a couple terms (cobalamin biosynthesis, larval lymph gland hemopoiesis) are less clearly connected, the dominant signal points to epigenetic regulation and control of protein synthesis.","confidence":"Medium","size":26,"edges":23,"triangles":4,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0035167","count":1}]},{"hash":"953328291511387403","title":"Vesicle trafficking and signaling regulation","description":"The top GO terms cluster around intracellular transport and vesicle dynamics (intracellular protein transport; ER to Golgi ceramide transport; synaptic vesicle priming; acrosome reaction), suggesting a core function in vesicle trafficking. Additional terms point to regulation of signaling pathways involving small GTPases (Rho and Ras) and related remodeling processes, which often coordinate vesicle movement and cellular responses. Together, these indicate a protein cluster focused on vesicle trafficking with linked regulatory signaling. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0046580","count":2},{"id":"GO:0060313","count":2}]},{"hash":"1311468697501125239","title":"Chromatin modification and transcription regulation","description":"The top GO terms point to histone modifications (H3-K36 methylation/trimethylation and H3-K9 acetylation regulation) and DNA-templated transcription elongation, with additional links to antisense RNA transcription regulation. Developmental and genome maintenance terms (vasculogenesis, placenta morphogenesis, DNA repair, apoptosis) are consistent with chromatin state influencing gene expression and genome integrity during development. Overall, these proteins seem to function in epigenetic regulation of transcription and related genome maintenance processes, hence the label.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097198","count":2},{"id":"GO:0097676","count":2},{"id":"GO:0006354","count":2},{"id":"GO:0035441","count":2},{"id":"GO:2000616","count":2}]},{"hash":"1725019752445964524","title":"G2/M cell cycle control and mitochondrial function","description":"The top GO terms are dominated by cell division and mitotic G2/M transition, indicating a core association with cell cycle regulation. Additional annotations point to mitochondrial electron transport and complex II assembly, as well as zinc ion transport, suggesting accompanying metabolic and metal homeostasis roles. Together these terms imply proteins that participate in cell cycle control with links to mitochondrial function and related metabolic processes, consistent with a cohesive though diverse cluster.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":1},{"id":"GO:0045792","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0032515","count":1},{"id":"GO:0000086","count":1}]},{"hash":"410970984385661844","title":"Ubiquitin-Mediated Protein Turnover and Aggresome Formation","description":"The top GO terms are dominated by ubiquitination-related processes: ubiquitin-dependent protein catabolic process, monoubiquitination/deubiquitination, and histone ubiquitination, plus aggresome assembly. This pattern points to a cluster whose proteins participate in protein quality control via the ubiquitin-proteasome system and related chromatin regulation, consistent with a cohesive functional theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010216","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0035520","count":1},{"id":"GO:0036353","count":1},{"id":"GO:0070842","count":1}]},{"hash":"337813195830137491","title":"RNA Methylation and Ribosome Biogenesis","description":"The GO terms point to RNA maturation and chemical modification, especially rRNA maturation (LSU and SSU), rRNA methylation (guanine-N7), and tRNA methylation, along with related peptidyl-glutamine methylation. This pattern indicates proteins involved in RNA processing that supports ribosome biogenesis and function; a few unrelated terms (telomerase assembly, kinase regulation) appear incidental but do not redefine the cluster\u2019s core theme.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000470","count":1},{"id":"GO:0018364","count":1},{"id":"GO:0030490","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0030488","count":1}]},{"hash":"971046117430733466","title":"Broad developmental differentiation","description":"This cluster is dominated by GO terms pointing to development across multiple tissues (spermatid development, facial nerve morphogenesis, erythrocyte differentiation, neuromuscular transmission), with supporting terms for cytoskeletal organization and transcriptional regulation, suggesting a broad, multi-lineage developmental theme. Some terms (cellular response to virus, A-to-I editing) are less obviously tied to development, so the overall cohesion is moderate.","confidence":"Medium","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007286","count":2},{"id":"GO:0030035","count":2},{"id":"GO:0034394","count":2},{"id":"GO:0048146","count":2},{"id":"GO:0045944","count":2}]},{"hash":"651428343221607589","title":"Unknown","description":"The GO terms span nervous system development, lipid metabolism, proteolysis, immune cell migration, cell adhesion, and host-symbiont interactions, with no dominant shared function or pathway. The lack of connections (edges/triangles) suggests the proteins are functionally diverse, so a single cohesive label is not apparent.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0022011","count":5},{"id":"GO:0061003","count":4},{"id":"GO:0010888","count":4},{"id":"GO:0097264","count":4},{"id":"GO:0061097","count":4}]},{"hash":"843126817711553254","title":"Embryonic neural and vascular morphogenesis","description":"Based on the top GO terms, this cluster centers on embryonic development with emphasis on neural crest/cranial nerve morphogenesis (branchiomotor axon guidance, vagus and facial nerve development) and endothelial/vasculature morphogenesis (endothelial morphogenesis, endothelial chemotaxis), plus limb bud formation, indicating a coordinated morphogenetic program in early development.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0007169","count":2},{"id":"GO:0033689","count":2},{"id":"GO:0021793","count":2},{"id":"GO:0050918","count":2}]},{"hash":"621077265646881065","title":"Neural Cytoskeleton Remodeling and Cell Cycle","description":"The cluster is dominated by GO terms tied to actin cytoskeleton dynamics (lamellipodium, filopodium, stress fiber assembly) and cell division/mitotic cell cycle, with additional neural development terms (hippocampus development, nervous system development). This suggests a shared functional theme where actin remodeling supports both mitosis and neural development processes, justifying a label that combines cytoskeletal dynamics with cell cycle and neural differentiation.","confidence":"High","size":25,"edges":140,"triangles":336,"max_degree":19,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":15},{"id":"GO:0000278","count":14},{"id":"GO:0051291","count":9},{"id":"GO:0010592","count":8},{"id":"GO:0033138","count":8}]},{"hash":"1053260729456721018","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":229,"triangles":1128,"max_degree":24,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000398","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0051301","count":8},{"id":"GO:0051260","count":7}]},{"hash":"1745427603598940814","title":"Plant lipid metabolism and signaling","description":"The term enrichment is dominated by lipid-related processes (lipid catabolic, phosphatidic acid and phosphatidylcholine biosynthesis, cardiolipin biosynthesis, inositol lipid signaling) and plant ABA-associated signaling (stomatal closure regulation), suggesting a cohesive cluster around lipid metabolism and ABA-mediated signaling in plants; a couple of non-lipid terms (DNA repair, P granule organization) may reflect multifunctional proteins or annotation noise.","confidence":"High","size":25,"edges":45,"triangles":31,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0016042","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0009789","count":1},{"id":"GO:0006654","count":1},{"id":"GO:0090333","count":1}]},{"hash":"1547539637237676281","title":"DNA replication, chromatin assembly, and transcription","description":"The cluster is enriched for DNA-templated transcription, DNA replication\u2013dependent chromatin assembly, DNA repair, and mRNA processing, indicating a core nuclear program of genome maintenance and gene expression; additional terms like GTPase regulation and tyrosine phosphorylation suggest accompanying signaling, while the defense term is less central.","confidence":"Medium","size":25,"edges":65,"triangles":60,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0008285","count":3},{"id":"GO:0006335","count":3},{"id":"GO:0018108","count":2},{"id":"GO:0035729","count":2}]},{"hash":"539977156053448530","title":"DNA transposition and proviral integration with actin remodeling","description":"This cluster combines GO terms for DNA transposition and DNA integration with those tied to cell cycle/division and chromosome segregation, and notably includes actin cytoskeleton processes (Arp2/3\u2013mediated nucleation and actin polymerization) as well as symbiont entry into host cells. The co-occurrence suggests a module where genome mobility events are linked to cytoskeletal dynamics and host interaction, hence a label that reflects both genome mobility/integration and cytoskeleton remodeling is appropriate.","confidence":"Medium","size":25,"edges":226,"triangles":1181,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0006313","count":2},{"id":"GO:0007049","count":2}]},{"hash":"327826427321170494","title":"Nucleotide metabolism and DNA replication","description":"The top GO terms dominate nucleotide metabolism: purine ribonucleotide interconversion, various nucleotide phosphorylation and biosynthesis processes (ADP, AMP, CDP; AMP salvage), and ITP metabolism, with an additional link to DNA replication initiation. The brain and liver development terms are likely tissue-specific annotations and not central to the cluster\u2019s primary function. Thus the proteins likely participate in nucleotide biosynthesis/utilization relevant to DNA replication, supporting a cohesive theme around nucleotide metabolism with a replication connection.","confidence":"Medium","size":25,"edges":25,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0015951","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0046939","count":2},{"id":"GO:0006172","count":2}]},{"hash":"96650964511368974","title":"Fatty acid biosynthesis and protein farnesylation in wound healing","description":"The cluster prominently features long-chain fatty acid biosynthesis and protein farnesylation, both lipid-modifying processes that can affect signaling, membrane dynamics, and enzyme localization. The inclusion of wound healing and fibroblast proliferation\u2013related terms, along with positive regulation of the cell cycle, suggests a link between lipid modification/metabolism and cell growth during tissue repair. A few isoprenoid/tuberculosinol\u2013related terms are present but do not override the main lipid/cell-proliferation theme.","confidence":"High","size":25,"edges":13,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042759","count":4},{"id":"GO:0018343","count":2},{"id":"GO:0051771","count":2},{"id":"GO:0045787","count":2},{"id":"GO:0051770","count":2}]},{"hash":"1793801924431520026","title":"Lamellipodium-Driven Motility and Polarity","description":"The cluster centers on actin-based motility and cell\u2013substrate interactions, as shown by lamellipodium assembly, cell migration, substrate adhesion\u2013dependent spreading, and establishment of epithelial polarity. Endothelial barrier organization and endocytosis further link motility with junctional dynamics and vesicular trafficking. Some terms (synaptic depression, insulin signaling) are broader, but the core theme ties to cytoskeletal rearrangements guiding movement and polarity.","confidence":"Medium","size":25,"edges":161,"triangles":480,"max_degree":24,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030032","count":7},{"id":"GO:0090162","count":6},{"id":"GO:1900026","count":6},{"id":"GO:0016477","count":6},{"id":"GO:1903753","count":6}]},{"hash":"790998440199333970","title":"ESCRT/MVB Trafficking and Viral Budding","description":"The top GO terms are dominated by ESCRT-mediated multivesicular body (MVB) formation, ubiquitin-dependent protein sorting to MVBs, and MVB-lysosome fusion, plus viral budding via the host ESCRT complex, indicating a cohesive module of ESCRT/MVB\u2013driven vesicle trafficking and degradation. Other terms such as ATP export and cell division\u2013related processes appear as ancillary connections but do not dominate the theme. This cluster most plausibly represents ESCRT/MVB\u2013based vesicle trafficking and protein turnover with involvement in viral budding.","confidence":"High","size":25,"edges":127,"triangles":276,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:1904669","count":3},{"id":"GO:0039702","count":3},{"id":"GO:0043162","count":3},{"id":"GO:0036258","count":3},{"id":"GO:1902188","count":3}]},{"hash":"546337325117460780","title":"Regulation of cytoskeleton dynamics and cell migration","description":"This cluster centers on regulation of Rho GTPase signaling and cytoskeletal processes (Rho signaling, GTPase activity, microspike assembly) along with membrane repair, and incorporates vascular/migration-related terms (negative regulation of extravasation and blood vessel remodeling). The common thread is regulation of cytoskeleton-driven cell movement and membrane integrity, linking immune cell trafficking and vascular dynamics.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0043314","count":5},{"id":"GO:0002692","count":5},{"id":"GO:0060313","count":5},{"id":"GO:0035023","count":4},{"id":"GO:0043087","count":4}]},{"hash":"1594472766346538538","title":"Organelle biogenesis and stress response","description":"The terms span ER-Golgi vesicle transport, mitochondrial inner membrane insertion and complex I assembly, microtubule severing, centriole elongation, heat acclimation, UV-damage repair, and oxidative protein catabolic processes. This mix suggests a broad theme of cellular maintenance of organelles and cytoskeletal structures, plus general stress-response and quality-control processes, rather than a single cohesive pathway. Therefore, a label centered on organelle biogenesis and stress response best captures the shared context, albeit with only weak, diverse connections. ","confidence":"Low","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0001319","count":1},{"id":"GO:0070914","count":1}]},{"hash":"1997430710295967031","title":"Chromatin Regulation and Transcription Control","description":"Top terms emphasize transcriptional regulation and chromatin organization (negative regulation of RNA Pol I transcription, heterochromatin formation, chromatin silencing), pointing to a nuclear regulatory theme. A few terms relate to cell differentiation and migration (skeletal muscle differentiation, megakaryocyte development, fibroblast migration), suggesting broader regulatory connections. The diverse, low-frequency terms and lack of strong co-occurrence imply a loosely connected cluster centered on chromatin/transcription control rather than a single pathway.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061188","count":1},{"id":"GO:0016479","count":1},{"id":"GO:0035914","count":1},{"id":"GO:0061408","count":1},{"id":"GO:0061186","count":1}]},{"hash":"2101076406708411006","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0043123","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0043420","count":1}]},{"hash":"2206720039914314259","title":"Cellular stress response and proteostasis","description":"The top GO terms point to a collection of stress-related processes: responses to various chemicals (curcumin, mercury, catechin), nucleotide-excision repair, ubiquitin-dependent protein turnover, selective autophagy (aggrephagy), ER-stress\u2013induced apoptosis, and broader signaling such as interferon pathways and miRNA-mediated silencing. Taken together, these terms suggest the proteins act in maintaining proteome integrity and coordinating cellular stress responses, rather than a single, narrow function. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904643","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0046689","count":1},{"id":"GO:1902168","count":1},{"id":"GO:0006289","count":1}]},{"hash":"2253274466445093262","title":"Nucleotide and Cofactor Catabolism","description":"The GO terms point to catabolic processes for nucleotides and cofactors (diadenosine derivatives, NAD+, CoA, folic acid) and RNA-related turnover (snoRNA) with RNA editing also present, suggesting the proteins are involved in breakdown and turnover of nucleotides and small-molecule cofactors. While there is some diversity, the common theme is catabolic metabolism of these molecules, supporting this label as representative without overstating a single precise pathway.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006382","count":1},{"id":"GO:0034656","count":1},{"id":"GO:0046057","count":1},{"id":"GO:1901909","count":1},{"id":"GO:0015938","count":1}]},{"hash":"1217222419436141512","title":"Wnt-regulated transcription and cell signaling","description":"The top GO terms point to DNA-templated transcription and the Wnt signaling pathway, suggesting a core link to transcriptional regulation driven by signaling. Additional terms indicate broader regulatory roles, including post-translational modification (ubiquitination, PARylation), responses to mechanical and heat stress, spindle assembly, and cell migration, which together imply these proteins participate in coordinating signaling with transcription, cell cycle progression, and cytoskeletal dynamics. ","confidence":"Medium","size":25,"edges":53,"triangles":31,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0016055","count":4},{"id":"GO:2001275","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0016567","count":3}]},{"hash":"977970836164797002","title":"Metal Ion Transport and Detoxification","description":"Proteins in this cluster are linked to transmembrane transport and homeostasis of metal ions (iron, zinc, cobalt, cadmium) and to detoxification responses, suggesting a coherent function in maintaining metal ion balance and handling toxic metals.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903874","count":4},{"id":"GO:0071577","count":4},{"id":"GO:0055072","count":4},{"id":"GO:0070574","count":4},{"id":"GO:0006877","count":4}]},{"hash":"1514156279185008364","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":217,"triangles":1054,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0000398","count":6},{"id":"GO:0042273","count":6},{"id":"GO:0000462","count":6},{"id":"GO:0000466","count":6}]},{"hash":"1731609383342606133","title":"Unknown","description":"The proteins show a mix of disparate processes (telomere-related localization, heat response, immune signaling, fertilization, nuclear pore complex assembly, and host-cell translocation) with no clear common function tying them together, so there isn\u2019t a coherent, representative label beyond Unknown.","confidence":"","size":24,"edges":276,"triangles":2024,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0009408","count":2},{"id":"GO:0051973","count":2},{"id":"GO:0014823","count":2},{"id":"GO:0007339","count":2}]},{"hash":"256329716283725530","title":"Mitotic progression and DNA damage response","description":"This cluster is enriched for terms tied to cell cycle control and genome maintenance: mitotic cell cycle, mitotic spindle assembly, DNA-templated transcription, and DNA replication, plus a G1 DNA damage checkpoint response. There are also signals of apoptosis, including neuron and cardiac muscle apoptotic processes, which may reflect downstream or tissue-specific roles of these proteins. Overall, the prevailing theme is coordination of mitosis with DNA damage response, with some involvement in apoptotic signaling.","confidence":"Medium","size":24,"edges":243,"triangles":1412,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0090307","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0006260","count":5}]},{"hash":"1834760587630151810","title":"Brush border actin and microvilli regulation","description":"Most terms cluster around actin cytoskeleton dynamics and microvillus structure: regulation of GTPase activity, actin filament depolymerization and capping, and terminal web assembly, plus regulation of microvillus length. The intestinal D-glucose absorption term supports a brush-border interpretation, since microvilli in the intestinal epithelium house glucose transporters. Together, these suggest a functional cluster of proteins coordinating actin-driven microvilli architecture and nutrient absorption. Some terms such as detection of mechanical stimulus in touch or cardiac membrane repolarization are less central but may reflect shared signaling or structural components.","confidence":"High","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":3},{"id":"GO:1902896","count":3},{"id":"GO:0030042","count":3},{"id":"GO:0032532","count":3},{"id":"GO:0001951","count":3}]},{"hash":"1153806829041800225","title":"Lipid and Aromatic Compound Catabolism","description":"Most top GO terms describe catabolic metabolism: triglyceride catabolic process, glucuronoside catabolic process, phospholipid dephosphorylation, and aromatic compound catabolism (3-phenylpropionate). Additional terms reference redox processes, nitrogen utilization, and antibiotic biosynthesis, suggesting broad metabolism-oriented roles. A few terms are plant- or regulatory-specific (secondary shoot formation, regulation of endocannabinoid signaling), which may reflect annotation noise or cross-species homology but do not override the primary lipid/aromatic catabolic signal.","confidence":"Medium","size":24,"edges":12,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":7},{"id":"GO:0055114","count":6},{"id":"GO:2000124","count":6},{"id":"GO:0097755","count":5},{"id":"GO:0019391","count":5}]},{"hash":"1475936898254651550","title":"Mitochondrial redox and stress response cluster","description":"The dominant GO terms point to mitochondrial function and redox balance, including oxidative stress response, redox homeostasis, iron ion homeostasis, and protein import into the mitochondrial intermembrane space, which together suggest a core theme of mitochondrial maintenance under stress. Some additional terms related to RNA silencing, ubiquitin-dependent protein degradation, and microtubule localization appear as secondary associations, but do not override the main mitochondrial stress signal.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0006879","count":1},{"id":"GO:0045041","count":1},{"id":"GO:0045454","count":1}]},{"hash":"1294370155247307338","title":"Vacuolar amino acid transporters","description":"The cluster\u2019s top GO terms are dominated by transmembrane transport of various amino acids into and out of the vacuole (e.g., histidine, arginine, serine, tyrosine, lysine, asparagine), indicating a cohesive function as vacuolar amino acid transporters, likely related to AVT-family proteins in yeast. Some unrelated terms are present, but the core signal is clear: a group of proteins mediating amino acid movement across the vacuolar membrane.","confidence":"High","size":24,"edges":94,"triangles":149,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0089708","count":4},{"id":"GO:0090513","count":4},{"id":"GO:0090518","count":4},{"id":"GO:0061402","count":4},{"id":"GO:0090516","count":4}]},{"hash":"872171531118684189","title":"Cell Cycle and Vesicle Trafficking","description":"The cluster is dominated by terms related to cell cycle and division (cell cycle, cell division, nuclear membrane reassembly) and, in addition, shows strong links to membrane trafficking processes (multivesicular body-lysosome fusion, protein retention in Golgi) and related cellular activities (ATP export, development-related follicle cell formation, host-virus interaction). This suggests a core theme around coordination of cell division with intracellular trafficking pathways.","confidence":"Medium","size":24,"edges":111,"triangles":249,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":4},{"id":"GO:0000920","count":3},{"id":"GO:0071454","count":3},{"id":"GO:0030713","count":3},{"id":"GO:0061763","count":3}]},{"hash":"2208169691268949683","title":"RNA processing and translation regulation","description":"The cluster is dominated by post-transcriptional RNA features: mRNA stabilization, regulation of mRNA splicing, miRNA-mediated silencing, and IRES-dependent translation initiation, indicating a shared theme of RNA processing and translational control. Some metabolic terms present are less coherent with this core signal, likely reflecting broader annotation or multifunctionality, but the RNA-focused terms define the cluster's main function.","confidence":"High","size":24,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":3},{"id":"GO:0032259","count":2},{"id":"GO:0010124","count":2},{"id":"GO:0006107","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1762619126094097611","title":"Sphingolipid Metabolism","description":"The strongest recurring GO terms are sphingomyelin catabolic process and sphingolipid metabolic process, both pointing to lipid metabolism involving sphingolipids. Other top terms appear more heterogeneous (prostate development, GPCR signaling, melatonin biosynthesis), which may reflect annotation noise or multi-function proteins, but the dominant signal centers on sphingolipid metabolism.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006685","count":3},{"id":"GO:0060736","count":3},{"id":"GO:0006665","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0060742","count":3}]},{"hash":"116834101844218835","title":"Plant nectar sugar secretion and transport","description":"The cluster features GO terms tied to plants' nectar production and sugar movement (nectar secretion, sucrose transport, fructose export from vacuole to cytoplasm) and core secretory machinery (ER to Golgi vesicle transport, protein secretion). This points to a cohesive theme around plant secretory pathways that supply nectar and mobilize sugars, with some outlier terms that are less central.","confidence":"Medium","size":24,"edges":131,"triangles":314,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0071836","count":2},{"id":"GO:0015770","count":2},{"id":"GO:1902334","count":2},{"id":"GO:0010930","count":2},{"id":"GO:0006888","count":2}]},{"hash":"898865599069556300","title":"Developmental Regulation and Growth","description":"The top GO terms point to developmental and growth-related processes, including heart development, visual perception, regulation of stem cell division, and budding growth, with supporting roles in cytoskeletal dynamics and protein transport. This suggests a broad theme of developmental regulation and cell growth rather than a single specific pathway. Some terms (like sperm DNA decondensation and histone acetylation regulation) are more divergent, indicating a mixed set of roles but still centered on development and growth. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0031116","count":1},{"id":"GO:0071442","count":1},{"id":"GO:2000617","count":1}]},{"hash":"145232722410690934","title":"Bacterial cell wall glycosylation and UDP-sugar biosynthesis","description":"This cluster is dominated by GO terms for UDP-sugar biosynthesis (UDP-glucose, UDP-galactose, UDP-GlcNAc), glycogen biosynthesis, and glycosylation, plus cell-wall\u2013associated processes like teichoic acid and hyaluronan biosynthesis and cell wall organization. Together these point to a cohesive theme of bacterial cell wall polysaccharide formation and glycosylation pathways that use UDP-sugar donors. Confidence: High","confidence":"","size":24,"edges":218,"triangles":1139,"max_degree":23,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0006011","count":7},{"id":"GO:0006486","count":5},{"id":"GO:0071555","count":4},{"id":"GO:0052573","count":4},{"id":"GO:0005978","count":4}]},{"hash":"511033966506695199","title":"Developmental chromatin regulation and proteostasis","description":"The top GO terms point to chromatin regulation (histone acetylation) together with multiple development-related processes (skeletal muscle, nervous system, multicellular organism development). Additionally, ubiquitin-dependent proteasomal catabolism and its regulation suggest proteostasis as a central theme, with some signaling and cell migration elements (B cell receptor signaling, fibroblast migration, nuclear export). Taken together, these terms imply a cluster focused on how chromatin state and protein turnover intersect to govern development and related signaling.","confidence":"Medium","size":24,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043966","count":2},{"id":"GO:0007519","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0031397","count":2}]},{"hash":"2008440155865960757","title":"TNF/NF-\u03baB signaling and innate immunity","description":"Dominated by TNF-mediated signaling and NF-\u03baB activation terms (I\u03baB phosphorylation, NF-\u03baB activity) and ubiquitination (K63-linked), with a consistent signal for innate immune response. This points to a cluster of proteins regulating inflammatory signaling and immune activation, with neural tube closure appearing incidental. Therefore, the name captures the core function.","confidence":"High","size":24,"edges":224,"triangles":1229,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":17},{"id":"GO:0090073","count":17},{"id":"GO:1903721","count":17},{"id":"GO:0033209","count":17},{"id":"GO:0007250","count":17}]},{"hash":"698743477298941485","title":"Unknown","description":"Top terms span innate immune response, transcription, DNA damage response to X-ray, T cell development, hematopoiesis, heart development, ovulation, and growth regulation. This diversity does not reveal a single cohesive function or pathway linking the proteins, so no specific label is appropriate.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0010165","count":2},{"id":"GO:0046638","count":1}]},{"hash":"1809063688572326893","title":"Unknown","description":"There are 24 proteins with no edges, no triangles, and no GO terms to indicate a shared function, so no coherent theme can be deduced. ReCIPE re-addition doesn\u2019t imply functional coherence here, hence a safe label is Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1974150369074804591","title":"Neurobehavioral signaling and homeostasis","description":"This cluster's GO terms point to neural signaling and behavior, including norepinephrine biosynthesis, regulation of glutamate receptor signaling, visual learning, maternal behavior, and behavioral responses to ethanol, suggesting brain-related signaling and behavioral functions. The presence of glucose homeostasis and homoiothermy indicates links to metabolic and temperature/homeostatic regulation, implying a broader neurobehavioral regulation theme rather than a single narrow process.","confidence":"Medium","size":24,"edges":229,"triangles":1210,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0042421","count":2},{"id":"GO:0042593","count":2},{"id":"GO:0048265","count":2},{"id":"GO:2001236","count":2},{"id":"GO:0042711","count":2}]},{"hash":"603025093314088801","title":"Chitin Cuticle Development and Catabolism","description":"The strongest signal is the trio of GO terms tied to chitin biology: ecdysis and chitin-based cuticle development, plus chitin catabolic process, pointing to cuticle formation/remodeling. Other terms (lung/cartilage development, NF-kappaB signaling, IL-6/IL-8 production) appear less central and may reflect broader annotations or cross-species data. Overall, the cluster is best described by its emphasis on chitin-containing cuticle metabolism.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":1},{"id":"GO:0018990","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0070741","count":1},{"id":"GO:0051216","count":1}]},{"hash":"645322167931818855","title":"Cellulose Catabolic Process","description":"This cluster is characterized by GO term cellulose catabolic process, implying possible cellulose degradation activity. Because only one protein carries this annotation and there are no other supporting terms, the link is weak and the label should be used cautiously.","confidence":"Low","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1}]},{"hash":"917964721718374334","title":"Mitotic Chromosome Condensation & Nuclear Transport","description":"Top GO terms point to mitosis and nuclear transport, including chromosome condensation, mitotic nuclear membrane disassembly, kinetochore-associated localization, and nuclear pore/ tRNA export processes. The dominant signal is cell-division related, with a few unrelated terms likely background noise.","confidence":"High","size":23,"edges":253,"triangles":1771,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006409","count":2},{"id":"GO:0051292","count":2},{"id":"GO:0007077","count":2},{"id":"GO:0007076","count":2}]},{"hash":"841960815200830285","title":"Megakaryocyte development and platelet exocytosis","description":"The cluster shows a clear tilt toward vesicle trafficking and secretion relevant to megakaryocytes and platelets: megakaryocyte development, regulation of platelet aggregation, calcium-dependent exocytosis, vesicle docking, and Golgi-to-endosome transport. RNA repair and DNA replication terms likely reflect the proliferative state and cell-cycle aspects of megakaryocyte precursors, but the dominant signal is vesicle trafficking and secretory processes tied to platelet formation and function.","confidence":"Medium","size":23,"edges":208,"triangles":1059,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0042245","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0035855","count":2}]},{"hash":"362629254445031306","title":"Neural development and cell morphogenesis","description":"Top terms point to neural development (forebrain development, neural tube closure), multicellular development, and cell morphogenesis, with Rho signaling and transcriptional regulation supporting these processes. The cluster appears enriched for genes coordinating neural tissue formation and changes in cell shape, though some terms reflect broader developmental regulation. Medium","confidence":"","size":23,"edges":20,"triangles":3,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0030900","count":3},{"id":"GO:0043552","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0007266","count":2}]},{"hash":"1937793144718197947","title":"GTPase-driven cell cycle and migration","description":"The cluster shows a focus on cell cycle regulation and division (regulation of the cell cycle, cell division, cell cycle) together with cell migration, and activation of GTPase activity, suggesting coordinated control of proliferation and motility via small GTPase signaling. Telomere maintenance via telomerase and protein tetramerization appear as secondary or ancillary themes, while a couple of niche terms (sperm binding to zona pellucida, heat response) may reflect broader or incidental associations. Overall, the dominant theme ties cell cycle control to cytoskeletal dynamics through GTPase signaling.","confidence":"Medium","size":23,"edges":84,"triangles":85,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0007050","count":3},{"id":"GO:0090630","count":3}]},{"hash":"1166861332588391144","title":"Rho GTPase-driven actin remodeling and cell migration","description":"The top GO terms converge on Rho signaling and GTPase activation, plus assembly of actin-rich structures like filopodia and lamellipodia, and adhesion-dependent cell spreading. This points to actin cytoskeleton remodeling driving cell movement and morphogenesis, with neural development terms suggesting tissue-specific morphogenetic roles as well. Edges are absent, but the functional theme remains cohesive around cytoskeleton dynamics and motility.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0090630","count":4},{"id":"GO:0046847","count":4},{"id":"GO:1900026","count":3},{"id":"GO:0043314","count":3}]},{"hash":"936865637058111671","title":"Tyrosine Phosphatases Regulating Signaling","description":"Top GO terms show consistent negative regulation of signaling via peptidyl-tyrosine dephosphorylation, including T cell receptor signaling, ERK cascade, and PI3K/AKT pathways, with additional hints from postsynaptic density assembly and synaptic vesicle regulation. This pattern strongly supports a set of proteins that dampen signaling through tyrosine dephosphorylation, across immune and neural contexts.","confidence":"High","size":23,"edges":148,"triangles":486,"max_degree":20,"top_function":"autophagy","top_go_terms":[{"id":"GO:0050860","count":10},{"id":"GO:0000200","count":10},{"id":"GO:0035335","count":10},{"id":"GO:0070373","count":10},{"id":"GO:0097107","count":9}]},{"hash":"1572726504429185173","title":"TNF-NF-\u03baB signaling and ubiquitination","description":"This cluster centers on TNF and NF-\u03baB pathway components, as evidenced by terms for TNF-mediated signaling, NF-\u03baB activation via I\u03baB phosphorylation, JNK cascade regulation, and ubiquitin-dependent protein catabolic processes. The presence of histone modification terms may reflect downstream chromatin remodeling during inflammatory gene expression. Overall, it describes inflammatory signaling with ubiquitin-regulated transcriptional responses.","confidence":"High","size":23,"edges":11,"triangles":1,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0046328","count":5},{"id":"GO:1903265","count":5},{"id":"GO:0090073","count":5},{"id":"GO:1903721","count":5}]},{"hash":"998167167111596258","title":"Ribosome Biogenesis and Translation","description":"The cluster shows strong representation of ribosome biogenesis and translation-related GO terms (ribosome biogenesis, translation, translational elongation, and translational fidelity), with additional links to mRNA export and RNAP II transcription regulation, pointing to a cohesive gene-expression machinery module centered on ribosome assembly and protein synthesis.","confidence":"High","size":23,"edges":29,"triangles":5,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0016973","count":2}]},{"hash":"122984598892759468","title":"RNA and protein methylation","description":"The cluster is strongly enriched for methylation-related GO terms, including RNA methylation (rRNA, guanine-N7 methylation; mRNA cap) and multiple protein methylation processes (N-terminal, lysine dimethylation/trimethylation). A chromatin-related term (rDNA heterochromatin formation) further supports involvement in methylation-based regulation. A single phagocytosis term is incidental. Overall, the dominant signal points to methylation-modifying enzymes and modifiers acting on RNA and proteins.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006909","count":2},{"id":"GO:0036265","count":1},{"id":"GO:0006370","count":1},{"id":"GO:1901052","count":1},{"id":"GO:0000183","count":1}]},{"hash":"1095493462731391080","title":"Fatty acid biosynthesis and catabolism","description":"This cluster centers on fatty-acyl-CoA biosynthesis and degradation, including long-chain and medium-chain fatty-acyl-CoA processes, palmitic acid biosynthesis, and related regulatory steps, indicating a coherent fatty acid metabolism module. Other GO terms appear incidental and do not override the dominant fatty acid theme. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035338","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0009239","count":1},{"id":"GO:0045892","count":1},{"id":"GO:1900535","count":1}]},{"hash":"118590573592609136","title":"Cellulose Degradation","description":"The only GO term is cellulose catabolic process, pointing to a possible role in cellulose breakdown, but with 23 proteins and just one annotation this link is weak; the label reflects a potential theme rather than a strong, representative function for the whole cluster.","confidence":"Low","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1}]},{"hash":"811398288896475957","title":"Actin cytoskeleton remodeling and cell migration signaling","description":"These proteins are enriched for actin-rich protrusions (filopodium, lamellipodium, microspike) and substrate adhesion-dependent spreading, indicating actin cytoskeleton remodeling essential for cell movement. Integrated receptor signaling (EGFR, integrin, ephrin) with Wnt pathways suggests coordinated signaling that drives protrusion formation and directional migration.","confidence":"High","size":23,"edges":136,"triangles":411,"max_degree":20,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:1900026","count":10},{"id":"GO:0046847","count":10},{"id":"GO:0043552","count":10},{"id":"GO:0007173","count":9},{"id":"GO:0090263","count":9}]},{"hash":"672805272888142456","title":"Unknown","description":"The GO terms are scattered across sphingolipid metabolism, development of prostate and brain regions, GPCR signaling, and general cellular processes, with no single cohesive function tying all proteins together, so a specific functional label isn\u2019t justifiable.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006685","count":1},{"id":"GO:0060736","count":1},{"id":"GO:0006665","count":1},{"id":"GO:1903206","count":1},{"id":"GO:0060742","count":1}]},{"hash":"515366047129339626","title":"Amino acid catabolism and porphyrin biosynthesis","description":"The cluster is dominated by amino-acid degradation terms (L-alanine, L-kynurenine, L-cysteine catabolic processes) and related metabolic steps (pyruvate biosynthesis, protoporphyrinogen IX biosynthesis), suggesting a metabolic module focused on amino-acid breakdown and interconnected pathways like heme biosynthesis; Notch signaling appears to be a less representative, possible secondary annotation.","confidence":"Medium","size":23,"edges":165,"triangles":681,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":14},{"id":"GO:0007219","count":13},{"id":"GO:0097053","count":13},{"id":"GO:0042866","count":9},{"id":"GO:0019265","count":8}]},{"hash":"102408570930620297","title":"Photoreceptor signaling and redox homeostasis","description":"This cluster is enriched for GO terms tied to light perception and visual stimulus detection, particularly photoreceptor function, plus several redox-related processes (redox homeostasis, cellular oxidant detoxification) and calcium-dependent exocytosis, which aligns with photoreceptor cells needing tight redox control and neurotransmitter release at synapses. The presence of GTPase regulation and tight junction terms may reflect signaling and junction dynamics in retinal tissue. Overall, the pattern points to retinal photoreceptor signaling with stress/oxidative response components.","confidence":"High","size":23,"edges":58,"triangles":103,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0034976","count":3},{"id":"GO:0043950","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0050908","count":3}]},{"hash":"92644679492296270","title":"Protein and RNA methyltransferases","description":"Most top GO terms point to methylation activities: N-terminal peptidyl-glycine/alanine/serine methylation, tRNA methylation, RNA guanine-N7 methylation, and mRNA capping. This clustering suggests a module enriched for methyltransferase enzymes that modify proteins or RNAs. A few terms related to biosynthetic methylation processes (cobalamin/antibiotic biosynthesis) also appear, consistent with methyltransferases participating in specialized metabolic pathways.","confidence":"High","size":23,"edges":120,"triangles":293,"max_degree":20,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0018013","count":9},{"id":"GO:0018012","count":8},{"id":"GO:0030488","count":7},{"id":"GO:0035573","count":6},{"id":"GO:0035572","count":6}]},{"hash":"1359511251379092671","title":"Nitrogen utilization and ammonium transport","description":"This cluster is dominated by GO terms related to nitrogen handling\u2014nitrogen utilization, ammonium and methylammonium transport, transepithelial transport, and regulation of nitrogen utilization\u2014suggesting a common theme of nitrogen metabolism and transport. Additional terms about carbon dioxide transport and iron ion homeostasis appear ancillary, and the absence of edges indicates a loosely connected set, but the nitrogen-focused terms provide the main functional thread.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019740","count":2},{"id":"GO:0007124","count":1},{"id":"GO:0072488","count":1},{"id":"GO:0015843","count":1},{"id":"GO:0001403","count":1}]},{"hash":"592084440047899668","title":"Developmental morphogenesis and ECM remodeling","description":"The top GO terms point to embryonic development and tissue morphogenesis, including vertebrate neural development (ventral spinal cord), craniofacial morphogenesis (palatal shelf), and bone-related processes (ossification, collagen regulation) with ECM interactions (integrin-mediated adhesion). Together these suggest a cluster of proteins involved in developmental processes and extracellular matrix remodeling, rather than a single pathway. The lone outlier term about symbiont entry is likely an annotation artifact and does not override the main theme.","confidence":"High","size":23,"edges":25,"triangles":11,"max_degree":13,"top_function":"wound healing","top_go_terms":[{"id":"GO:0061419","count":6},{"id":"GO:0046718","count":6},{"id":"GO:1990134","count":6},{"id":"GO:0021517","count":6},{"id":"GO:0010710","count":6}]},{"hash":"754798511989861954","title":"RNA Processing and Telomere Maintenance","description":"Based on the top terms, the cluster centers on RNA metabolism (DNA-templated transcription, tRNA processing) with a secondary tie to genome stability via telomere maintenance. The presence of an obsolete term and no edges among proteins suggests a loosely connected set rather than a tightly defined function, so the name emphasizes the strongest shared theme (RNA processing/transcription) while acknowledging the telomere maintenance hint. ","confidence":"Low","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0090342","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0008033","count":1}]},{"hash":"1437150245599528295","title":"Membrane Transport Proteins","description":"These proteins are annotated with multiple transmembrane transport GO terms across ions (K+, Na+, phosphate, nitrate) and small molecules (galactose, arabinose, vitamins, 4-hydroxyphenylacetate), plus neurotransmitter loading into synaptic vesicles. The shared theme is transport across membranes, suggesting a cluster of membrane transporter proteins rather than a single substrate. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":4},{"id":"GO:0035725","count":4},{"id":"GO:1900754","count":4},{"id":"GO:0035435","count":4},{"id":"GO:0042128","count":4}]},{"hash":"1360935738012733299","title":"RIG-I\u2013Mediated Antiviral Immunity and MHC I Regulation","description":"The cluster is dominated by innate immune and antiviral topics: innate immune response, defense against virus, and positive regulation of RIG-I signaling, along with MHC I biosynthesis. Additional terms point to ubiquitin-related regulation, PML body organization, and microtubule localization, all of which can participate in antiviral signaling and antigen presentation. Despite some obsolete terms, the core functions converge on antiviral innate immunity and MHC I regulation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045087","count":7},{"id":"GO:0051607","count":7},{"id":"GO:0045345","count":7},{"id":"GO:1900246","count":5},{"id":"GO:2000059","count":5}]},{"hash":"582133600222238849","title":"Cardiac development and Rac signaling","description":"The cluster features strong enrichment for heart development (GO:0007507) and cardiac muscle contraction (GO:0060048), along with Rac-mediated cytoskeleton dynamics (GO:0016601, GO:0030032) and GTPase activation (GO:0090630). These point to a set of proteins involved in cardiomyocyte development and contractile signaling, with lamellipodium assembly suggesting actin remodeling required for heart tissue formation. Some neural terms appear but the cardiac signals dominate.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043552","count":4},{"id":"GO:0090630","count":4},{"id":"GO:0007507","count":4},{"id":"GO:1903526","count":4},{"id":"GO:0030032","count":4}]},{"hash":"562781224589508754","title":"DNA replication and transcription machinery","description":"This cluster is enriched for GO terms centered on DNA-templated transcription, DNA replication initiation and elongation, RNA-templated DNA biosynthetic processes, and nucleotide metabolism, with additional ties to UV-damage repair synthesis and translesion synthesis, pointing to a set of nuclear DNA-processing proteins involved in replication and transcription.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009164","count":1},{"id":"GO:0009117","count":1},{"id":"GO:0006271","count":1},{"id":"GO:0006278","count":1}]},{"hash":"578278344482840531","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904744","count":1},{"id":"GO:0008380","count":1},{"id":"GO:1902570","count":1},{"id":"GO:0097309","count":1},{"id":"GO:0051096","count":1}]},{"hash":"951225874014959747","title":"Bacterial cell wall remodeling and sporulation","description":"The top GO terms cluster around cell wall metabolism (peptidoglycan and chitin catabolic/biosynthetic processes), cell wall organization, and regulation of cell shape, with an additional term for sporulation. This pattern suggests proteins involved in cell wall synthesis/remodeling and spore formation in bacteria, rather than a single isolated pathway.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009253","count":3},{"id":"GO:0016998","count":3},{"id":"GO:1902083","count":3},{"id":"GO:0008360","count":3},{"id":"GO:0071323","count":3}]},{"hash":"628937706085367281","title":"Transmembrane Transporters for Ions and Small Molecules","description":"The top GO terms point to membrane transport activity across a broad range of substrates, including sodium and potassium ions and various small molecules (nitrates, sialic acid, arabinose, vitamins, xenobiotics). The presence of neurotransmitter loading into synaptic vesicles also supports a transport-centered function. Overall, these proteins appear to function as diverse membrane transporters rather than a single substrate-specific group.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"transmembrane transport","top_go_terms":[{"id":"GO:0042128","count":11},{"id":"GO:0006855","count":11},{"id":"GO:0071805","count":10},{"id":"GO:0035725","count":10},{"id":"GO:1900754","count":10}]},{"hash":"636448859491877975","title":"Diverse Membrane Transporters","description":"This cluster shows a clear enrichment for transmembrane transport GO terms across a wide range of substrates and ions, including potassium, sodium, phosphate, nitrate, sugars, vitamins, xenobiotics, and even neurotransmitter loading. The shared function is membrane transport activity, suggesting these proteins are membrane transporters with broad substrate specificity. Edges and triangular connections are absent, but the GO profile supports a transporter-centric grouping.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0035725","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0042128","count":2}]},{"hash":"1879206467564157563","title":"Lysosomal Lipid Metabolism and Trafficking","description":"The GO terms point to lysosome-related processes (protein targeting to lysosome, secretion of lysosomal enzymes, Cvt/vacuole targeting) and sphingolipid metabolism (sphingomyelin catabolic and sphingolipid metabolic processes). Together, they suggest a core theme of lysosomal processing and lipid metabolism, with a few unrelated annotations likely contributing noise. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006685","count":1},{"id":"GO:0060736","count":1},{"id":"GO:0006665","count":1},{"id":"GO:1903206","count":1},{"id":"GO:0060742","count":1}]},{"hash":"2206246356118261832","title":"Neural signaling and synaptic plasticity","description":"This cluster centers on neural signaling and plasticity, highlighted by long-term potentiation and visual learning, and complemented by calcium-linked pathways (calcineurin-NFAT, JNK) and growth-factor\u2013related signaling (PDGF), as well as vesicle trafficking (COPII, intracellular transport). The heart development and innate immune terms are broader annotations, but the core signal points to neural communication and synaptic adaptation with supporting trafficking and signaling processes.","confidence":"Medium","size":22,"edges":58,"triangles":40,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0036120","count":3},{"id":"GO:0008542","count":3},{"id":"GO:0045087","count":3}]},{"hash":"2142153946726481824","title":"Nucleocytoplasmic transport and transcription regulation","description":"These terms cluster around nuclear transport: mRNA export and ribosomal subunit export from the nucleus, import of proteins into the nucleus (including NLS-bearing proteins), and regulation of transcription. The pattern suggests a module of nucleocytoplasmic transport coupled to transcription control.","confidence":"High","size":22,"edges":225,"triangles":1426,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006406","count":4},{"id":"GO:0000056","count":3},{"id":"GO:0042176","count":3},{"id":"GO:0010824","count":3}]},{"hash":"1774175714113882925","title":"Neuronal development and synaptic signaling","description":"This cluster is enriched for terms related to neural development and synaptic function, such as substantia nigra development, skeletal muscle fiber development (reflecting neuromuscular connections), ephrin receptor signaling, and excitatory postsynaptic potential, plus cell polarity and vesicle transport processes that support neuronal structure and trafficking. While there are some broader signaling associations (e.g., Wnt signaling), the strongest cohesive theme centers on neural development and synaptic activity.","confidence":"Medium","size":22,"edges":45,"triangles":14,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071963","count":6},{"id":"GO:0000001","count":6},{"id":"GO:0006888","count":5},{"id":"GO:0021762","count":5},{"id":"GO:0048741","count":4}]},{"hash":"2302595560542291335","title":"Developmental signaling and cytoskeletal remodeling","description":"This cluster centers on signaling pathways (Wnt, Rho/Rac, EGFR) that regulate actin dynamics (actin depolymerization) and sarcomere organization, linking these processes to developmental outcomes (hippocampus development) and regeneration (liver regeneration). The GO terms point to proteins that coordinate signaling with cytoskeletal remodeling during development and tissue regeneration. ","confidence":"Medium","size":22,"edges":14,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:0007266","count":2},{"id":"GO:0045214","count":2},{"id":"GO:0021766","count":2},{"id":"GO:0016601","count":2}]},{"hash":"609243356384303815","title":"Embryonic and Organ Development","description":"The top GO terms cover forebrain, cerebellum, inner ear, heart, skeletal muscle, placenta development and related organs, indicating a broad embryonic development and organogenesis program.","confidence":"High","size":22,"edges":184,"triangles":812,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":7},{"id":"GO:0007275","count":6},{"id":"GO:0008045","count":5},{"id":"GO:0048839","count":5},{"id":"GO:0021549","count":5}]},{"hash":"1925689004198957254","title":"Ubiquitination-Linked Signaling and Cell Cycle Regulation","description":"The cluster centers on protein ubiquitination and I-kappaB phosphorylation, which points to ubiquitin- and phosphorylation-driven signaling (including NF-kB pathways). Additional terms like spindle assembly, epithelial polarity, and calcium import indicate broader connections to cell cycle control, cytoskeletal organization, and signaling processes. This combination suggests a general theme of regulatory signaling intertwined with cell cycle and cellular architecture.","confidence":"Medium","size":22,"edges":74,"triangles":104,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0007252","count":2},{"id":"GO:0043486","count":2},{"id":"GO:0045736","count":1}]},{"hash":"321544201286758144","title":"Unknown","description":"The Top Terms include cell growth, heat response, immune cell apoptosis, endothelial differentiation, calcium transport, synaptic plasticity regulation, IL-12 production, epithelial polarity, and RNA processing. This mix spans immune, neural, vascular, and gene-expression processes with no clear unifying function or pathway. Given the heterogeneity and lack of cohesive biological theme, there isn\u2019t a single intuitive label other than Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":8},{"id":"GO:0009408","count":8},{"id":"GO:0033028","count":8},{"id":"GO:0060843","count":8},{"id":"GO:0098703","count":8}]},{"hash":"1482659288858395421","title":"Symbiont dormancy and stress response","description":"The top GO term is dormancy entry of symbiont in host, suggesting these proteins work together to enter or maintain a dormant state within a host. Additional terms emphasize stress response, including oxidative stress, and proteostasis via ubiquitin-dependent degradation and proteasome assembly, which are common in conditions of dormancy or host-associated stress. Some terms like chlorophyll biosynthesis and stamen formation appear distant, likely noise or cross-species annotations, but the core pattern centers on host-associated dormancy and stress adaptation.","confidence":"Medium","size":22,"edges":135,"triangles":428,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0085014","count":7},{"id":"GO:0006950","count":7},{"id":"GO:0019358","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0006979","count":2}]},{"hash":"422865243104369408","title":"Ribosome Biogenesis and Cell Division","description":"Proteins in this cluster are enriched for ribosome biogenesis and translation-related processes (ribosome biogenesis, small subunit biogenesis, tRNA modification) alongside cell division and septum formation, with occasional links to conjugation and stress responses. This combination points to a module coordinating ribosome assembly with bacterial proliferation and division.","confidence":"High","size":22,"edges":16,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0090529","count":2}]},{"hash":"704878179897477329","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042113","count":1},{"id":"GO:0030500","count":1},{"id":"GO:1904744","count":1},{"id":"GO:0008380","count":1},{"id":"GO:1902570","count":1}]},{"hash":"742662812241529862","title":"GPI-anchor biosynthesis and N-linked glycosylation","description":"The top GO terms cluster around protein glycosylation, especially GPI anchor biosynthesis and dolichol-linked oligosaccharide synthesis, plus N-linked glycosylation. This suggests the proteins function in attaching sugar chains and GPI anchors to proteins. A few terms (DNA replication, signaling, sensory perception) appear less central, likely background or secondary associations. ","confidence":"High","size":22,"edges":206,"triangles":1117,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":5},{"id":"GO:0030433","count":3},{"id":"GO:0006488","count":3},{"id":"GO:0070389","count":2},{"id":"GO:0006260","count":2}]},{"hash":"173819802449453376","title":"Neuronal ion transport and synaptic loading","description":"The cluster contains multiple transmembrane transport terms for ions and small molecules (Na+, K+, phosphate, sugars, etc.) and a key function related to neurotransmitter loading into synaptic vesicles, with an additional note on peripheral nervous system myelination. This points to a cohesive theme of neuronal membrane transport and synaptic function, so a label emphasizing ion transport and neurotransmission fits well.","confidence":"Medium","size":22,"edges":13,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":3},{"id":"GO:0071805","count":2},{"id":"GO:0035725","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0035435","count":2}]},{"hash":"1297010193697542017","title":"Mitochondrial translation and ribosome biogenesis","description":"Based on GO terms, the cluster centers on protein synthesis and ribosome assembly, including mitochondrial translation, maturation of LSU rRNA, and ribosomal large subunit assembly, suggesting a shared role in mitochondrial protein synthesis and ribosome biogenesis. A few other terms (SNARE complex disassembly, ER-to-Golgi transport, microtubule severing, heat acclimation, UV-damage repair) appear as occasional functions but do not define the overall theme.","confidence":"Medium","size":22,"edges":29,"triangles":4,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0051013","count":1},{"id":"GO:0070370","count":1}]},{"hash":"898678069542545841","title":"Phosphate homeostasis and vacuolar transport","description":"The top GO terms cluster around phosphate starvation response, phosphate transmembrane transport, intracellular phosphate homeostasis, polyphosphate biosynthesis, and vacuole-related processes such as microautophagy and vacuole fusion, suggesting a shared function in phosphate management and vacuolar/ion transport. Peripheral terms like sodium transport and cold response are present but do not define the core theme.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016036","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0030643","count":1},{"id":"GO:0048016","count":1},{"id":"GO:0006814","count":1}]},{"hash":"2108604435896386424","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":1},{"id":"GO:0006432","count":1},{"id":"GO:0043622","count":1},{"id":"GO:0010119","count":1},{"id":"GO:0009737","count":1}]},{"hash":"1983091319426302257","title":"Mitochondrial import and ERAD regulation","description":"This cluster highlights GO terms tied to mitochondrial matrix protein import, ER-associated degradation (ERAD) and its regulation, plus lipid droplet organization and related organelle processes. Together they suggest a theme of intracellular protein handling and organelle quality control (mitochondria/ER), rather than a single, uniform cytosolic pathway, despite some divergent immune-related terms.","confidence":"Medium","size":22,"edges":33,"triangles":22,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":2},{"id":"GO:0051289","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0031134","count":1},{"id":"GO:1904293","count":1}]},{"hash":"2174984874370295581","title":"PI3K-AKT Signaling and Development","description":"This cluster shows strong participation of PI3K/AKT-related signaling (GO:0043491), insulin signaling (GO:0008286), AKT activation (GO:0032148), and peptide phosphorylation (GO:0018107), pointing to growth-factor\u2013mediated signaling. Developmental processes such as heart development (GO:0007507) and glycogen cell differentiation in placenta (GO:0060709), along with hemopoiesis (GO:0030097) and IL-7 response (GO:0098761), suggest a broader program of tissue differentiation and immune-related signaling coordinated via AKT pathways. A DNA-templated transcription term (GO:0006351) may reflect downstream transcriptional responses. Overall, this cluster likely represents PI3K-AKT\u2013driven signaling linked to development and differentiation.","confidence":"Medium","size":22,"edges":59,"triangles":50,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0043491","count":3},{"id":"GO:0060709","count":3},{"id":"GO:0018107","count":3},{"id":"GO:0008286","count":3}]},{"hash":"1282730491723879208","title":"Unknown","description":"The GO terms are very diverse, ranging from autophagy-related trafficking (Cvt pathway) and endosomal transport to cytotoxic T cell degranulation, cytoskeletal remodeling (stress fibers, filopodia, pseudopodia), and even hair follicle proliferation and vascular regulation. There isn\u2019t a clear, single biological theme tying these proteins together, so a cohesive functional label cannot be confidently assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":1},{"id":"GO:0043316","count":1},{"id":"GO:0035646","count":1},{"id":"GO:0051496","count":1},{"id":"GO:0071338","count":1}]},{"hash":"1892228240996289782","title":"Mitochondrial respiration and ATP synthesis","description":"The top GO terms are strongly centered on mitochondrial electron transport and ATP production, including NADH to ubiquinone, cytochrome c to oxygen, and assembly of respiratory chain complexes II and IV, pointing to mitochondrial energy metabolism as the cluster\u2019s core function. A few terms related to cannabinoid biosynthesis and inflorescence development appear incidental noise relative to the dominant respiration-related terms.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":2},{"id":"GO:0006120","count":2},{"id":"GO:1901696","count":1},{"id":"GO:1901697","count":1},{"id":"GO:0033617","count":1}]},{"hash":"231441493557007314","title":"Transmembrane transport of ions and amino acids","description":"This cluster is dominated by GO terms describing transmembrane transport of ions (sodium and potassium) and L-alpha-amino acids, plus a transport term for 4-hydroxyphenylacetate; with intracellular water homeostasis and osmotic-stress response also present, indicating a shared function in transport and osmoregulation across membranes. Although there are some generic terms like metabolic process and a DNA repair term that may be incidental, the preponderance of transport-related terms supports a membrane transport/theme for this group.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902475","count":1},{"id":"GO:0008152","count":1},{"id":"GO:0009992","count":1},{"id":"GO:0071470","count":1},{"id":"GO:0034220","count":1}]},{"hash":"1177942100843909859","title":"Steroid hormone biosynthesis and lipid metabolism","description":"This cluster is dominated by GO terms for steroid hormone production and related lipid metabolism, notably testosterone and estrogen biosynthesis and C21-steroid hormone metabolism, suggesting a core theme of steroid biosynthesis. Additional terms for sphinganine lipid metabolism and diverse secondary metabolite biosynthesis (antibiotics, alkaloids, mycolic acids) indicate broader metabolic capabilities, but the steroid/lipid theme appears most representative of the group.","confidence":"Medium","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045150","count":22},{"id":"GO:0071768","count":22},{"id":"GO:0006666","count":22},{"id":"GO:0006710","count":22},{"id":"GO:0061370","count":22}]},{"hash":"842087273785678519","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":13,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0009311","count":2},{"id":"GO:0009272","count":2},{"id":"GO:0070880","count":2},{"id":"GO:0006487","count":2}]},{"hash":"1227373012491720065","title":"Translational Control and mRNA Decay","description":"Reason: The top GO terms are dominated by translation-related processes (translation, translational initiation/elongation/termination, positive regulation of cytoplasmic translation, selenocysteine incorporation) and mRNA decay, indicating a cluster of proteins involved in protein synthesis and mRNA turnover; a few outlier terms (BDNF response, actin cytoskeleton reorganization, antibiotic response) may reflect broader cellular context or noise.","confidence":"High","size":22,"edges":39,"triangles":19,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0031532","count":3},{"id":"GO:0045901","count":2},{"id":"GO:1990416","count":2},{"id":"GO:2000767","count":2}]},{"hash":"1803421990313459858","title":"Steroid and lipid metabolism","description":"The top GO terms are dominated by steroid hormone biosynthesis and metabolism (testosterone, estrogen, C21-steroid), along with lipid biosynthesis pathways (mycolic acid, 3-keto-sphinganine) and related catabolic processes. Additional terms for antibiotic and alkaloid biosynthesis suggest broader secondary metabolism. Overall, the cluster aligns with lipid and steroid biosynthesis and turnover, with secondary metabolite production as a supporting theme.","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045150","count":22},{"id":"GO:0071768","count":22},{"id":"GO:0006666","count":22},{"id":"GO:0006710","count":22},{"id":"GO:0061370","count":22}]},{"hash":"529412235330842688","title":"Unknown","description":"The GO terms are highly heterogeneous (digestion development, sulfur oxidation, tRNA processing, peptidoglycan and cell wall macromolecule catabolism, viral release by cytolysis, carbohydrate metabolism, and defense against bacteria) with little overlap or a clear shared pathway, so there isn\u2019t a cohesive function to label. Confidence: None","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055123","count":1},{"id":"GO:0019417","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0009253","count":1},{"id":"GO:0016998","count":1}]},{"hash":"1384201072907011197","title":"Lymphocyte development and cytokine signaling","description":"This cluster is dominated by GO terms related to lymphocyte biology and cytokine pathways: NK T cell differentiation, B cell affinity maturation, interleukin-4 production, cellular response to interleukin-7, and hemopoiesis, along with cell migration and small GTPase\u2013mediated signaling. While there are a few metabolic signaling terms (insulin and growth hormone receptor pathways) that are less central to lymphocyte development, the core theme is immune cell development and cytokine-driven signaling. Overall, the proteins appear to participate in lymphocyte differentiation and cytokine responses.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0032633","count":5},{"id":"GO:0001865","count":5},{"id":"GO:0002344","count":5},{"id":"GO:2001275","count":5}]},{"hash":"1179077851739023291","title":"Unknown","description":"No GO terms or interaction signals are provided for this cluster (22 proteins, 0 edges, 0 triangles). Without functional terms to connect the members, a unifying function cannot be inferred.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"598673271486592305","title":"Neural development and axon guidance","description":"These GO terms cluster around developmental processes, particularly neural development and morphogenesis. The presence of axonogenesis and chemorepulsion of branchiomotor axons, along with vagus nerve morphogenesis, limb bud formation, and endothelial morphogenesis, supported by receptor tyrosine kinase signaling, suggests a role in signaling-driven neural patterning and tissue morphogenesis during development. A minor component relates to broader development, such as bone-related regulation, but the dominant theme is neural and morphological development.","confidence":"High","size":22,"edges":116,"triangles":320,"max_degree":19,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0007275","count":9},{"id":"GO:0007169","count":6},{"id":"GO:0035563","count":6},{"id":"GO:0033689","count":6},{"id":"GO:0021793","count":6}]},{"hash":"1691171562360538190","title":"Mitochondrial respiration and ion transport","description":"This cluster shows strong signals for mitochondrial respiration (NADH to ubiquinone, complex II assembly) alongside several transmembrane transport processes (K+, Na+, sialic acid, vitamin). The combination points to a functional theme around energy production via mitochondrial pathways and membrane transport, with a few outliers related to iron/erythrocyte biology. Overall it maps best to a transport-and-respiration module.","confidence":"Medium","size":22,"edges":20,"triangles":9,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0006120","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0035725","count":1},{"id":"GO:1900754","count":1}]},{"hash":"1422602819062032602","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0070535","count":2},{"id":"GO:0070842","count":2}]},{"hash":"849661793866050764","title":"Antiviral Innate Immunity","description":"This cluster centers on innate immune defense against viruses, highlighted by terms like innate immune response, positive regulation of RIG-I signaling, and suppression of viral release by host, with PML body organization and related chromatin modifiers providing supporting links to antiviral signaling and transcriptional control.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900246","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0035372","count":1},{"id":"GO:0036353","count":1},{"id":"GO:0070562","count":1}]},{"hash":"1669908655365765991","title":"Unknown","description":"There are no GO terms or network connections to suggest a shared function, and the zero edges/triangles indicate no apparent interactions; the ReCIPE re-additions imply a data-assembly artifact rather than a cohesive functional cluster, so the label remains Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1711148895466377772","title":"Plant lipid biosynthesis and ER-Golgi trafficking","description":"The top GO terms blend lipid/fatty acid and dolichol-linked glycan biosynthesis with secretory pathway transport (ER to Golgi and endosome-to-Golgi), consistent with a plant-centered cluster where lipid metabolism interfaces with protein processing and trafficking, including brassinosteroid biosynthesis.","confidence":"Medium","size":22,"edges":185,"triangles":841,"max_degree":21,"top_function":"lipid metabolic process","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0016132","count":3},{"id":"GO:0006629","count":3},{"id":"GO:0042761","count":3},{"id":"GO:0042147","count":2}]},{"hash":"1137253460861992168","title":"Chemokine Production Regulation and Inflammatory Signaling","description":"The cluster is enriched for GO terms related to positive regulation of chemokine production, notably CXCL1, CCL5, and MIP-1 alpha (MIP-1\u03b1), suggesting a core role in modulating inflammatory signaling and chemokine-mediated immune responses. Supporting terms point to vesicle trafficking and lipid catabolism, which can facilitate chemokine processing and secretion, along with calcium signaling. While some terms touch on sensory (pain) or cardiac (SA node) processes, they appear peripheral to the dominant chemokine/inflammatory theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048016","count":3},{"id":"GO:0042144","count":3},{"id":"GO:0046475","count":3},{"id":"GO:0098703","count":2},{"id":"GO:2000340","count":2}]},{"hash":"379237925372949276","title":"Ion and Metabolite Transmembrane Transporters","description":"The top GO terms are dominated by transmembrane transport activities across a broad range of substrates\u2014ions (potassium, sodium, phosphate), metabolites (arabinose, 4-hydroxyphenylacetate, nitrate), vitamins, and sialic acid, plus a vesicular neurotransmitter loading term. This pattern points to proteins whose primary role is transporting substances across membranes, rather than catalyzing chemical reactions, so a transporter-focused label fits best.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":7},{"id":"GO:0035725","count":7},{"id":"GO:1900754","count":7},{"id":"GO:0035461","count":7},{"id":"GO:0015739","count":7}]},{"hash":"2098680347863857172","title":"Unknown","description":"The GO terms span lipid and carbohydrate catabolic processes, cell wall organization, a developmental process, apoptosis, and multiple stress responses, with little cohesive overlap to define a single biological theme. Therefore, there isn\u2019t a clear, representative function for the entire cluster.","confidence":"","size":22,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031161","count":2},{"id":"GO:0046338","count":2},{"id":"GO:0046843","count":2},{"id":"GO:0006309","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1917047602553485844","title":"Unknown","description":"The top GO terms cover innate immunity (innate immune response, cellular response to lipopolysaccharide, lipopolysaccharide signaling), cell death (necroptotic process), metabolism (cholesterol and oligosaccharide catabolic processes, hydrolase activity), and neural functions (learning or memory, neuromuscular process controlling balance). This wide scatter across divergent biological processes provides no single cohesive function or pathway to define the cluster, so Unknown is the most appropriate label.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1},{"id":"GO:0070266","count":1},{"id":"GO:0008203","count":1},{"id":"GO:0007611","count":1},{"id":"GO:0009313","count":1}]},{"hash":"88190090520900839","title":"Axon guidance and vascular morphogenesis","description":"Most terms cluster around neural development (axonogenesis, chemorepulsion of branchiomotor axons, vagus nerve morphogenesis) and vascular development (endothelial morphogenesis, endothelial chemotaxis, limb bud formation), linked by cell surface receptor tyrosine kinase signaling. This suggests a cohesive theme of developmental signaling coordinating nerve and blood vessel formation, so the label is appropriate. ","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0007169","count":15},{"id":"GO:0035563","count":15},{"id":"GO:0033689","count":15},{"id":"GO:0021793","count":15},{"id":"GO:0050918","count":15}]},{"hash":"182960417913493575","title":"Cytoskeletal Remodeling and Cell Polarity","description":"The top GO terms converge on cytoskeletal organization and dynamics (actin cytoskeleton reorganization, mitotic spindle assembly), regulation of cell shape and polarity, and signaling/turnover processes (GTPase activity regulation, ubiquitin-dependent proteolysis). This suggests a cohesive theme around cytoskeleton-driven cell polarity and division, with some ancillary signaling links.","confidence":"High","size":21,"edges":133,"triangles":423,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:2000009","count":2},{"id":"GO:0071963","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0048633","count":2},{"id":"GO:0031532","count":2}]},{"hash":"307039122395610871","title":"Siderophore biosynthesis and transport","description":"This cluster is characterized by GO terms for rhizobactin 1021 biosynthetic process, aerobactin biosynthetic process, and siderophore transmembrane transport, indicating proteins involved in siderophore production and transport for iron acquisition in bacteria. The combination of two distinct siderophore biosynthesis terms with a transport term strongly points to a cohesive siderophore-mediated iron acquisition pathway.","confidence":"High","size":21,"edges":23,"triangles":13,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0019289","count":1},{"id":"GO:0019270","count":1},{"id":"GO:0044718","count":1}]},{"hash":"2301745457170650417","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":11,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071360","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0048137","count":2},{"id":"GO:0000381","count":1},{"id":"GO:0040039","count":1}]},{"hash":"1600713934805482856","title":"Drosophila embryonic morphogenesis and axis patterning","description":"The GO terms are dominated by embryonic tissue morphogenesis across multiple organs (epidermis, hindgut, foregut, wing disc, spiracle) and axis specification via torso signaling and proximal/distal patterning, pointing to a developmental program governing embryonic tissue formation and body axis patterning in Drosophila. A few neuronal/exocytosis terms appear but do not define the main theme. Confidence reflects a coherent morphogenesis/axis patterning theme across this cluster.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008544","count":1},{"id":"GO:0048619","count":1},{"id":"GO:0035220","count":1},{"id":"GO:0008293","count":1},{"id":"GO:0009946","count":1}]},{"hash":"1964923841668743471","title":"Signaling-Regulated Cell Migration","description":"The cluster centers on regulatory signaling processes (regulation of GTPase activity, regulation of protein tyrosine kinase activity) and migratory events (sprouting angiogenesis, T cell migration), suggesting a theme of signaling-controlled cell movement in development and immunity. Some terms like sarcomere organization and symbiont entry are less cohesive with the core theme, but the dominant pattern supports a migration-signaling connection.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"wound healing","top_go_terms":[{"id":"GO:0043087","count":8},{"id":"GO:0097264","count":7},{"id":"GO:0045214","count":7},{"id":"GO:0061003","count":6},{"id":"GO:0010888","count":6}]},{"hash":"213059874274415490","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":183,"triangles":911,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":8},{"id":"GO:0055114","count":6},{"id":"GO:0006740","count":6},{"id":"GO:0006103","count":4},{"id":"GO:0042853","count":4}]},{"hash":"167382919842108216","title":"Lipid metabolism and detoxification","description":"Most terms point to lipid metabolism and lipid-derived signaling (triglyceride catabolism, phospholipid dephosphorylation, regulation of endocannabinoid signaling) and oxidative detoxification; a few terms reflect broader metabolism or development, but the dominant theme is lipid processing and detox pathways.","confidence":"Medium","size":21,"edges":76,"triangles":133,"max_degree":18,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0019433","count":13},{"id":"GO:2000124","count":12},{"id":"GO:0098869","count":11},{"id":"GO:0097755","count":10},{"id":"GO:0019391","count":10}]},{"hash":"200974061123900398","title":"Ubiquitin-Mediated Antiviral Defense","description":"This cluster is dominated by ubiquitin-related processes (autoubiquitination, ubiquitin-dependent ERAD and degradation, and K63-linked ubiquitination) alongside innate immune and antiviral responses (innate immune response, defense response to virus, TNF signaling). The peroxisomal protein import term may reflect broader metabolic-immune coordination. Together, these suggest a core theme of ubiquitin-regulated antiviral defense.","confidence":"High","size":21,"edges":43,"triangles":31,"max_degree":10,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:1903762","count":6},{"id":"GO:1901253","count":6},{"id":"GO:0045087","count":5}]},{"hash":"1676681260256906412","title":"Ribosome Biogenesis and Translation","description":"The top GO terms cluster around translation and ribosome biogenesis, including maturation of rRNA and ribosomal subunit assembly/biogenesis, indicating a cohesive group of ribosomal proteins and maturation factors involved in ribosome production and function. Hence the label Ribosome Biogenesis and Translation best describes the functional theme.","confidence":"High","size":21,"edges":179,"triangles":881,"max_degree":20,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":18},{"id":"GO:0000027","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0006407","count":3}]},{"hash":"1050063710528504012","title":"Retinoid metabolism and neural regeneration with ECM remodeling","description":"This cluster is driven by retinol and retinoic acid biosynthesis terms and the peripheral nervous system axon regeneration term, with supporting extracellular matrix organization and redox/detoxification signals. Together these suggest a theme where retinoid metabolism influences neural repair and tissue remodeling through ECM interactions, aided by oxidative stress management.","confidence":"Medium","size":21,"edges":21,"triangles":7,"max_degree":5,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042619","count":4},{"id":"GO:0017000","count":3},{"id":"GO:0030198","count":3},{"id":"GO:0016032","count":3}]},{"hash":"2000597711075704385","title":"Calcium-Driven Immune and Purinergic Signaling","description":"The terms cluster around innate immune defense against Gram-positive bacteria and cytokine production (IL-1\u03b2, IL-6), with prominent calcium signaling (import and release) and purinergic receptor pathways that also relate to nociception (pain, electrical stimulus). This suggests a cohesive module of calcium-dependent immune and purinergic signaling.","confidence":"High","size":21,"edges":39,"triangles":19,"max_degree":7,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0050718","count":4},{"id":"GO:0032755","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0098703","count":4}]},{"hash":"20935159952502076","title":"Developmental and Reproductive Processes","description":"The top GO terms span developmental pathways (SMAD signaling, cell shape regulation, myelination, astrocyte migration, skeletal development) and reproductive biology (oogenesis, sexual reproduction, male courtship behavior), suggesting a broad theme of development with reproductive aspects.","confidence":"Medium","size":21,"edges":53,"triangles":64,"max_degree":12,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0008049","count":4},{"id":"GO:0008360","count":4},{"id":"GO:0009313","count":4},{"id":"GO:0019953","count":4}]},{"hash":"1667002801915957277","title":"RIG-I\u2013driven innate antiviral signaling","description":"This cluster is characterized by terms pointing to innate immunity and antiviral sensing, especially positive regulation of RIG-I signaling and broad innate immune responses, plus host restriction of viral processes. The ubiquitin-dependent protein regulation and PML body-related terms suggest regulatory layers that modulate signaling and chromatin during antiviral responses, while retinoic acid and vitamin D receptor signaling imply metabolic-immune modulation connected to defense. Overall, the dominant theme is RIG-I\u2013mediated innate antiviral signaling with supporting ubiquitin- and nuclear-body\u2013related regulation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900246","count":2},{"id":"GO:2000059","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0036353","count":2},{"id":"GO:0070562","count":2}]},{"hash":"1598913917725977102","title":"Unknown","description":"The top GO terms are highly diverse (RNA localization, NF-kappaB signaling, integrin regulation, mitotic spindle checkpoint, cyclic nucleotide biosynthesis, miRNA processing, DNA replication initiation, voltage-gated sodium channel regulation, and chromatin silencing). There is no single cohesive biological function or pathway linking the majority of terms, and the cluster has no edges, suggesting the proteins do not form a clearly connected functional group. Therefore, a specific label is not justifiable.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051237","count":1},{"id":"GO:0007249","count":1},{"id":"GO:0033624","count":1},{"id":"GO:0044810","count":1},{"id":"GO:0009190","count":1}]},{"hash":"1505631033045510833","title":"Membrane Transporters","description":"The GO terms show multiple transmembrane transport activities across ions, sugars, vitamins, and organic substrates, including nitrite, sodium, potassium, phosphate, nitrate assimilation, galactose/arabinose transport, and even neurotransmitter loading. This suggests a cluster of membrane transporter proteins with broad substrate specificity.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":4},{"id":"GO:0071805","count":3},{"id":"GO:0035725","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0035435","count":3}]},{"hash":"1243640166196801645","title":"Innate antiviral immune response","description":"The dominant GO terms indicate antiviral defense and innate immunity, including defense against virus, innate immune response, suppression of viral release, and regulatory interactions with viral entry\u2014pointing to a cohesive antiviral defense theme. Related terms about cellular stress and microtubule localization may reflect immune signaling and trafficking; one outlier about meristem structure is likely annotation noise.","confidence":"Medium","size":21,"edges":14,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":5},{"id":"GO:0045087","count":4},{"id":"GO:0009934","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0071260","count":3}]},{"hash":"172274108515880719","title":"Antiviral innate immunity and chromatin regulation","description":"These proteins cluster around innate antiviral functions, including RIG-I signaling and host suppression of viral release, plus chromatin- and transcription-related processes such as PML body organization and histone ubiquitination. A carbohydrate metabolism term is present but likely incidental; the dominant theme appears to be host antiviral defense linked to chromatin regulation. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":2},{"id":"GO:1900246","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0035372","count":1},{"id":"GO:0036353","count":1}]},{"hash":"1956384227247924308","title":"Oxidative stress response and cell death","description":"This cluster\u2019s top GO terms center on redox biology and detoxification (oxidation-reduction process, cellular oxidant detoxification) and include programmed necrotic cell death, suggesting a common theme of responding to oxidative stress and coordinating cell fate. A few terms (cellulose catabolic process, flocculation, protein homooligomerization) are less consistent with this theme, likely reflecting broader or pleiotropic functions or dataset noise. Overall, the oxidative stress and cell death signal dominates, justifying the label.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0044533","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0000501","count":2}]},{"hash":"1974827914626266946","title":"Endosome-to-Melanosome Trafficking and Recycling","description":"The cluster is dominated by GO terms for endocytic and secretory vesicle transport\u2014endosome-to-melanosome transport, melanosome transport, Golgi-to-endosome transport\u2014and endocytic recycling, indicating a cohesive vesicle trafficking module within the endomembrane system; related terms on secretory pathways (Cvt/autophagy targeting, degranulation) reinforce a broad vesicle handling theme.","confidence":"High","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035646","count":3},{"id":"GO:0032402","count":3},{"id":"GO:0032456","count":3},{"id":"GO:0071260","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1146785092517626358","title":"Neural development and cortical layering","description":"The prominent GO terms focus on neuron guidance (serotonergic and dopaminergic axon guidance, planar polarity) and cortical organization (layer formation in cerebral cortex), pointing to neural development and brain structuring. Calcium signaling and growth-related processes are consistent with developmental signaling, while electron transport and angiogenesis can support broader cellular and vascular aspects of developing neural tissue. Overall, the cluster centers on neural development, cortical layering, and associated signaling pathways.","confidence":"Medium","size":21,"edges":63,"triangles":45,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0022900","count":6},{"id":"GO:0048105","count":5},{"id":"GO:0036515","count":5},{"id":"GO:1904938","count":5},{"id":"GO:0036514","count":5}]},{"hash":"2101819191275932234","title":"Neural development and glial differentiation","description":"Dominant signals include Schwann cell development and substantia nigra development, both neural tissue\u2013related; cell-cell adhesion supports developmental tissue organization, and sphingomyelin catabolic processes align with myelin/lipid metabolism important for glial function. While some terms touch on general DNA repair and transcription, the strongest theme is nervous system development and glial differentiation.","confidence":"Medium","size":21,"edges":106,"triangles":238,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006685","count":11},{"id":"GO:0031573","count":10},{"id":"GO:0014044","count":10},{"id":"GO:1905205","count":10},{"id":"GO:0030847","count":10}]},{"hash":"1287860637687870006","title":"Cytoskeleton dynamics and polarity signaling","description":"This cluster centers on cytoskeleton regulation (Rac signaling, spindle assembly) and membrane trafficking (pinocytosis), tied to epithelial polarity; supporting signaling pathways (calcium, cGMP) suggest broader signal integration, with ubiquitination potentially modulating these processes. ","confidence":"Medium","size":21,"edges":16,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0045736","count":1},{"id":"GO:0098703","count":1},{"id":"GO:0071321","count":1},{"id":"GO:0048549","count":1}]},{"hash":"2257861206744011501","title":"Immune signaling and wound repair","description":"The cluster shows enrichment for adaptive immune response, positive regulation of T cell proliferation, fibroblast proliferation, wound healing, and blood coagulation, plus phosphatidylinositol-mediated signaling. These together suggest a theme of immune activation linked to tissue repair/remodeling, despite some peripheral/obsolete terms present.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048146","count":2},{"id":"GO:0042102","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0007286","count":2}]},{"hash":"1403769141227053690","title":"Insulin signaling and secretory vesicle trafficking","description":"The cluster\u2019s top GO terms center on insulin receptor signaling regulation, insulin secretion, secretory granule localization, and vesicle transport along actin\u2014together indicating a core theme of insulin-regulated secretory pathways and vesicle trafficking. Additional terms about transcription regulation and ubiquitination are present but appear less central, suggesting these proteins primarily participate in insulin-related signaling and vesicle dynamics with some multifunctionality.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046626","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0042098","count":2},{"id":"GO:0032252","count":2}]},{"hash":"468485881268176457","title":"Metabolism and DNA Repair","description":"This cluster centers on metabolic processes (metabolic process, L-alpha-amino acid transport, regulation of nitrogen utilization, toxin catabolic process) and genome maintenance (nucleotide-excision repair, apoptotic DNA fragmentation). There are some outliers like erythrocyte differentiation and auxin signaling, which are not tightly aligned with metabolism/repair and may reflect broader or cross-species annotations. Overall, the dominant theme suggests metabolism with a DNA repair/maintenance component, but the connections are moderate rather than strong.","confidence":"Medium","size":21,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030218","count":6},{"id":"GO:0006309","count":6},{"id":"GO:1902475","count":2},{"id":"GO:0008152","count":2},{"id":"GO:0006289","count":2}]},{"hash":"1850258095290328899","title":"Unknown","description":"There are no GO terms or network connections to define a shared function for this cluster; with 0 edges and no top terms, a common theme cannot be inferred. Although 20 proteins were re-added by ReCIPE, this does not establish a cohesive functional signal.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1693636061490335611","title":"Unknown","description":"There are no top GO terms listed, and the cluster shows no edges or triangles, so there is no shared functional signal to define a specific process or location. With 21 proteins and no functional hints, the safest label is Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1797023419720346137","title":"Actin Cytoskeleton Dynamics","description":"Dominant GO terms cluster around actin cytoskeleton organization and actin filament\u2013based movement (barbed-end capping, bundling), with additional terms touching on neural/immune development contexts. The strongest common theme is actin remodeling and cytoskeletal dynamics, suggesting the proteins collectively influence cell motility and cytoskeletal rearrangements, even across different tissue contexts.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035855","count":1},{"id":"GO:0002625","count":1},{"id":"GO:0051016","count":1},{"id":"GO:0030048","count":1},{"id":"GO:0030046","count":1}]},{"hash":"1306663062971854834","title":"Golgi sugar-nucleotide transport and glycosylation","description":"The top terms point to membrane transport with a strong focus on Golgi lumen import/export of nucleotide sugars (UDP-glucose, GDP-fucose) and fucosylation-related glycosylation steps, indicating a cluster centered on Golgi-associated sugar transport and glycosylation. Some terms also reflect general transmembrane transport (amino acids, calcium, nitrate) and carbohydrate metabolism, but the Golgi sugar transport/glycosylation theme is the most representative.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0032973","count":7},{"id":"GO:1990034","count":7},{"id":"GO:0036085","count":6},{"id":"GO:0015786","count":6},{"id":"GO:0042149","count":5}]},{"hash":"2234652445096250877","title":"Neuro-Muscular Development and Movement","description":"The cluster is enriched for neural development and motor function terms: somatic motor neuron differentiation, neuromuscular process controlling posture, and musculoskeletal movement, complemented by neural-support factors like neurofilament organization and Schwann cell migration. Glutamate reuptake points to neurotransmitter handling, while collagen biosynthesis hints at ECM roles in nerve-muscle connectivity. Together, these indicate a cohesive theme around neural development and the control of movement, with supporting tissue remodeling.","confidence":"High","size":21,"edges":199,"triangles":1136,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0060052","count":3},{"id":"GO:0050884","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0006655","count":3},{"id":"GO:0021523","count":2}]},{"hash":"1001206177398039254","title":"Lipid metabolism and GPCR signaling","description":"This cluster is characterized by lipid-related processes, notably sphingomyelin catabolic process and lysobisphosphatidic acid metabolic process, suggesting a theme of sphingolipid/lysosomal lipid turnover. It also includes an adenylate cyclase-inhibiting GPCR signaling term, pointing to GPCR-mediated regulation of cAMP. While there are some tissue-specific terms related to prostate gland development, the dominant signals tie lipids to signaling pathways, making this a cohesive lipid-metabolism\u2013signaling cluster.","confidence":"Medium","size":21,"edges":9,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006685","count":2},{"id":"GO:0060736","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0060742","count":2},{"id":"GO:0007193","count":2}]},{"hash":"2007583278257995050","title":"Nucleotide metabolism and RNA editing","description":"The cluster includes multiple GO terms centered on nucleotides and RNA-related processes (uridine/UMP salvage, cytidine/cytosine metabolism, deoxycytidine catabolism, guanine catabolic process) and RNA modification such as tRNA wobble adenosine to inosine editing, with a broader flavor including riboflavin biosynthesis. Together these suggest a core theme of nucleic acid/nucleotide metabolism and RNA editing, though a few outlier terms (e.g., cellulose catabolic process, antibiotic response) contribute less to the main signal.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0006147","count":1},{"id":"GO:0002100","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0046109","count":1}]},{"hash":"1416185503628059173","title":"Neuronal vesicle trafficking and exocytosis","description":"The top GO terms cluster around intracellular vesicle transport pathways (Golgi\u2013plasma membrane, lysosomal, endocytic recycling, retrograde transport) and vesicle tethering/exocytosis, including dense core granule transport. The inclusion of nervous system development and visual learning terms suggests a neuronal/secretory context, consistent with proteins coordinating vesicle trafficking and secretion in neurons. ","confidence":"High","size":20,"edges":189,"triangles":1122,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006893","count":3},{"id":"GO:0090326","count":3},{"id":"GO:0007041","count":3},{"id":"GO:0032456","count":3},{"id":"GO:0006896","count":3}]},{"hash":"754176990391745505","title":"ABA-Driven Stomatal Regulation and Microtubule Dynamics","description":"The cluster is dominated by GO terms for abscisic acid response and regulation of stomatal movement, indicating ABA-mediated control of stomatal aperture. The presence of cortical microtubule organization suggests associated cytoskeletal remodeling in guard cells during stomatal opening/closing. Other terms (e.g., transcription, autophagy, DNA damage response) may reflect broad stress responses, but the core theme aligns with ABA signaling regulating stomata via microtubule dynamics.","confidence":"Medium","size":20,"edges":20,"triangles":15,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0043622","count":2},{"id":"GO:0010119","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0006351","count":1},{"id":"GO:0010165","count":1}]},{"hash":"2256658008203808164","title":"DNA replication and chromatin assembly","description":"The top GO terms center on DNA replication and CENP-A\u2013chromatin assembly, with supporting signals from cell division and microtubule dynamics, pointing to replication-associated chromatin maintenance and chromosome segregation. Some vesicle trafficking-related terms appear but are likely less central to the cluster\u2019s core function. Overall, the cluster seems enriched for nuclear replication and chromatin organization processes rather than a single cytosolic pathway.","confidence":"Medium","size":20,"edges":132,"triangles":503,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0070651","count":4},{"id":"GO:0051013","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0051301","count":3}]},{"hash":"196854123048888512","title":"Seed Coat Lipid and Phenylpropanoid Metabolism","description":"The cluster centers on seed-related processes (seed coat development and regulation of seed germination) and lipid metabolism (medium- and long-chain fatty acid metabolism and transport), with phenylpropanoid metabolism supporting seed coat chemistry, suggesting a plant seed metabolism program; a couple of terms (lipoteichoic acid biosynthetic process, bioluminescence) appear as potential noise or cross-species annotations.","confidence":"Medium","size":20,"edges":145,"triangles":559,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0036112","count":7},{"id":"GO:0001579","count":7},{"id":"GO:0010214","count":7},{"id":"GO:0008218","count":7},{"id":"GO:0001676","count":7}]},{"hash":"2264068394401717704","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":46,"triangles":41,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006574","count":13},{"id":"GO:0017000","count":12},{"id":"GO:0010124","count":11},{"id":"GO:0006635","count":11},{"id":"GO:0009234","count":11}]},{"hash":"695610822583645473","title":"Apoptosis and Immune Signaling","description":"The terms point to a stress-response network where innate immune and TNF signaling intersect with cell-cycle control and the execution phase of apoptosis, governed by transcriptional programs. This suggests a cohesive module centered on inflammation-linked cell fate decisions, with some developmental terms likely reflecting broader signaling roles. ","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0097194","count":2}]},{"hash":"1563244066790920533","title":"Adipogenesis and Angiogenesis","description":"The cluster is dominated by terms linking fat cell differentiation and vascular development, notably adipocyte formation and responses to VEGF, along with supporting signals for cell migration and proliferation (G1/S transition) that would enable expansion and remodeling of adipose tissue and its vasculature. Telomere maintenance and capping terms suggest genomic stability in proliferating progenitors, while muscle stretch response may reflect mechanotransduction during tissue remodeling. Overall, these terms point to coordinated adipogenesis with concurrent angiogenesis and tissue remodeling.","confidence":"Medium","size":20,"edges":38,"triangles":15,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006397","count":5},{"id":"GO:0000082","count":4},{"id":"GO:0035924","count":4},{"id":"GO:1904355","count":4},{"id":"GO:0035994","count":4}]},{"hash":"79228810711142638","title":"Nucleolar RNA Processing and Cell Cycle Control","description":"The proteins are enriched for nucleolar localization and RNA processing activities (mRNA capping, splicing, helicase regulation) alongside cell cycle control (CDK activity regulation, ubiquitination). This suggests a cohesive nucleolar RNA-processing module that interfaces with cell-cycle regulation, despite a few outliers. ","confidence":"High","size":20,"edges":190,"triangles":1140,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:1902570","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0016567","count":2}]},{"hash":"692453917402974359","title":"Neuronal development and signaling","description":"These proteins appear linked to nervous system development and synaptic signaling, as shown by terms like visual perception, excitatory postsynaptic potential, and Schwann cell development. Additionally, they are enriched for signaling pathway regulation and protein modification (ERK/JNK cascades, ubiquitination, phosphorylation) and apoptosis, suggesting a coordinated network governing neural signaling and cell fate in this cluster.","confidence":"Medium","size":20,"edges":16,"triangles":0,"max_degree":7,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007601","count":4},{"id":"GO:0001403","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0014044","count":4},{"id":"GO:0070374","count":3}]},{"hash":"728720238260539152","title":"Immunoglobulin diversification and DNA repair","description":"This cluster is dominated by GO terms for somatic hypermutation of immunoglobulin genes and class-switch recombination (IgG/IgA), indicating immunoglobulin diversification. It also features DNA repair and cell-cycle related terms (mismatch repair, helicase regulation, intra-S checkpoint), suggesting genome maintenance during antibody diversification. A few terms related to germ cell development and energy metabolism appear, but the dominant signal is immunoglobulin diversification coupled with DNA repair processes.","confidence":"High","size":20,"edges":11,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016446","count":2},{"id":"GO:0006119","count":2},{"id":"GO:0043570","count":2},{"id":"GO:0031573","count":2},{"id":"GO:0051096","count":2}]},{"hash":"788965729089386843","title":"Unknown","description":"The Top Terms are a mix of cell-cycle regulation (CDK activity, spindle assembly) and diverse processes (calcium transport, pinocytosis, epithelial polarity, ubiquitination) plus immune/differentiation signals. The cluster does not converge on a single clear function or theme, making a coherent high-level label inappropriate.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":3},{"id":"GO:0045736","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0090162","count":2}]},{"hash":"40862301543400330","title":"RNAi and miRNA processing machinery","description":"The top GO terms cluster around RNA interference and small RNA biogenesis (RISC assembly, miRNA processing and metabolism, primary miRNA processing), with additional RNA-processing terms suggesting a broader RNA metabolism role; the dominant signal is RNA silencing.","confidence":"High","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031152","count":2},{"id":"GO:1903669","count":2},{"id":"GO:1903665","count":2},{"id":"GO:0008033","count":1},{"id":"GO:0045589","count":1}]},{"hash":"1860933580573238217","title":"LPS Core and O-antigen Biosynthesis","description":"The top GO terms cluster around lipopolysaccharide biosynthesis, including core region and O-antigen assembly and sugar donor pathways (dTDP-rhamnose, ADP-L-glycero-beta-D-manno-heptose), indicating a cohesive role in LPS and related polysaccharide biosynthesis in Gram-negative bacteria. Some other terms appear ancillary.","confidence":"High","size":20,"edges":94,"triangles":246,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":8},{"id":"GO:0006541","count":8},{"id":"GO:0009244","count":7},{"id":"GO:0019835","count":7},{"id":"GO:0055114","count":6}]},{"hash":"1778967383613416380","title":"Translation","description":"The only annotated function is translation (GO:0006412), indicating a possible focus on protein synthesis; with no other shared GO terms or interactions evident, the label reflects the minimal but explicit translation-related function observed in this cluster.","confidence":"Low","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1}]},{"hash":"2239282503964808811","title":"Nucleotide metabolism and phosphorylation","description":"The cluster is dominated by GO terms related to phosphorylation and nucleotide biosynthesis/ salvage (phosphorylation, dephosphorylation, nucleoside monophosphate phosphorylation, NAD+ and coenzyme A biosynthesis, UMP salvage, and pyrimidine metabolism), suggesting a cohesive theme around nucleotide metabolism and nucleotide-derivative biosynthesis. Some ancillary terms like DNA repair and viral process appear but do not define the main function.","confidence":"High","size":20,"edges":136,"triangles":496,"max_degree":19,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046939","count":7},{"id":"GO:0046940","count":7},{"id":"GO:0015937","count":7},{"id":"GO:0016310","count":7},{"id":"GO:0009435","count":6}]},{"hash":"172419195576058362","title":"Aromatic amino acid catabolism and cofactor biosynthesis","description":"The top GO terms cluster around breakdown of phenylalanine and tyrosine (phenylalanine/tyrosine catabolic and homogentisate catabolic processes) and synthesis of cofactors (molybdenum cofactor/MoCo and protoporphyrinogen IX). This points to a cohesive theme of aromatic compound degradation coupled with cofactor biosynthesis, despite a few broader terms (DNA-templated transcription, apoptotic process) present. Overall, a metabolic enzyme/cofactor assembly focus best fits the cluster.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0006559","count":2},{"id":"GO:0006572","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0006782","count":2}]},{"hash":"1133887632134198200","title":"Bacterial Type III secretion and flagellum assembly","description":"The top GO terms are dominated by bacterial virulence/motility components: protein secretion via the Type III secretion system and bacterial-type flagellum assembly, with energy aspects tied to proton motive force-driven ATP synthesis. While there are a few general transcriptional and amino acid homeostasis terms present, the strongest and most coherent signal across the cluster points to bacterial secretion and flagellar machinery. This suggests a functionally related group of proteins involved in secretion and motility systems in bacteria, rather than a single eukaryotic process.","confidence":"Medium","size":20,"edges":122,"triangles":392,"max_degree":19,"top_function":"lipid metabolic process","top_go_terms":[{"id":"GO:0030254","count":3},{"id":"GO:0042776","count":3},{"id":"GO:0043536","count":3},{"id":"GO:0006626","count":3},{"id":"GO:0090465","count":3}]},{"hash":"1202746018855912473","title":"Glycosylation and ER-Golgi Trafficking","description":"Based on the top GO terms, the proteins are enriched for N- and O-linked glycosylation and for ER-to-Golgi vesicle transport, including SNARE complex disassembly, which points to processing and trafficking in the secretory pathway. Additional terms like ribosomal subunit assembly and microtubule severing may reflect broader cytoskeletal or ribosome-related roles, but the strongest shared function appears to be protein modification via glycosylation and trafficking through the ER-Golgi network.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:0035269","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0051013","count":1},{"id":"GO:0070370","count":1}]},{"hash":"2115807877731478962","title":"Innate antiviral defense and viral restriction","description":"The prevalent GO terms center on innate immune response and antiviral signaling, including positive regulation of RIG-I signaling, innate immune response, suppression of viral release by host, and PML body organization, all indicating host antiviral defense. Additional terms related to retinoic acid and vitamin D receptor signaling suggest immunomodulatory context, while ubiquitin and microtubule localization terms can support antiviral processes. Overall, the cluster seems to group proteins involved in innate antiviral sensing and restriction.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900246","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0035372","count":1},{"id":"GO:0036353","count":1},{"id":"GO:0070562","count":1}]},{"hash":"1538450283042196879","title":"Embryonic development and organogenesis","description":"Terms cluster around developmental processes and morphogenesis across multiple tissues\u2014gastrulation cell migration, convergent extension in organogenesis/axis elongation, pancreas and prostate development, primitive hematopoiesis, and cardioblast differentiation\u2014plus regulation of transcription. The shared theme is embryonic development and tissue formation rather than a specific pathway. With no evident protein\u2013protein interactions (edges/triangles zero), the label captures a broad developmental theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042074","count":1},{"id":"GO:0014812","count":1},{"id":"GO:0060029","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0031016","count":1}]},{"hash":"2053982475991147266","title":"Neural signaling and plasticity","description":"This cluster centers on brain-related processes: hippocampus development, visual perception, dopamine response, and regulation of synaptic plasticity, all linked through ERK/MAPK signaling. While there are a few non-neural terms (e.g., T cell signaling, heart development), the predominant signals point to neural development and synaptic communication. ","confidence":"Medium","size":20,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0033138","count":7},{"id":"GO:0070374","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0021766","count":5},{"id":"GO:0000186","count":5}]},{"hash":"467665825109666534","title":"Negative regulation of NF-kappaB and immune signaling","description":"These proteins cluster around suppression of immune and inflammatory signaling: multiple terms describe negative regulation of canonical NF-kappaB signaling, leukocyte migration, B cell activation, germinal center formation, and TNF production. The presence of ubiquitination and deubiquitination terms (K48- and K11-linked) implies regulation via post-translational modifications, reinforcing a theme of downregulation of immune responses.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043124","count":2},{"id":"GO:0002686","count":1},{"id":"GO:0002634","count":1},{"id":"GO:0002677","count":1},{"id":"GO:0045736","count":1}]},{"hash":"2052342868839181062","title":"Neuronal development and axon growth signaling","description":"The top GO terms cluster around nervous system development, axon extension, and glutamatergic synaptic transmission, with supporting involvement of growth hormone and insulin receptor signaling. This points to a neuronal development program focusing on neuron formation, axon outgrowth, and synaptic communication, with accompanying transcriptional regulation. Hence the theme is coherent and specific to neuronal development and axon growth.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0045773","count":3},{"id":"GO:0060396","count":3},{"id":"GO:0035249","count":3}]},{"hash":"1591181800760564028","title":"Unknown","description":"The top GO terms span very different contexts\u2014plant reproductions (pollen sperm differentiation, sexual reproduction), animal development (germ-band extension, apical constriction in gastrulation), and bacterial processes (protein secretion by Type I secretion system, bacteriocin transport), plus general cellular functions like cellulose catabolic process, glycosylation, and proteolysis\u2014indicating no cohesive functional theme linking these proteins. Therefore a single descriptive label is not supported.","confidence":"","size":20,"edges":58,"triangles":69,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0007377","count":2},{"id":"GO:0048235","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0003384","count":1}]},{"hash":"1711200275367128162","title":"Unknown","description":"The GO terms are highly diverse, spanning heart/brain development, mitochondrial complex IV assembly and cytochrome c oxidase activity, protein farnesylation, copper ion transfer, ion transport, lipid digestion, salt stress response, and actin cytoskeleton polarity. With no clear shared function or pathway linking these terms, there isn\u2019t a cohesive theme to name the cluster; thus, Unknown is most appropriate.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":1},{"id":"GO:0033617","count":1},{"id":"GO:0018343","count":1},{"id":"GO:1904960","count":1},{"id":"GO:0015680","count":1}]},{"hash":"2039929966252833620","title":"Amino acid biosynthesis and N-terminal acetylation","description":"This cluster shows several specific biosynthetic processes (e.g., L-arginine, glucosamine, mycothiol, melatonin) together with multiple N-terminal acetylation/propionylation terms, suggesting a group of proteins tied to amino acid/small-molecule biosynthesis and protein N-terminal modification. Confidence reflects a coherent but broad linkage across diverse biosynthetic pathways and modification activities.","confidence":"Medium","size":20,"edges":67,"triangles":102,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":7},{"id":"GO:0045150","count":6},{"id":"GO:0017198","count":6},{"id":"GO:0030187","count":6},{"id":"GO:0018002","count":6}]},{"hash":"2118634755534143248","title":"Bacterial cell wall and teichoic/lipoteichoic acid biosynthesis","description":"These terms emphasize biosynthesis of lipid A, fatty acids, teichoic and lipoteichoic acids, and cell wall organization, indicating a cluster centered on bacterial cell envelope construction and modification. The inclusion of antibiotic and nonribosomal peptide biosynthesis hints at secondary metabolites linked to cell wall\u2013active compounds, reinforcing the envelope-biosynthesis theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009245","count":1},{"id":"GO:0043041","count":1},{"id":"GO:0070395","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0006633","count":1}]},{"hash":"695574312114395490","title":"Unknown","description":"The top GO terms span innate immunity, transcription, microtubule localization, Schwann cell and heart development, plant ABA signaling, visual perception, and cell cycle transitions, with no clear unifying biological process. The proteins show no evidence of interactions (Edges: 0), so a single cohesive label cannot be justified.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0035372","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0014044","count":2}]},{"hash":"952725318501238791","title":"Unknown","description":"There are no shared GO terms or network connections among the 20 proteins (no edges, triangles, or annotated terms), so a coherent common function cannot be inferred from the data provided. The safest label is Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"540875265070275647","title":"Developmental transcription and growth signaling regulators","description":"This cluster centers on transcriptional regulation and developmental signaling, with GO terms for DNA-templated transcription and its regulation, plus pathways related to growth hormone and insulin signaling, and muscle/heart development. The presence of B cell receptor signaling and hemopoiesis hints at broader immune-development roles within the same developmental program.","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0060396","count":3},{"id":"GO:0046626","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0006355","count":2}]},{"hash":"2028457404968015668","title":"Ubiquitin-dependent proteolysis and cell cycle control","description":"This cluster centers on ubiquitin-mediated protein catabolism (ubiquitin-dependent proteolysis and autoubiquitination) and cell cycle regulation (including negative regulation of CDK kinase activity and general cell cycle processes), with references to mitotic spindle\u2013associated localization. Together, these terms imply proteins that tag regulators for degradation to control cell cycle progression, particularly mitosis. Additional terms touching JNK and TNF signaling, and transcriptional regulation, reflect broader roles of ubiquitination in signaling and gene expression, supporting a cohesive theme of ubiquitin-driven regulation. Edge absence does not negate this shared functional theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0051865","count":3},{"id":"GO:0045736","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0035853","count":2}]},{"hash":"546590433853078801","title":"Unknown","description":"The top GO terms span diverse biological themes\u2014neural development (synapse assembly, innervation), cardiac and heart outflow tract development (outflow tract morphogenesis, regulation of atrial cardiac muscle cell action potential), bone and pancreatic development (ossification, pancreatic cell apoptosis), general cellular processes (protein localization to microtubule, calcium transporter activity), and innate immunity (innate immune response, suppression of viral release). There is no single coherent function across the cluster, so a specific, high-level label cannot be meaningfully assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060386","count":3},{"id":"GO:0003151","count":2},{"id":"GO:0097050","count":2},{"id":"GO:0035372","count":2},{"id":"GO:1901896","count":2}]},{"hash":"2003646562727687719","title":"Vacuolar acidification and organelle ion transport","description":"Top GO terms indicate processes tied to vacuoles and ion transport: vacuolar acidification, vacuole organization, protein targeting to vacuole; proton transmembrane transport and proton motive force-driven ATP synthesis; sodium ion transport; copper ion homeostasis. Together these suggest a cohesive role in maintaining organelle ion gradients and vacuolar pH, with involvement in protein trafficking to the vacuole. Confidence in this theme is moderate, given some terms are broad or orthogonal to a single pathway.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0006878","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0007035","count":2}]},{"hash":"331183618488556216","title":"Axon Guidance and Vascular/Limb Morphogenesis","description":"The cluster prominently features terms related to neural development and axon guidance (positive regulation of axonogenesis, chemorepulsion of branchiomotor axon, vagus nerve morphogenesis) alongside endothelial and limb morphogenesis (endothelial morphogenesis, limb bud formation, positive regulation of endothelial chemotaxis), suggesting a cohesive role in developmental signaling across neural and vascular/limb tissues. Additional GO terms on receptor tyrosine kinase signaling and chromatin regulation support a broad developmental regulatory theme.","confidence":"Medium","size":20,"edges":138,"triangles":485,"max_degree":19,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0007169","count":3},{"id":"GO:0035563","count":3},{"id":"GO:0033689","count":3},{"id":"GO:0021793","count":3},{"id":"GO:0050918","count":3}]},{"hash":"133725244253414153","title":"Unknown","description":"There are no top GO terms and no edges or connections among the 20 proteins, so there is no identifiable shared function or common theme to define a label.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1646933996096321997","title":"Mitochondrial Apoptosis Regulation","description":"The top GO terms point to mitochondrial-dependent control of cell death, including cytochrome c release and regulation of mitochondrial depolarization, suggesting a coherent theme of apoptosis regulation via mitochondrial pathways. Other terms about development and lysosomal processes may be incidental or reflect multi-function proteins, but the apoptosis-mitochondria signal is strong.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001240","count":1},{"id":"GO:0001836","count":1},{"id":"GO:0043154","count":1},{"id":"GO:0051902","count":1},{"id":"GO:0001889","count":1}]},{"hash":"241795209631730096","title":"Cell Migration and Tissue Morphogenesis","description":"The main GO terms point to movement and shaping of tissues (dendritic spine morphogenesis, prostate gland morphogenesis, cardiac muscle differentiation, sprouting angiogenesis-related migration) and adhesion (cell-matrix adhesion), with several entries emphasizing various forms of cell migration. While there are a few outliers (lipid storage regulation, self proteolysis, symbiont entry), the dominant theme is cells migrating and contributing to tissue morphogenesis, suggesting a cohesive cluster around developmental remodeling and movement.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"wound healing","top_go_terms":[{"id":"GO:0061003","count":4},{"id":"GO:0010888","count":4},{"id":"GO:0097264","count":4},{"id":"GO:0061097","count":4},{"id":"GO:0060740","count":4}]},{"hash":"113378436109341385","title":"DNA damage repair and genome maintenance","description":"This cluster is dominated by GO terms for DNA replication and multiple DNA repair pathways (nucleotide-excision repair, base-excision repair, and classical nonhomologous end joining) as well as a general response to DNA damage (e.g., X-ray exposure). The presence of V(D)J recombination and pro-B cell differentiation terms aligns with repair processes used during immune receptor diversification, supporting a cohesive theme of genome maintenance and DNA damage response.","confidence":"High","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006297","count":4},{"id":"GO:0010165","count":4},{"id":"GO:0006288","count":4},{"id":"GO:0000466","count":4}]},{"hash":"398515741157591385","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":171,"triangles":969,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006268","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0000184","count":5},{"id":"GO:0048026","count":4}]},{"hash":"1691789213677929091","title":"Cell Cycle Regulation and Ubiquitin-Mediated Control","description":"The cluster centers on regulatory processes linked to cell cycle control\u2014DNA replication initiation, and spindle assembly in meiosis\u2014tied to protein turnover via ubiquitination (protein polyubiquitination and its positive regulation). While some GO terms point to broader regulatory roles (circadian rhythm regulation) or stress responses (arsenic exposure, oxidative stress\u2013induced neuronal apoptosis), the dominant theme is regulators of cell-cycle transitions and ubiquitin signaling that modulate protein levels during division.","confidence":"Medium","size":19,"edges":15,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":4},{"id":"GO:0021678","count":3},{"id":"GO:0006516","count":3},{"id":"GO:1903378","count":3},{"id":"GO:0042752","count":3}]},{"hash":"26732694288869311","title":"Proviral integration and latency","description":"This cluster centers on retroviral-like steps: reverse transcription (RNA-templated DNA synthesis), DNA replication and recombination, DNA integration, and establishment of integrated proviral latency, plus viral entry into host cells and suppression of host RNAi processing\u2014unifying around the retroviral life cycle and genome integration.","confidence":"High","size":19,"edges":84,"triangles":178,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0075713","count":1},{"id":"GO:0039651","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0015074","count":1}]},{"hash":"1467306293051297627","title":"Diverse Metabolism and Transport Functions","description":"The cluster centers on basic metabolic and transport-related processes: fatty acid biosynthesis, GTP biosynthesis, magnesium ion transmembrane transport, glycine betaine transport, and L-homocysteine catabolic activity, suggesting a broad metabolic/transport theme. The presence of additional terms related to retina development and immune signaling likely reflects multifunctional proteins or annotation noise, but the dominant signals point to metabolism and transport rather than a single, cohesive pathway.","confidence":"Medium","size":19,"edges":11,"triangles":1,"max_degree":4,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0060041","count":4},{"id":"GO:0071353","count":4},{"id":"GO:0030071","count":3},{"id":"GO:1903830","count":3},{"id":"GO:0046651","count":3}]},{"hash":"1601134124319467202","title":"Nuclear RNA Export and Telomere Tethering","description":"The cluster shows multiple RNA export (tRNA, mRNA, ribosomal subunits) and nuclear pore organization terms, together with telomere/periphery tethering and chromatin regulation at telomeres, indicating a shared theme of nuclear transport and genome organization at the nuclear periphery.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006409","count":1},{"id":"GO:0006607","count":1},{"id":"GO:0035392","count":1},{"id":"GO:0016973","count":1},{"id":"GO:0000973","count":1}]},{"hash":"2029552720219768113","title":"DNA replication and cell cycle regulation","description":"This cluster centers on core DNA metabolism and cell cycle processes, including DNA replication, mitotic chromatid cohesion, and DNA-templated transcription, with supporting chromatin regulation via deubiquitination and methylation. These terms together suggest a cohesive role in DNA replication and cell-cycle control, with chromatin-modifying activities modulating these processes.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0035753","count":1},{"id":"GO:1900264","count":1}]},{"hash":"1830331819407129131","title":"Actin Cytoskeleton Remodeling","description":"Dominant enrichment for actin-related processes (filament polymerization, lamellipodium/ bundle assembly, and cytoskeleton organization) plus dendritic spine morphogenesis points to a cluster of proteins involved in actin remodeling and protrusive structures, with a few peripheral terms (vacuole inheritance, lymphocyte migration) that are less central. ","confidence":"High","size":19,"edges":28,"triangles":15,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030041","count":3},{"id":"GO:1903526","count":3},{"id":"GO:0030032","count":3},{"id":"GO:0030036","count":3},{"id":"GO:0051497","count":3}]},{"hash":"783308948192376812","title":"ER-Golgi Vesicle Trafficking and Golgi Localization","description":"Top GO terms cluster around secretory pathway organization and Golgi dynamics, including ER-to-Golgi vesicle transport, retrograde endosome-to-Golgi transport, endocytosis, Golgi inheritance/localization, and protein targeting to vacuole. These collectively point to a group of proteins involved in ER-Golgi trafficking and Golgi function, with a few outlier terms such as viral genome replication and pigmentation that are less representative. ","confidence":"High","size":19,"edges":110,"triangles":341,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0043547","count":4},{"id":"GO:0019079","count":3},{"id":"GO:0042989","count":3},{"id":"GO:0006897","count":3}]},{"hash":"2237890245405230470","title":"DNA Replication and Gene Expression Control","description":"Most terms cluster around genome maintenance (DNA recombination, DNA replication) and core gene-expression steps (transcription by RNA Pol II, translation), with SOS response supporting a DNA-damage signaling context. This suggests a module coordinating DNA repair with transcription/translation control, despite a few peripheral terms that are less central to this theme.","confidence":"Medium","size":19,"edges":98,"triangles":220,"max_degree":15,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1719659706400799504","title":"Steroid and Prostaglandin Lipid Biosynthesis","description":"The cluster shows strong enrichment for biosynthesis and metabolism of lipid-derived signaling molecules, including steroid hormones (testosterone, androgens, aldosterone, ecdysone) and prostaglandins, plus related lipid oxidation and retinoid metabolism, indicating a cohesive role in lipid hormone production and signaling.","confidence":"High","size":19,"edges":72,"triangles":144,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":14},{"id":"GO:0061370","count":9},{"id":"GO:0008209","count":9},{"id":"GO:0061298","count":9},{"id":"GO:0009636","count":8}]},{"hash":"1995401842139952495","title":"Mitotic cell cycle and microtubule transport","description":"This cluster is dominated by terms for cell division and cell cycle, plus tubulin complex assembly and plus-end-directed vesicle transport along microtubules, pointing to mitotic microtubule dynamics and microtubule-based trafficking. The presence of autophagosome maturation and Rab/Rap signaling suggests related vesicle trafficking and autophagy processes linked to the microtubule network; translation/RNA processing terms may be background functions. ","confidence":"Medium","size":19,"edges":76,"triangles":155,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0007021","count":2},{"id":"GO:0006412","count":2}]},{"hash":"166705143921392463","title":"Innate immune signaling and xenophagy","description":"Proteins cluster around innate immune responses to pathogens, including dsRNA sensing, LPS signaling, interferon-beta production, and general innate defense, with a clear drive toward xenophagy/autophagy-based pathogen clearance, plus related regulation of apoptosis and cell migration.","confidence":"High","size":19,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043330","count":4},{"id":"GO:0031663","count":4},{"id":"GO:1904417","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0045359","count":4}]},{"hash":"739515529558238475","title":"Dendritic Spine Actin Remodeling","description":"The Top Terms cluster around actin cytoskeleton regulation and dendritic spine biology, with emphasis on barbed-end actin capping, spine morphogenesis, and motility, plus localization to actin-rich patches. This points to actin remodeling in dendritic spines and related cellular movement, rather than unrelated pathways. Some outliers (host-virus and fungal defense terms) exist but do not dominate the set. ","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000814","count":1},{"id":"GO:0061001","count":1},{"id":"GO:0014823","count":1},{"id":"GO:0044794","count":1},{"id":"GO:1902951","count":1}]},{"hash":"856120086856962000","title":"Nuclear RNA Surveillance and Decay","description":"The terms are dominated by nuclear RNA quality-control and decay processes (nuclear mRNA surveillance, histone mRNA decay, and catabolic processes for snoRNA and snRNA, including polyadenylation-dependent routes), pointing to a shared function in nuclear RNA turnover. The other terms (ion transport, plastid DNA replication, growth regulation) seem peripheral and do not define a stronger alternative theme, so the strongest signal is nuclear RNA surveillance/decay.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0071048","count":1},{"id":"GO:0071036","count":1},{"id":"GO:0040009","count":1}]},{"hash":"1587957451983650497","title":"Bone formation and limb development","description":"The top GO terms point to embryonic skeletal development and ossification (limb bud formation, intramembranous ossification, regulation of osteoblast activity) and accompanying vascular and tissue morphogenesis (endothelial morphogenesis, multicellular development), with supportive developmental signaling cues. This suggests a cohesive theme around bone formation and limb patterning during development.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060174","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0005975","count":2},{"id":"GO:0001957","count":2},{"id":"GO:0007169","count":1}]},{"hash":"1099090496653783289","title":"Developmental Signaling and Metabolism","description":"The top GO terms cluster around developmental processes (post-embryonic development, heart development, meristem identity maintenance, germ-line masculinization) and signaling regulation (negative regulation of TGF-beta signaling, peptidyl-threonine dephosphorylation), with accompanying metabolic and stress-related terms (response to starvation, leucine catabolic process) and plant-specific processes (photosystem stoichiometry adjustment). This suggests a theme of developmental regulation coordinated with signaling and metabolic state, across diverse organisms. ","confidence":"Medium","size":19,"edges":51,"triangles":47,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0009791","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0006552","count":3},{"id":"GO:0061191","count":3}]},{"hash":"1619172334163188871","title":"Chloroplast Metabolism and ABA-Driven Stomatal Signaling","description":"Top GO terms cluster around plastid-focused metabolism (protein import into chloroplast stroma; molybdenum cofactor biosynthesis in plastids; plastidic amino acid biosynthesis like tryptophan and arginine) together with abscisic acid biosynthesis and stomatal movement, indicating a plastid-centric metabolic program linked to ABA-regulated gas exchange in plants.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0010118","count":2},{"id":"GO:0018315","count":2},{"id":"GO:0006727","count":2}]},{"hash":"1705104260237815779","title":"Neural development and synaptic plasticity","description":"Based on the prominent neural-related terms (Schwann cell development, axonogenesis, long-term potentiation, excitatory postsynaptic potential, visual perception), the proteins in this cluster likely participate in neural development and synaptic function. Other terms such as mitotic cell cycle and NF-kappaB signaling may reflect broader cellular regulation or annotation noise, but do not define the main theme.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0014044","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0010800","count":3},{"id":"GO:0009738","count":3}]},{"hash":"1786334948641879877","title":"DNA replication, repair, and SOS response","description":"The top terms are dominated by DNA-related processes: replication, repair, transcription linked to DNA templates, and the SOS/damage response. There are also entries for restriction-modification and transcription regulation in the context of DNA maintenance, suggesting this cluster groups proteins involved in genome integrity and DNA damage response pathways. Confidence is High.","confidence":"","size":19,"edges":9,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009307","count":1},{"id":"GO:0090305","count":1},{"id":"GO:0009432","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0006281","count":1}]},{"hash":"796719136033461507","title":"Transport and stress-response proteins","description":"The top GO terms cluster around transport activities (auxin polar transport, malate transport, phosphatidylcholine catabolic process) and stress/detoxification responses (response to UV-B, cellular oxidant detoxification). This points to a general theme of proteins involved in moving metabolites or ions and mitigating oxidative or environmental stress, with a few terms related to host\u2013microbe interactions appearing as well. Thus a label like \"Transport and stress-response proteins\" captures the core shared function without overemphasizing any single process.","confidence":"Medium","size":19,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009926","count":2},{"id":"GO:0010224","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0044148","count":1}]},{"hash":"2167928732268786084","title":"Neural development and chromatin regulation","description":"The cluster is dominated by terms for DNA-templated transcription and histone modifications, pointing to chromatin-level control of gene expression. Several terms specifically reference neural development (cerebellar cortex development, regulation of gliogenesis), supporting a neural-context function, with other terms (muscle regeneration, drug response) likely incidental. Overall, the common theme is transcriptional regulation tied to neural development via chromatin marks.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0097198","count":1},{"id":"GO:0071314","count":1},{"id":"GO:2001040","count":1},{"id":"GO:0051154","count":1}]},{"hash":"1471441384041575911","title":"Chaperone-driven protein folding and quality control","description":"These terms cluster around proteostasis: chaperone- and cofactor-dependent protein folding, ER folding, membrane targeting, ATP-dependent chaperone activity, and redox homeostasis, plus assembly/maturation of protein complexes and stress response regulation. The overall pattern points to a coordinated protein folding and quality-control system rather than a single enzymatic pathway.","confidence":"High","size":19,"edges":167,"triangles":902,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0090084","count":17},{"id":"GO:0031204","count":17},{"id":"GO:0070389","count":17},{"id":"GO:1900035","count":17},{"id":"GO:0006260","count":17}]},{"hash":"608755581246063243","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0042823","count":1},{"id":"GO:0008614","count":1},{"id":"GO:0006543","count":1},{"id":"GO:0000304","count":1}]},{"hash":"478758751716440375","title":"Plant development and cell cycle regulation","description":"This cluster centers on plant-specific growth control: auxin- and ethylene-activated signaling, multicellular development, and links to cell cycle progression (G2/M) and microtubule organization, with ubiquitin-mediated regulation. While a few terms are broader or outliers (e.g., viral process, obsolete histone ubiquitination), the dominant theme ties plant development to growth/division control. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":1},{"id":"GO:0035518","count":1},{"id":"GO:0000086","count":1},{"id":"GO:0000226","count":1},{"id":"GO:0007275","count":1}]},{"hash":"1602801887243915827","title":"Cell stress response and organelle homeostasis","description":"The GO terms center on ER unfolded protein response, vacuolar acidification, and V-ATPase complex assembly, all tied to maintaining protein folding and organelle function under stress. Additional terms reflect general stress responses (response to antibiotic) and signaling (phosphorylation), with some seemingly less connected metabolic or developmental terms. Overall, the cluster appears to reflect cellular stress responses and organelle homeostasis.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0019509","count":1},{"id":"GO:0019284","count":1},{"id":"GO:0009088","count":1}]},{"hash":"1594679605045671674","title":"RNA polymerase assembly and transcription regulation","description":"This cluster is dominated by GO terms related to RNA polymerase I/II/III assembly and regulation of transcription elongation, pointing to a shared role in assembling and modulating the transcription machinery. While other terms touch on general cellular processes like protein folding and cytoskeleton formation, the strongest signal is the coordination of RNAP complexes and transcription control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:1990115","count":1},{"id":"GO:0007021","count":1},{"id":"GO:1990113","count":1},{"id":"GO:0006457","count":1}]},{"hash":"380183773962770275","title":"Cardiac protein trafficking and heart development","description":"The top GO terms include intracellular transport (ER-to-Golgi, endosome organization) indicating a shared protein trafficking function, while heart-related terms (heart development, coronary artery morphogenesis, cardiac muscle contraction) point to a cardiac development context. The cluster thus seems to combine protein trafficking with cardiac development signals, though the connections are not tight and there\u2019s no network connectivity observed; this label is a best-effort, with Medium confidence.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0007275","count":2}]},{"hash":"1931555993574335009","title":"Gene Expression Regulation and Cell Cycle Control","description":"The GO terms emphasize regulation of gene expression and genome maintenance, including transcriptional signaling (NF-kappaB), RNA processing (miRNA processing), chromatin dynamics (heterochromatin formation), and cell cycle\u2013related processes (mitotic spindle checkpoint signaling, DNA replication initiation). While some terms relate to broader signaling (integrin or ion channel regulation), the dominant theme ties gene expression control to genome stability during the cell cycle, which this label reflects.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051237","count":1},{"id":"GO:0007249","count":1},{"id":"GO:0033624","count":1},{"id":"GO:0044810","count":1},{"id":"GO:0009190","count":1}]},{"hash":"995836636653334327","title":"Developmental cell migration and signaling","description":"The top GO terms cluster around cell movement and signaling pathways that regulate migration (cell migration; positive regulation of fibroblast migration) and cytoskeletal/kinase signaling (Rho and GTPase activation, phosphorylation, JNK regulation), plus related developmental contexts (insulin signaling, VEGF response, placental development). This suggests a coherent theme of signaling networks coordinating migration and developmental processes, rather than a single isolated function. Confidence: Medium","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008286","count":4},{"id":"GO:0035924","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0060709","count":3},{"id":"GO:0035023","count":3}]},{"hash":"935065661556717333","title":"Unknown","description":"There are no GO terms or shared functional annotations to tie these proteins to a common function, and the interaction metrics show no edges or triangles, so no unified pathway or process is evident. The note about \u201c20 proteins re-added by ReCIPE\u201d suggests computational reassembly rather than real connectivity, leaving the cluster without a clear theme.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"657782710210869530","title":"Vacuolar trafficking and microautophagy","description":"This cluster\u2019s top GO terms are dominated by vacuole-related processes: vacuole fusion (non-autophagic), vacuolar transport, and microautophagy, plus polyphosphate biosynthesis linked to vacuoles. These point to a cohesive theme of vesicle sorting and degradation within the vacuole/lysosome. A few scattered terms (rRNA maturation, germarium-derived cyst formation, RNA destabilization) appear sparsely and may reflect annotation noise or multifunctional proteins rather than a core theme. The absence of edges suggests loose connectivity, but the prevalent vacuolar/autophagic signals justify a unified label around vacuolar trafficking and autophagy.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0048016","count":1},{"id":"GO:0007034","count":1},{"id":"GO:0006799","count":1},{"id":"GO:0016237","count":1}]},{"hash":"506458459172348877","title":"Unknown","description":"There are no top GO terms or connections among the 19 proteins (no edges, no triangles), so there is no discernible shared function to label this cluster. Unable to assign a specific theme beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"587000613216421349","title":"Unknown","description":"The top GO terms show a mix of immune signaling (positive regulation of IL-1 production) and a variety of developmental/physiological processes (foregut morphogenesis, germ-line cyst formation, left/right nervous system asymmetry, anesthetic response, defecation rhythm), with no clear shared pathway or function. With no edges or interactions, there isn\u2019t a cohesive theme tying these proteins together, so a single representative label isn\u2019t justifiable. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050718","count":1},{"id":"GO:0007440","count":1},{"id":"GO:0030727","count":1},{"id":"GO:0036098","count":1},{"id":"GO:0072347","count":1}]},{"hash":"1525529595253864001","title":"Unknown","description":"The two GO terms are disjoint\u2014ER-to-Golgi vesicle transport vs. regulation of fibroblast apoptotic process\u2014and there are no edges or a shared enriched function linking the proteins, so there is no coherent theme to name the cluster beyond Unknown.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1},{"id":"GO:2000269","count":1}]},{"hash":"2012229119854030780","title":"ER Quality Control and ERAD/Retrograde Transport","description":"This cluster centers on ER-associated protein fate: retention in the ER lumen, retrograde transport from ER to cytosol, and ER-associated degradation pathways (ERAD). These GO terms (GO:0006621, GO:0030970, GO:0030433, GO:1904153) point to a coherent theme of ER quality control and proteostasis. The other terms appear more divergent (developmental processes in various tissues, self proteolysis, kinase regulation) and may reflect incidental annotations rather than a shared function. Overall, the strongest signal is ER retention/ERAD/retrograde trafficking.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055123","count":1},{"id":"GO:0006621","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0030433","count":1},{"id":"GO:1904153","count":1}]},{"hash":"1375262476061099816","title":"Cell cycle and protein synthesis","description":"The top GO terms cluster around mitotic cell cycle and cell division, along with protein production steps (ribosomal large subunit biogenesis, translation preinitiation complex formation) and trafficking (ER to Golgi transport) and microtubule dynamics, indicating a cohesive theme of cell growth and division tied to protein synthesis and trafficking.","confidence":"High","size":18,"edges":145,"triangles":706,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0071276","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0000278","count":4}]},{"hash":"2157208604927815265","title":"Plant gravitropism and plastid organization","description":"The cluster is dominated by terms related to gravity sensing in plants (negative gravitropism, detection of gravity) and plastid organization (amyloplast organization), which together point to plastid-mediated gravity perception. Additional terms about vesicle fusion, lipid droplets, and mitochondrial fission suggest broader organelle dynamics but do not outweigh the gravitropism/plastid theme.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0009959","count":1},{"id":"GO:0009660","count":1},{"id":"GO:0008542","count":1},{"id":"GO:0019433","count":1},{"id":"GO:0034389","count":1}]},{"hash":"911572629269517365","title":"Unknown","description":"The terms span diverse processes from xenobiotic/chemical responses and metabolism to development and transcription, with one very specific RNA modification term and an obsolete term, showing no clear, single shared function or pathway tying all proteins together.","confidence":"","size":18,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042220","count":4},{"id":"GO:0016049","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0035690","count":3},{"id":"GO:0002098","count":3}]},{"hash":"70925380054365962","title":"Developmental Signaling and Polarity","description":"This cluster is dominated by GO terms related to development (forebrain, nervous system, skeletal muscle) and signaling pathways (B cell receptor, growth hormone signaling, Rho signaling) as well as polarity establishment. The convergence on developmental processes and signaling suggests proteins acting in developmental signaling networks and cell polarity regulation, with some DNA repair/cell-cycle terms present as broader cellular maintenance roles. Overall, the label reflects the most coherent theme across the terms, with DNA repair being a secondary feature.","confidence":"Medium","size":18,"edges":97,"triangles":251,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0007519","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0006281","count":2}]},{"hash":"759528704952844591","title":"Otolith morphogenesis","description":"The only top GO term is otolith morphogenesis (GO:0032474), suggesting a shared involvement in ear stone formation. Despite a dense interaction network, the annotation is sparse (1 member annotated with this term), so the label reflects the strongest available signal rather than broad functional coverage.","confidence":"Medium","size":18,"edges":142,"triangles":664,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0032474","count":1}]},{"hash":"1158963956014110948","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":151,"triangles":785,"max_degree":17,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0000463","count":6},{"id":"GO:0000472","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0000480","count":5}]},{"hash":"295705495163544442","title":"Unknown","description":"The set of terms covers mRNA processing, spindle assembly, telomere maintenance, actin bundle assembly, vesicle transport, and growth processes like pollen tube development, with no single dominant function. The diversity suggests there isn\u2019t a cohesive functional theme tying these proteins together in this cluster.","confidence":"","size":18,"edges":134,"triangles":562,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":1},{"id":"GO:0051225","count":1},{"id":"GO:0032212","count":1},{"id":"GO:0090501","count":1},{"id":"GO:0051017","count":1}]},{"hash":"1436699011850056402","title":"Mitosis and genome maintenance","description":"This cluster shows strong links to cell division and genome integrity: mitotic sister chromatid cohesion and segregation, Okazaki fragment processing in DNA replication, homologous recombination repair, and general cell division; plus supporting terms for ribosome biogenesis, nuclear pore localization, and actin dynamics, suggesting coordinated cell-cycle progression and genome maintenance.","confidence":"Medium","size":18,"edges":35,"triangles":21,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000462","count":5},{"id":"GO:0000724","count":4},{"id":"GO:0007064","count":4},{"id":"GO:1903461","count":4},{"id":"GO:0051301","count":4}]},{"hash":"1364217062388342203","title":"Innate antiviral signaling and NF-kB regulation","description":"The GO terms cluster around innate immune response and antiviral sensing (RIG-I signaling) with modulation of NF-kB activity, including suppression of viral release and positive regulation of related pathways. Additional terms point to nuclear/nuclear body involvement (PML bodies) and ubiquitin-related protein turnover, suggesting a cohesive theme of antiviral signaling tightly regulated at both cytoplasmic and nuclear levels.","confidence":"High","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":3},{"id":"GO:1900246","count":2},{"id":"GO:2000059","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0036353","count":2}]},{"hash":"1814680718846126972","title":"Neural development and Eph signaling","description":"The top GO terms point strongly to neural development processes (forebrain development, neuronal/multicellular organism development, neuronal migration) and Eph receptor signaling, with connections to synaptic activity (excitatory postsynaptic potential) and downstream ERK/MAPK pathways. This combination suggests a cluster of proteins coordinating neural patterning, migration, and synaptic signaling via Eph-ephrin signaling, alongside transcriptional regulation during development. Confidence reflects a coherent theme centered on neural development and Eph signaling, though some general transcription/cell-cycle terms may broaden the group.","confidence":"High","size":18,"edges":14,"triangles":5,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0016477","count":6},{"id":"GO:0030900","count":5},{"id":"GO:0048013","count":5}]},{"hash":"889275503472292039","title":"Neurodevelopment and cell cycle regulation","description":"The cluster shows prominent neural development signals (forebrain development, neuron apoptotic process) alongside cell cycle-related terms (mitotic cell cycle, mitotic sister chromatid cohesion, regulation of G0 to G1). Transcription and protein oligomerization terms provide supporting context for regulatory networks involved in neural development and cell-cycle control, with ubiquitin ligase activity hinting at proteostasis. Overall, the proteins appear linked to neural development with concurrent cell-cycle regulation, justifying the label.","confidence":"Medium","size":18,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0051260","count":7},{"id":"GO:0030900","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0051402","count":7}]},{"hash":"1203520357685427847","title":"Neuronal development and axon guidance signaling","description":"The cluster is dominated by neural-related terms such as hippocampus development, ephrin receptor signaling, excitatory postsynaptic potential, and positive regulation of axon extension, along with ERK/MAPK and PI3K pathway associations, pointing to neuronal development and synaptic signaling. The presence of a T cell receptor signaling term appears more like a general signaling pathway overlap rather than the cluster\u2019s primary function. ","confidence":"High","size":18,"edges":33,"triangles":14,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":8},{"id":"GO:0021766","count":7},{"id":"GO:0048013","count":6},{"id":"GO:0060079","count":6},{"id":"GO:0043552","count":6}]},{"hash":"672001607297158905","title":"Selective autophagy and nucleophagy","description":"Dominant autophagy signals: Cvt pathway, nucleophagy, and mitochondrion autophagy, with a lipidation-related step. These suggest a cluster of autophagy-related proteins, especially selective autophagy; the other terms likely reflect regulatory or contextual aspects.","confidence":"High","size":18,"edges":66,"triangles":65,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0051726","count":3},{"id":"GO:0032258","count":3},{"id":"GO:0034727","count":3},{"id":"GO:0044805","count":3},{"id":"GO:0006501","count":3}]},{"hash":"141967688873862931","title":"Neural development and signaling","description":"Dominant terms point to neural development (motor neuron axon guidance, forebrain development, bipolar cell polarity) and signaling pathways (PI3K/AKT signaling, phosphorylation). While there are a few non-neural terms (lung mesenchyme, placenta-associated differentiation), the recurring theme is developmental processes with neural emphasis, making this label a reasonable fit. The lack of observed interactions (Edges: 0) reduces confidence somewhat, so medium confidence. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008045","count":1},{"id":"GO:0045736","count":1},{"id":"GO:0071375","count":1},{"id":"GO:0043491","count":1},{"id":"GO:0060709","count":1}]},{"hash":"1405602222396494356","title":"Fatty acid metabolism and oxidative stress response","description":"The top GO terms cluster around fatty acid beta-oxidation (unsaturated, long- and very long-chain acyl-CoA metabolism) and fatty acid biosynthesis regulation, with associated oxidative stress detoxification and apoptotic signaling terms. A transcription-related term is present but less dominant, so the lipid metabolism and redox/homeostasis linkage best explains the cluster.","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:0036112","count":2},{"id":"GO:0033542","count":2},{"id":"GO:0036111","count":2},{"id":"GO:0042759","count":2}]},{"hash":"1874419261995935189","title":"Glutamatergic synaptic plasticity regulation","description":"The cluster is dominated by GO terms related to synaptic function and plasticity (glutamatergic transmission, long-term potentiation, and both positive and negative regulation of synaptic plasticity), with supplementary signals related to glial/neuronal survival. This points to a coherent theme of neuronal signaling and plasticity control, despite some peripheral terms. ","confidence":"High","size":18,"edges":8,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031914","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0090153","count":3}]},{"hash":"1636637784464471386","title":"Virus-host Entry and Attachment Proteins","description":"Based on the top GO terms, three of the four annotations describe steps in viral infection and host cell entry: viral process, virion attachment to host cell, and symbiont entry into host cell. The mitochondrial complex II assembly term is likely incidental. Overall, the cluster appears to be characterized by virus\u2013host entry processes, hence the label, though there is no observed network connectivity (edges) among proteins.","confidence":"Low","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034553","count":1},{"id":"GO:0016032","count":1},{"id":"GO:0019062","count":1},{"id":"GO:0046718","count":1}]},{"hash":"101872864719939448","title":"Chloroplast RNA Processing and Plant Development","description":"Dominant GO terms center on chloroplast/plastid RNA processing (chloroplast mRNA processing and polycistronic mRNA processing) and plant development (meristem development and regulation of organ growth). Additional terms align with plastid/mitochondrial metabolism (ubiquinone biosynthetic process, iron-sulfur cluster assembly), supporting a plastid-associated functional theme. Some outliers exist but do not overturn the plastid-development signal.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":1},{"id":"GO:0010239","count":1},{"id":"GO:0031426","count":1},{"id":"GO:0006744","count":1},{"id":"GO:0043086","count":1}]},{"hash":"2092823053261044484","title":"Monoaminergic Neuron Axon Guidance and Calcium Signaling","description":"This cluster is enriched for GO terms related to neuron development and pathfinding, specifically serotonergic and dopaminergic axon guidance, and includes related cytoskeletal polarity and PCP pathway involvement. Calcium signaling terms (positive regulation of cytosolic Ca2+ concentration) further support a neuronal signaling/axon guidance theme. An electron transport chain term appears but likely reflects general cellular metabolism shared by many proteins. Together these terms point to a functional group involved in monoaminergic neuron axon guidance and calcium-mediated signaling.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0022900","count":9},{"id":"GO:0048105","count":6},{"id":"GO:0036515","count":6},{"id":"GO:1904938","count":6},{"id":"GO:0036514","count":6}]},{"hash":"1888750239526387998","title":"Mitotic G2/M Transition Regulation","description":"The cluster\u2019s top GO terms cluster around cell division and mitotic control, especially the G2/M transition of the mitotic cell cycle, with additional hints of transcriptional regulation and mRNA stabilization. While one term touches lipid catabolism, the dominant theme is regulation of mitosis, making a mitotic/G2M regulatory label appropriate.","confidence":"High","size":18,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":1},{"id":"GO:0045792","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0032515","count":1},{"id":"GO:0000086","count":1}]},{"hash":"1573544523815143652","title":"Nervous system development and myelination","description":"The cluster is enriched for GO terms tied to neural and glial development, especially Schwann cell development and myelination in the peripheral nervous system, plus brain region development (substantia nigra) and neuronal morphology processes. While there are a few broader developmental terms (EMT, vascular branching, etc.), the strongest and most representative signals point to nervous system formation and nerve insulation.","confidence":"Medium","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0014044","count":2},{"id":"GO:1905205","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0050774","count":2}]},{"hash":"243293205568403110","title":"Metabolism and Transport","description":"The top GO terms cluster around metabolic processes (transsulfuration, L-homocysteine catabolic, GTP biosynthesis, fatty acid biosynthesis) and transport activities (magnesium ion transmembrane transport, glycine betaine transport), suggesting a core theme of cellular metabolism coupled with solute/ion transport. A few terms related to cell cycle regulation and lymphocyte proliferation appear peripheral rather than central to this core. Confidence in this label is Medium.","confidence":"Medium","size":18,"edges":88,"triangles":207,"max_degree":16,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0019346","count":11},{"id":"GO:0030071","count":10},{"id":"GO:1903830","count":10},{"id":"GO:0046651","count":10},{"id":"GO:0051289","count":10}]},{"hash":"479358570972668642","title":"Protein quality control and stress response","description":"This cluster is dominated by proteostasis-related terms (proteolysis, ubiquitin-dependent ERAD) and autophagy regulation, with antibiotic response and metabolic regulation as supporting stress-related signals; a few terms are more peripheral (cell wall organization, tRNA modification), but the core theme is proteostasis and stress response.","confidence":"Medium","size":18,"edges":35,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045541","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0043085","count":2}]},{"hash":"1146114113391610036","title":"Bacterial LPS and Capsule Biosynthesis","description":"The top GO terms center on biosynthesis of surface polysaccharides: lipopolysaccharide core and O-antigen, colanic acid (capsule), and related sugar nucleotide pathways (dTDP-rhamnose). While some plant metabolic terms appear, the dominant theme is bacterial cell envelope polysaccharide production, indicating a capsule/LPS biosynthesis program. ","confidence":"High","size":18,"edges":140,"triangles":648,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":15},{"id":"GO:0009718","count":14},{"id":"GO:0006012","count":14},{"id":"GO:0009242","count":14},{"id":"GO:0009699","count":14}]},{"hash":"967827396600460246","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2001275","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0042997","count":2},{"id":"GO:0048240","count":2},{"id":"GO:0034501","count":2}]},{"hash":"1911209136950298491","title":"Neural RNA processing and chromatin regulation","description":"The cluster shows strong signals for nuclear processes: RNA splicing, mRNA processing, and spliceosome assembly, along with chromatin organization, all of which are key to neural development and gene regulation in the brain. Additional terms like brain development and sumoylation support a theme of transcriptional/nuclear control in neural contexts, with some peripheral hints at neural function (flight behavior) and growth regulation. Overall, the proteins appear connected through RNA maturation and chromatin-based regulation in neural development.","confidence":"High","size":18,"edges":99,"triangles":266,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0006471","count":2},{"id":"GO:0031497","count":2},{"id":"GO:0008380","count":1},{"id":"GO:0006397","count":1}]},{"hash":"1996545226712965154","title":"Lipid transport and vesicle trafficking","description":"GO terms converge on intracellular lipid movement (ceramide, sterol, triglyceride transport) and vesicle trafficking (ER\u2013Golgi and post-Golgi), with incidental hints of broader transport roles (cell polarity maintenance, nuclear pore localization). This supports a cohesive label for a cluster centered on lipid handling and vesicle transport.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035621","count":2},{"id":"GO:0030011","count":2},{"id":"GO:0044128","count":2},{"id":"GO:0010891","count":2},{"id":"GO:0006892","count":2}]},{"hash":"683670012172467683","title":"Cytoskeletal dynamics and signaling","description":"This cluster centers on actin cytoskeleton organization, focal adhesion regulation, and small GTPase\u2013mediated signaling, with links to PKC and insulin receptor pathways, all of which drive cytoskeletal remodeling and cell movement (including migration in neural and developmental contexts). While a few terms touch on development or immune differentiation, the dominant theme is cytoskeletal dynamics and associated signal transduction.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051895","count":4},{"id":"GO:0030183","count":3},{"id":"GO:0007480","count":3},{"id":"GO:0090038","count":3},{"id":"GO:0046626","count":3}]},{"hash":"1799521417433533935","title":"Unknown","description":"There are no top GO terms or network edges to suggest a common function among these proteins, so a meaningful label cannot be inferred from the available data.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"2150981751084641539","title":"Ectodermal and motor neuron development","description":"The GO terms cluster around ectodermal derivatives (ectoderm formation, sebaceous gland development) and neural/motor neuron processes (medial motor column neuron differentiation, visceral motor neuron differentiation, motor neuron axon guidance), suggesting a shared theme of ectoderm-derived tissue and neural development. Some terms like palmitoylation and vacuole fusion are broader cellular processes that may support development but are not central. Overall, a coherent theme is ectodermal/neural differentiation. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048733","count":1},{"id":"GO:0018230","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0007160","count":1},{"id":"GO:0001705","count":1}]},{"hash":"1176629727675662312","title":"Retinoic Acid\u2013Mediated Adipose Browning","description":"The top terms center on brown fat differentiation and heat generation, indicating adipose tissue browning and thermogenesis, with retinoic acid signaling guiding this process (response to retinoic acid, retinoic acid catabolic process). Prostaglandin biosynthesis also ties into adipose metabolic regulation. Other signals (response to bacteria/mycotoxin) are less central, but the core theme remains retinoic acid\u2013driven adipose remodeling. ","confidence":"Medium","size":18,"edges":67,"triangles":86,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":2},{"id":"GO:0032526","count":2},{"id":"GO:0070207","count":2},{"id":"GO:0050873","count":2},{"id":"GO:0031649","count":1}]},{"hash":"984962987387373270","title":"Unknown","description":"The terms span very different biological areas\u2014from microbial cellulose degradation and flocculation to programmed necrotic cell death and endothelial barrier regulation\u2014plus several obsolete GO entries. There is no coherent, shared function that ties these proteins together, so a single interpretable label cannot be assigned.","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0044533","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0000501","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0035897","count":2}]},{"hash":"1086785723556393302","title":"Unknown","description":"The terms span very different biological areas (cellulose catabolic process, flocculation, various cell death and barrier-related processes) with no clear, shared function among the proteins, and several GO terms are obsolete, so a concise, representative label isn\u2019t supported.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0009405","count":3},{"id":"GO:0044533","count":2},{"id":"GO:0000501","count":2},{"id":"GO:0051260","count":2}]},{"hash":"1507381435376580030","title":"Mitochondrial redox, transport, and apoptosis regulation","description":"The top GO terms cluster around mitochondria: redox response to superoxide, regulation of mitochondrial membrane potential, apoptotic mitochondrial changes, and diverse metabolite transports (malate-aspartate shuttle, glycine, thiamine pyrophosphate, thiosulfate, magnesium). This points to coordinated mitochondrial redox balance, energetic metabolism, and control of cell death pathways, justifying a label focused on mitochondrial redox, transport, and apoptosis regulation.","confidence":"High","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0000303","count":18},{"id":"GO:0051881","count":18},{"id":"GO:0060546","count":17},{"id":"GO:0036233","count":17},{"id":"GO:1990845","count":17}]},{"hash":"1759085196533223736","title":"Unknown","description":"The top terms are a mix of disparate processes (bone remodeling, morphogenesis, peptide catabolism, autophagy regulation, inflammation-related catabolism) with no clear shared function. Only a few terms touch on tissue remodeling, while others are unrelated or obsolete, suggesting no coherent biological theme tying these proteins together. Therefore there is no strong, representative label for the cluster.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903955","count":1},{"id":"GO:0010813","count":1},{"id":"GO:0051603","count":1},{"id":"GO:0071888","count":1},{"id":"GO:0001957","count":1}]},{"hash":"376897130135669481","title":"Glycosylation in neural and immune processes","description":"Top GO terms point to diverse glycosylation-related activities (L-fucose catabolism, Lewis a epitope biosynthesis, N-glycan fucosylation, deglycosylation, regulation of glycosylation) alongside neural development and immune cell migration signals (neuronal stem cell maintenance, cortical neuron migration, leukocyte migration, regulatory T cell differentiation). The common thread appears to be glycosylation-modulated functions in neural and immune contexts, justifying a label focused on glycosylation in neural and immune processes.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097150","count":1},{"id":"GO:0042355","count":1},{"id":"GO:0006486","count":1},{"id":"GO:0010493","count":1},{"id":"GO:0021799","count":1}]},{"hash":"1153198125733349583","title":"Ribosome maturation and RNA modification","description":"Most of the top GO terms point to RNA processing and ribosome biogenesis, notably maturation of LSU rRNA and 5.8S rRNA from tricistronic transcripts and rRNA/tRNA methylation. This suggests a functional cluster of proteins involved in ribosome assembly and RNA modification. A few terms about heart development appear incidental and do not align with the core RNA-processing theme. Overall, the dominant signal supports ribosome biogenesis and RNA modification as the cluster\u2019s function.","confidence":"Medium","size":17,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:2000620","count":2},{"id":"GO:0085020","count":2},{"id":"GO:0070512","count":2}]},{"hash":"982720682745956538","title":"APC/C-Mediated Mitosis and K11 Ubiquitination","description":"The top GO terms cluster around mitotic progression and ubiquitin-dependent proteolysis, notably mitotic cell cycle, cell division, and the metaphase/anaphase transition, with K11-linked ubiquitination strongly indicating APC/C-driven substrate degradation. This combination points to proteins that regulate mitosis via ubiquitin tagging and degradation. While a few terms relate to DNA repair or histone mRNA turnover, they do not override the dominant mitotic-ubiquitin theme. Overall, this label captures the core function of the cluster.","confidence":"High","size":17,"edges":129,"triangles":586,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0031145","count":4},{"id":"GO:0070301","count":2}]},{"hash":"468493525841449030","title":"Cell cycle and mitochondrial dynamics with autophagy","description":"The cluster strongly enriches cell division and cell cycle terms, with multiple mitochondrial dynamics and autophagy-related terms (fusion, membrane organization, macroautophagy) and some endocytic recycling. Together they point to a module of cell-cycle\u2013coupled mitochondrial maintenance and membrane trafficking, with minor supporting signals from protein oligomerization and GABAergic signaling.","confidence":"Medium","size":17,"edges":18,"triangles":9,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0007049","count":5},{"id":"GO:0016236","count":3},{"id":"GO:0032456","count":3},{"id":"GO:0051260","count":3}]},{"hash":"2185884201020493017","title":"Migration and adhesion signaling","description":"This cluster is dominated by GO terms tied to cell movement and attachment across diverse contexts: various forms of cell migration (sprouting angiogenesis, T cell migration, germ cell migration) and adhesion signaling (integrin-mediated signaling, hemidesmosome assembly). Additional terms reference development in heart and nervous system and host\u2013cell interaction, suggesting a cohesive theme of migratory and adhesive processes with supporting lipid signaling aspects. Confidence: Medium","confidence":"","size":17,"edges":37,"triangles":28,"max_degree":12,"top_function":"wound healing","top_go_terms":[{"id":"GO:0010888","count":12},{"id":"GO:0002042","count":12},{"id":"GO:2000406","count":12},{"id":"GO:0046718","count":12},{"id":"GO:0055007","count":12}]},{"hash":"159641942292005444","title":"Neural synapse regulation and glial differentiation","description":"The cluster centers on neural/synaptic processes, including positive regulation of synaptic vesicle endocytosis, regulation of synaptic assembly at the neuromuscular junction, and glial cell differentiation, with IL-18 production suggesting a neuroinflammatory aspect. Some terms (iodide transport, lipid/carb catabolism) appear more general or noisy and do not fit the core theme. Overall, the data point to a neural synapse\u2013glial development theme with potential inflammatory signaling.","confidence":"Medium","size":17,"edges":39,"triangles":19,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0015705","count":2},{"id":"GO:0042136","count":2},{"id":"GO:0046340","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0016042","count":2}]},{"hash":"708979290971215649","title":"Amino acid biosynthesis and peptide catabolism","description":"This cluster centers on amino acid biosynthesis (notably lysine via diaminopimelate and arginine biosynthesis) and peptide/protein degradation (proteolysis, peptide catabolic process), with related nitrogen metabolism (purine base metabolism, allantoin assimilation). The mix of biosynthetic and catabolic GO terms suggests a coherent theme of amino acid metabolism coupled with protein turnover, making this label representative. ","confidence":"High","size":17,"edges":47,"triangles":45,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":5},{"id":"GO:0010136","count":5},{"id":"GO:0009089","count":5},{"id":"GO:0006526","count":5},{"id":"GO:0009442","count":5}]},{"hash":"1790958801724885715","title":"Antiviral Innate Immunity and Ubiquitination","description":"The cluster is enriched for innate immune and antiviral functions, including defense against virus, host suppression of viral release and transcription, and ubiquitin-related processes (K63-linked ubiquitination and actin ubiquitination) often involved in signaling and cytoskeletal dynamics, suggesting a cohesive antiviral defense program.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:0035372","count":4},{"id":"GO:0051092","count":4},{"id":"GO:0045087","count":4},{"id":"GO:1902187","count":4},{"id":"GO:0007014","count":4}]},{"hash":"800764038301886794","title":"Central Carbon Metabolism and Biosynthesis","description":"The cluster shows enrichment in glycolysis, glucose metabolism, PPP, TCA cycle, and related biosynthetic processes such as thiamine and terpenoid synthesis, indicating a cohesive set of energy-generation and building-block pathways; one GO term appears unrelated (olfactory bulb development) and may be annotation noise.","confidence":"High","size":17,"edges":112,"triangles":446,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":5},{"id":"GO:0006006","count":5},{"id":"GO:0006098","count":5},{"id":"GO:0009228","count":5},{"id":"GO:0055114","count":5}]},{"hash":"1901505810994419444","title":"Neural Stress and Redox Metabolism","description":"The terms cluster around neural stress responses (lipopolysaccharide and corticosterone responses, aluminum ion response), redox biology (cell redox homeostasis, hydrogen peroxide biosynthetic process), mitochondrial/metabolic processes (ubiquinone biosynthesis) and brain-specific pathways (substantia nigra development, tryptophan catabolism linked to NAD synthesis). Together they suggest a cohesive theme of neuronal stress signaling intertwined with redox balance and mitochondrial metabolism.","confidence":"Medium","size":17,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0006569","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0050665","count":2}]},{"hash":"670891874603640151","title":"Ubiquitin-Proteasome Regulation and Nuclear Bodies","description":"The cluster centers on ubiquitination-related processes (autoubiquitination, aggresome assembly, negative regulation of ubiquitin-dependent protein catabolic process) and nuclear body-associated functions (PML body organization, snRNA export, and related localization). This suggests a cohesive theme around proteostasis via the ubiquitin-proteasome system with ties to nuclear architecture and trafficking.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070842","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0006408","count":1},{"id":"GO:1900246","count":1},{"id":"GO:2000059","count":1}]},{"hash":"2163914928832584595","title":"Membrane transport and glycosylation proteins","description":"The Top Terms point mainly to membrane transport (malate transport, general transport, D-glucose transmembrane transport, L-cystine transport) and to protein processing in the secretory pathway (protein N-linked glycosylation, dolichol-linked oligosaccharide biosynthetic process). This suggests a cohesive cluster of proteins involved in transport across membranes and in N-linked glycosylation, with a few less-related terms as outliers. Therefore, the label emphasizes transport and glycosylation functions. ","confidence":"Medium","size":17,"edges":57,"triangles":61,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0044148","count":1},{"id":"GO:0015743","count":1},{"id":"GO:0006810","count":1},{"id":"GO:0006487","count":1},{"id":"GO:0006488","count":1}]},{"hash":"1684251076777826178","title":"Actin Cytoskeleton Remodeling in Development","description":"The cluster is dominated by GO terms related to actin dynamics\u2014actin filament polymerization, stress fiber and ruffle assembly and their regulation\u2014alongside development-associated terms like neural tube closure and multicellular organism development. This pattern suggests proteins that coordinate actin remodeling during morphogenesis and cell-shape changes, rather than a single pathway, so a label highlighting actin dynamics in development fits best.","confidence":"High","size":17,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":2},{"id":"GO:0051496","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0030041","count":2},{"id":"GO:1900029","count":2}]},{"hash":"2259027006493071317","title":"Embryonic heart and immune development","description":"Top GO terms indicate a developmental program combining cardiovascular formation (heart development, cardiac smooth muscle differentiation) with embryogenesis and immune signaling (primitive streak formation, B cell homeostasis, germinal center regulation, IL-4 response). This suggests a cohesive theme of developmental processes that coordinate heart development with aspects of immune system maturation and signaling.","confidence":"Medium","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001782","count":3},{"id":"GO:0071364","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0097011","count":3},{"id":"GO:0060947","count":3}]},{"hash":"1314344428075312288","title":"Bacterial metabolism and envelope biosynthesis","description":"The terms point to metabolic pathways (lactate and methanol metabolism) alongside biosynthesis of envelope components (capsule and cell wall polysaccharides), plus core growth functions (DNA-templated transcription, cell division) and antibiotic response. While a few terms seem noisy (e.g., cytokinin catabolic process) or obsolete, the overall theme aligns with bacterial growth and envelope construction, suggesting a cohesive, bacteria-focused cluster rather than random functions.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006351","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0046677","count":2},{"id":"GO:1903457","count":2}]},{"hash":"605936525903747605","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (proteasome assembly, transcription, aging regulation, telomere maintenance, tRNA processing, cannabinoid/olivetolic acid biosynthesis, chloroplast organization, and light response), with no clear shared functional theme among the proteins. This scattered annotation suggests no single cohesive function for this cluster, making it hard to assign a specific label.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0090342","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0008033","count":1}]},{"hash":"2057641361908363677","title":"Photoreception and Circadian Regulation","description":"The term set centers on light perception and circadian control, with red/far-red light phototransduction and far-red light signaling, plus positive regulation of circadian rhythm and development, suggesting a theme where light signaling interfaces with circadian and developmental processes. The presence of viral-related and proteolysis terms appears tangential or noisy relative to this core theme, so the label reflects the dominant photo-signaling/circadian signals rather than the entire mix.","confidence":"Medium","size":17,"edges":78,"triangles":164,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0042753","count":1},{"id":"GO:0010018","count":1},{"id":"GO:0009585","count":1}]},{"hash":"2295624562056537182","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0008033","count":2},{"id":"GO:0045006","count":2},{"id":"GO:0000964","count":2},{"id":"GO:0070481","count":2}]},{"hash":"252523057177290415","title":"Unknown","description":"The GO terms cover diverse areas\u2014from lipopolysaccharide biosynthesis (bacterial) and cell cycle to embryonic development, translational fidelity, amino acid/vitamin biosynthesis, calcium transport, and muscle relaxation\u2014showing no single cohesive function across the cluster. Because there isn't a common theme that encompasses most members, a precise label would be misleading, so this cluster is best described as Unknown.","confidence":"","size":17,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0006450","count":2}]},{"hash":"1091585393983219028","title":"Multitissue morphogenesis","description":"The terms cluster around morphogenesis across tissues (outflow tract, kidney ureteric bud, Schwann cells, photoreceptors) with supporting calcium\u2013NFAT signaling and mitochondrial calcium handling, suggesting a theme of multitissue developmental morphogenesis and signaling.","confidence":"Medium","size":17,"edges":27,"triangles":13,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097274","count":4},{"id":"GO:0035502","count":3},{"id":"GO:0033234","count":3},{"id":"GO:0097264","count":3},{"id":"GO:0003151","count":3}]},{"hash":"2166724141556147266","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":105,"triangles":341,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0034965","count":3},{"id":"GO:0000294","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0006412","count":2}]},{"hash":"672463716494320312","title":"Proteolytic processing and LDL receptor regulation","description":"The GO terms point to proteolytic maturation and processing at dibasic sites (insulin processing; dibasic protein processing; peptide pheromone maturation) and to regulation of cholesterol uptake through LDL receptor activity and endocytosis (negative regulation of LDL particle clearance; LDL receptor catabolic process; receptor-mediated endocytosis involved in cholesterol transport). This suggests a theme around proprotein convertases and related proteases that process hormones/peptides and modulate LDL receptor degradation, with a few ancillary terms reflecting broader proteolysis roles in development and bone remodeling.","confidence":"High","size":17,"edges":13,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030070","count":3},{"id":"GO:0010989","count":2},{"id":"GO:0032902","count":2},{"id":"GO:0007354","count":2},{"id":"GO:0045453","count":2}]},{"hash":"900891224777611749","title":"Unknown","description":"Top GO terms are highly diverse, including multiple transporters (oligosaccharide, cobalt ion, thiamine, cysteine, abscisic acid), phospholipid translocation, plus cellulose catabolic process, SOS response, nucleotide-excision repair, and sporocarp morphogenesis. The lack of a cohesive, shared function across these terms makes a single interpretable theme unlikely, so Unknown is the most appropriate label.","confidence":"","size":17,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0009432","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0045332","count":1},{"id":"GO:0015772","count":1}]},{"hash":"732759818926012687","title":"Unknown","description":"No shared GO terms or network connections are reported for this cluster (edges 0, max degree 0, and an empty Top Terms list), so there is no evident common function tying these proteins together. In the absence of a unifying theme, the safe label is Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1090696694124513526","title":"Actin dynamics in morphogenesis","description":"The terms show a clear emphasis on actin cytoskeleton regulation (positive regulation of actin filament polymerization; stress fiber assembly) and cell movement/morphogenesis (epithelial migration, histoblast and larval salivary gland morphogenesis). While there are a few neuronal signaling and other processes, the dominant theme is cytoskeletal remodeling during developmental morphogenesis, suggesting the proteins cluster around actin dynamics in development.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":1},{"id":"GO:0051496","count":1},{"id":"GO:0007436","count":1},{"id":"GO:0007488","count":1},{"id":"GO:2000300","count":1}]},{"hash":"893463579244720220","title":"Motor Neuron Development and Axon Guidance","description":"These proteins show GO terms focused on neural development, especially motor neuron differentiation (medial motor column neuron differentiation; visceral motor neuron differentiation) and motor neuron axon guidance. Additional terms touch on ectoderm formation and neural differentiation, with a few broader processes, but the motor neuron\u2013related terms provide the strongest cohesive theme. Therefore, the label captures the primary function of the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007160","count":1},{"id":"GO:0001705","count":1},{"id":"GO:0021526","count":1},{"id":"GO:2000691","count":1},{"id":"GO:2000768","count":1}]},{"hash":"2042370781187652598","title":"Chromatin regulation and chromosome maintenance","description":"The cluster is enriched for terms involving chromatin localization, histone modification regulation, dosage compensation, cohesion maintenance, and transcriptional control, all indicating a chromatin- and chromosome-centric function. Some terms (keratinocyte differentiation, Wnt signaling) are peripheral but may reflect broader regulatory roles. Overall, the theme is chromatin regulation and chromosome maintenance.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":2},{"id":"GO:0007549","count":2},{"id":"GO:0033128","count":2},{"id":"GO:0051572","count":2},{"id":"GO:0061086","count":2}]},{"hash":"851732043423726095","title":"Unknown","description":"GO terms across the cluster are highly diverse and do not point to a single shared function. They include energy metabolism (mitochondrial electron transport, ATP synthesis, photosynthesis), cellulose catabolic process, stress responses, transport, pH/homeostasis, and even skin development, which are unlikely to reflect a cohesive molecular module. The cluster shows minimal connectivity (one edge, no triangles) and disparate annotations, suggesting no clear functional theme. ","confidence":"","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0046690","count":1},{"id":"GO:0006950","count":1},{"id":"GO:0051452","count":1},{"id":"GO:0043588","count":1}]},{"hash":"650374451047672882","title":"Bacterial sugar metabolism and envelope biosynthesis","description":"The top GO terms are dominated by carbohydrate metabolism (glucose, glycogen, starch biosynthesis) and biosynthesis of cell-surface/lipid components (GPI anchor), along with bacterial thiol biosynthesis (mycothiol, bacillithiol) and a sorbitol response. This suggests a cohesive theme around sugar metabolism and the production of cell-surface envelopes in bacteria, despite some obsolete terms. Confidence: Medium","confidence":"","size":17,"edges":51,"triangles":76,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0007631","count":4},{"id":"GO:0009405","count":4},{"id":"GO:0006490","count":4},{"id":"GO:0010125","count":4},{"id":"GO:0019252","count":4}]},{"hash":"1161926283630853035","title":"Unknown","description":"The GO terms are highly diverse (sporulation, proteolysis, myelination, LDL regulation, nerve growth factor production, embryonic axis determination, pheromone maturation, insulin processing), and there are no connecting edges or a unifying function, so a coherent, specific label cannot be assigned.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0010989","count":1},{"id":"GO:0032902","count":1}]},{"hash":"120708669902089979","title":"RIG-I-driven Antiviral Innate Immunity","description":"The top GO terms strongly point to innate antiviral defense, especially defense against virus and positive regulation of the RIG-I signaling pathway, suggesting RNA-sensing\u2013driven antiviral responses. Additional terms about PML body organization and suppression of viral release fit with cellular antiviral compartments and host restriction activity. Regulatory ubiquitin-related terms imply modulation of signaling stability and turnover in antiviral pathways. Overall, the cluster appears to group proteins involved in RIG-I\u2013mediated innate immune signaling and antiviral defense.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:1900246","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0035372","count":1}]},{"hash":"1736083968473986765","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":115,"triangles":496,"max_degree":15,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000480","count":14},{"id":"GO:0000472","count":14},{"id":"GO:0042273","count":14},{"id":"GO:0016441","count":14},{"id":"GO:0009432","count":13}]},{"hash":"2150139413887225353","title":"Prostaglandin biosynthesis and immune-related processes","description":"This cluster is driven by prostaglandin biosynthetic process as the top term, with supporting immune-related terms such as immunoglobulin production and regulation of TNF production, suggesting involvement in inflammatory signaling and secretory immune functions. The presence of glycosylation-related terms and various metabolic processes (fatty acid oxidation, aldosterone biosynthesis) indicates broader secretory/metabolic roles, but the strongest cohesive signal points to lipid mediator production and immune modulation.","confidence":"Medium","size":16,"edges":10,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":3},{"id":"GO:0045944","count":2},{"id":"GO:0032720","count":2},{"id":"GO:0018242","count":2},{"id":"GO:0016266","count":2}]},{"hash":"105708104600347456","title":"Vascular and cardiac cell signaling","description":"GO terms cluster around vascular cell migration and differentiation, calcium import and membrane depolarization in cardiac tissue, and related signaling processes, suggesting a cardiovascular signaling-centric theme. Some terms (e.g., stress response and cell cycle regulation) may be peripheral, but the core pattern aligns with signaling in vascular/endocardial contexts.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0000083","count":5},{"id":"GO:0016049","count":4},{"id":"GO:0009408","count":4},{"id":"GO:0033028","count":4}]},{"hash":"1037313978534559885","title":"N-terminal acetylation and mycothiol biosynthesis","description":"The cluster\u2019s strongest signals are mycothiol biosynthesis and N-terminal acetylation-related processes, including acetylation of specific N-terminal residues and propionylation, along with cellular oxidant detoxification. This points to a theme of redox balancing and post-translational modification in a bacterial context (likely Actinobacteria), with additional metabolic links such as arginine biosynthesis and lipid-related processes. Confidence: Medium","confidence":"","size":16,"edges":9,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010125","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0043651","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0017198","count":2}]},{"hash":"1625400551651486627","title":"Unknown","description":"The proteins map to a highly diverse set of functions: heat response, cell cycle and division, chromatin remodeling, tissue development, signaling, and metabolic/growth responses. There is no single dominant function or pathway that ties these terms together, and most terms have low representation, making a coherent and specific label inappropriate.","confidence":"","size":16,"edges":10,"triangles":1,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0007049","count":2},{"id":"GO:1901998","count":2},{"id":"GO:0050821","count":2}]},{"hash":"2080220618692241615","title":"Cellular Stress Response and Apoptosis","description":"This cluster is best described by a theme of cellular stress management and signaling leading to apoptosis. The top GO terms emphasize redox homeostasis, responses to xenobiotics, and apoptotic processes, alongside signaling-related terms (cellular response to cAMP and phosphatidylinositol dephosphorylation) and peptide hormone signaling. While a couple terms are obsolete, the dominant pattern centers on how cells sense stress and transduce signals to decide survival or programmed cell death, fitting a cohesive stress-response module.","confidence":"Medium","size":16,"edges":11,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0071320","count":3},{"id":"GO:0046856","count":3},{"id":"GO:0042493","count":3}]},{"hash":"729284553443643730","title":"DNA repair and ubiquitin signaling","description":"This cluster is enriched for DNA repair terms (DNA repair and nucleotide-excision repair) and multiple ubiquitin-related processes (monoubiquitination, autoubiquitination, ubiquitin-dependent protein catabolic process, and K63-linked ubiquitination), suggesting a set of proteins involved in the DNA damage response and ubiquitin-mediated regulation of signaling pathways (including Wnt and Hippo). The deglycosylation term is less central but can relate to protein turnover. Overall, the dominant theme is DNA repair coupled with ubiquitin-driven regulation of cellular signaling.","confidence":"Medium","size":16,"edges":84,"triangles":216,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0006517","count":2},{"id":"GO:0006513","count":2},{"id":"GO:0090263","count":2}]},{"hash":"1788599028729341969","title":"Placental development and embryonic morphogenesis","description":"Top GO terms indicate placenta morphogenesis and placenta development, suggesting a placenta-associated developmental program. The inclusion of cell-cycle related terms (mitotic spindle organization, G1/S transition) aligns with cellular proliferation during placental formation, supporting a theme of placental development with embryonic morphogenesis. Overall, the cluster centers on placental formation and early developmental regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060669","count":2},{"id":"GO:0006970","count":1},{"id":"GO:0030472","count":1},{"id":"GO:0032515","count":1},{"id":"GO:0032516","count":1}]},{"hash":"2265526810155330715","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0042274","count":1}]},{"hash":"1180357088488597664","title":"ER Stress Response and Developmental Signaling","description":"This cluster shows enrichment for PERK-mediated unfolded protein response and responses to ER stress, indicating an overarching ER stress\u2013related signaling theme. Additional terms point to developmental and differentiation processes, such as leading edge cell differentiation and outflow tract morphogenesis, plus muscle stretch response. While some terms (ABA response, microglial activation) reflect broader stress or tissue-specific roles, the most coherent connection across the subset is the cellular stress response pathway (UPR/ER stress) coupled with developmental signaling.","confidence":"Medium","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0035026","count":2},{"id":"GO:0003151","count":2},{"id":"GO:1990441","count":2}]},{"hash":"2243523695650598421","title":"ER Stress\u2013Associated Translation and Folding","description":"The cluster is enriched mainly for translation and translational initiation terms (GO:0006412, GO:0006413), especially in the context of endoplasmic reticulum (ER) stress and the unfolded protein response, along with protein folding and ER-associated quality control (e.g., chaperone-assisted refolding, ERAD). Some mitochondrial and rRNA maturation terms are present but less central, so the core theme centers on translation regulation during ER stress and protein quality control.","confidence":"High","size":16,"edges":50,"triangles":99,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0036494","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0051301","count":2}]},{"hash":"697386826095914547","title":"Insulin signaling and glucose uptake regulation","description":"The cluster\u2019s top GO terms center on insulin receptor internalization and negative regulation of insulin receptor signaling and PI3K/AKT signaling, along with negative regulation of glucose import, pointing to modulation of insulin signaling and glucose uptake. Other terms (GPI anchor biosynthesis, autophagosome assembly, ER protein folding) appear ancillary, but the dominant theme is insulin pathway regulation affecting glucose handling.","confidence":"High","size":16,"edges":109,"triangles":423,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0046325","count":2},{"id":"GO:0038016","count":2},{"id":"GO:0046627","count":2},{"id":"GO:0042733","count":2},{"id":"GO:0051898","count":2}]},{"hash":"411485024264127228","title":"Neuronal excitability and mechanosensory signaling","description":"The top GO terms cluster around neural electrical activity and sensory perception: action potentials, membrane hyperpolarization, and regulation of potassium channels, along with detection of mechanical stimuli (pain and touch) and optic nerve organization. Circadian rhythm regulation also ties into neural function, supporting a broader nervous-system\u2013focused group. While one term mentions an obsolete Wnt pathway in neural crest, the dominant pattern points to neuronal signaling and mechanosensation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019228","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0044335","count":1},{"id":"GO:0045188","count":1},{"id":"GO:0060081","count":1}]},{"hash":"1791573343252660696","title":"Metabolic and Innate Immune-Neural Signaling","description":"The Top Terms include multiple metabolic processes (carbohydrate and cholesterol metabolism) alongside innate immune responses (innate immune response, cellular response to LPS, lipopolysaccharide signaling) and even neural-related terms (learning or memory, neuromuscular balance). This suggests a cluster centered on metabolism with intertwined innate immune signaling and neural functions, hence the combined label.","confidence":"Medium","size":16,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":3},{"id":"GO:0070266","count":2},{"id":"GO:0008203","count":2},{"id":"GO:0007611","count":2},{"id":"GO:0009313","count":2}]},{"hash":"863195600268245000","title":"Translation Machinery and Ribosome Biogenesis","description":"The top GO terms cluster around core translation processes (initiation, elongation, termination, cytoplasmic translation, and selenocysteine incorporation) and ribosome biogenesis, suggesting these proteins primarily belong to the protein synthesis apparatus and ribosome assembly. Some peripheral terms (antibiotic response, glial cell proliferation, mRNA decay) may be incidental to the main translation-centric function.","confidence":"High","size":16,"edges":102,"triangles":373,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0045901","count":7},{"id":"GO:2000767","count":7},{"id":"GO:0006415","count":7},{"id":"GO:0001514","count":7}]},{"hash":"284027999604771339","title":"Unknown","description":"The Top Terms are highly heterogeneous across species and processes (fungal ergosterol biosynthesis, plant pollen rejection, cellulose catabolism, dopamine signaling, TLR signaling, chromatin localization, epithelial polarity, mitotic control, AMPK signaling, neural migration), with no clear shared function or common pathway tying the proteins together. This lack of a cohesive theme suggests there is no single interpretable label beyond Unknown.","confidence":"","size":16,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060320","count":1},{"id":"GO:0006696","count":1},{"id":"GO:0030245","count":1},{"id":"GO:0060161","count":1},{"id":"GO:0034130","count":1}]},{"hash":"909017475963740319","title":"Antioxidant Defense and Redox Homeostasis","description":"The top GO terms show oxidative stress and redox-related processes (removal of superoxide radicals, glutathione catabolic process, oxidation-reduction processes) and selenium ion response, which together point to antioxidant defense mechanisms and redox balance. While there are some neural/vascular terms in the list, the strongest shared theme across the terms is redox regulation and antioxidant metabolism, suggesting these proteins function in managing oxidative stress. ","confidence":"Medium","size":16,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0048485","count":2},{"id":"GO:0071291","count":1},{"id":"GO:0010447","count":1},{"id":"GO:0001320","count":1},{"id":"GO:0001302","count":1}]},{"hash":"619734229174921218","title":"Ubiquitin-Dependent Protein Degradation","description":"The top terms are all tied to ubiquitination and proteasomal or ubiquitin-mediated protein catabolism (e.g., ubiquitin-dependent ERAD, K48-linked ubiquitination, other protein degradation terms, and autoubiquitination). This points to a cohesive theme of protein turnover and quality control. A few terms about Wnt receptor catabolism and X-chromosome dosage regulation appear tangential but can reflect broader ubiquitin-regulated regulatory processes; overall, the cluster seems centered on the ubiquitin-proteasome system.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0060816","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0046621","count":2}]},{"hash":"1053701657839116418","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms for translation, ribosome biogenesis, and SSU-rRNA maturation, pointing to a core function in ribosome assembly and protein synthesis. The additional terms (protease regulation, cytokine production, TLR3 signaling, podocyte development, mitochondrial fusion) likely reflect broader roles of these proteins or pleiotropy, but do not diminish the central ribosome/translation theme.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":12},{"id":"GO:0042254","count":6},{"id":"GO:0000462","count":3},{"id":"GO:0045861","count":2},{"id":"GO:0060355","count":2}]},{"hash":"2145278830293948729","title":"Membrane transporters (ions and nutrients)","description":"GO terms cluster around transmembrane transport of ions (K+, Na+, phosphate) and diverse substrates (nitrate, sialic acid, arabinose, vitamins), plus a related neurotransmitter loading term, indicating a set of membrane transporter proteins.","confidence":"High","size":16,"edges":18,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":4},{"id":"GO:0071805","count":3},{"id":"GO:0035725","count":3},{"id":"GO:1900754","count":3},{"id":"GO:0035461","count":3}]},{"hash":"1143602993526568975","title":"Motor neuron development and axon guidance","description":"This cluster\u2019s terms strongly emphasize neural development, especially motor neuron differentiation (medial motor column, visceral motor neurons, ectoderm formation) and axon guidance, with supporting roles from cell-matrix adhesion. Additional terms touching on miRNA silencing and signaling pathways (NFAT/calcineurin, glucocorticoid signaling) can influence neural differentiation but don\u2019t change the core theme. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007160","count":1},{"id":"GO:0001705","count":1},{"id":"GO:0021526","count":1},{"id":"GO:2000691","count":1},{"id":"GO:2000768","count":1}]},{"hash":"1567351125931493787","title":"Ubiquitin-dependent TNF and NF-\u03baB signaling","description":"The terms cluster around ubiquitination (autoubiquitination, K48- and K6-linked ubiquitination, ubiquitin-dependent proteolysis) and TNF/NF-\u03baB signaling (TNF-mediated signaling, IKK activation, I\u03baB phosphorylation, NF-\u03baB induction), with histone turnover also present, indicating a coherent theme of ubiquitin-mediated regulation of TNF and NF-\u03baB pathways.","confidence":"High","size":16,"edges":23,"triangles":13,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1903265","count":14},{"id":"GO:0051865","count":14},{"id":"GO:0070936","count":13},{"id":"GO:0090073","count":13},{"id":"GO:1903721","count":13}]},{"hash":"1452658022106406770","title":"GTPase Signaling Regulation (Rho/Ras)","description":"This cluster is dominated by GO terms about regulating small GTPase pathways, especially Rho and Ras (e.g., regulation of Rho and Ras signal transduction, positive regulation of GTPase activity). Many terms point to processes influenced by these pathways, like neutrophil degranulation, blood vessel remodeling, and cellular extravasation, suggesting a shared theme of signaling control governing cell movement and immune\u2013vascular functions. Some terms (like acrosome reaction) are more context-specific but do not overturn the central theme of GTPase-mediated signaling regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0035023","count":5},{"id":"GO:0043314","count":5},{"id":"GO:0060313","count":5},{"id":"GO:0002692","count":5},{"id":"GO:0006886","count":4}]},{"hash":"1194330775564114312","title":"Golgi- and SNARE-mediated vesicle trafficking","description":"The term cluster centers on vesicle transport from ER to Golgi and within the Golgi, SNARE complex assembly, and vesicle fusion, including exocytic insertion of receptors at the postsynaptic membrane and related synaptic plasticity. Additional terms about Golgi ribbon formation and Golgi-to-vacuole transport reinforce a Golgi-focused vesicle trafficking module, making this a coherent, high-level functional cluster.","confidence":"High","size":16,"edges":98,"triangles":317,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":7},{"id":"GO:0006891","count":7},{"id":"GO:0048280","count":7},{"id":"GO:0090161","count":7},{"id":"GO:0098967","count":6}]},{"hash":"1186288981288605397","title":"RNA splicing and translation regulation","description":"The terms center on mRNA processing and spliceosome-regulated splicing, with several items relating to translation initiation and miRNA-mediated silencing, indicating a shared role in post-transcriptional gene expression control.","confidence":"High","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":7},{"id":"GO:1901407","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0035278","count":6},{"id":"GO:0075522","count":6}]},{"hash":"2207105666699447418","title":"Mitochondrial Energy Homeostasis and Stress Response","description":"The cluster\u2019s GO terms cluster strongly around mitochondrial function and energy management, including pathways for energy production (malate-aspartate shuttle, adaptive thermogenesis, membrane potential regulation), redox stress response (superoxide/reactive oxygen species), and apoptosis-related mitochondrial changes, plus ion handling within mitochondria (magnesium export). This coherence indicates a focus on mitochondria-driven energy metabolism and stress responses.","confidence":"High","size":16,"edges":89,"triangles":264,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097274","count":13},{"id":"GO:0061179","count":11},{"id":"GO:0060546","count":9},{"id":"GO:0036233","count":9},{"id":"GO:0000303","count":9}]},{"hash":"1100634313043282182","title":"Unknown","description":"No GO terms or connections to define a shared function; with no top terms and zero edges, there is no detectable common theme to assign a specific function.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1858409909253545900","title":"Neural development and PI3K signaling","description":"This cluster is dominated by neural-development related terms (motor neuron axon guidance, forebrain development, bipolar cell polarity) and by key signaling and phosphorylation processes (PI3K/AKT signaling, peptidyl-threonine phosphorylation, CDK activity regulation). Together these suggest a cohesive module involved in neural differentiation and development governed by signaling cascades, with a few broader developmental terms indicating accompanying mesenchymal/placental processes. ","confidence":"Medium","size":16,"edges":27,"triangles":28,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008045","count":16},{"id":"GO:0045736","count":16},{"id":"GO:0071375","count":16},{"id":"GO:0043491","count":16},{"id":"GO:0060709","count":16}]},{"hash":"1556316018379903621","title":"Proteostasis and cytoskeletal remodeling","description":"The top GO terms point to protein quality control (aggresome assembly, autoubiquitination) and actin cytoskeleton dynamics (filopodium, stress fiber assembly), with additional terms touching nuclear organization (PML bodies) and developmental processes. While several terms are diverse, the common thread centers on proteostasis and cytoskeletal regulation rather than a single unified pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0022011","count":2},{"id":"GO:0030578","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0007480","count":1}]},{"hash":"2011504848117701481","title":"Embryonic organogenesis and neural development","description":"This cluster's GO terms center on developmental processes across organs: heart development (cardioblast differentiation and migration), kidney development (nephric duct formation and ureteric bud formation), and nervous system development (sympathetic nervous system development). A few other terms touch on metabolism or chromatin regulation but are secondary to the main theme of organogenesis and morphogenesis.","confidence":"Medium","size":16,"edges":25,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1902660","count":2},{"id":"GO:0051891","count":1},{"id":"GO:2000734","count":1},{"id":"GO:0060975","count":1},{"id":"GO:2000664","count":1}]},{"hash":"69143993103825530","title":"ER-Golgi Vesicle Transport and Golgi Organization","description":"The cluster is dominated by GO terms describing ER and Golgi dynamics, including regulation of Golgi organization, ER membrane organization and fusion, and vesicle-mediated transport between the ER and Golgi (retrograde Golgi\u2192ER and ER\u2192Golgi routes). This suggests proteins in this set participate in assembling and maintaining Golgi structure and coordinating ER-Golgi trafficking; a few other terms appear ancillary or context-specific. ","confidence":"High","size":16,"edges":26,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:1903358","count":2},{"id":"GO:0048279","count":1},{"id":"GO:1902117","count":1},{"id":"GO:0090158","count":1},{"id":"GO:0006890","count":1}]},{"hash":"705465188457214012","title":"Energy Metabolism and Nutrient Sensing","description":"Based on the GO terms, several are tied to energy production and metabolic signaling: canonical glycolysis; ATP and pyruvate biosynthesis; responses to glucose, insulin, nutrients, and epinephrine. A subset also mentions heat and hypoxia, which can influence metabolic state. Collectively these terms point to metabolic energy production and nutrient-responsive signaling as the core theme of this protein cluster.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":1},{"id":"GO:0007584","count":1},{"id":"GO:0009749","count":1},{"id":"GO:0061621","count":1},{"id":"GO:0009408","count":1}]},{"hash":"1327435710430480572","title":"Unknown","description":"Insufficient functional signal: there are no top GO terms and no edges to tie the proteins into a common function, so a general Unknown label is most appropriate.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1920855743063263784","title":"Actin Cytoskeleton Remodeling","description":"This cluster centers on GO terms for lamellipodium assembly and actin filament\u2013based movement, along with barbed-end capping and parallel actin filament bundle assembly, indicating actin cytoskeleton remodeling and cell motility as the core theme. A few terms touch on immune cell processes and development in megakaryocytes and oligodendrocytes, which also rely on actin dynamics, supporting a broader theme of actin-driven cellular movement and maturation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030032","count":2},{"id":"GO:0032973","count":1},{"id":"GO:1990034","count":1},{"id":"GO:0035855","count":1},{"id":"GO:0002625","count":1}]},{"hash":"94976921194162331","title":"Unknown","description":"The terms span toxin/hormone responses, development in plants and animals, and various metabolic processes, with no single cohesive function linking all members. Because of this mixed signal, a precise, representative label cannot be determined reliably.","confidence":"","size":16,"edges":20,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":5},{"id":"GO:0043627","count":3},{"id":"GO:0060374","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0010223","count":3}]},{"hash":"1996449756385480886","title":"Mitochondrial respiration and ribosome assembly","description":"The GO terms converge on mitochondrial energy metabolism: electron transport chain components and their assembly (Complex III and IV), pyruvate import, aerobic respiration, and mitochondrial ribosome assembly, plus related metabolic processes such as ethanol metabolism and glucose-stimulated insulin secretion in a mitochondrial context. This indicates a cohesive cluster of mitochondrial bioenergetics and ribosome biogenesis proteins.","confidence":"High","size":16,"edges":119,"triangles":546,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0034551","count":1},{"id":"GO:0006122","count":1},{"id":"GO:0061668","count":1}]},{"hash":"491292997652302443","title":"Neural Axon Guidance and Vascular Morphogenesis","description":"The top terms cluster around neural development (axonogenesis/axon guidance and chemotaxis, vagus nerve morphogenesis) and endothelial/vascular morphogenesis (endothelial cell morphogenesis and chemotaxis), with cell surface receptor tyrosine kinase signaling tying these signaling pathways. Limb bud formation and chromatin regulation further point to embryonic development and patterning. Together, they suggest a program coordinating neural pathfinding with blood vessel formation, hence this label.","confidence":"High","size":16,"edges":120,"triangles":560,"max_degree":15,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0007169","count":9},{"id":"GO:0035563","count":9},{"id":"GO:0033689","count":9},{"id":"GO:0021793","count":9},{"id":"GO:0050918","count":9}]},{"hash":"1449539314354020021","title":"Sterol and lipid biosynthesis","description":"Most top GO terms point to lipid metabolism and sterol biosynthesis, including ergosterol biosynthetic process, cholesterol biosynthetic process via lathosterol, and various sterol oxidation steps, as well as fatty acid and ether lipid metabolic processes. This suggests these proteins participate in membrane lipid synthesis/remodeling. While a few terms relate to immune or neural differentiation, the lipid-related signals dominate, supporting the label.","confidence":"High","size":16,"edges":98,"triangles":333,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":8},{"id":"GO:0001949","count":8},{"id":"GO:0032286","count":8},{"id":"GO:0006696","count":6},{"id":"GO:0033490","count":6}]},{"hash":"1586423363860213984","title":"Steroid, retinoid, and lipid metabolism","description":"The top GO terms cluster around metabolism of lipids, steroids, and retinoids (retinoic acid, cholesterol, testosterone, aldosterone, ecdysone), with additional xenobiotic and catabolic pathways (camphor, alkaloids). This shared theme points to enzymes involved in processing lipid-based molecules and related signaling compounds, justifying a label centered on steroid/retinoid and lipid metabolism.","confidence":"High","size":16,"edges":10,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034653","count":16},{"id":"GO:0010430","count":16},{"id":"GO:0032342","count":16},{"id":"GO:0006697","count":16},{"id":"GO:0002677","count":16}]},{"hash":"1736292590902436923","title":"ER Folding and Secretory Trafficking","description":"This cluster centers on ER quality control and the secretory pathway, with terms like ER unfolded protein response, ER membrane localization, ER-to-Golgi transport, ERAD, and chaperone-mediated assembly; a few terms touch on nuclear or other organelle processes, but the dominant signal is ER folding/trafficking.","confidence":"Medium","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030968","count":2},{"id":"GO:0097051","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1904874","count":2},{"id":"GO:0051131","count":2}]},{"hash":"878581101704345379","title":"Nuclear RNA Processing and Transcription Regulation","description":"The top GO terms cluster around nuclear RNA metabolism (tRNA processing/transport, ribosomal subunit export from the nucleus) and transcriptional control (regulation of RNA Pol II), with some cell-cycle related terms (centrosome duplication). This combination suggests a theme of nuclear gene expression and RNA processing, despite a few outliers.","confidence":"Medium","size":15,"edges":84,"triangles":260,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0071894","count":4},{"id":"GO:0006311","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0045465","count":3},{"id":"GO:0006656","count":3}]},{"hash":"1849942798398843560","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":66,"triangles":133,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006310","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000472","count":3}]},{"hash":"744651734497753616","title":"Antiviral innate immune response","description":"This cluster's GO terms predominantly describe defense against viruses and innate immune signaling, including regulation of RIG-I signaling, host suppression of viral release, and PML body organization. While a few terms touch on chromatin modification and hormone signaling, the central theme is antiviral innate immunity.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900246","count":2},{"id":"GO:2000059","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0036353","count":2},{"id":"GO:0070562","count":2}]},{"hash":"1270985086405285759","title":"Endosomal trafficking and exosomal secretion","description":"The terms cluster around vesicle and endosome routing: plasma membrane to endosome transport, MVB/vacuolar sorting with ubiquitin-dependent protein turnover, and exosomal secretion, plus polarity maintenance. TNF signaling and NF-kappaB regulation suggest these trafficking events influence signaling pathways, while a note on G1/S address a broader cell-cycle tie-in. Overall, the dominant theme is vesicle-mediated transport and exosome-related secretion.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902306","count":2},{"id":"GO:1902072","count":2},{"id":"GO:2000009","count":2},{"id":"GO:0048227","count":2},{"id":"GO:0032088","count":2}]},{"hash":"2093987615254121072","title":"Cell Cycle and DNA Damage Response Regulation","description":"The GO terms point to regulation of cell division and DNA damage response, including asymmetric neuroblast division, regulation of DSB repair via NHEJ, and meiotic checkpoint signaling, plus mitotic DNA damage checkpoint regulation. While some terms touch on broader signaling and metabolism, the core theme appears to be modulation of cell cycle processes and DNA repair.","confidence":"Medium","size":15,"edges":71,"triangles":155,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0055059","count":2},{"id":"GO:2001034","count":1},{"id":"GO:0006470","count":1},{"id":"GO:0072462","count":1},{"id":"GO:0045722","count":1}]},{"hash":"702376348667825973","title":"Epigenetic Regulation and Cell Cycle","description":"The top GO terms emphasize epigenetic and transcriptional control (RNA guanine-N7 methylation; histone H3-K27 methylation; positive regulation of transcription via transcription factor localization; TORC1 signaling) together with cell cycle processes (mitotic sister chromatid cohesion; negative regulation of G0 to G1 transition). This combination suggests a cluster of proteins involved in chromatin state regulation and cell cycle control, with some developmental annotations that may reflect broader regulatory roles. ","confidence":"Medium","size":15,"edges":39,"triangles":33,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":1},{"id":"GO:0070317","count":1},{"id":"GO:1904668","count":1},{"id":"GO:0036265","count":1},{"id":"GO:0050909","count":1}]},{"hash":"1607630067973411847","title":"Developmental gene regulation and chromatin remodeling","description":"The proteins in this cluster show enrichment across diverse developmental processes (multicellular growth; brain and gonad development; osteoblast differentiation; single fertilization) and transcription/chromatin control (DNA-templated transcription; negative regulation of transcription by RNA Pol II; histone H3 acetylation; CENP-A chromatin assembly). The combination suggests a cohesive role in regulating gene expression during development via chromatin remodeling.","confidence":"Medium","size":15,"edges":102,"triangles":419,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0035264","count":6},{"id":"GO:0008584","count":6},{"id":"GO:0007338","count":6},{"id":"GO:0043966","count":6},{"id":"GO:0007420","count":6}]},{"hash":"1141830563704155646","title":"DNA replication, RNA processing, and ribosome biogenesis","description":"These proteins cluster around core cellular machinery: genome maintenance (DNA replication/recombination, cell division), RNA processing (spliceosome activity and ncRNA-mediated silencing), and protein synthesis (ribosome biogenesis and translation). The combination points to a cohesive theme of fundamental gene expression and cell-cycle processes rather than a specific signaling pathway. Some outlier terms related to proviral latency and host apoptosis are present but do not dominate the cluster.","confidence":"High","size":15,"edges":27,"triangles":17,"max_degree":7,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3}]},{"hash":"290323994308005633","title":"Steroid hormone and lipid metabolism","description":"Enrichment is dominated by steroid/hormone biosynthesis terms (prostaglandin, testosterone, aldosterone, ecdysone) and by lipid metabolism processes (fatty acid omega-oxidation, retinoic acid catabolism). This suggests a cohesive theme around lipid-derived hormone production and broader lipid catabolism, with some inflammation regulation signals. The label Steroid hormone and lipid metabolism reflects the common functional thread.","confidence":"High","size":15,"edges":67,"triangles":165,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":14},{"id":"GO:0061370","count":11},{"id":"GO:0008209","count":11},{"id":"GO:0034653","count":10},{"id":"GO:0010430","count":10}]},{"hash":"1536914660488182562","title":"Ubiquitin-Dependent Proteostasis and ERAD","description":"The cluster is centered on ubiquitin-related functions: ubiquitin-dependent protein catabolic processes, regulation of ubiquitin ligase activity, and multiple deubiquitination pathways (monoubiquitinated, linear, and K11-linked). This points to protein quality control and targeted degradation via the ubiquitin-proteasome system and ER-associated degradation (ERAD). The presence of spliceosomal assembly and transcription regulation terms suggests additional connection to gene expression control, but the dominant signal is proteostasis through ubiquitin-mediated processes.","confidence":"Medium","size":15,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060013","count":3},{"id":"GO:1904667","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0035520","count":2}]},{"hash":"921872133592665464","title":"Ephrin signaling in neural development","description":"The proteins cluster around nervous system development and synaptic signaling, with strong representation for ephrin receptor signaling, excitatory synaptic activity, hippocampus development, and axon extension, plus ERK cascade regulation. This pattern suggests a role in ephrin-regulated neural differentiation and synaptic maturation.","confidence":"High","size":15,"edges":51,"triangles":62,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":6},{"id":"GO:0048013","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0043552","count":5},{"id":"GO:0070374","count":5}]},{"hash":"364872057761313786","title":"RNA Modification and Ribosome Biogenesis","description":"The cluster shows several RNA-centric terms: tRNA wobble uridine modification, RNA (guanine-N7)-methylation, and ribosomal large subunit assembly, plus arginine methylation, which together point to RNA processing and translation machinery. While a few terms relate to other processes (muscle development, dendrite morphogenesis, ubiquitin-mediated proteolysis), the strongest signal is RNA modification and ribosome biogenesis, justifying this label as representative of the cluster\u2019s core function.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0043950","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0050774","count":2},{"id":"GO:0000027","count":2}]},{"hash":"1319908725892016877","title":"Signaling and Trafficking Regulators","description":"The proteins in this cluster appear to regulate multiple signaling and trafficking-related processes rather than a single enzyme activity. Top GO terms point to modulation of signaling cascades (positive regulation of GTPase activity; calcineurin-NFAT signaling), nuclear and mRNA transport (NLS-bearing protein import into nucleus; mRNA transport), and organelle dynamics (mitochondrial calcium regulation; non-autophagic vacuole fusion; ciliary basal body docking). The inclusion of midbrain dopaminergic neuron differentiation hints at roles in neural development where signaling regulation and intracellular transport are critical. Together, these terms suggest a group of regulators coordinating signaling with intracellular transport and organelle interactions.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904948","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0051561","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0051028","count":2}]},{"hash":"783614594120018872","title":"Exocrine gland and neuronal development","description":"The top GO terms emphasize exocrine system development and neural differentiation (submandibular gland formation and midbrain dopaminergic neuron differentiation), with supporting cytoskeletal remodeling and junction assembly indicating epithelial morphogenesis. Together, these suggest a cluster focused on exocrine gland development and neuronal differentiation, shaped by cytoskeletal dynamics.","confidence":"High","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070830","count":15},{"id":"GO:0051496","count":15},{"id":"GO:0051489","count":15},{"id":"GO:1903542","count":15},{"id":"GO:0016567","count":15}]},{"hash":"1205604468273340503","title":"Redox Stress and Sulfate and Nitrate Assimilation","description":"Many top terms point to redox biology (oxidation-reduction, nitrosative stress) and inorganic nutrient metabolism (nitrate and sulfate assimilation, L-cysteine biosynthesis). This suggests a cohesive theme around cellular redox balance linked to sulfur and nitrogen metabolism. A few terms (response to antibiotic, sodium ion transport, regulation of integrin biosynthesis) appear less central or represent broader stress responses, but do not override the main redox-nutrient theme.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0042128","count":4},{"id":"GO:0006814","count":4},{"id":"GO:0045726","count":3}]},{"hash":"1607142805646336113","title":"Ribosome biogenesis and ER-targeted translation","description":"This cluster centers on ribosome biogenesis, cytoplasmic translation, and SRP-dependent cotranslational targeting to the membrane, with accompanying glycosylation steps (GPI anchor biosynthesis and related glycosylation) that align with secretory pathway maturation. Together, these terms point to a module combining ribosome assembly/translation with ER-associated processing of nascent polypeptides.","confidence":"Medium","size":15,"edges":50,"triangles":78,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":2},{"id":"GO:0035269","count":1},{"id":"GO:0018279","count":1},{"id":"GO:0015693","count":1},{"id":"GO:0071353","count":1}]},{"hash":"1454848529697446341","title":"Amino acid and cofactor biosynthesis","description":"These proteins show enrichment for multiple biosynthetic pathways: amino acid biosynthesis (tyrosine, alanine), oxaloacetate metabolism, biotin biosynthesis, and protoporphyrinogen IX biosynthesis (a heme pathway precursor), as well as antibiotic biosynthetic processes. Together, these terms point to a cohesive theme of metabolic production and cofactor assembly, indicating a biosynthesis-focused cluster. ","confidence":"Medium","size":15,"edges":85,"triangles":301,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006107","count":5},{"id":"GO:0019878","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006782","count":4},{"id":"GO:0042853","count":4}]},{"hash":"893815887793836911","title":"Vacuolar phosphate homeostasis and transport","description":"The cluster is dominated by GO terms related to phosphate metabolism and transport, including cellular responses to phosphate starvation, phosphate transmembrane transport, intracellular phosphate ion homeostasis, polyphosphate biosynthesis, and regulation of phosphate transport, with added links to vacuolar processes such as non-autophagic vacuole fusion and microautophagy. This points to a cohesive theme of phosphate handling within the vacuolar compartment and associated trafficking, with a few peripheral terms (sodium transport, cold response) that are less central to the core theme.","confidence":"Medium","size":15,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016036","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0048016","count":3},{"id":"GO:0030643","count":3},{"id":"GO:0006814","count":3}]},{"hash":"505720224120669532","title":"Fatty acid metabolism and lipid biosynthesis","description":"The cluster shows a strong enrichment for fatty acid metabolic processes (medium- and long-chain fatty acids), carnitine-related metabolism, and lipid transport, along with lipoteichoic acid biosynthesis. While some GO terms pertain to seed development or other organism-specific processes, the dominant theme tying these proteins together is lipid metabolism and related biosynthetic pathways, suggesting this label accurately reflects the core function of the cluster.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0009437","count":15},{"id":"GO:0036112","count":15},{"id":"GO:0001579","count":15},{"id":"GO:0010214","count":15},{"id":"GO:0008218","count":15}]},{"hash":"424545785040763134","title":"Translation Regulation and Ribosome Function","description":"This cluster is dominated by GO terms tied to protein synthesis and ribosome activity, including cytoplasmic and mitochondrial translation, translation elongation and termination, ribosome disassembly, and maintenance of translational fidelity, suggesting a cohesive theme around translation control and ribosome biology. Some terms, like spliceosomal assembly or brain-derived neurotrophic factor response, appear ancillary but do not override the central translation-related signal.","confidence":"Medium","size":15,"edges":48,"triangles":68,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0003009","count":6},{"id":"GO:1990145","count":4},{"id":"GO:1902802","count":4},{"id":"GO:0045901","count":4},{"id":"GO:0000244","count":4}]},{"hash":"1185051782925767884","title":"Unknown","description":"There are no shared GO terms or interactions linking these proteins (edges 0, top terms empty), so a coherent functional label cannot be inferred from the data provided.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1329115791004208045","title":"Neuronal calcium signaling and pain response","description":"This cluster centers on calcium dynamics across the plasma membrane and neuronal signaling, including purinergic receptor pathways and responses to pain and electrical stimuli. Additional terms related to membrane remodeling (proteolysis, phospholipid translocation, pore assembly) may reflect membrane processes linked to signaling, and a modest signal for glycolytic regulation suggests metabolic support for active signaling. Overall, a coherent theme around calcium-mediated neuronal signaling and pain perception.","confidence":"Medium","size":15,"edges":103,"triangles":429,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006509","count":3},{"id":"GO:0045332","count":3},{"id":"GO:0051209","count":2},{"id":"GO:0048266","count":2},{"id":"GO:0051602","count":2}]},{"hash":"658201802107195349","title":"Developmental Differentiation and Signaling","description":"The proteins are enriched for diverse developmental processes (forebrain development, keratinocyte and placenta-related differentiation) and also for signaling pathways (PI3K/AKT) and regulation of protein turnover, suggesting a common theme of developmentally related differentiation linked with signaling rather than a single tissue-specific function.","confidence":"Medium","size":15,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043277","count":13},{"id":"GO:0030216","count":13},{"id":"GO:0032436","count":13},{"id":"GO:0008045","count":12},{"id":"GO:0045736","count":12}]},{"hash":"1486652961741951415","title":"Ribosome Biogenesis and Translation","description":"The cluster centers on translation-related GO terms (cytoplasmic and general translation), ribosome biogenesis, and rRNA maturation, with associated terms for ribosomal subunit assembly and translational fidelity. These themes point to proteins involved in the protein synthesis machinery and ribosome assembly, making the label representative of the cluster\u2019s function.","confidence":"High","size":15,"edges":71,"triangles":181,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0046677","count":4},{"id":"GO:0002181","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006353","count":2}]},{"hash":"236968284179969177","title":"Mitochondrial translation and tRNA charging","description":"The cluster shows strong signals for translation and multiple tRNA aminoacylation activities (methionyl-, isoleucyl-, valyl-, leucyl-tRNA synthetases) as well as regulation of translational fidelity, indicating a focus on protein synthesis. The mitochondrial-specific GO terms (protein import into the mitochondrial matrix and respiratory chain) further support that these proteins function together in mitochondrial translation machinery, consistent with imported synthetases and related factors.","confidence":"High","size":15,"edges":22,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006431","count":3},{"id":"GO:0006428","count":3},{"id":"GO:0006438","count":3},{"id":"GO:0006429","count":3}]},{"hash":"1769709574546456210","title":"Endomembrane transport in development","description":"Rationale: The strongest signals are vesicle trafficking terms (ER to Golgi, Golgi to endosome, endosome to melanosome), implying a core function in endomembrane transport. The other terms reflect developmental and immune contexts in which such trafficking proteins operate (eyelid development, macrophage differentiation, vitellogenesis), plus general cellular processes. Overall, the cluster appears to be endomembrane transport proteins involved in development.","confidence":"Medium","size":15,"edges":32,"triangles":24,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0009737","count":4},{"id":"GO:0030225","count":3},{"id":"GO:0061029","count":3},{"id":"GO:0006366","count":3},{"id":"GO:0042832","count":3}]},{"hash":"468087335470138133","title":"Unknown","description":"There are 15 proteins with no reported edges or shared GO terms, and ReCIPE-added proteins do not reveal a common functional theme. Without functional terms or interaction data linking them, a meaningful, specific label cannot be inferred.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"829685361352348086","title":"Lipid catabolism and endocannabinoid signaling","description":"The cluster is dominated by GO terms for lipid breakdown (triglyceride catabolic, monoacylglycerol catabolic, phosphatidylserine catabolic) and regulation of endocannabinoid signaling, indicating a cohesive theme around lipid metabolism and lipid signaling. A few outlier terms (sensory perception of sound, cellulose and antibiotic biosynthesis, and an obsolete GPCR pathway term) are present but do not override the lipid-centric pattern. Overall, the proteins likely participate in lipid catabolic processes and related signaling pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":3},{"id":"GO:0090630","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0051262","count":3}]},{"hash":"905193282235059758","title":"Innate Antiviral Immunity and MHC I Processing","description":"This cluster centers on innate antiviral defense, including RIG-I signaling and upregulation of MHC I biosynthesis, pointing to antiviral sensing and antigen presentation; other terms touch nuclear immune signaling (PML bodies) and ubiquitin-dependent regulation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045345","count":2},{"id":"GO:1900246","count":1},{"id":"GO:2000059","count":1}]},{"hash":"2106217366251690156","title":"Amino acid and sugar transport and homeostasis","description":"The cluster is dominated by transport and homeostasis terms: L-cystine transport, D-glucose transmembrane transport, and basic amino acid export from the vacuole, along with intracellular amino acid homeostasis, suggesting a membrane transport/metabolic regulation theme. Additional terms like dolichol-linked oligosaccharide biosynthesis and JNK cascade regulation may relate to broader cellular processes, but do not override the central transport/metabolism signal. Some terms (lens development, grooming behavior) are organism-specific annotations and likely not central to the cluster\u2019s core function.","confidence":"Medium","size":15,"edges":41,"triangles":25,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":2},{"id":"GO:0006488","count":2},{"id":"GO:0080144","count":2},{"id":"GO:0002088","count":2},{"id":"GO:0015811","count":2}]},{"hash":"1641878469038835831","title":"Neuronal Axon Guidance and Embryonic Axis Patterning","description":"The GO terms point to neuronal axon guidance (serotonergic and dopaminergic) and planar polarity, along with multiple axis specification processes (anterior/posterior, left/right) and segmentation in embryonic development, indicating a cluster centered on neural connectivity and body axis patterning during development. A lone electron transport chain term is less cohesive but does not override the overarching developmental theme.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0048105","count":4},{"id":"GO:0036515","count":4},{"id":"GO:0036514","count":4},{"id":"GO:0022900","count":4},{"id":"GO:1904938","count":4}]},{"hash":"1144018183151506529","title":"Neurovascular Development","description":"This cluster centers on neural development processes (axonogenesis, branchiomotor axon guidance, vagus nerve morphogenesis) and endothelial/vascular morphogenesis and chemotaxis, plus limb bud formation, suggesting a cohesive theme of neurovascular patterning and developmental morphogenesis supported by cell surface receptor tyrosine kinase signaling.","confidence":"Medium","size":15,"edges":105,"triangles":455,"max_degree":14,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0007169","count":5},{"id":"GO:0035563","count":5},{"id":"GO:0033689","count":5},{"id":"GO:0021793","count":5},{"id":"GO:0050918","count":5}]},{"hash":"1974791951635035900","title":"Developmental transcription and signaling","description":"This cluster shows enrichment for DNA-templated transcription and multiple developmental processes (forebrain development, neural tube closure, skeletal muscle development, multicellular organism development) plus signaling regulation (GTPase activity, PI3K-related activity). The core theme appears to be regulation of development through transcriptional control and signaling pathways, with some accompanying immune signaling terms as broader regulatory context.","confidence":"Medium","size":14,"edges":30,"triangles":19,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0030900","count":2},{"id":"GO:0060313","count":2},{"id":"GO:0043552","count":2}]},{"hash":"1901289282938243443","title":"Neural development and ER stress-related trafficking","description":"GO terms in this cluster highlight neural development (forebrain development, neural tube closure) alongside general cellular processes (DNA-templated transcription, DNA replication, ribosomal large subunit assembly) and secretory pathway activity (ER to Golgi transport) with ER-stress\u2013induced apoptotic signaling. The overarching theme appears to be neurodevelopment coupled with core cellular machinery and trafficking/stress responses, justifying this label.","confidence":"Medium","size":14,"edges":79,"triangles":248,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0030900","count":3}]},{"hash":"1684882234333747695","title":"DNA Repair and Membrane Transport","description":"The cluster includes GO terms for SOS response and nucleotide-excision repair, indicating a DNA damage\u2013response facet, alongside several transport-related terms (oligosaccharide, thiamine, cobalt, cysteine, abscisic acid) and phospholipid translocation, plus cytochrome complex assembly, suggesting a shared theme of stress response coupled with membrane transport/assembly processes.","confidence":"Medium","size":14,"edges":21,"triangles":12,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":5},{"id":"GO:0006289","count":5},{"id":"GO:0045332","count":5},{"id":"GO:0015772","count":5},{"id":"GO:0006824","count":5}]},{"hash":"1293054036657879479","title":"RNA and histone methylation cluster","description":"Top GO terms show a strong enrichment for methylation activities across RNA species and histones (tRNA/rRNA methylation,RNA methylation, mRNA capping, arginine/histone methylation), indicating a cluster of methyltransferases involved in RNA processing and chromatin modification. Some metabolism-related terms (cobalamin and antibiotic biosynthesis) may reflect methyltransferase functions in those pathways, but the central theme is methylation-based regulation of nucleic acids and chromatin.","confidence":"High","size":14,"edges":10,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":6},{"id":"GO:0016049","count":5},{"id":"GO:0030488","count":5},{"id":"GO:0031167","count":5},{"id":"GO:0090398","count":5}]},{"hash":"1989838135109930602","title":"Gluconeogenesis and lipid metabolism","description":"Proteins in this cluster are enriched for energy-related processes, including gluconeogenesis, fatty-acyl-CoA biosynthesis, carnitine metabolism, and NADPH regeneration, with a broader theme of starvation response. The presence of liver development and post-embryonic development hints at metabolic remodeling rather than a single pathway. Overall, the cluster appears to group enzymes involved in central carbon metabolism and lipid processing with redox balance.","confidence":"Medium","size":14,"edges":57,"triangles":111,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0019878","count":3},{"id":"GO:0001889","count":3},{"id":"GO:0042594","count":3},{"id":"GO:0006552","count":3}]},{"hash":"796588981763390258","title":"Unknown","description":"The top GO terms are diverse and include obsolete annotations (pathogenesis, proteolysis in other organism) along with disparate processes like cellulose catabolic, flocculation, protein homooligomerization, programmed necrotic cell death, and endothelial barrier regulation. There is no clear shared function linking these terms across the proteins, so a coherent cluster name cannot be assigned with confidence.","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009405","count":3},{"id":"GO:0044533","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0000501","count":2},{"id":"GO:0051260","count":2}]},{"hash":"84113709127486385","title":"Epithelial junctions and cytoskeletal remodeling in development","description":"The top GO terms point to epithelial tight junction assembly and cytoskeletal dynamics (stress fiber and filopodium assembly), along with developmental processes such as exocrine system and gland formation and neural differentiation. This suggests a theme where cell adhesion and actin remodeling coordinate tissue morphogenesis and organ development, spanning epithelial, glandular, and neural contexts. ","confidence":"Medium","size":14,"edges":72,"triangles":194,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070830","count":14},{"id":"GO:0051496","count":14},{"id":"GO:0051489","count":14},{"id":"GO:1903542","count":14},{"id":"GO:0016567","count":14}]},{"hash":"1457761675142155678","title":"Embryonic development and organ morphogenesis","description":"Most of the top GO terms point to developmental processes across organs (gastrulation, outflow tract morphogenesis, metanephric ureteric bud development). While there are some general cellular processes and sensory terms present, the preponderance of embryonic development terms suggests the cluster reflects embryonic development and organ morphogenesis rather than a single, tightly defined molecular function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007602","count":2},{"id":"GO:0007369","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0006096","count":1},{"id":"GO:0050787","count":1}]},{"hash":"1311772895758131547","title":"Nucleotide and Cofactor Catabolism","description":"The top GO terms are dominated by catabolic processes for nucleotides and small-molecule cofactors (adenosine-related, NAD+, CoA, diadenosine nucleotides) along with a general nucleobase-containing small molecule catabolic process, suggesting a shared theme of breakdown of nucleotides and cofactors. There is one outlier related to RNA editing, but the prevailing pattern supports a catabolic/metabolic theme around nucleotide and cofactor turnover.","confidence":"Medium","size":14,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006382","count":1},{"id":"GO:0034656","count":1},{"id":"GO:0046057","count":1},{"id":"GO:1901909","count":1},{"id":"GO:0015938","count":1}]},{"hash":"1531511983935763546","title":"Differentiation and growth regulation","description":"The top GO terms point to differentiation processes (brown fat cell differentiation and pollen sperm cell differentiation) and a general growth regulation term (negative regulation of multicellular organism growth). Although each term has only 1 occurrence and there are no edges, the common theme is developmental differentiation and growth control, suggesting the cluster may reflect proteins involved in differentiation pathways. However, the sparse annotations mean this label is tentative.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040015","count":1},{"id":"GO:0050873","count":1},{"id":"GO:0048235","count":1}]},{"hash":"2000905656897373175","title":"Mitochondrial translation and tRNA charging","description":"The terms are dominated by translation-related processes and multiple mitochondrial tRNA aminoacylation activities (glycyl, threonyl, seryl, prolyl), along with regulation of translational fidelity, indicating a mitochondrial protein synthesis module. The inclusion of mitochondrial-specific tRNA biosynthesis and a respiratory chain context further supports a cohesive theme around mitochondrial translation machinery and tRNA charging. ","confidence":"High","size":14,"edges":39,"triangles":54,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0006450","count":6},{"id":"GO:0006433","count":5},{"id":"GO:0070150","count":5},{"id":"GO:0070159","count":5}]},{"hash":"1976057126192635658","title":"Unknown","description":"These terms cover diverse cellular processes: responses to various chemical stimuli (curcumin, mercury, catechin, sorbitol), cell adhesion, regulation of calcium-dependent exocytosis, TORC1 signaling, meiotic checkpoint signaling, axon guidance, and regulation of CDK activity. There is no single coherent biological theme or pathway tying the proteins together, so a unified functional label cannot be confidently assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904643","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0046689","count":1},{"id":"GO:1902168","count":1},{"id":"GO:0045956","count":1}]},{"hash":"2043326116710109005","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":20,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006338","count":1},{"id":"GO:0031063","count":1},{"id":"GO:0048254","count":1},{"id":"GO:0000492","count":1},{"id":"GO:0070475","count":1}]},{"hash":"1044159263436934849","title":"Ubiquitin-Dependent Cell Cycle Regulation","description":"The top GO terms highlight mitotic cell cycle and cell division alongside ubiquitin-related processes (notably K11-linked ubiquitination), pointing to a cluster of proteins involved in regulating mitosis via ubiquitin-mediated proteolysis. Some terms appear unrelated (e.g., prostate gland development, cytokinin signaling) and may reflect noise or cross-species annotations, but the core pattern supports a cell-cycle/ubiquitin regulation theme.","confidence":"High","size":14,"edges":5,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051291","count":7},{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":5},{"id":"GO:1903071","count":5},{"id":"GO:0030850","count":5}]},{"hash":"98542680731087169","title":"Detoxification and small-molecule metabolism","description":"The proteins cluster around a mix of small-molecule catabolic processes (sorbitol, ethanol, formaldehyde, D-xylulose 5-phosphate biosynthesis), metal- and microbe-associated stress responses (response to copper ion, response to lipopolysaccharide), plus redox-related signaling (peptidyl-cysteine S-nitrosylation) and extracellular signal regulation. This combination suggests a functional theme centered on detoxification/metabolism of diverse xenobiotics with modulation of signaling, rather than a single straightforward pathway. ","confidence":"Medium","size":14,"edges":70,"triangles":210,"max_degree":12,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0046688","count":13},{"id":"GO:0006062","count":13},{"id":"GO:0010430","count":13},{"id":"GO:0018119","count":13},{"id":"GO:0045777","count":13}]},{"hash":"2130292598085463781","title":"Negative regulation of immune and vascular processes","description":"This cluster is dominated by GO terms that describe negative regulation of immune and vascular functions\u2014e.g., Rho signaling inhibition, neutrophil degranulation suppression, respiratory burst suppression, cellular extravasation inhibition, vascular permeability regulation, and reduced blood vessel remodeling. These consistently point to a theme of dampening inflammatory and vascular responses, with a few outliers related to broader developmental differentiation that do not contradict the core regulatory pattern. ","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035024","count":3},{"id":"GO:2001170","count":2},{"id":"GO:2000973","count":2},{"id":"GO:0007480","count":2},{"id":"GO:0043314","count":2}]},{"hash":"468913075322484628","title":"Ion transport and cytoskeletal signaling","description":"The cluster is enriched in potassium ion transmembrane transport along with signaling pathways (Rho, semaphorin-plexin) and mechanotransduction-related terms, plus a few notes on organelle dynamics (mitochondrial autophagy, vacuole fusion). This suggests a theme where membrane transport is linked to cytoskeletal signaling and mechanosensitive regulation, rather than a single isolated process.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0000422","count":1},{"id":"GO:0010259","count":1},{"id":"GO:0043457","count":1},{"id":"GO:0007266","count":1}]},{"hash":"222277611224162683","title":"N-terminal acetylation and related metabolism","description":"This cluster is dominated by GO terms for N-terminal acetylation of various amino acids (serine, glutamic acid, methionine) and related propionylation, indicating a common theme of protein N-terminal modification. While a few terms touch broader metabolic pathways (acetoin, glucosamine, mycothiol biosynthesis), the strongest and most coherent signal is N-terminal acetylation and related acylation processes, suggesting these proteins function in or with N-terminal modification pathways.","confidence":"High","size":14,"edges":87,"triangles":319,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":14},{"id":"GO:0017198","count":14},{"id":"GO:0030187","count":14},{"id":"GO:0018002","count":14},{"id":"GO:0006526","count":14}]},{"hash":"1126063669999082939","title":"Cardiac and Muscle Development","description":"The top GO terms are dominated by heart development and muscle cell homeostasis, suggesting a focus on cardiac/muscle biology. While additional terms point to broad developmental processes across other tissues, the strongest signal is cardiac/muscle development, justifying the label. ","confidence":"Medium","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046716","count":2},{"id":"GO:1903526","count":2},{"id":"GO:0030259","count":2},{"id":"GO:0051262","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1397890626361917478","title":"Muscle and neural development","description":"The terms cluster around development of heart and skeletal muscle (heart development, regulation of striated muscle differentiation, muscle satellite cell maintenance) and neural lineage (cerebellar cortex development, regulation of gliogenesis), with supporting references to transcriptional regulation and histone methylation (DNA-templated transcription, H3-K36 methylation). This suggests a developmental program coordinating muscle and brain lineages, rather than a single, unified pathway. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0097198","count":2},{"id":"GO:0071314","count":2},{"id":"GO:2001040","count":2}]},{"hash":"592865657164800321","title":"Ubiquitin-Regulated Immune Signaling and Transcription","description":"The cluster concentrates on immune signaling and transcriptional control linked by ubiquitin processes: innate immune response, TNF signaling, JNK cascade regulation, and K48-linked ubiquitination appear together with DNA-templated transcription and growth regulation terms. This suggests a coherent theme of ubiquitin-dependent regulation of signaling and transcription in immune and growth pathways, despite a few miscellaneous terms. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0071374","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0038018","count":2}]},{"hash":"412875293881173447","title":"Unknown","description":"The top GO terms describe very disparate processes\u2014maintenance of rDNA, mitochondrial ATP synthesis, and negative regulation of insulin secretion in response to glucose\u2014without a common functional theme or interaction pattern (no edges or triangles). This lack of a cohesive shared function among the proteins suggests no meaningful label beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043007","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0061179","count":1}]},{"hash":"687894131228525974","title":"Amino acid biosynthesis and metabolic signaling","description":"This cluster is enriched for several amino acid biosynthetic processes (tryptophan, arginine, histidine) and glutamine metabolism, indicating a core theme of amino acid biosynthesis. The presence of a triglyceride biosynthetic process and cellular responses to cAMP and oleic acid suggests broader metabolic regulation and nutrient signaling. Overall, the proteins appear grouped around amino acid production with related metabolic signaling roles.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":2},{"id":"GO:0071400","count":2},{"id":"GO:0019432","count":2},{"id":"GO:1903718","count":1},{"id":"GO:0000162","count":1}]},{"hash":"753409531388883797","title":"Rho-Driven Actin Cytoskeleton Remodeling","description":"This cluster shows enrichment for actin cytoskeleton organization, actin filament depolymerization, and regulation of Rho signaling, with thrombin-activated receptor signaling supporting a theme of cytoskeletal dynamics and signal transduction. DNA replication-related terms appear infrequently and do not define the main function of the group.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070493","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0030036","count":2},{"id":"GO:0071165","count":1}]},{"hash":"1783149275885669573","title":"Cell Cycle and Vesicle Transport","description":"Based on the top GO terms, the cluster centers on cell division and cell cycle, coupled with multiple intracellular transport processes (protein transport, ER-to-Golgi vesicle transport, and endosome-to-Golgi retrograde transport). This points to proteins coordinating cell cycle progression with vesicle trafficking and organelle dynamics, with a few secondary terms (mitochondrial fusion regulation, prenylated protein turnover) that fit within broader intracellular protein handling during cellular division.","confidence":"Medium","size":14,"edges":20,"triangles":10,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0042147","count":1}]},{"hash":"46889775520637351","title":"DNA damage response and RNA turnover","description":"Genes in this cluster show links to DNA-templated transcription, DNA repair, and mRNA decay pathways, along with an apoptotic/stress response (cellular response to menadione). Although a few terms relate to metabolism (lipid and purine catabolism), the dominant theme centers on nucleic acid maintenance and cellular stress response. ","confidence":"Medium","size":14,"edges":10,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:2000757","count":1},{"id":"GO:0044240","count":1},{"id":"GO:0009154","count":1},{"id":"GO:1901919","count":1}]},{"hash":"1082227962825911184","title":"Endocytic Receptor Trafficking and Lysosome Targeting","description":"These proteins appear linked to internalization of cell-surface receptors, trafficking through endosomes toward lysosomal compartments, and associated signaling pathways (receptor signaling, integrin, VEGF). The GO terms include receptor internalization, protein localization to lysosome, endosome-to-melanosome transport, and receptor-mediated interactions, suggesting a cohesive role in endocytic trafficking coupled with signaling.","confidence":"Medium","size":14,"edges":43,"triangles":60,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0035646","count":3},{"id":"GO:0043128","count":3},{"id":"GO:0090528","count":3},{"id":"GO:0031623","count":3},{"id":"GO:0061462","count":3}]},{"hash":"200644673565142971","title":"Unknown","description":"There are no edges, no triangles, and no enriched GO terms to tie the proteins to a shared function, so a meaningful label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"242020191267606057","title":"Unknown","description":"The GO terms span meiosis, gene expression regulation, muscle adaptation, endocytosis, development (retina, substantia nigra, mesenchyme), and behavior, with no single dominant function tying them together. This heterogeneous mix makes a cohesive cluster label unlikely.","confidence":"","size":14,"edges":18,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016344","count":1},{"id":"GO:0010628","count":1},{"id":"GO:0043503","count":1},{"id":"GO:0030100","count":1},{"id":"GO:0090131","count":1}]},{"hash":"266249153102797499","title":"Secretory trafficking and Wnt signaling in development","description":"The top terms point to COPI-coated vesicles and ER\u2013Golgi transport, lysosome targeting, and secretion of Wnt proteins, with supporting hints from rhodopsin biosynthesis and axis/developmental processes. This implies a cluster of proteins involved in the secretory/trafficking machinery that supports developmental signaling and specialized protein production, rather than a single linear pathway. ","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006622","count":3},{"id":"GO:0016063","count":3},{"id":"GO:0043277","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0032525","count":2}]},{"hash":"1356720408176985618","title":"Unknown","description":"There are no GO terms or network connections to point to a common function among the 14 proteins (no edges/triangles, and no top terms provided). With the data available, no coherent functional theme can be inferred, so a generic Unknown label is appropriate.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1904131565587305109","title":"Unknown","description":"This cluster has no edges and no top GO terms to indicate a shared function among the proteins, so a coherent biological theme cannot be inferred from the available data.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1088025622228670039","title":"Sphingolipid Metabolism and Signaling","description":"The cluster shows multiple terms tied to sphingosine/sphinganine metabolism and sphingolipid-mediated signaling, along with phospholipid turnover, suggesting a coherent lipid metabolism/signaling module. Obsolete Wnt-related terms appear less informative and do not define the core theme.","confidence":"High","size":14,"edges":53,"triangles":84,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0044328","count":3},{"id":"GO:0035233","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0006668","count":3},{"id":"GO:0046839","count":3}]},{"hash":"2092410255074627017","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048542","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0000461","count":1}]},{"hash":"2111176701436674345","title":"Skin lipid metabolism and adipogenesis","description":"The cluster centers on lipid biosynthesis and metabolism, including monounsaturated fatty acid biosynthesis, sphinganine/sphingosine pathways, and cholesterol esterification, with related skin/adipose biology signals such as tarsal gland development and white fat cell differentiation. Despite some obsolete terms, the overarching theme is lipid production/storage and adipocyte-related processes in skin, suggesting sebaceous gland and adipose tissue lipid functions.","confidence":"High","size":14,"edges":63,"triangles":148,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0034435","count":5},{"id":"GO:0010205","count":4},{"id":"GO:0033561","count":4},{"id":"GO:1903966","count":4},{"id":"GO:0006667","count":4}]},{"hash":"1078247759877077292","title":"Unknown","description":"The top GO terms mix diverse polymer/antibiotic catabolic processes with plant defense responses and cell wall remodeling, plus an outlier like sexual reproduction; there isn\u2019t a single cohesive function tying all proteins together, so a clear label isn\u2019t supported.","confidence":"","size":14,"edges":14,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0045493","count":2},{"id":"GO:0019876","count":1},{"id":"GO:0030655","count":1},{"id":"GO:0046677","count":1}]},{"hash":"1934030613057000757","title":"Zinc transport and homeostasis","description":"This cluster is dominated by GO terms related to zinc import across membranes, intracellular zinc ion homeostasis, zinc detoxification, and cellular response to zinc ion starvation, indicating a cohesive group of proteins involved in zinc uptake and maintenance of cellular zinc levels. The presence of related metal ion transport terms (e.g., cadmium) supports a broader metal transport context, but the zinc-focused terms are most prominent, suggesting a specific zinc homeostasis module.","confidence":"High","size":14,"edges":54,"triangles":105,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0044749","count":7},{"id":"GO:1903615","count":7},{"id":"GO:0070574","count":7},{"id":"GO:0034224","count":7},{"id":"GO:0010312","count":7}]},{"hash":"1951859135988348008","title":"Siderophore biosynthesis and transport","description":"This cluster shows strong signals for siderophore biosynthesis (rhizobactin 1021, aerobactin) and siderophore transmembrane transport, suggesting proteins involved in iron-chelating molecule production and uptake. Some other GO terms appear unrelated background terms, but the siderophore-related terms provide the cohesive theme. ","confidence":"Medium","size":13,"edges":72,"triangles":226,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0019289","count":1},{"id":"GO:0019270","count":1},{"id":"GO:0044718","count":1},{"id":"GO:1990834","count":1},{"id":"GO:0097500","count":1}]},{"hash":"593419196245759805","title":"Nuclear RNA processing and ribosome biogenesis","description":"The top GO terms cluster around splicing and rRNA maturation (mRNA splicing via spliceosome; maturation of SSU/LSU/5.8S rRNA), ribosome biogenesis (ribosomal large subunit biogenesis), chromatin remodeling, and transcription termination, all pointing to coordinated nuclear RNA processing and assembly of ribosomes, with additional links to cell cycle processes. ","confidence":"High","size":13,"edges":64,"triangles":161,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000462","count":3}]},{"hash":"375275511907474935","title":"DNA Replication and Repair Machinery","description":"This cluster is dominated by GO terms for DNA replication, DNA repair, mitotic checkpoint signaling, and replication-associated double-strand break repair, indicating a group specialized in genome maintenance and cell-cycle control. Oxidative stress and xenobiotic response terms fit into the broader DNA damage response context, while a peroxisome import term appears ancillary. Overall, the theme centers on genome integrity during replication and division.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0034599","count":3}]},{"hash":"2259893230849463476","title":"Cell Cycle and Telomere Maintenance","description":"The cluster is enriched for core cell-cycle processes (cell division, cell cycle, mitotic G2 DNA damage checkpoint signaling) and telomere maintenance via telomerase, along with DNA damage repair-related activity (poly-ADP-ribosylation). While a few terms (migration, morphogenesis) are less central, the dominant theme centers on cell proliferation with genome maintenance.","confidence":"Medium","size":13,"edges":55,"triangles":116,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032212","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0016477","count":3},{"id":"GO:0000902","count":3}]},{"hash":"854848467784965188","title":"DNA replication and ribosome biogenesis","description":"These proteins are linked to core nuclear processes: DNA replication and recombination (DNA replication, DNA recombination, RNA-templated DNA biosynthetic process) and ribosome biogenesis (ribosome assembly, preribosome large subunit precursor assembly, LSU-rRNA maturation). While a couple of terms (silencing, proviral latency) are less directly connected, the dominant signals point to DNA handling and ribosome production as the cluster\u2019s theme.","confidence":"Medium","size":13,"edges":60,"triangles":137,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006310","count":4},{"id":"GO:0006268","count":3},{"id":"GO:0042255","count":3},{"id":"GO:1902626","count":3}]},{"hash":"1879981061081091848","title":"Neural development and cell migration","description":"This cluster is dominated by GO terms tied to neural development and cell movement, including forebrain development, neural tube closure, cell migration, and integrin-mediated signaling, plus transcriptional regulation and multicellular development. The presence of metallopeptidase activity suggests extracellular matrix remodeling linked to migratory processes, consistent with neural development and tissue remodeling. Some terms like cytosine metabolism or stress-induced invasive growth may reflect broader cellular states or housekeeping links but do not override the central neural-development/migration theme.","confidence":"Medium","size":13,"edges":36,"triangles":40,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0007229","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1052804997871992455","title":"ER Stress and Redox Homeostasis","description":"The cluster is enriched in GO terms for redox balance, oxidant detoxification, and ER-related quality control (protein folding in the ER and ER stress response), plus cytochrome complex assembly linked to electron transport. While there are some transcription-related terms, the dominant themes point to managing oxidative stress and ER function, suggesting a cohesive role in ER stress response and redox homeostasis.","confidence":"Medium","size":13,"edges":38,"triangles":52,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045454","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0098869","count":6},{"id":"GO:0034975","count":5},{"id":"GO:0006351","count":4}]},{"hash":"1710125124542888753","title":"RNA processing and nucleotide biosynthesis","description":"The listed GO terms cluster around two main themes: mRNA export from the nucleus (GO:0006406) and various steps of pyrimidine ribonucleotide biosynthesis (dUTP/dITP/dUMP and related biosynthetic processes). A smaller set mentions [2Fe-2S] cluster assembly and transcription-related regulation, which can tie into maturation of RNA-processing and transcriptional machinery. Overall, the proteins appear to be involved in nucleic-acid metabolism, spanning RNA processing/export and nucleotide biosynthesis. ","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0046081","count":1},{"id":"GO:0006229","count":1},{"id":"GO:0035863","count":1},{"id":"GO:0006226","count":1}]},{"hash":"1304619521844229132","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071549","count":2},{"id":"GO:0031123","count":1},{"id":"GO:0043631","count":1},{"id":"GO:0019827","count":1},{"id":"GO:0045665","count":1}]},{"hash":"1256679453194680631","title":"Spliceosome-regulated RNA processing and translation control","description":"This cluster centers on post-transcriptional regulation: multiple GO terms point to splicing regulation via the spliceosome (positive/negative regulation, alternative splicing) and to translation control (translation preinitiation complex formation, reinitiation, IRES-driven initiation, and miRNA-mediated silencing). The coexistence of splicing and translation-related terms suggests a cohesive role in RNA processing and translational regulation, with a hint of RNA silencing components.","confidence":"High","size":13,"edges":12,"triangles":7,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0002188","count":6}]},{"hash":"764549811527109270","title":"Mitochondrial dynamics and apoptosis","description":"The cluster is dominated by GO terms tied to mitochondria, including mitochondrial fission and fusion, release of cytochrome c, and intrinsic apoptotic signaling, with neuron-specific apoptosis and calcium-regulated stress responses. An outlier term like cellulose catabolic process is likely noise, but the core pattern clearly centers on mitochondrial stress leading to apoptosis, consistent across the proteins. ","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1},{"id":"GO:1904579","count":1},{"id":"GO:0007204","count":1},{"id":"GO:0097237","count":1},{"id":"GO:0008053","count":1}]},{"hash":"317662473662751466","title":"Ribosome biogenesis and translation regulation","description":"The cluster is dominated by GO terms for translation, cytoplasmic translation, ribosome biogenesis, and regulation of translational fidelity/elongation, with some ribosome disassembly signals and antibiotic response, indicating a cohesive ribosome- and translation-focused module.","confidence":"High","size":13,"edges":54,"triangles":115,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":3},{"id":"GO:0045903","count":3},{"id":"GO:1990145","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2000226254577237516","title":"Macrophage lipid metabolism and foam cell formation","description":"The cluster centers on lipid handling: triglyceride biosynthesis, VLDL particle assembly, and cholesterol efflux, plus protein lipidation (palmitoylation) and foam cell differentiation. While there are a few general metabolic terms (lipoylation, glycine decarboxylation), the dominant signal is macrophage lipid metabolism and lipid-modification processes linked to foam cell formation.","confidence":"Medium","size":13,"edges":67,"triangles":186,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0009249","count":1},{"id":"GO:0019464","count":1},{"id":"GO:0018009","count":1},{"id":"GO:0010742","count":1},{"id":"GO:0034379","count":1}]},{"hash":"2149525611697134170","title":"Unknown","description":"The top GO terms span DNA repair, toxin metabolism, nitrogen utilization, inflammatory signaling, hormone responses (auxin and estradiol), development, and olfactory perception, with no single unifying function linking them. The diversity suggests a mixed or misannotated cluster rather than a coherent biological module, so a specific label cannot be confidently assigned.","confidence":"","size":13,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":2},{"id":"GO:0009407","count":2},{"id":"GO:0006808","count":2},{"id":"GO:0019371","count":2},{"id":"GO:0071638","count":2}]},{"hash":"677300059536028215","title":"DNA Transcription and RNA Pol II Initiation","description":"The cluster\u2019s strongest, most frequent GO terms center on DNA-templated transcription, transcription initiation, and RNA polymerase II preinitiation complex assembly, suggesting a core link to transcription machinery. There are also outlier terms related to meiosis and other processes, but the dominant signal supports transcriptional regulation and initiation as the main theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0007129","count":2},{"id":"GO:0048666","count":2},{"id":"GO:0043966","count":1},{"id":"GO:0009736","count":1}]},{"hash":"1558934534600029698","title":"Nucleocytoplasmic Transport and Membrane Trafficking","description":"The cluster shows enrichment for nucleocytoplasmic transport terms (protein import into nucleus, protein export from nucleus, and regulation of import) along with general membrane/transport terms (protein transmembrane transport, monoatomic cation transmembrane transport) and related processes like ATP synthesis and cytokinesis, suggesting a group of proteins involved in nucleocytoplasmic exchange and vesicle/membrane transport, with ancillary links to cytoskeletal regulation.","confidence":"Medium","size":13,"edges":14,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006606","count":2},{"id":"GO:0099132","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0051016","count":1},{"id":"GO:0007294","count":1}]},{"hash":"2158139708442204406","title":"Antiviral Innate Immune Signaling","description":"This cluster centers on innate antiviral defense: RIG-I signaling, innate immune response, and suppression of viral release by host. Additional terms point to immune-modulatory signaling (retinoic acid and vitamin D receptor pathways) and nuclear structures (PML bodies) that can influence antiviral responses, along with microtubule localization for intracellular trafficking of immune components. Together, these terms suggest proteins involved in antiviral innate immunity and related host defense pathways.","confidence":"High","size":13,"edges":3,"triangles":1,"max_degree":2,"top_function":"autophagy","top_go_terms":[{"id":"GO:1900246","count":3},{"id":"GO:2000059","count":3},{"id":"GO:0035372","count":3},{"id":"GO:0036353","count":3},{"id":"GO:0070562","count":3}]},{"hash":"995819977184824794","title":"Unknown","description":"There is no coherent shared function among the proteins in this cluster: the top GO terms are separate (peptidyl-cysteine oxidation and detection of hypoxia) with only single counts, and the cluster has no edges or connectivity to suggest a common pathway or process. Confidence: None","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018171","count":1},{"id":"GO:0070483","count":1}]},{"hash":"885917504579303322","title":"N-terminal acetylation cluster","description":"The top GO terms are dominated by N-terminal acetylation events on various amino acids (serine, glutamic acid, methionine) and related acetylation/protein modification processes, indicating this cluster centers on N-terminal modification of proteins. While a few terms point to broader metabolic processes (acetoin/melatonin biosynthesis, mycothiol biosynthesis, sporulation), the strongest signal is N-terminal acetylation. ","confidence":"High","size":13,"edges":23,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":7},{"id":"GO:0017198","count":7},{"id":"GO:0030187","count":7},{"id":"GO:0018002","count":7},{"id":"GO:0006526","count":7}]},{"hash":"823947142858287429","title":"Redox homeostasis and transcriptional regulation","description":"This cluster centers on redox-related processes (oxidant detoxification and redox homeostasis) alongside transcription-related terms (DNA-templated transcription and regulation of DNA binding), implying a link between cellular redox state and transcriptional control. Although also featuring protein repair, proline hydroxylation, and a viral process term, the dominant theme appears to be redox regulation coupled with transcriptional regulation.","confidence":"Medium","size":13,"edges":64,"triangles":168,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0098869","count":11},{"id":"GO:0043388","count":10},{"id":"GO:0055114","count":10},{"id":"GO:0045454","count":10},{"id":"GO:0006351","count":9}]},{"hash":"1266376284902992386","title":"Plant nitrogen and iron metabolism","description":"These proteins appear linked to nitrogen metabolism (ureide catabolic and allantoin assimilation pathways, arginine biosynthesis) and iron handling (iron import across the membrane, transferrin transport, receptor-mediated endocytosis). The presence of a plant growth term (regulation of inflorescence meristem growth) suggests additional developmental roles, but the core theme across the GO terms points to nutrient processing and transport in plants, especially nitrogen and iron pathways.","confidence":"Medium","size":13,"edges":51,"triangles":98,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0010136","count":1},{"id":"GO:0098707","count":1},{"id":"GO:0006526","count":1},{"id":"GO:0009442","count":1},{"id":"GO:0042135","count":1}]},{"hash":"467375180690871465","title":"ER stress-driven transcriptional regulation","description":"This cluster is enriched for terms tied to the endoplasmic reticulum unfolded protein response, transcription by RNA polymerase II, and regulation of transcription, along with protein ubiquitination, suggesting a coherent function in ER stress\u2013related transcriptional control and quality control. Some development-related terms appear but are secondary to this core theme.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":3},{"id":"GO:0000209","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0021615","count":2},{"id":"GO:1900103","count":2}]},{"hash":"828367555472228327","title":"Nucleic acid repair and tRNA modification","description":"The cluster centers on RNA processing, RNA/DNA repair, and tRNA wobble modification, including regulation of translational initiation by tRNA modification and mRNA processing, with additional, smaller links to programmed cell death. This points to a cohesive theme of nucleic acid quality control and RNA metabolism.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1990983","count":1},{"id":"GO:0042245","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0006307","count":1}]},{"hash":"673053455467111101","title":"Cilium-Related Morphogenesis and Vesicle Trafficking","description":"This label fits because the top GO terms cluster around cilium-related processes (cilium assembly regulation, centrosome localization), cell morphogenesis, and vesicle trafficking (endosome transport, vesicle fusion), with lens fiber morphogenesis supporting a morphogenesis-centric role tied to ciliary/centrosomal functions.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090630","count":2},{"id":"GO:0045737","count":2},{"id":"GO:0000902","count":2},{"id":"GO:0051661","count":2},{"id":"GO:1902543","count":1}]},{"hash":"1444572618048269680","title":"Epigenetic Regulation of Neural and Muscle Development","description":"This cluster centers on DNA-templated transcription and histone modification activities (H3K36 and H3K4 methylation), suggesting chromatin-level control of gene expression. The presence of neural development terms (cerebellar cortex development, regulation of gliogenesis) together with muscle-related terms (muscle satellite cell maintenance, regulation of striated muscle differentiation) points to a set of epigenetic regulators involved in both neural and muscular development. Drug-response terms appear but are secondary to the core epigenetic and developmental theme.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0097198","count":2},{"id":"GO:0071314","count":2},{"id":"GO:2001040","count":2},{"id":"GO:0051154","count":2}]},{"hash":"490241329193618002","title":"Unknown","description":"The GO terms are spread across muscle and nervous system development, innate immune responses, signaling pathways (PI, CAMKK-AMPK, Rho), cell cycle regulation, and protein ubiquitination, with no single unifying function that ties the cluster together. This diversity makes it hard to assign a cohesive label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":3},{"id":"GO:0007399","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0045842","count":2},{"id":"GO:1905289","count":2}]},{"hash":"2249737726081405261","title":"Prostaglandin and leukotriene biosynthesis in inflammation","description":"The proteins are enriched for prostaglandin biosynthetic process, lipoxygenase pathway, and leukotriene production, with concurrent responses to lipopolysaccharide and cytokines and oxidative detoxification\u2014strongly indicating generation of inflammatory lipid mediators (eicosanoids). A couple of terms like plant-type cell wall assembly and heme biosynthesis are less coherent with this theme but do not dominate the cluster.","confidence":"High","size":13,"edges":20,"triangles":11,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006783","count":1},{"id":"GO:0070453","count":1},{"id":"GO:0071668","count":1},{"id":"GO:1902001","count":1},{"id":"GO:0032496","count":1}]},{"hash":"882510637097198594","title":"Strigolactone-responsive shoot development","description":"This cluster is anchored by GO terms related to strigolactone signaling (cellular response to strigolactone) and secondary shoot formation, pointing to plant hormone\u2013driven regulation of shoot architecture. The other terms are diverse metabolic processes and do not form a cohesive theme, so the label emphasizes the strongest, most specific link. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097755","count":1},{"id":"GO:0019391","count":1},{"id":"GO:0010223","count":1},{"id":"GO:0019740","count":1},{"id":"GO:0046839","count":1}]},{"hash":"1995720687395779716","title":"Transmembrane Ion and Metabolite Transport","description":"This cluster is dominated by GO terms for transporting substances across membranes, including ions (potassium, sodium, phosphate), small molecules (arabinose, 4-hydroxyphenylacetate), vitamins, and even neurotransmitter loading into synaptic vesicles; some terms also touch nitrate assimilation and obsolete antibiotic transport. The overall pattern points to membrane transport proteins or transport-associated functions rather than enzymes, making \u201cTransmembrane Ion and Metabolite Transport\u201d an apt label.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0035725","count":2},{"id":"GO:1900754","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0015739","count":2}]},{"hash":"628588785065769177","title":"Amino-acid catabolism and xenobiotic metabolism","description":"The GO terms show multiple amino-acid catabolic pathways (glutamine, phenylalanine, tyrosine), glutathione metabolism, and xenobiotic/antibiotic catabolism, suggesting a cluster focused on metabolic detoxification and breakdown of amino acids, with only minor transcription-related signals.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0046677","count":1},{"id":"GO:0006749","count":1}]},{"hash":"930638753780855188","title":"Unknown","description":"The proteins in this cluster show a scattered mix of GO terms spanning neural development, reproduction, apoptosis, redox and metabolism, chromatin regulation, and other unrelated processes, with only small counts per term and minimal connectivity. This lack of a clear, shared function across members makes it difficult to assign a cohesive, meaningful name.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048240","count":3},{"id":"GO:0021987","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045793","count":3}]},{"hash":"1857101626059038511","title":"Genome transcription and DNA maintenance with proviral integration","description":"The top GO terms center on transcription across RNA polymerases I\u2013III, RNA-templated transcription, transcription-coupled repair, plus core DNA metabolism activities (DNA replication, recombination) and DNA integration including proviral latency. A unifying theme is nucleic acid metabolism and genome regulation, with hints of viral integration and host interaction, justifying a label that emphasizes transcription and DNA maintenance with integration aspects.","confidence":"Medium","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006367","count":3},{"id":"GO:0042797","count":2},{"id":"GO:0006363","count":2},{"id":"GO:0001172","count":2},{"id":"GO:0006283","count":2}]},{"hash":"598269359231125449","title":"Retroviral integration and latency","description":"The GO terms point to a retroviral life cycle: reverse transcription (RNA-templated DNA synthesis), DNA replication and recombination, DNA integration, viral entry and penetration into the host nucleus, and establishment of integrated proviral latency, with hints of RNAi suppression and host apoptosis manipulation. This constellation strongly supports a retroviral infection/latency theme rather than general DNA replication alone. ","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":12},{"id":"GO:0006260","count":12},{"id":"GO:0006278","count":11},{"id":"GO:0046718","count":11},{"id":"GO:1903704","count":11}]},{"hash":"2006989168311035639","title":"Golgi-to-ER Retrograde Trafficking","description":"The top GO term is retrograde vesicle-mediated transport from the Golgi to the endoplasmic reticulum (GO:0006890), pointing to a core function in Golgi\u2013ER trafficking. Although developmental and signaling terms appear, the strongest and most specific signal is vesicle transport between Golgi and ER, making this the most representative label for the cluster.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":3},{"id":"GO:0001501","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0060789","count":2},{"id":"GO:0010255","count":2}]},{"hash":"877806519720885430","title":"Neural development and cell-cycle proliferation","description":"The top GO terms point to brain development (including substantia nigra development) and overall neural growth, together with mitotic processes (cell division, mitotic cell cycle, spindle assembly) and proliferation. This pattern suggests a cluster of proteins involved in neural development that also coordinate cell division and growth, possibly reflecting proliferative neural progenitors or developmentally regulated signaling tied to brain formation. The vesicle transport term hints at intracellular trafficking supporting these processes in developing neural tissue.","confidence":"High","size":12,"edges":42,"triangles":73,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0043547","count":6},{"id":"GO:0021762","count":5},{"id":"GO:0035264","count":5},{"id":"GO:0000278","count":5}]},{"hash":"191189990672054261","title":"Neural development and cell cycle regulation","description":"The cluster shows strong signals for neural development (forebrain development, neural tube closure) alongside general developmental processes (multicellular organism development) and core cell cycle/transcription activities (mitotic cell cycle, cell division, DNA-templated transcription). The combination points to proteins involved in coordinating development with proliferation and gene expression, with some stress-related terms likely reflecting common regulatory intersections. ","confidence":"Medium","size":12,"edges":17,"triangles":6,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0030900","count":4},{"id":"GO:0070059","count":4},{"id":"GO:0051301","count":4}]},{"hash":"372887233183978971","title":"RNA Splicing Regulation and Translation Initiation","description":"The top GO terms cluster around mRNA processing and spliceosome-mediated regulation of splicing (positive/negative, alternative), indicating a core focus on RNA maturation and splicing control. Additional terms touch on translation initiation (preinitiation complex formation, IRES-dependent initiation) and ncRNA-mediated gene silencing, suggesting the proteins collectively participate in coordinating RNA processing with post-transcriptional gene regulation. This combination supports a label centered on spliceosome-driven RNA processing with a translational initiation connection.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":4},{"id":"GO:0006397","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0035278","count":3},{"id":"GO:0075522","count":3}]},{"hash":"1504643370434866900","title":"Unknown","description":"GO terms are diverse, including nitrogen fixation, ubiquitin-related regulation, microtubule localization, oxidative stress response, and signaling pathways, with some obsolete terms. There is no clear unifying function or pathway linking the proteins, suggesting a heterogeneous cluster rather than a distinct module.","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009399","count":1},{"id":"GO:0051725","count":1},{"id":"GO:0071451","count":1},{"id":"GO:1900246","count":1},{"id":"GO:2000059","count":1}]},{"hash":"1125105969984348464","title":"Vesicle trafficking and cytoskeletal remodeling","description":"The cluster centers on processes like retrograde Golgi-ER transport, endocytosis, and regulation of actin structures (stress fibers, filopodia), combined with cell division/proliferation and osteoclast development signals. This points to a coordinated program of vesicle trafficking and cytoskeletal dynamics in proliferating cells.","confidence":"Medium","size":12,"edges":56,"triangles":142,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":7},{"id":"GO:0008283","count":7},{"id":"GO:0036035","count":7},{"id":"GO:0006897","count":7},{"id":"GO:0051301","count":7}]},{"hash":"977200385583884116","title":"Nucleotide Excision Repair and Cell Cycle Regulation","description":"The cluster is enriched for global genome nucleotide-excision repair terms and preincision complex components, with accompanying cell-cycle control terms; sumoylation also appears, supporting regulation of DNA repair processes. Some transcription-related terms are present but appear secondary to the core NER and cell-cycle theme.","confidence":"High","size":12,"edges":42,"triangles":74,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0000717","count":1},{"id":"GO:0006294","count":1}]},{"hash":"47412196547367843","title":"Central Metabolism and Translation","description":"Contains major metabolic pathways (glycolysis, TCA cycle, lipid biosynthesis, malonyl-CoA, cobalamin biosynthesis) plus protein synthesis (translation and tRNA aminoacylation). This combination points to a core, housekeeping cluster integrating metabolism with translation.","confidence":"Medium","size":12,"edges":31,"triangles":34,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042759","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0006431","count":3},{"id":"GO:0006429","count":3},{"id":"GO:0006096","count":3}]},{"hash":"1923741910268150069","title":"Embryonic development and tissue morphogenesis","description":"Top GO terms point to development and morphogenesis across diverse tissues (exocrine gland formation, multicellular growth, dopaminergic neuron differentiation, trabecula morphogenesis) as well as cytoskeletal remodeling (stress fiber and filopodium assembly) and gene regulation (protein ubiquitination, negative regulation of gene expression). Together these imply a cluster of proteins involved in developmental regulation and morphogenetic processes, with cytoskeletal dynamics facilitating tissue formation and regulatory controls ensuring proper expression during development.","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051496","count":12},{"id":"GO:0051489","count":12},{"id":"GO:1903542","count":12},{"id":"GO:0016567","count":12},{"id":"GO:0060661","count":12}]},{"hash":"1081784948050431775","title":"Neuronal lipid metabolism and neuroimmune signaling","description":"This cluster\u2019s terms point to lipid/glycolipid turnover in neurons (cholesterol metabolic process, ganglioside catabolic process) and nervous system functions (learning or memory, neuromuscular balance). The presence of innate immune terms (innate immune response, cellular response to lipopolysaccharide, positive regulation of LPS signaling) suggests neuroimmune signaling. Although necroptosis is a single term, the overall mix fits a theme of neural lipid metabolism coupled with neuroimmune interactions rather than a single pure pathway.","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070266","count":1},{"id":"GO:0008203","count":1},{"id":"GO:0007611","count":1},{"id":"GO:0009313","count":1},{"id":"GO:0031666","count":1}]},{"hash":"1264640602635065077","title":"DNA replication, repair, and telomere maintenance","description":"The cluster\u2019s top GO terms center on DNA replication, DNA repair, recombination, and telomere maintenance, with a connected cell cycle checkpoint signal, pointing to genome maintenance and genome stability as the core function. Translation-related terms and mitochondrial tRNA aminoacylation appear but seem secondary to the dominant DNA metabolism signals.","confidence":"Medium","size":12,"edges":38,"triangles":58,"max_degree":11,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0010833","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0072581","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1372798436752762884","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":21,"triangles":14,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":1},{"id":"GO:0045006","count":1},{"id":"GO:0000964","count":1},{"id":"GO:0070481","count":1},{"id":"GO:0010323","count":1}]},{"hash":"363195944494887048","title":"Exocrine gland development and epithelial organization","description":"The top GO terms align with exocrine system development, submandibular gland formation, and multicellular growth, together with epithelial remodeling activities such as tight junction and cytoskeletal (stress fiber, filopodium) assembly. This suggests a unified role in gland morphogenesis and epithelial structure, with supportive regulatory processes like ubiquitination and cell division. Confidence reflects the coherent gland- and epithelial-focused theme.","confidence":"High","size":12,"edges":41,"triangles":61,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":12},{"id":"GO:0070830","count":11},{"id":"GO:0051496","count":11},{"id":"GO:0051489","count":11},{"id":"GO:1903542","count":11}]},{"hash":"354932127703466418","title":"Developmental and Immune Signaling","description":"The cluster includes GO terms spanning tissue development and differentiation (heart development, axonogenesis, fat cell differentiation, response to muscle stretch), alongside innate immune signaling (innate immune response, lipopolysaccharide-mediated signaling). There are also general regulatory processes like mRNA processing, regulation of cyclin-dependent protein kinase activity, and telomere capping. Taken together, these proteins seem to participate in signaling networks that coordinate development, differentiation, and immune responses, rather than a single cohesive pathway.","confidence":"Medium","size":12,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":3},{"id":"GO:0031663","count":3},{"id":"GO:0007507","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0035994","count":3}]},{"hash":"1651215462799282111","title":"Skeletal ossification and bone remodeling","description":"The cluster is dominated by terms related to bone biology, including intramembranous ossification, bone resorption, and collagen catabolic processes, as well as Wnt signaling components linked to bone development. While some terms reference broader hormonal or connective-tissue processes, the coherence of ossification, remodeling, and extracellular matrix turnover points to a bone formation/resorption program as the core theme.","confidence":"High","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":10},{"id":"GO:0097067","count":10},{"id":"GO:0001957","count":10},{"id":"GO:0060448","count":10},{"id":"GO:0010815","count":10}]},{"hash":"1646084048038713371","title":"Lipid Biosynthesis and Membrane Trafficking","description":"This cluster is dominated by lipid metabolism and secretory pathway signals: ergosterol biosynthesis, palmitic acid and long-chain fatty-acyl-CoA biosynthesis, and protein transport between the ER, Golgi, and endosomes, suggesting a shared role in membrane lipid synthesis and vesicular trafficking. An outlier term (enterobactin biosynthesis) may reflect annotation noise or broader metabolic capacity, but the core theme remains lipid production linked to membrane trafficking.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006696","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0015031","count":1},{"id":"GO:0035338","count":1}]},{"hash":"960567865150716832","title":"Inflammation-driven angiogenesis and vascular remodeling","description":"The terms cluster around inflammatory signaling and vascular remodeling: inflammatory response, promotion of angiogenesis, fibroblast proliferation, smooth muscle and calcium signaling, and NF-kappaB/S1P pathway involvement, suggesting coordinated immune-vascular crosstalk.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":3},{"id":"GO:0045766","count":2},{"id":"GO:0045987","count":2},{"id":"GO:0042346","count":2},{"id":"GO:0019722","count":2}]},{"hash":"267397134649191208","title":"Chaperone-assisted folding and mitochondrial import","description":"This cluster is dominated by GO terms related to protein quality control and folding (chaperone-mediated complex assembly, unfolded protein response, chaperone-dependent refolding) and mitochondrial protein import, plus oxidative stress regulation, suggesting a coherent theme around chaperone machinery and mitochondrial protein handling. The viral assembly terms appear incidental and do not define the core function of the cluster.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051131","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0006986","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0045041","count":1}]},{"hash":"555506205998199972","title":"Lysosomal glycosylation and secretion","description":"This cluster centers on lysosome biology and glycosylation: lysosome organization, secretion of lysosomal enzymes, and N-/O-glycosylation pathways, with UDP-glucose metabolism supporting glycan assembly. Together these suggest roles in glycoprotein maturation and trafficking to lysosomes or secretory pathways, with some links to extracellular matrix and immune-related secretory processes.","confidence":"High","size":12,"edges":55,"triangles":135,"max_degree":11,"top_function":"lysosome organization","top_go_terms":[{"id":"GO:0071555","count":5},{"id":"GO:0016266","count":4},{"id":"GO:0006011","count":4},{"id":"GO:0033299","count":4},{"id":"GO:0046835","count":4}]},{"hash":"18664388593336713","title":"RNA processing and mRNA turnover","description":"This cluster is enriched for RNA processing and mRNA metabolism terms, notably mRNA splicing, regulation of splicing, mRNA deadenylation/decay, and localization, suggesting a core theme around RNA processing. Some outlier terms (e.g., host interaction concepts) are present but do not override the main RNA-focused signal.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":2},{"id":"GO:0006574","count":1},{"id":"GO:0061470","count":1},{"id":"GO:0033120","count":1}]},{"hash":"989761800222685949","title":"Neural development and glial differentiation","description":"This cluster is dominated by GO terms related to cerebellar cortex formation, Bergmann glial cell differentiation, and regulation of axon regeneration, pointing to neural development and glial signaling as the core theme. Immune-related terms (e.g., T/B cell receptor signaling, macrophage differentiation) appear but are less central, suggesting they may reflect broader signaling components or annotation noise rather than defining the cluster. Overall, neural development with glial involvement best captures the shared function of these proteins.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045650","count":4},{"id":"GO:0008285","count":3},{"id":"GO:0090334","count":3},{"id":"GO:0060396","count":3},{"id":"GO:0050859","count":3}]},{"hash":"1597149913005372197","title":"Mitochondrial dynamics and cell cycle regulation","description":"This cluster centers on mitochondrial functions (import into the mitochondrial matrix, regulation of mitochondrial membrane permeability, intracellular distribution of mitochondria) and core cell cycle processes (negative regulation of G1/S transition, mitotic cell cycle, cell division). Some terms touch lipid metabolism and protein interactions, which may relate to mitochondrial signaling and complex formation, but the dominant themes are mitochondrial dynamics combined with cell cycle control.","confidence":"Medium","size":12,"edges":10,"triangles":2,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:2000134","count":4},{"id":"GO:0046902","count":4},{"id":"GO:0070940","count":4},{"id":"GO:0010867","count":4},{"id":"GO:1903740","count":4}]},{"hash":"317984578257466162","title":"Chromatin modification and DNA repair","description":"This cluster is driven by GO terms for histone acetylation and histone exchange, coupled with DNA repair processes (including replication-born DSB repair via sister chromatid exchange). The combined signal points to chromatin remodeling and genome maintenance as the core theme, with a few peripheral terms like gibberellin response being less central.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043967","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0043968","count":1},{"id":"GO:0045892","count":1},{"id":"GO:0043486","count":1}]},{"hash":"1714125627215292852","title":"ER-Golgi trafficking and protein maturation","description":"The top GO terms cluster around secretory pathway processes: ER\u2013Golgi and Golgi\u2013ER vesicle transport, GPI-anchor biosynthesis, ER retention, unfolded protein response, and protein localization to the plasma membrane, all pointing to ER quality control and trafficking to membranes. Some terms (NK cell activation, wing development) seem less related and may reflect broader annotations, but the core theme is ER/Golgi transport and membrane targeting. ","confidence":"Medium","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":2},{"id":"GO:0006506","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0071340","count":1},{"id":"GO:0006621","count":1}]},{"hash":"224059671984432100","title":"Neurovascular development signaling","description":"The cluster's top GO terms center on neural morphogenesis (vagus nerve morphogenesis, chemorepulsion/axon guidance, axonogenesis) and endothelial morphogenesis/chemotaxis, with receptor tyrosine kinase signaling linking these processes, suggesting coordinated neurovascular development programs.","confidence":"High","size":12,"edges":64,"triangles":201,"max_degree":11,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0007169","count":3},{"id":"GO:0035563","count":3},{"id":"GO:0033689","count":3},{"id":"GO:0021793","count":3},{"id":"GO:0050918","count":3}]},{"hash":"1754069712323844517","title":"Unknown","description":"The top GO terms are split between sphingolipid metabolism and prostate gland development on one side and bacterial cell wall/peptidoglycan processes on the other, with no connecting pathway or interaction (no edges/triangles). This mix suggests no coherent functional theme for the cluster, so a confident, representative label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006685","count":1},{"id":"GO:0060736","count":1},{"id":"GO:0006665","count":1},{"id":"GO:1903206","count":1},{"id":"GO:0060742","count":1}]},{"hash":"2224962656378020422","title":"Unknown","description":"The top GO terms are highly diverse, spanning development (sebaceous gland and metanephric ureteric bud), post-translational modification (palmitoylation), various organelle and nuclear processes, ion transport, and even gravitaxis, with no cohesive biological function linking the proteins; plus there are no observed edges, suggesting this set does not form a single functional cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048733","count":1},{"id":"GO:0018230","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0010761","count":1},{"id":"GO:0007097","count":1}]},{"hash":"1281233936118754546","title":"GPCR signaling and secretory transport","description":"The cluster shows strong representation of G protein-coupled receptor signaling and pheromone response, along with vesicle trafficking from the ER to the Golgi, suggesting roles in receptor signaling linked to the secretory pathway. While there are additional terms related to lipid signaling and metabolism, the dominant themes are signaling and intracellular transport.","confidence":"Medium","size":12,"edges":11,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019236","count":2},{"id":"GO:0007186","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0044328","count":1},{"id":"GO:0035233","count":1}]},{"hash":"1170517808948614975","title":"Signaling and cytoskeletal dynamics with protein turnover","description":"This cluster centers on dynamic signaling and cytoskeletal changes, as highlighted by GO terms for Wnt and EGFR signaling alongside actin filament network formation and stress fiber assembly. The enrichment of ubiquitin-dependent proteolysis (SCF and related pathways) suggests coordinated protein turnover accompanying signaling and structural remodeling. A few terms point to broader stress or immune contexts (muramyl dipeptide response, viral process, UV repair), but the dominant theme is signaling-driven regulation of the cytoskeleton with proteostasis.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071225","count":2},{"id":"GO:2000973","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0051639","count":2},{"id":"GO:0070914","count":2}]},{"hash":"1313323169273985984","title":"Retroviral Integration and Reverse Transcription","description":"This cluster centers on DNA synthesis and genome integration steps characteristic of retroviral life cycles, including RNA-templated DNA biosynthesis, DNA integration, DNA replication, and proviral latency, plus terms about viral entry into the host nucleus. Some GO terms (like rRNA maturation) may be incidental noise not central to the core theme. ","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000462","count":3},{"id":"GO:0075713","count":2},{"id":"GO:0039651","count":2},{"id":"GO:0006278","count":2}]},{"hash":"1329289145926032687","title":"Spliceosome-Mediated mRNA Processing and Translation Initiation","description":"The cluster shows strong enrichment for spliceosome-related mRNA processing and splicing regulation (including multiple terms about alternative splicing), alongside terms related to translation initiation (preinitiation complex formation and IRES-dependent initiation) and miRNA-mediated translational silencing, indicating a group of proteins involved in post-transcriptional gene expression control at splicing and translation levels.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0045292","count":4},{"id":"GO:1901407","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0035278","count":2}]},{"hash":"148795747326218158","title":"Unknown","description":"The terms cover a mix of stress responses (response to heat/ATP), immune signaling (B cell cytokine production), reproductive interaction (binding of sperm to zona pellucida), and cellular processes (pore complex assembly, translocation into host cell cytoplasm, telomere localization). There isn\u2019t a single cohesive biological theme tying these terms together, so a unified, specific cluster label isn\u2019t supported.","confidence":"","size":11,"edges":24,"triangles":19,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0014823","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0051973","count":3},{"id":"GO:0007339","count":3},{"id":"GO:0046931","count":3}]},{"hash":"1521220063371867548","title":"Ribosome Biogenesis and Translation Initiation","description":"The cluster is dominated by GO terms for rRNA maturation (5.8S, LSU), ribosome biogenesis, and translation initiation/reinitiation, pointing to proteins involved in assembling ribosomes and starting translation. While a few terms touch on cell cycle regulation and ubiquitin signaling, they are less central to the core theme, which is ribosome production and translation control.","confidence":"Medium","size":11,"edges":53,"triangles":148,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000463","count":6},{"id":"GO:0001731","count":5},{"id":"GO:0002188","count":5},{"id":"GO:0000466","count":5},{"id":"GO:0042254","count":5}]},{"hash":"2106441303394432397","title":"Unknown","description":"The top GO terms are highly diverse (cell division; heat response; telomere-related regulation; sperm-zona pellucida binding; pore complex assembly; B cell cytokine production; translocation into host cytoplasm; chaperone-related refolding; etc.), indicating no single cohesive function or pathway tying these proteins together. Some terms are even marked obsolete, suggesting annotation noise. Therefore no clear cluster-specific theme can be assigned beyond Unknown.","confidence":"","size":11,"edges":18,"triangles":9,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0009408","count":4},{"id":"GO:0051973","count":4},{"id":"GO:0014823","count":4},{"id":"GO:0007339","count":4}]},{"hash":"1763227107880368670","title":"Antiviral Innate Immune Response","description":"The cluster centers on innate antiviral defense activities: innate immune response, defense against virus, and RIG-I signaling, with links to MHC class I biosynthesis regulation and PML body organization, all characteristic of intracellular antiviral surveillance and antigen presentation processes.","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045345","count":2},{"id":"GO:1901536","count":2},{"id":"GO:1900246","count":1}]},{"hash":"762318988975182878","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":41,"triangles":83,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0043248","count":2},{"id":"GO:0000288","count":1},{"id":"GO:0006397","count":1},{"id":"GO:0031990","count":1},{"id":"GO:0006281","count":1}]},{"hash":"2270975011337219583","title":"Ribosome Biogenesis and Cell Division","description":"The cluster is enriched for ribosome-related processes (ribosome biogenesis, tRNA and rRNA processing, ribosomal small subunit biogenesis) along with cell cycle, cell division, and cell septum assembly terms, suggesting a coordinated module for ribosome production linked to cell division. Some stress-response terms are present but secondary to the ribosome/division theme.","confidence":"High","size":11,"edges":6,"triangles":0,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0008033","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1396505518783357684","title":"Neural development and cell cycle signaling","description":"The cluster features neural development terms such as forebrain development, motor neuron axon guidance, and bipolar cell polarity, alongside cell cycle/ DNA replication terms like mitotic cell cycle and DNA replication. This combination suggests proteins involved in neural progenitor proliferation and differentiation, with signaling pathways (e.g., PI3K/AKT) and hormonal responses supporting neural development.","confidence":"Medium","size":11,"edges":26,"triangles":21,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0000278","count":3},{"id":"GO:0008045","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0071375","count":2}]},{"hash":"1690606771796719381","title":"Transcription Regulation and Ubiquitin Signaling","description":"The strongest GO signals point to DNA-templated transcription and its regulation, suggesting a core role in gene expression. Several terms (COP9 signalosome assembly, K11-linked deubiquitination) imply ubiquitin-related protein regulation, consistent with transcription factor turnover or chromatin remodeling. Biotin/lipoylation-related terms and sporadic metabolic/ergosterol terms add some noise, but overall the cluster appears centered on transcription control with ubiquitin-mediated processes.","confidence":"Medium","size":11,"edges":23,"triangles":18,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070781","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0071110","count":2},{"id":"GO:0009107","count":2}]},{"hash":"1531087808137157845","title":"Energy metabolism: photosynthesis and respiration","description":"The top GO terms point to energy generation across chloroplasts and mitochondria\u2014photosynthesis light reactions, mitochondrial electron transport, and ATP synthesis\u2014with supporting transport and redox processes. While there are a few outliers, the dominant theme is cellular energy metabolism spanning photosynthetic and respiratory pathways, justifying this label.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0019684","count":3},{"id":"GO:0006810","count":3},{"id":"GO:0006120","count":2},{"id":"GO:0042775","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1856655225546624110","title":"Membrane Ion Transport and Gradient Maintenance","description":"The top GO terms point to multiple ion transport processes across membranes (potassium, zinc, cadmium, sodium) and to establishing or maintaining transmembrane electrochemical gradients, along with intracellular potassium homeostasis. These recurring themes indicate the cluster is driven by membrane transport and ion homeostasis functions, with a few unrelated terms present but not dominant.","confidence":"Medium","size":11,"edges":39,"triangles":69,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0097755","count":9},{"id":"GO:0000749","count":9},{"id":"GO:1990573","count":9},{"id":"GO:0070574","count":9},{"id":"GO:0010107","count":9}]},{"hash":"636664720808628925","title":"Actin Cytoskeleton Remodeling and Cell Motility","description":"The dominant terms are actin cytoskeleton organization and assembly of filopodia and lamellipodia, driven by small GTPase\u2013mediated signaling. This points to actin dynamics controlling cell movement and protrusion formation. Some terms also touch on development and immune/vascular processes, which can be linked to cytoskeletal remodeling in those contexts.","confidence":"High","size":11,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030036","count":3},{"id":"GO:0030097","count":2},{"id":"GO:0051489","count":2},{"id":"GO:0043314","count":2},{"id":"GO:0030032","count":2}]},{"hash":"1680262412030809155","title":"Splicing regulation and translation initiation","description":"These proteins appear to be involved in post-transcriptional gene expression control, with strong signals for spliceosome-mediated regulation of mRNA splicing (including alternative splicing) and components of translation initiation (formation of the preinitiation complex and IRES-dependent initiation). Additional RNA-based regulatory activities (regulatory ncRNA-mediated silencing and poly(A) tail regulation) further support a cohesive role in RNA processing and translation control. Overall, the cluster likely comprises splicing regulators and translation-associated factors coordinating post-transcriptional gene expression.","confidence":"High","size":11,"edges":26,"triangles":25,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0000381","count":2}]},{"hash":"217551293974418226","title":"NF-kB Signaling and Translation Regulators","description":"This cluster centers on canonical NF-kappaB signaling and translation-related processes (translation, cap-dependent initiation) with stress-responsive cues (dexamethasone) and autophagy regulation, suggesting a core theme of NF-kB\u2013driven immune/stress signaling linked to translation control. Some developmental terms appear, possibly reflecting broader roles or annotation breadth, but the strongest signals point to NF-kB\u2013mediated signaling connected to translation and stress responses. ","confidence":"Medium","size":11,"edges":43,"triangles":87,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0007249","count":2},{"id":"GO:0019827","count":1},{"id":"GO:0045665","count":1},{"id":"GO:0007112","count":1}]},{"hash":"1482420308082702736","title":"Motor neuron differentiation and axon guidance","description":"The GO terms center on neural development, especially motor neuron differentiation (medial motor column and visceral motor neuron differentiation) and motor neuron axon guidance, with related terms for ectoderm formation and cell-matrix adhesion. Some entries reflect miRNA-mediated post-transcriptional regulation and glucocorticoid signaling, indicating regulatory inputs rather than core function but still compatible with development and connectivity. Overall, this cluster seems to reflect proteins involved in motor neuron development and their pathfinding, with supporting adhesion and regulatory context.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":3},{"id":"GO:0007160","count":2},{"id":"GO:0001705","count":2},{"id":"GO:0021526","count":2},{"id":"GO:2000691","count":2}]},{"hash":"1199854495585071913","title":"Copper transport and copper-dependent maturation","description":"The top terms cluster around copper ion transport and homeostasis (copper import, copper ion transport, intracellular copper homeostasis) and copper-dependent protein maturation, indicating a cohesive set of proteins involved in copper handling and maturation processes. Supporting signals include xenobiotic transport and cellular response to cisplatin, while DNA repair is present but not dominant, so the copper-focused theme best explains the cluster.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":1},{"id":"GO:2000185","count":1},{"id":"GO:0006817","count":1},{"id":"GO:0051604","count":1},{"id":"GO:1902311","count":1}]},{"hash":"346186478454500307","title":"Differentiation and transcription regulation","description":"The Top Terms point to various differentiation processes across distinct lineages (brown fat, pollen sperm, monocytes) plus a central term on regulating transcription. This suggests a general theme around differentiation with transcriptional control rather than a single specific pathway, justifying a broad label that captures both aspects.","confidence":"Low","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040015","count":1},{"id":"GO:0050873","count":1},{"id":"GO:0048235","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0030224","count":1}]},{"hash":"512586005929578296","title":"Unknown","description":"The top GO terms are a mixed bag (erythrocyte differentiation, apoptotic DNA fragmentation, LDL particle remodeling, cellulose catabolic process, flocculation, protein homooligomerization) with several obsolete entries, offering no clear shared function or pathway among the 11 proteins. This lack of a cohesive theme makes it inappropriate to assign a specific, representative label.","confidence":"","size":11,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030218","count":2},{"id":"GO:0006309","count":2},{"id":"GO:0034374","count":2},{"id":"GO:0044533","count":2},{"id":"GO:0030245","count":2}]},{"hash":"2203180680367460740","title":"LDL cholesterol uptake and processing","description":"This cluster is most strongly associated with LDL/cholesterol handling: negative regulation of LDL particle clearance, regulation of LDL receptor activity, LDL receptor\u2013mediated endocytosis in cholesterol transport, and related receptor-mediated receptor endocytosis processes. There are also terms for insulin and dibasic protein processing, suggesting secretory pathway involvement that can accompany lipid metabolism. A few terms (bone resorption, embryo axis determination) seem less connected and may reflect broader or overlapping annotations. Overall, the dominant theme is lipoprotein uptake and processing.","confidence":"Medium","size":11,"edges":18,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0010989","count":2},{"id":"GO:0032902","count":2},{"id":"GO:0007354","count":2},{"id":"GO:0045453","count":2},{"id":"GO:0007323","count":2}]},{"hash":"1484779392087201496","title":"Heat and radiation stress response with microtubule dynamics","description":"The top GO terms point to cellular responses to heat, UV-A, and gamma radiation, plus regulation of ROS and microtubule polymerization, as well as anterograde axonal transport and lens morphogenesis. Together, these suggest a cluster centered on environmental stress responses that are tightly linked to cytoskeletal dynamics and intracellular transport, rather than a single specialized pathway. Hence, a label that captures stress responses and cytoskeletal regulation fits well.","confidence":"Medium","size":10,"edges":26,"triangles":28,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":5},{"id":"GO:0009408","count":4},{"id":"GO:0099641","count":4},{"id":"GO:0030308","count":4},{"id":"GO:0070141","count":4}]},{"hash":"1724589090100727510","title":"Exocyst-Mediated Vesicle Trafficking","description":"The GO terms are dominated by vesicle transport processes centered on the exocyst complex (exocyst assembly, exocyst localization, Golgi to vacuole transport, endocytic recycling, lysosomal transport, ER inheritance), suggesting a shared role in secretory and endocytic trafficking. A few development terms appear but likely reflect broader contexts rather than a core function. Confidence: High","confidence":"","size":10,"edges":44,"triangles":112,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0090326","count":1},{"id":"GO:1904810","count":1},{"id":"GO:0007041","count":1},{"id":"GO:0010668","count":1},{"id":"GO:0032456","count":1}]},{"hash":"2100123257476614753","title":"Proviral latency and DNA replication proteins","description":"The top GO terms point to viral lifecycle steps: establishment of integrated proviral latency, DNA replication, DNA integration, RNA-templated DNA biosynthesis, DNA recombination, and viral penetration into the host nucleus, plus symbiont-related host interactions. This combination strongly suggests proteins involved in proviral genome maintenance and replication within the host, i.e., the proviral latency and replication machinery cluster.","confidence":"High","size":10,"edges":40,"triangles":90,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0075713","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0039651","count":3},{"id":"GO:0006278","count":3},{"id":"GO:0015074","count":3}]},{"hash":"1797134751321775344","title":"Membrane Signaling and Trafficking","description":"The cluster's terms cluster around ER membrane organization, phosphatidylinositol-mediated signaling, intracellular protein transport, and phospholipid catabolic processes, pointing to membrane dynamics and signaling pathways that govern trafficking and cytoskeletal interactions; regulation of Rho signaling and neutrophil degranulation reflect related signaling networks, while some items (salt stress, tRNA processing) are less central. Overall, core theme is membrane-associated signaling and trafficking.","confidence":"Medium","size":10,"edges":10,"triangles":5,"max_degree":5,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0030579","count":4},{"id":"GO:0031914","count":4},{"id":"GO:0009395","count":4},{"id":"GO:1901002","count":4},{"id":"GO:0006886","count":4}]},{"hash":"1517127082021807898","title":"Ubiquitin-Dependent Regulation of Mitosis and DNA Repair","description":"The GO terms show ubiquitin-mediated pathways (SCF, APC/C, K11-linked ubiquitination, ERAD) intertwined with mitotic processes (mitotic cell cycle, cell division, spindle checkpoint) and DNA repair (homologous recombination) plus chromatin organization, suggesting a cohesive role in tagging and degrading regulators to coordinate mitosis and genome maintenance, with ties to ER stress\u2013related apoptosis.","confidence":"High","size":10,"edges":25,"triangles":36,"max_degree":7,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0030433","count":8},{"id":"GO:0000278","count":7},{"id":"GO:0031497","count":7},{"id":"GO:0070059","count":7},{"id":"GO:0000724","count":7}]},{"hash":"160544212440746039","title":"Vesicle Trafficking and Cargo Sorting","description":"The cluster centers on vesicle trafficking within the endomembrane system: ER-Golgi and Golgi-ER transport, clathrin-mediated cargo loading, endosome-to-melanosome transport, receptor internalization, plus melanosome organization and mRNA transport. This indicates a common function in intracellular cargo sorting via vesicles.","confidence":"High","size":10,"edges":29,"triangles":48,"max_degree":8,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0006890","count":5},{"id":"GO:0035652","count":4},{"id":"GO:0035646","count":4},{"id":"GO:0099590","count":4}]},{"hash":"503734260773428540","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":33,"triangles":66,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006207","count":5},{"id":"GO:0044205","count":5},{"id":"GO:0006351","count":3},{"id":"GO:0006189","count":3},{"id":"GO:0046651","count":3}]},{"hash":"432597885070095280","title":"Plant organogenesis and cell wall biosynthesis","description":"The GO terms show strong enrichment for plant development processes, including shoot organ boundary specification, internode patterning, and secondary cell wall biogenesis, as well as mucilage biosynthesis and cytokinin signaling. A few terms relate to transcription regulation, mitochondrial fission, and menaquinone biosynthesis, which may reflect broader cellular roles or annotation noise. Overall, the cluster seems dominated by plant developmental and cell wall\u2013related functions, justifying the label.","confidence":"Medium","size":10,"edges":13,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0090141","count":2},{"id":"GO:2000652","count":1},{"id":"GO:0009722","count":1}]},{"hash":"630928312487616487","title":"Endosome trafficking and receptor recycling","description":"The proteins cluster around endosomal transport and recycling functions, supported by terms like Golgi to endosome transport, protein localization to endosome, receptor recycling, and Rab signaling regulation, plus endosome-related transport to melanosomes and endosome size control, indicating a cohesive endosomal trafficking module. Some outliers (e.g., nucleosome positioning) are less representative but don\u2019t override the main theme.","confidence":"High","size":10,"edges":6,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016584","count":2},{"id":"GO:0035646","count":1},{"id":"GO:0006895","count":1},{"id":"GO:0031914","count":1},{"id":"GO:0001881","count":1}]},{"hash":"1932614697046675895","title":"Membrane trafficking and signaling","description":"The GO terms emphasize regulation of exocytosis, endosome-lysosome transport, and small GTPase\u2013mediated signaling, together with epithelial polarity establishment, suggesting a core theme of membrane trafficking and cell signaling. A few terms relate to development or rhythms, likely downstream processes, but the primary signal points to trafficking/signaling across membranes.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":2},{"id":"GO:0061000","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0010227","count":2},{"id":"GO:0007264","count":2}]},{"hash":"353689355803951181","title":"Translation initiation and telomere maintenance cluster","description":"The top GO terms cluster around translation initiation (translation reinitiation; formation of translation preinitiation complex) and telomere maintenance via telomerase (with its positive regulation), suggesting core themes of protein synthesis initiation and genome maintenance. Supporting terms touch on cell cycle control and protein/RNA modification, indicating a broader nuclear gene expression and genome stability context. Overall, the translation initiation and telomere maintenance signals are the strongest throughlines, with ancillary regulation roles. ","confidence":"Medium","size":10,"edges":31,"triangles":45,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0007004","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0007064","count":1}]},{"hash":"1262305466835064383","title":"Ribosome biogenesis and rRNA processing","description":"The cluster is dominated by GO terms related to ribosome biogenesis and ribosomal large subunit assembly, including LSU rRNA maturation and preribosome assembly. Additional transcription-related terms (Pol II/III) and a couple of DNA repair terms appear but the core signal centers on ribosome biogenesis and rRNA maturation, suggesting a nucleolar/biogenesis-focused functional theme.","confidence":"High","size":10,"edges":15,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0042255","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0042273","count":1}]},{"hash":"253881244856491666","title":"Protein maturation and intracellular trafficking","description":"Based on the GO terms, the cluster centers on intracellular handling of proteins: assembly of proteasome components (quality control), vesicle transport between ER and Golgi and SNARE complex disassembly, mitochondrial protein import and complex I assembly, and cytoskeletal remodeling via microtubule severing that can affect transport. Radiation/damage repair and heat acclimation terms suggest ancillary stress-response roles, but the strongest signal is protein maturation and trafficking within the cell across organelles. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0051013","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0006888","count":1}]},{"hash":"1899303244917839727","title":"RNA Processing and Decay","description":"The top GO terms cluster around RNA maturation and turnover: mRNA splicing via the spliceosome, spliceosomal complex assembly, tRNA processing, and rRNA maturation indicate RNA processing and maturation. Concomitant terms for P-body assembly and deadenylation-dependent decapping point to mRNA decay/turnover. The presence of ABA- and water deprivation-related responses and hair cycle suggests broader plant developmental and stress regulatory connections, but the core signals are clearly RNA processing and decay machinery.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":10},{"id":"GO:0042633","count":9},{"id":"GO:0030490","count":9},{"id":"GO:0009737","count":9},{"id":"GO:0008033","count":9}]},{"hash":"1719726125462456563","title":"Metabolic growth signaling and differentiation","description":"This cluster's top GO terms cluster around metabolic regulation and growth signaling: insulin receptor signaling, cholesterol biosynthesis, fat cell differentiation, and glucose-related responses, plus cell cycle regulatory and telomere maintenance terms suggesting a broader growth/gene expression program. While there are a few outliers (synaptic transmission, muscle stretch, mRNA processing), the dominant themes are insulin-mediated metabolic signaling and differentiation processes, with some overlap into cell cycle control.","confidence":"Medium","size":10,"edges":15,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0051968","count":2},{"id":"GO:0045736","count":2},{"id":"GO:0008286","count":2},{"id":"GO:1904355","count":2}]},{"hash":"1431352264560954000","title":"Choline and phospholipid biosynthesis","description":"The majority of terms cluster around choline metabolism and phospholipid assembly, including choline metabolic process, CDP-choline pathway, ethanolamine metabolism, and phosphatidylethanolamine biosynthetic process, indicating a lipid biosynthesis module. A secondary theme is less represented amino-acacid or stress-related terms (L-threonine biosynthesis, response to antibiotic, response to 3-methylcholanthrene) that appear as noise. Overall, the core function is phospholipid biosynthesis via the CDP-choline pathway.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009088","count":2},{"id":"GO:0046677","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0006580","count":1},{"id":"GO:0019509","count":1}]},{"hash":"2233497450841869837","title":"DNA Repair and Oxidative Stress Response","description":"The top GO terms cluster around genomic maintenance and stress responses: base-excision repair and DNA recombination indicate DNA repair processes, while cellular response to hydrogen peroxide points to oxidative stress response. Some terms about mRNA stability regulation may reflect post-transcriptional control during stress, though a few outliers appear noise. Overall, a coherent theme is DNA damage repair coupled with stress adaptation. ","confidence":"Medium","size":10,"edges":30,"triangles":46,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006284","count":3},{"id":"GO:0044179","count":2},{"id":"GO:0080111","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0006310","count":2}]},{"hash":"1039580606600480233","title":"TLR-NF-kappaB Innate Immunity Cluster","description":"Dominant GO terms point to innate immunity, especially TLR signaling (TLR1/2) and NF-kappaB pathways, with supportive links to mitochondrial fission and receptor trafficking that modulate these signals.","confidence":"High","size":10,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090141","count":2},{"id":"GO:0007169","count":1},{"id":"GO:0042346","count":1},{"id":"GO:1900155","count":1},{"id":"GO:0034130","count":1}]},{"hash":"1770652005223827152","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":36,"triangles":65,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006401","count":4},{"id":"GO:0006364","count":4},{"id":"GO:0090503","count":4},{"id":"GO:0035900","count":3},{"id":"GO:0008033","count":3}]},{"hash":"530713835194822132","title":"Nuclear processes and chromatin regulation","description":"These terms point to nuclear-centric roles: mRNA splicing via spliceosome, export of ribosomal subunits from the nucleus, chromatin-related regulation such as histone H2A ubiquitination and PML body organization, and regulation of transcription-related processes (DNA replication initiation, RNA polymerase II regulatory region binding, and nuclear receptor signaling). A subset also touches innate immune signaling (RIG-I pathway) but can intersect with transcriptional regulation through chromatin state. Overall, the cluster appears to group nuclear RNA processing, chromatin modification, and transcriptional regulation functions.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0032298","count":1},{"id":"GO:1903026","count":1},{"id":"GO:1900246","count":1}]},{"hash":"1566714491131275883","title":"LDL-Cholesterol Transport and Receptor Endocytosis Regulation","description":"The top GO terms cluster around LDL particle handling, cholesterol transport, and receptor-mediated endocytosis (LDL receptor activity, LDL particle catabolic process, and related regulatory processes). Additional terms point to protein processing and secretory pathway roles (insulin processing, dibasic protein processing), which can tie into broader membrane trafficking. A few terms (cellulose catabolic process, embryo axis determination, pheromone maturation) seem unrelated noise. Overall, the dominant theme is lipid transport and LDL receptor\u2013mediated endocytosis regulation. ","confidence":"Medium","size":10,"edges":28,"triangles":29,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0010989","count":2},{"id":"GO:0032902","count":2},{"id":"GO:0007354","count":2},{"id":"GO:0007323","count":2}]},{"hash":"1676991133730922763","title":"Glycosylation and sugar metabolism","description":"The top GO terms are dominated by glycosylation- and carbohydrate-processing processes (N-glycan processing, protein deglycosylation,obsolete protein glycosylation, galactose and mannose metabolic processes), suggesting a common theme around glycan maturation and sugar metabolism. Some terms like erythrocyte differentiation, rhodopsin biosynthetic process, encapsulation of foreign target, and apoptotic DNA fragmentation appear less directly related and may reflect broader annotations within this set. Overall, the core signal points to glycosylation-related functions, with ancillary terms contributing noise. ","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030218","count":1},{"id":"GO:0006309","count":1},{"id":"GO:0016063","count":1},{"id":"GO:0006013","count":1},{"id":"GO:0006486","count":1}]},{"hash":"1186557470821214958","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":22,"triangles":26,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1901710","count":1},{"id":"GO:0048680","count":1},{"id":"GO:0016925","count":1},{"id":"GO:0006939","count":1},{"id":"GO:0022417","count":1}]},{"hash":"1165530568574982427","title":"Specialized metabolite biosynthesis and lipid oxidation","description":"The top GO terms cluster around biosynthetic processes for ectoine and verruculogen, plus fatty acid alpha-oxidation and methyl-branched fatty acid metabolism, suggesting a group of proteins involved in production and modification of specialized metabolites and related lipid metabolism. There are also hints of post-translational modification and redox-related processes, but the common thread appears to be biosynthesis/ modification of small molecules and lipids. ","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042400","count":3},{"id":"GO:1902181","count":3},{"id":"GO:0001561","count":3},{"id":"GO:0019491","count":3},{"id":"GO:0097089","count":3}]},{"hash":"849858275126601316","title":"Lipid metabolism and membrane remodeling","description":"Top terms show lipid catabolic processes (phosphatidylinositol and phosphatidylethanolamine) and lipid droplet organization, indicating lipid turnover and membrane-associated remodeling. Viral fusion/release terms further support membrane dynamics. A couple of developmental terms (dorsal appendage formation, sepal formation) seem incidental. Together these point to lipid metabolism and membrane remodeling as the cluster's shared theme.","confidence":"Medium","size":10,"edges":9,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031161","count":3},{"id":"GO:0046338","count":3},{"id":"GO:0046843","count":3},{"id":"GO:1901407","count":1},{"id":"GO:0048453","count":1}]},{"hash":"301690771769486839","title":"Glycan processing during organ development","description":"GO terms point to organ development (renal system and liver) together with glycan-related processes (carbohydrate phosphorylation and N-glycan processing to lysosome), suggesting a cluster of proteins involved in glycan remodeling/lysosomal trafficking during development.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072001","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0016256","count":1},{"id":"GO:0001889","count":1}]},{"hash":"2076555946764301600","title":"RNA processing and methylation","description":"This cluster centers on RNA maturation: tRNA processing, tRNA/rRNA methylation, RNA capping, and related RNA modification processes. While a couple terms (DNA methylation, CD40 signaling) are outliers, the dominant themes point to RNA processing and chemical modification.","confidence":"Medium","size":9,"edges":24,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0032775","count":1},{"id":"GO:0009452","count":1},{"id":"GO:0070476","count":1}]},{"hash":"247201369205565725","title":"RNA Splicing Regulation and Translation Initiation","description":"Most GO terms cluster around spliceosome-mediated regulation of mRNA splicing (positive/negative regulation, alternative splicing) and processes related to translation initiation (formation of the preinitiation complex, IRES-dependent initiation), suggesting a cohesive theme of RNA processing and translational control. Some outlier terms (immunoglobulin diversification, apoptotic process) exist, but the dominant signal is splicing and translation regulation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016445","count":1},{"id":"GO:0006915","count":1},{"id":"GO:1901407","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0035278","count":1}]},{"hash":"1941246022987280118","title":"Nuclear RNA Processing and Transport","description":"Top GO terms link ribosomal subunit and mRNA export from the nucleus, import of splicing factors/hnRNPs, and regulation of nuclear transcription and protein export, with some cell-cycle related localization (centrosome/kinetochore). This points to a cohesive module centered on nuclear RNA processing and nucleocytoplasmic transport. ","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042176","count":4},{"id":"GO:0000056","count":4},{"id":"GO:0010824","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0035048","count":4}]},{"hash":"1674714564509083538","title":"Chromatin regulation and cell cycle control","description":"This cluster centers on chromatin and transcriptional regulation, with terms like histone H3-K27 methylation, RNA guanine-N7 methylation, and positive regulation of transcription via transcription factor localization, plus links to cell-cycle control such as mitotic sister chromatid cohesion and G0 to G1 transition. The inclusion of ubiquitin ligase activity regulation and TORC1 signaling supports a broader theme of coordinating protein turnover and nutrient signaling with gene expression during the cell cycle. A few terms about development or sensory functions appear incidental, but do not override the dominant epigenetic/gene-expression and cell-cycle signal.","confidence":"Medium","size":9,"edges":19,"triangles":23,"max_degree":7,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007064","count":8},{"id":"GO:0070317","count":8},{"id":"GO:1904668","count":8},{"id":"GO:0036265","count":8},{"id":"GO:0050909","count":8}]},{"hash":"2088227016873535275","title":"Unknown","description":"There are no GO terms or functional terms provided for this cluster (Top Terms are empty), so there is no clear shared function to name it after. With 9 proteins and 8 edges but no enrichment signal, I cannot infer a specific, representative label.","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[]},{"hash":"1118539235019002373","title":"Ubiquitin signaling and translation initiation","description":"Top GO terms cluster around ubiquitin-related regulation and processes that control protein synthesis and growth, such as positive regulation of ubiquitin ligase activity and K11-linked ubiquitination, formation of the translation preinitiation complex, TORC1 and SREBP signaling, and RNA methylation, with accompanying cell-cycle cues like mitotic cohesion and G0\u2192G1 transition. This points to a theme of ubiquitin-mediated regulation of translation and cell-growth pathways.","confidence":"Medium","size":9,"edges":31,"triangles":59,"max_degree":8,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:1904668","count":8},{"id":"GO:0032933","count":8},{"id":"GO:0046784","count":8},{"id":"GO:0001731","count":8},{"id":"GO:1904263","count":8}]},{"hash":"1173969405728486010","title":"Aromatic amino acid derived secondary metabolite biosynthesis","description":"These GO terms cluster around biosynthesis of aromatic compounds from phenylalanine and tyrosine (e.g., cinnamic acid), plus related alkaloid, antibiotic, and toxin biosynthesis. The presence of catabolic processes for phenylalanine and tyrosine supports the aromatic metabolite theme, suggesting a focus on aromatic secondary metabolism. The zinc stress term is less central but may reflect broader stress-regulated secondary metabolism.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":1},{"id":"GO:0009821","count":1},{"id":"GO:0051289","count":1},{"id":"GO:0006559","count":1},{"id":"GO:0006572","count":1}]},{"hash":"2225619361672376715","title":"Neural development and cell cycle regulation","description":"The terms point to neural development (axonogenesis; sensory perception of pain) alongside cell cycle/dna maintenance processes (mitotic cell cycle; centrosome localization; DNA repair). Inflammation-related signaling (cytokine production) and morphogenesis also fit into broader developmental contexts, though the connection is not to a single tight pathway. Overall, the cluster seems to reflect proteins involved in neural development with concurrent cell-cycle and stress-response roles, rather than a narrowly defined function. ","confidence":"Medium","size":9,"edges":12,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0000902","count":2},{"id":"GO:1900015","count":2},{"id":"GO:0019233","count":2},{"id":"GO:0006281","count":2}]},{"hash":"1435521143910355374","title":"Membrane nutrient transporters","description":"The terms largely reflect membrane transport of nutrients (thiamine, branched-chain amino acids, cysteine, cobalt, vitamins) and lipid-related processes (lipoprotein transport, phospholipid translocation) with cytochrome complex assembly, while SOS response and nucleotide-excision repair terms are less central.","confidence":"Medium","size":9,"edges":30,"triangles":50,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":8},{"id":"GO:0006289","count":8},{"id":"GO:0045332","count":8},{"id":"GO:0006824","count":8},{"id":"GO:0015888","count":8}]},{"hash":"938391830250507003","title":"Vesicle Trafficking Regulation","description":"The predominant GO terms point to intracellular transport, endosome vesicle movement, and Rab-regulated signaling, with activation of GTPase activity and intracellular protein transport appearing repeatedly. While a couple of terms touch on spindle/cilium processes or lens morphogenesis, the common thread across the cluster is regulation of vesicle trafficking and membrane transit. Thus \"Vesicle Trafficking Regulation\" captures the shared function of these proteins.","confidence":"Medium","size":9,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902543","count":1},{"id":"GO:0031030","count":1},{"id":"GO:0031338","count":1},{"id":"GO:1902018","count":1},{"id":"GO:0070309","count":1}]},{"hash":"1403512107763007651","title":"Developmental Signaling and Cytoskeletal Regulation","description":"This cluster features terms pointing to developmental signaling and differentiation (midbrain dopaminergic neuron differentiation, hair follicle placode formation, Wnt signalosome assembly, GPCR signaling) along with cytoskeletal dynamics (positive regulation of pseudopodium assembly) and protein turnover (ubiquitination). While there are outliers like immune-related terms, the dominant theme is signaling pathways governing development and structural remodeling. ","confidence":"Medium","size":9,"edges":8,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1904948","count":5},{"id":"GO:0032467","count":5},{"id":"GO:0060789","count":5},{"id":"GO:0031274","count":5},{"id":"GO:0016567","count":4}]},{"hash":"1364280339986480745","title":"Chromatin assembly and cell cycle regulation","description":"This cluster is dominated by GO terms tied to chromatin dynamics and cell division\u2014CENP-A\u2013containing chromatin assembly, histone H3 acetylation, mitotic sister chromatid cohesion, and control of the G0 to G1 transition\u2014indicating a core function in chromatin organization and cell cycle progression. The developmental terms (brain, gonad, osteoblast differentiation) likely reflect broader regulatory contexts or shared networks rather than a single, cohesive pathway, so the chromatin/cell cycle theme best captures the main signal.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035264","count":5},{"id":"GO:0008584","count":5},{"id":"GO:0007338","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0001649","count":5}]},{"hash":"1847808164851928362","title":"Neural development and axon guidance","description":"These proteins cluster around neural development processes: motor neuron axon guidance, forebrain development, bipolar cell polarity, and neural signaling via PI3K/AKT and phosphorylation. While a few terms reference other developmental contexts (lung mesenchyme, placental differentiation), the strongest signals point to a neural development theme with axon guidance as a hallmark.","confidence":"High","size":9,"edges":16,"triangles":7,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0008045","count":9},{"id":"GO:0045736","count":9},{"id":"GO:0071375","count":9},{"id":"GO:0043491","count":9},{"id":"GO:0060709","count":9}]},{"hash":"259927515756892918","title":"Ubiquitination-driven protein quality control","description":"The cluster centers on ubiquitination and proteolysis: several terms involve ubiquitin-dependent protein degradation, autoubiquitination, and specific linkages (K6-linked ubiquitination), paired with a strong signal for response to unfolded protein, all pointing to proteostasis. Additional terms for TNF signaling and immune-related processes suggest stress-response signaling integrated with protein turnover, while the DNA damage checkpoint term aligns with cell-cycle quality control. Taken together, these proteins appear to function in ubiquitin-mediated protein quality control and associated stress responses.","confidence":"High","size":9,"edges":24,"triangles":35,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":3},{"id":"GO:0006986","count":3},{"id":"GO:1903265","count":3},{"id":"GO:0036205","count":3},{"id":"GO:0042787","count":3}]},{"hash":"2283403537496139643","title":"Unknown","description":"The GO terms show a mix of metabolic catabolic/biosynthetic processes and diverse developmental and behavioral terms with no clear shared function tying the proteins together, suggesting there is no cohesive cluster function to label beyond Unknown.","confidence":"","size":9,"edges":17,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0009450","count":6},{"id":"GO:0009447","count":6},{"id":"GO:0055129","count":6},{"id":"GO:0030902","count":5},{"id":"GO:0031016","count":5}]},{"hash":"1355226406839521300","title":"Mitotic Cell Cycle and Ribosome Biogenesis","description":"The top GO terms cluster around mitosis and cell division (mitotic cell cycle, cell division, mitotic sister chromatid cohesion, spindle pole regulation) and include ubiquitin-related regulation of protein ligases, which ties into checkpoints and progression. There is also a signal for ribosome biogenesis and RNA methylation, suggesting a broader link to cellular growth and biosynthesis that accompanies cell cycle progression. A stray term for sensory perception of taste appears, but the dominant theme is mitotic control with supporting biosynthetic processes.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0007064","count":3},{"id":"GO:0070317","count":3}]},{"hash":"1152296636210552528","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":8,"triangles":2,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0008283","count":5},{"id":"GO:0006888","count":5},{"id":"GO:0000398","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0042273","count":4}]},{"hash":"48750911365441853","title":"Proteostasis and Autophagy Regulation","description":"The top GO terms cluster around protein quality control mechanisms: sumoylation, deubiquitination, and ER-associated degradation (proteostasis machinery), along with autophagy-related processes (mitophagy, aggrephagy). Additional terms about responses to toxins and stress (and a touch of DNA repair signaling) fit within cellular stress responses that often engage ubiquitin/sumoylation pathways and autophagy. Taken together, the dominant theme is regulation of protein turnover and clearance via ubiquitin/SUMO pathways and autophagy.","confidence":"High","size":8,"edges":25,"triangles":40,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":7},{"id":"GO:0006289","count":5},{"id":"GO:0097237","count":5},{"id":"GO:0016579","count":5},{"id":"GO:0045648","count":5}]},{"hash":"2057243730662593064","title":"Antiviral IFN signaling and ubiquitination","description":"Proteins cluster around type I interferon\u2013mediated signaling, ISG15-conjugation, and ubiquitin-related activities (including K11-linked ubiquitination), all of which are hallmarks of antiviral innate immune responses. The presence of viral process and apoptotic process terms supports a coordinated defense against viral infection, with peroxisome import potentially reflecting antiviral signaling routes. While there is a DNA repair term present, the dominant theme is interferon-driven antiviral defense and ubiquitin/ISGylation pathways. ","confidence":"High","size":8,"edges":21,"triangles":30,"max_degree":6,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0042275","count":7},{"id":"GO:0060340","count":7},{"id":"GO:0051092","count":7},{"id":"GO:0051443","count":7},{"id":"GO:0032020","count":7}]},{"hash":"2240033608906831146","title":"DNA replication and protein quality control","description":"This cluster centers on DNA-centric processes such as DNA replication and cell division, and on proteostasis through proteasome assembly and ubiquitin-dependent protein degradation, with supporting RNA quality control (nonsense-mediated decay) and mitotic machinery (microtubule severing). These terms together suggest a coordinated role in DNA replication during the cell cycle while maintaining protein and RNA integrity via degradation and surveillance pathways.","confidence":"Medium","size":8,"edges":23,"triangles":32,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0032508","count":2},{"id":"GO:0090305","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1221261592575572683","title":"Ubiquitin-Mediated Proteostasis and Autophagy","description":"This cluster is enriched for autophagy-related terms (aggrephagy, mitophagy) and ubiquitin/protein turnover processes (deubiquitination, sumoylation, ER-associated degradation), along with stress-response signals (cellular response to toxic substance, TNF signaling). The combination suggests a cohesive module coordinating protein quality control via ubiquitin signaling, ERAD, and autophagy.","confidence":"High","size":8,"edges":24,"triangles":33,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035973","count":5},{"id":"GO:0006289","count":4},{"id":"GO:0016925","count":4},{"id":"GO:0097237","count":4},{"id":"GO:0016579","count":4}]},{"hash":"2280712551213998404","title":"Developmental transcriptional regulation and chromatin modification","description":"The terms point to developmental processes (brain, skeletal, cardiac morphogenesis) alongside regulatory mechanisms of gene expression, including transcription factor localization, ubiquitin ligase activity, RNA methylation, and histone modification, indicating a theme of developmental gene regulation through chromatin and RNA-level controls.","confidence":"Medium","size":8,"edges":16,"triangles":20,"max_degree":6,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007420","count":5},{"id":"GO:0007064","count":4},{"id":"GO:0070317","count":4},{"id":"GO:1904668","count":4},{"id":"GO:0036265","count":4}]},{"hash":"1143148069613469820","title":"Bacterial cell wall biosynthesis and amino acid metabolism","description":"The cluster shows strong representation of peptidoglycan biosynthetic process, D-alanine biosynthetic process, cell wall organization, and related antibiotic biosynthesis, all indicative of bacterial cell wall construction and amino acid metabolism. Some terms (e.g., cardiac muscle hypertrophy) appear unrelated noise or cross-annotation. Overall, a cohesive theme around bacterial cell wall pathways with some stray terms.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0014898","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006212","count":2}]},{"hash":"1250858224021871868","title":"Neural Development and Transcription Regulation","description":"The set is dominated by neural and developmental GO terms (forebrain development, neural tube closure, multicellular organism development, skeletal system development) and a DNA-templated transcription term, suggesting regulation of gene expression during neural development. Positive regulation of TORC1 signaling fits growth signaling in development, while some outliers (defense response, ER stress\u2013related apoptosis, mitotic cell cycle) are less central to the theme. Overall, the cluster points to a neural development program with transcriptional regulation.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1904263","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0001843","count":3}]},{"hash":"2224701434072555250","title":"Steroid and natural product biosynthesis","description":"The GO terms are dominated by biosynthetic processes for steroids, lipids, and other natural products (steroid hormones, alkaloids, antibiotics, mycolic acid, sphinganine), suggesting the cluster centers on enzymes involved in diverse small-molecule production. While a few terms (acetoin catabolism, regulation of transcription) are present, they appear peripheral to the main theme. ","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":2},{"id":"GO:0071768","count":2},{"id":"GO:0006666","count":2},{"id":"GO:0006710","count":2},{"id":"GO:0061370","count":2}]},{"hash":"1120832468603429066","title":"Cross-Tissue Developmental Regulation","description":"The top GO terms span developmental processes in diverse tissues (kidney, retina, Schwann cells, brain regions like substantia nigra) and include regulatory signaling (NFAT), exocytosis, complement activation, ROS generation, and cytoskeletal/terminal web assembly. There isn\u2019t a single cohesive pathway across all terms, suggesting a broad, cross-tissue developmental regulatory theme rather than a specific organ-focused function.","confidence":"Medium","size":8,"edges":6,"triangles":2,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035502","count":7},{"id":"GO:0008594","count":7},{"id":"GO:0014044","count":7},{"id":"GO:1905205","count":7},{"id":"GO:0070886","count":7}]},{"hash":"2106757736181007611","title":"Actin cytoskeleton remodeling and cell adhesion","description":"The cluster is dominated by GO terms for actin organization, actin cortical patch assembly, regulation of Rho signaling, and cell adhesion, all pointing to cytoskeletal dynamics and cell\u2013surface interactions. Plasma membrane tubulation further supports membrane remodeling linked to actin. A blastocyst formation term fits developmental context but is less central. A few RNA processing terms appear but are minor. Thus the label reflects the core theme: actin cytoskeleton remodeling and adhesion. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001825","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0007015","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0000147","count":2}]},{"hash":"2125564989660305079","title":"Translation Initiation Regulation Under Stress","description":"The strongest terms describe initiation of translation: IRES-dependent viral translational initiation, formation of translation preinitiation complex, and regulation of translational initiation, pointing to a coherent cluster focused on control of protein synthesis initiation. The additional terms\u2014response to ethanol, COP9 signalosome assembly, deubiquitination, and unfolded protein response regulation\u2014likely reflect cellular stress and proteostasis-related regulation that accompany translational control. Overall, the cluster seems to capture regulated translation initiation in a stress context.","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0075522","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0045471","count":3},{"id":"GO:0010387","count":2}]},{"hash":"157494599650949004","title":"Actin-driven motility and vesicle trafficking","description":"The cluster is dominated by GO terms tied to cytoskeletal dynamics (positive regulation of stress fiber, filopodium, and pseudopodium assembly) and vesicle/organelle transport (CVT pathway, endosome to melanosome transport, general vesicle targeting). This suggests proteins work together in actin-based cell movement and intracellular trafficking, with supporting signals from related developmental or immune-related processes. While some terms (like hair follicle proliferation and vasoconstriction) are peripheral, the central theme appears to be cytoskeleton remodeling coupled to vesicle transport.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032258","count":8},{"id":"GO:0043316","count":8},{"id":"GO:0035646","count":8},{"id":"GO:0051496","count":8},{"id":"GO:0071338","count":8}]},{"hash":"1854193340092495243","title":"Signaling and Developmental Processes","description":"These terms cluster around broad signaling roles (immune sensing via TLR/MyD88, dopamine signaling) and developmental processes (neural morphogenesis, polarity establishment, chromatin localization), with an additional cell-cycle regulation term. This suggests a general theme of signaling coordinating development rather than a single cohesive pathway.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060161","count":1},{"id":"GO:0034130","count":1},{"id":"GO:0071169","count":1},{"id":"GO:0016336","count":1},{"id":"GO:0045842","count":1}]},{"hash":"1561926776401019059","title":"RNA transcription and ribosome biogenesis","description":"The Top Terms are strongly dominated by transcription-related GO terms (RNA polymerase II and III transcription, transcription elongation and termination, RNA-templated transcription) and ribosome biogenesis, pointing to a cluster involved in nuclear gene expression and ribosome assembly. Some terms about proteasomal degradation regulation and ER stress are present but less central. ","confidence":"High","size":8,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":2},{"id":"GO:1902236","count":2},{"id":"GO:0070893","count":1},{"id":"GO:0042797","count":1},{"id":"GO:0006366","count":1}]},{"hash":"1210605755732216005","title":"Cardiac electrophysiology and calcium handling regulation","description":"The GO terms show strong focus on regulation of action potential, potassium channel activity, cardiac muscle contraction, and calcium transporter activity, all hallmark features of cardiac electrophysiology and calcium homeostasis. There are additional terms related to post-translational modification and stress/immune signaling that may be peripheral to the core function, but the dominant theme points to regulation of cardiac electrical activity and calcium transport.","confidence":"High","size":8,"edges":18,"triangles":17,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":4},{"id":"GO:0006517","count":3},{"id":"GO:0045759","count":2},{"id":"GO:0051572","count":2},{"id":"GO:0043392","count":2}]},{"hash":"1282916347424648915","title":"Unknown","description":"No functional terms or network connections are provided for this cluster, so there is no clear theme to name it; hence Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"285111823863122903","title":"Mycolic acid and steroid lipid biosynthesis","description":"The top GO terms cluster around lipid and steroid biosynthesis and metabolism, including mycolic acid biosynthesis, 3-keto-sphinganine metabolism (a sphingolipid), and several steroid-related processes (testosterone, C21-steroid hormone, androgen). While there is also an antibiotic biosynthetic term, the dominant theme is lipid/steroid biosynthesis pathways, suggesting a functionally cohesive group of enzymes tied to mycolic acid and related lipid metabolism.","confidence":"High","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0042619","count":8},{"id":"GO:0045150","count":4},{"id":"GO:0071768","count":4},{"id":"GO:0006666","count":4}]},{"hash":"1267704822646704561","title":"Glycoprotein Processing and ECM Secretion","description":"The GO terms cluster around protein glycosylation (O-linked via Ser/Thr and via N-acetyl-galactosamine), secretion of extracellular matrix components, and metabolism of plant-associated carbohydrates (arabinose, arabinan, xylan), suggesting secreted glycoproteins involved in extracellular matrix remodeling and carbohydrate processing. Immunoglobulin production and translation regulation appear ancillary but do not outweigh the core theme of glycosylation and ECM-associated secretion. ","confidence":"Medium","size":8,"edges":8,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0031221","count":2},{"id":"GO:0070278","count":2},{"id":"GO:0046373","count":2},{"id":"GO:0018242","count":2},{"id":"GO:0016266","count":2}]},{"hash":"2279199411516335706","title":"Retroviral integration and proviral latency","description":"The GO terms strongly point to a retroviral life cycle: reverse transcription (RNA-templated DNA biosynthetic process), integration into host DNA, DNA recombination, and DNA replication, alongside establishment of proviral latency and viral entry into the host nucleus. Additional terms about host\u2013symbiont interactions and RNA silencing defense support a virus\u2013host interaction context. This cohesive theme suggests proteins involved in retroviral replication and provirus maintenance.","confidence":"High","size":7,"edges":11,"triangles":10,"max_degree":5,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0075713","count":6},{"id":"GO:0039651","count":6},{"id":"GO:0006278","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0015074","count":6}]},{"hash":"265739231915964146","title":"Mitotic spindle regulation and cell division control","description":"Enriched for mitosis-related processes (spindle assembly, chromatid cohesion, cytokinesis, and general cell division) with some ubiquitin-pathway regulation hints, indicating proteins that regulate mitotic progression rather than just structural components.","confidence":"High","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0007064","count":1},{"id":"GO:0051016","count":1},{"id":"GO:1902426","count":1},{"id":"GO:1903461","count":1}]},{"hash":"110332242157084902","title":"Antiviral Interferon-Ubiquitination Module","description":"The top GO terms cluster around antiviral defense and protein regulation: interferon signaling, ISG15 conjugation, and ubiquitin-mediated regulation (including K11-linked ubiquitination), with links to viral processes and apoptosis. Although some terms are older/less-relevant, the dominant theme is innate antiviral signaling and ubiquitin-dependent control of protein activity, fitting a cohesive antiviral/ubiquitination module. ","confidence":"High","size":7,"edges":13,"triangles":8,"max_degree":6,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0042275","count":7},{"id":"GO:0060340","count":7},{"id":"GO:0051092","count":7},{"id":"GO:0051443","count":7},{"id":"GO:0032020","count":7}]},{"hash":"1727028656670550796","title":"Ubiquitin-mediated cell cycle control","description":"Enriched terms cluster around cell-cycle regulation with emphasis on ubiquitin signaling (K11-linked ubiquitination, histone H2A ubiquitination) and G2/M transition, suggesting a module of ubiquitin-dependent cell-cycle control. Developmental terms are supplementary but not central.","confidence":"Medium","size":7,"edges":16,"triangles":16,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0001831","count":2},{"id":"GO:0019102","count":2},{"id":"GO:0044346","count":2},{"id":"GO:2000819","count":2},{"id":"GO:0030853","count":2}]},{"hash":"2130230408236410674","title":"Translation initiation and ribosome biogenesis","description":"This cluster's top GO terms cluster around protein synthesis: cytoplasmic translational initiation, regulation of translational initiation, and ribosome biogenesis, plus associated regulation of GTPase activity and cell division, suggesting a functional module focused on early stages of ribosome assembly and control of translation. Some entries like amino acid starvation response and a couple of methionine salvage terms may reflect broader stress responses or annotation noise, but the core signal is translation initiation and ribosome production.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":2},{"id":"GO:1903833","count":2},{"id":"GO:0002183","count":2}]},{"hash":"1617585060137841253","title":"RNA and Protein Methylation","description":"This cluster is dominated by GO terms for methylation: rRNA methylation, tRNA methylation, peptidyl-lysine methylation (mono/di/tri), N-terminal peptidyl-glycine methylation, and RNA guanine-N7-methylation, plus general protein methylation. This suggests the proteins function as methyltransferases acting on RNA and protein substrates, with some related links to chromatin methylation and methyl-donor pathways. Overall, the label captures the shared function motif of the cluster.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":5},{"id":"GO:0018027","count":4},{"id":"GO:0018013","count":3},{"id":"GO:0030488","count":3},{"id":"GO:0006479","count":3}]},{"hash":"965745580347641711","title":"Endomembrane Vesicle Trafficking","description":"The top GO terms cluster around vesicle transport within the endomembrane system: retrograde and forward trafficking between the ER and Golgi, endosome-to-Golgi transport, general protein transport, endocytosis, targeting to vacuoles, and exocytic insertion. This suggests a cohesive role in intracellular protein trafficking across compartments.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006890","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0042147","count":6},{"id":"GO:0015031","count":4},{"id":"GO:0006897","count":4}]},{"hash":"1390216579217948193","title":"Neural Development and Transcriptional Regulation","description":"Despite some stress- and metabolism-related terms, the strongest recurring signals are vertebrate neural development terms (forebrain development, neural tube closure) along with broader development and DNA-templated transcription. This suggests proteins linked to neural development and transcriptional control, with some notes of cell cycle and stress response that may reflect pleiotropy.","confidence":"Medium","size":7,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0070059","count":3},{"id":"GO:0001501","count":3},{"id":"GO:0007275","count":3}]},{"hash":"1300092465958158798","title":"Mitotic Chromosome Segregation and Cytokinesis","description":"This cluster centers on mitotic processes and cytokinesis, with terms covering sister chromatid cohesion, metaphase/anaphase transition regulation, spindle assembly checkpoint deactivation, and cytokinesis regulation, plus supporting roles in mitotic DNA replication and actin-based cytokinetic machinery, all linked by ubiquitin-mediated regulation. ","confidence":"High","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":1},{"id":"GO:0030071","count":1},{"id":"GO:0051016","count":1},{"id":"GO:1902426","count":1},{"id":"GO:1903461","count":1}]},{"hash":"307289656333069321","title":"Neural development and neurotransmitter metabolism","description":"The cluster is dominated by neural-development terms (hindbrain development, neural tube development, righting reflex, neuromuscular control of balance) and by metabolism-related GO terms (retinoic acid biosynthesis, GABA and other catabolic processes), suggesting a CNS patterning and neurotransmitter regulation theme; a couple of non-neural terms (pancreas/ureter development) may be incidental. ","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030902","count":7},{"id":"GO:0031016","count":7},{"id":"GO:0042904","count":7},{"id":"GO:0006068","count":7},{"id":"GO:0009450","count":7}]},{"hash":"1215930428426319160","title":"Embryonic morphogenesis and neural crest migration","description":"The top GO terms cluster around embryonic development and organogenesis\u2014digestive tract morphogenesis, bronchus cartilage development, ureter smooth muscle differentiation, limb bud formation, and neural crest cell migration\u2014suggesting a focus on organogenesis and tissue differentiation. While there are also generic cellular-process terms (splicing, sumoylation, nucleotide-excision repair), the strongest signal is developmental morphogenesis, especially neural crest migration. This justifies a label centered on embryonic development and tissue morphogenesis.","confidence":"Medium","size":7,"edges":13,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0033234","count":1},{"id":"GO:0060784","count":1},{"id":"GO:2000819","count":1},{"id":"GO:0048546","count":1}]},{"hash":"2294209711026893038","title":"Isoprenoid and Sterol Biosynthesis","description":"Most top GO terms point to biosynthetic steps for terpenoids and related isoprenoids (geranyl, farnesyl, and geranylgeranyl diphosphates; monoterpene biosynthesis) as well as sterol/quinone production (cholesterol, quinone biosynthesis). This suggests a cohesive theme around prenyl lipid biosynthesis and lipid-terpenoid pathways, with a couple of ancillary protein-related terms that are less central to the core function.","confidence":"High","size":7,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0033384","count":4},{"id":"GO:1901663","count":4},{"id":"GO:0051290","count":4},{"id":"GO:0043693","count":4},{"id":"GO:0006695","count":4}]},{"hash":"1983213021942639764","title":"Glycoprotein ER quality control and ERAD","description":"The terms converge on N-glycan trimming (mannose trimming) during ER/Golgi processing and on the ubiquitin-dependent ERAD pathway, including positive regulation of retrograde transport from the ER to the cytosol for degradation. This points to a cohesive function in glycoprotein maturation, quality control, and disposal of misfolded proteins via ERAD. ","confidence":"High","size":7,"edges":11,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:1904154","count":3},{"id":"GO:1904381","count":3},{"id":"GO:0036511","count":3},{"id":"GO:0006486","count":3},{"id":"GO:0036509","count":3}]},{"hash":"933111341331503907","title":"Transcriptional control and genome stability in neural development","description":"This cluster centers on transcriptional regulation (DNA-templated transcription, chromatin-related terms) coupled with genome integrity processes (SCE repair, rDNA heterochromatin, telomere capping) and cell cycle control, with additional hints of neural development and morphogenesis (hippocampus development, bipolar cell polarity) and stress response signals (senescence, HGF signaling, muscle stretch). The convergence suggests a module integrating gene expression regulation and genome maintenance in a neural development context.","confidence":"Medium","size":7,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0090400","count":4},{"id":"GO:0035729","count":4},{"id":"GO:0021766","count":3},{"id":"GO:1990414","count":3}]},{"hash":"917281221835235285","title":"Steroid and secondary metabolite biosynthesis","description":"The top GO terms include steroid hormone metabolism (testosterone biosynthesis, C21-steroid hormone metabolic process) and androgen-related processes, along with antibiotic and alkaloid biosynthetic processes and mycolic acid synthesis, suggesting a theme around production of steroids/lipids and other secondary metabolites. While there is some functional diversity, the common thread appears to be biosynthesis of small molecules and lipid-associated metabolites, hence the label Steroid and secondary metabolite biosynthesis.","confidence":"Medium","size":7,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0045150","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0071768","count":3},{"id":"GO:0006666","count":3},{"id":"GO:0006710","count":3}]},{"hash":"815458783844074203","title":"Neuronal development and synaptic trafficking","description":"The cluster\u2019s top GO terms center on excitatory postsynaptic potential and secretory/trafficking processes, including protein transport and ER-to-Golgi vesicle transport, with references to neuronal development terms (substantia nigra) and broader developmental contexts. This points to a group of proteins involved in establishing synaptic signaling and the neuronal secretory pathway, supporting a label that emphasizes both neuronal development and synaptic trafficking.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0015031","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0021762","count":2}]},{"hash":"394129274196003667","title":"Lipid and isoprenoid biosynthesis","description":"The top GO terms are dominated by lipid and isoprenoid pathways: cholesterol biosynthesis, phosphatidylcholine biosynthesis, farnesyl diphosphate biosynthesis, and IPP biosynthesis via the MEP pathway, indicating a metabolic cluster focused on lipid and isoprenoid production and regulation. Some terms like blastocyst development or galactose metabolism appear less central and may reflect broader cellular metabolism or annotation noise, but the core signal supports lipid/isoprenoid biosynthesis as the cluster theme.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2001246","count":2},{"id":"GO:2001247","count":2},{"id":"GO:0001824","count":2},{"id":"GO:0042352","count":1},{"id":"GO:0061623","count":1}]},{"hash":"1073559954321016258","title":"Spliceosome-Mediated RNA Processing and Translation Regulation","description":"The top GO terms are dominated by mRNA splicing via the spliceosome, including cis splicing, regulation and alternative splicing, and preinitiation complex formation, with additional signals for translation initiation and miRNA-mediated silencing, pointing to a cohesive role in RNA processing and post-transcriptional gene expression control.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0045292","count":6},{"id":"GO:1901407","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0035278","count":4},{"id":"GO:0075522","count":4}]},{"hash":"1780782935115424278","title":"Intracellular vesicle trafficking and organelle transport","description":"The top GO terms are dominated by vesicle trafficking and transport among the endomembrane system: ER-Golgi and Golgi-ER pathways, endosome to melanosome transport, endocytosis, and protein targeting to vacuoles. This points to a cohesive theme centered on intracellular transport and organelle organization, with some ancillary terms relating to cell polarity and inheritance that can accompany such processes. Confidence reflects the strong alignment to membrane trafficking, with minor outliers.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":6},{"id":"GO:0010628","count":6},{"id":"GO:0071963","count":6},{"id":"GO:0000001","count":6},{"id":"GO:0006348","count":5}]},{"hash":"138307820394579659","title":"ABA-Driven Stomatal Regulation and Chloroplast Import","description":"This cluster is enriched for plant-specific processes centered on abscisic acid biosynthesis and stomatal movement, plus protein import into the chloroplast stroma, suggesting a link to ABA signaling and plastid targeting. While a few terms relate to other biosynthetic or RNA processing activities, the dominant signals point to ABA-mediated stomatal control and chloroplast import.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009688","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0010118","count":2},{"id":"GO:0018315","count":2},{"id":"GO:0006727","count":2}]},{"hash":"2176692243633238313","title":"Epithelial Signaling and Polarity","description":"The top terms cluster around epithelial cell polarity and junctions (establishment of epithelial cell polarity, bicellular tight junction assembly) and related signaling pathways (EGFR and GPCR signaling, including acetylcholine receptor signaling and bitter taste GPCRs) as well as calcium-dependent exocytosis. This suggests a cohesive function centered on epithelial cell\u2013level signaling and polarity, with a few outliers related to broader GPCR signaling or housekeeping processes like copper homeostasis. Overall, the core theme is epithelial signaling and polarity.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045956","count":6},{"id":"GO:0070830","count":6},{"id":"GO:0007173","count":6},{"id":"GO:0007213","count":6},{"id":"GO:0090162","count":6}]},{"hash":"2094452602254652119","title":"Steroid and lipid hormone metabolism and signaling","description":"The top GO terms cluster around lipid/hormone metabolism (testosterone biosynthesis, cholesterol catabolic process, prostaglandin biosynthetic process, retinol metabolism) and related signaling (positive regulation of receptor signaling via JAK-STAT), with implications for endothelial cell behavior. While some terms (fructose biosynthetic process, doxorubicin metabolic process) are ancillary, the dominant theme ties metabolism of steroids/lipids to signaling contexts, particularly in vascular/hormonal settings.","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046370","count":7},{"id":"GO:0042572","count":7},{"id":"GO:0071805","count":6},{"id":"GO:2000353","count":6},{"id":"GO:2000224","count":6}]},{"hash":"237935939310272241","title":"P53-mediated translation and cell cycle regulation","description":"The cluster combines translation-related terms (translation, cytoplasmic translation) with cell-cycle regulation and p53 pathway signaling (positive regulation of signal transduction by p53 class mediator), plus ubiquitin-related regulation and protein stabilization. This pattern suggests a coordinated program linking protein synthesis, stability, and cell-cycle control in a stress response, potentially involving p53-driven regulatory axes and DNA-damage responses such as to actinomycin D. Hence the label emphasizes the p53-associated control of translation and the cell cycle as the core theme.","confidence":"Medium","size":7,"edges":6,"triangles":1,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0002181","count":3},{"id":"GO:1904667","count":2},{"id":"GO:2000059","count":2},{"id":"GO:0072717","count":2}]},{"hash":"377199514697150785","title":"Autophagy and cell death regulation","description":"This cluster shows enrichment for autophagy-related terms (macroautophagy, negative regulation of autophagosome assembly), apoptotic and necroptotic processes, and vesicle trafficking components (protein targeting to vacuole, Golgi retention, membrane fusion) as well as mitochondrial fusion. Together these terms suggest a shared function in coordinating autophagy with programmed cell death and organelle dynamics.","confidence":"High","size":7,"edges":13,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006623","count":3},{"id":"GO:0045053","count":3},{"id":"GO:0006915","count":3},{"id":"GO:1902902","count":2},{"id":"GO:0070266","count":2}]},{"hash":"1348185904408515668","title":"Plant hormone signaling and cell wall regulation","description":"The terms are dominated by plant hormone responses (ABA, GA, ethylene) and processes linked to cell wall biogenesis and cytoskeletal regulation (tubulin deacetylation, secondary cell wall biogenesis), suggesting a theme around hormone-driven growth and structural control, despite an outlier term from a different lineage.","confidence":"Low","size":7,"edges":12,"triangles":7,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051534","count":2},{"id":"GO:1904911","count":1},{"id":"GO:0035066","count":1},{"id":"GO:0035855","count":1},{"id":"GO:1990414","count":1}]},{"hash":"1549050768468203555","title":"Unknown","description":"The GO terms are scattered across very different biological areas, including meiosis, gene expression regulation, muscle adaptation, endocytosis regulation, mesenchyme migration, retina homeostasis, histone acetylation, cell polarity, brain/nervous system development, and aggressive behavior. There is no single, coherent function that ties these proteins together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016344","count":7},{"id":"GO:0010628","count":7},{"id":"GO:0043503","count":7},{"id":"GO:0030100","count":7},{"id":"GO:0090131","count":7}]},{"hash":"1208743841253400881","title":"Mitotic Chromosome Segregation and Endosome Trafficking","description":"The top GO terms point to mitotic cell cycle and chromosome passenger complex localization to the kinetochore, signaling a core mitosis function. Additional terms regarding endosome size regulation and receptor recycling suggest linked membrane trafficking, with cilium assembly aligning with centrosome-related processes. Taken together, the cluster seems to combine mitotic machinery with endosomal/trafficking roles.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0072356","count":6},{"id":"GO:0001881","count":6},{"id":"GO:0019236","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0051036","count":6}]},{"hash":"1529292636449633222","title":"Redox Homeostasis and Hydrogen Peroxide Response","description":"This cluster is dominated by GO terms for redox homeostasis, response to hydrogen peroxide, and hydrogen peroxide catabolic processes, indicating a core role in oxidative stress management. The inclusion of cytochrome complex assembly supports a mitochondrial/respiratory angle linked to redox biology. Some terms (extracellular matrix organization, lipoprotein biosynthesis) may reflect broader or contextual annotations, but the strongest signal across members is redox balance and hydrogen peroxide detoxification.","confidence":"Medium","size":7,"edges":12,"triangles":11,"max_degree":5,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0070301","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0042267","count":3},{"id":"GO:0022417","count":3}]},{"hash":"2198925394129415854","title":"Unknown","description":"The list includes core proliferation terms (cell division, cell cycle) but also a broad mix of disparate metabolic and biosynthetic processes (lactate, methanol, alkaloid, cytokinin metabolism; capsule and cell wall polysaccharide biosynthesis). With only isolated GO terms and no clear shared pathway across the cluster, there isn\u2019t a cohesive function to label; hence Unknown with no confidence. ","confidence":"","size":7,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":1},{"id":"GO:0046677","count":1},{"id":"GO:1903457","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0009823","count":1}]},{"hash":"1352899368272888166","title":"Bone formation and remodeling","description":"The cluster shows strong enrichment for bone-related processes such as intramembranous ossification, bone resorption, and collagen catabolic/proteolytic remodeling, pointing to extracellular matrix turnover and skeletal development as the core theme, with some regulatory terms included as broader context.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":7},{"id":"GO:0097067","count":7},{"id":"GO:0001957","count":7},{"id":"GO:0060448","count":7},{"id":"GO:0010815","count":7}]},{"hash":"130482353990242211","title":"Tissue Development and Remodeling","description":"The top GO terms cluster around developmental tissue formation and remodeling (ossification, lung branching morphogenesis, decidualization, collagen catabolic process) with regulatory aspects such as regulation of catalytic activity and thyroid hormone response supporting coordinated development. Some terms (short-term memory, bradykinin catabolic process) may be peripheral or broader annotations, but overall the group points to proteins involved in tissue remodeling during development. ","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050790","count":7},{"id":"GO:0007614","count":7},{"id":"GO:0010839","count":7},{"id":"GO:0097067","count":7},{"id":"GO:0001957","count":7}]},{"hash":"879967468610548996","title":"Prostate gland development and epithelial differentiation","description":"This cluster is dominated by GO terms tied to prostate biology, notably prostate gland growth (GO:0060736) and epithelial cell differentiation involved in prostate gland development (GO:0060742), suggesting the proteins are enriched for prostate lineage differentiation. Lipid metabolism terms (sphingolipid metabolism and sphingomyelin catabolic process) appear as supporting context but are less central to the main theme. A few terms related to facial/hair morphogenesis appear but at low frequency and do not outweigh the prostate-focused signals. Overall, the core theme is prostate gland development and epithelial differentiation.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060736","count":3},{"id":"GO:0006665","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0060742","count":3},{"id":"GO:0007193","count":3}]},{"hash":"936987876123039152","title":"Signaling Regulation and Protein Modification","description":"The proteins show annotations linking immune signaling (positive regulation of TNF production, response to cytokine), neuromuscular signaling (acetylcholine-gated channel clustering), and post-translational modification processes (protein farnesylation, regulation of deacetylase activity, NOS biosynthetic regulation), suggesting a broad role in modulating signaling pathways through enzymatic activity and modifications rather than a single pathway.","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051770","count":3},{"id":"GO:0032760","count":2},{"id":"GO:0018343","count":2},{"id":"GO:0090045","count":2},{"id":"GO:0071340","count":2}]},{"hash":"208772697603243911","title":"NOD-like receptor\u2013mediated innate immunity","description":"This cluster centers on innate immune responses, including defense against virus and NOD-like receptor signaling, pointing to a core antiviral innate immunity function. Some terms touch on NF-kappaB regulation, calcium signaling, and cell-cycle references, which may reflect ancillary signaling roles or annotation noise, but the dominant theme is innate antiviral signaling via NOD-like receptors.","confidence":"High","size":6,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2}]},{"hash":"251203873043952859","title":"Ubiquitin-regulated protein quality control and DNA repair","description":"The proteins are dominated by ubiquitin-related processes: autoubiquitination, ubiquitin-dependent ERAD, sumoylation, and deubiquitination, plus aggrephagy, pointing to protein turnover and quality control as a core theme. The presence of nucleotide-excision repair terms suggests these factors also participate in DNA repair pathways, indicating a broader stress-response role. Together, these terms support a label capturing both ubiquitin-mediated proteostasis and DNA repair connections.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0070911","count":5},{"id":"GO:0006289","count":4},{"id":"GO:0016925","count":4}]},{"hash":"31533459580141680","title":"Growth signaling and cell-cycle control","description":"This cluster centers on growth signaling and cell-cycle control. The presence of TORC1 signaling, ubiquitin ligase activity and K11-linked ubiquitination, and cell-cycle terms (G0 to G1 transition, sister chromatid cohesion) points to a module coordinating nutrient sensing with progression through the cell cycle, with RNA processing and dephosphorylation providing regulatory layers.","confidence":"High","size":6,"edges":11,"triangles":6,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0038202","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0070262","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0007064","count":1}]},{"hash":"446065979528391095","title":"DNA replication and genome maintenance","description":"Based on GO terms, the proteins cluster around DNA replication and chromosomal processes such as sister chromatid cohesion, cohesin-related loading, chromatin condensation, and homologous recombination repair, with a weaker hint of DNA damage response (SOS). Even though some terms are obsolete, the recurring theme is genome maintenance during replication and chromosome segregation.","confidence":"High","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000733","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0009432","count":1},{"id":"GO:0007064","count":1}]},{"hash":"709926376294781056","title":"DNA damage response and repair","description":"These proteins cluster around genome stability: multiple GO terms point to DNA recombination and DSB repair via HR, telomere maintenance, and cellular responses to ionizing radiation, suggesting a shared function in DNA damage response and repair. The remaining terms are more peripheral noise.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0008045","count":1},{"id":"GO:0060218","count":1},{"id":"GO:0071481","count":1},{"id":"GO:0000723","count":1}]},{"hash":"93752867959095705","title":"Developmental Cell Cycle Regulation","description":"The cluster centers on centrosome cycle and DNA replication with related regulation of the cell cycle, indicating a core role in developmental cell-cycle control. While there are development-specific terms (embryonic skeletal morphogenesis, placenta-associated differentiation) and signaling components (PI3K/AKT, peptide hormone response) that place these proteins in broader growth and differentiation contexts, the dominant theme is regulation of cell cycle progression during development, with a hint of neural development from the axon guidance term.","confidence":"High","size":6,"edges":7,"triangles":2,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0010571","count":6},{"id":"GO:0008045","count":5}]},{"hash":"1821702642032146495","title":"Cell cycle regulation and vesicle trafficking","description":"This cluster centers on cell growth and division signals (TORC1, mitotic cohesion, G0\u2192G1 transition) and intracellular trafficking (ER\u2013Golgi transport, GTPase regulation, ubiquitin ligase activity), with mRNA transport as a related growth-related process. The convergence of cell cycle control and vesicle transport suggests a cohesive theme coordinating growth with division and cargo movement.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0038202","count":4},{"id":"GO:0051028","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0070262","count":4},{"id":"GO:0006890","count":4}]},{"hash":"606691920356418648","title":"Unknown","description":"The top terms include a mix of metabolic biosynthesis (glycerol-3-phosphate, pantothenate, polysaccharide biosynthesis) and immune/defense processes (interleukin-1 and interferon-\u03b1 production, defense against Gram-negative bacteria), along with unrelated tasks like RNA import into the nucleus and cell polarity maintenance. This lack of a coherent, single functional theme across the cluster makes it unclear what common function to label, so Unknown is most appropriate.","confidence":"","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046167","count":2},{"id":"GO:0033317","count":1},{"id":"GO:0046168","count":1},{"id":"GO:0000271","count":1},{"id":"GO:0055114","count":1}]},{"hash":"232334622636046208","title":"Embryonic neural development with transcriptional regulation","description":"This cluster is enriched for embryonic/neural development terms such as forebrain development, neural tube closure, skeletal system and multicellular organism development, together with DNA-templated transcription and cell cycle processes, suggesting proteins involved in transcriptional regulation during embryogenesis and neural tissue formation. The inclusion of ER-stress\u2013related apoptotic signaling indicates cellular stress responses that can accompany development, reinforcing a developmental/regulatory theme.","confidence":"High","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0070059","count":3}]},{"hash":"278336961455859426","title":"Unknown","description":"The terms span transport (calcium import), endocytosis regulation, epithelial polarity, protein ubiquitination, spindle assembly, immune differentiation, chemokine production, and epithelial maturation, with no obvious common function. With zero edges and mixed processes, there isn\u2019t a single coherent function tying the proteins together, so the cluster is best labeled Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098703","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0090162","count":1},{"id":"GO:0090501","count":1},{"id":"GO:0016567","count":1}]},{"hash":"49256816254736254","title":"Steroid Hormone Biosynthesis and Androgen Metabolism","description":"The top GO terms are dominated by testosterone biosynthetic process, androgen metabolic process, and C21-steroid hormone metabolic process, indicating the proteins cluster around steroid hormone production and androgen metabolism. There are also related lipid/secondary metabolite biosynthesis terms (e.g., 3-keto-sphinganine metabolic and mycolic acid biosynthetic) and some oddities like acetoin catabolic and regulation of transcription, which may reflect annotation noise or broader metabolic links. Overall, the core theme is steroid hormone biosynthesis and androgen metabolism.","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0061370","count":4},{"id":"GO:0008209","count":4},{"id":"GO:0045150","count":3},{"id":"GO:0071768","count":3},{"id":"GO:0006666","count":3}]},{"hash":"1998989329918123709","title":"Glutamatergic Synapse Function and Plasticity","description":"The dominant GO terms point to glutamatergic synaptic transmission and receptor regulation (AMPA/NMDA) with associated plasticity processes (learning, receptor internalization, vesicle clustering, and terminal button organization), suggesting proteins that modulate excitatory synapses and their plastic changes.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000463","count":3},{"id":"GO:0051968","count":3},{"id":"GO:2000969","count":3},{"id":"GO:0050783","count":2},{"id":"GO:0007612","count":2}]},{"hash":"1389503633483579466","title":"Unknown","description":"The top GO terms span diverse processes (cell cycle regulation, calcium transport, pinocytosis, epithelial polarity, ubiquitination, spindle assembly, immune differentiation, chemokine production, and NF-kappaB signaling) with no single cohesive theme linking all proteins, so a precise, representative label is not apparent.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045736","count":1},{"id":"GO:0098703","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0090162","count":1},{"id":"GO:0090501","count":1}]},{"hash":"796387461488889513","title":"Membrane Targeting and Protein Folding","description":"The GO terms cluster around SRP-dependent and post-translational targeting of proteins to membranes, plus cellular responses to unfolded proteins, pointing to membrane-associated protein biogenesis and quality control. While a couple of terms (iron-sulfur cluster assembly, DNA replication) are present, the strongest signal is membrane targeting and folding/quality control.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0016226","count":6},{"id":"GO:1902037","count":6},{"id":"GO:0034620","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0006616","count":6}]},{"hash":"1557786011708522827","title":"Gene Expression Regulation and Proteostasis","description":"The cluster contains GO terms spanning transcriptional regulation (negative regulation of transcription by RNA polymerase II, chromatin/heterochromatin formation), RNA processing (nuclear mRNA surveillance), translation initiation and regulation (translation preinitiation complex formation, IRES-dependent translation), and protein turnover (ubiquitin-dependent protein catabolic process, proteasome assembly). This combination points to control of gene expression at multiple levels plus protein quality control, even though a few terms touch on development (neuron differentiation, germ-line cyst encapsulation) that may reflect broader regulatory roles. Confidence: Medium","confidence":"","size":6,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090054","count":3},{"id":"GO:0006511","count":3},{"id":"GO:0030182","count":3},{"id":"GO:0070321","count":3},{"id":"GO:0075522","count":3}]},{"hash":"1060343943816497160","title":"T cell activation and antigen presentation","description":"The cluster features strong immune-related terms: T cell receptor signaling, MHC class I antigen processing and presentation (TAP-dependent), Fc-epsilon receptor signaling, non-canonical NF-kappaB signaling, and protein deubiquitination with regulation of mRNA stability, all suggesting coordinated signaling for antigen recognition and T cell\u2013mediated responses. Some related regulatory and stress-response terms appear, but the dominant theme is adaptive immune activation and antigen processing.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0002479","count":5},{"id":"GO:0038095","count":5},{"id":"GO:0043488","count":5}]},{"hash":"2155535183432835237","title":"Ribosome Biogenesis and Translation Control","description":"This cluster is dominated by translation-related terms (GO:0006412, translation, 6 annotations) and includes ribosome assembly (GO:0042255) plus negative regulation of translation, including initiation complex formation, pointing to regulation of protein synthesis and ribosome assembly. The observed responses to antibiotic and cycloheximide further support a link to translation stress. A few transcription/DNA repair terms appear but are secondary to the main translation/ribosome theme.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0046677","count":3},{"id":"GO:0046898","count":2},{"id":"GO:1901194","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1482508860050132888","title":"Proteostasis and Vesicle Trafficking","description":"The GO terms cluster around proteasome regulatory particle assembly and various aspects of intracellular transport and protein handling, including ER-Golgi vesicle transport, SNARE complex disassembly, ribosomal subunit assembly, and mitochondrial inner-membrane protein insertion. These together point to a theme of protein quality control and intracellular trafficking, with some stress response terms (heat acclimation, UV repair, aging) that modulate proteostasis. Thus the label reflects a coherent, albeit broad, functional group. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070682","count":2},{"id":"GO:0051013","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0001319","count":1}]},{"hash":"1966394561414692501","title":"Regulators of Morphogenesis and Signaling","description":"This cluster gathers proteins linked to developmental morphogenesis across multiple tissues (heart outflow tract, photoreceptor, Schwann cell development) and to regulation of signaling pathways (negative regulation of protein kinase activity, negative regulation of sumoylation, calcineurin-NFAT signaling), suggesting a shared role in coordinating developmental processes through signaling control. The presence of self proteolysis and mitochondrial calcium import adds some functional diversity but does not override the overarching theme of developmental regulation via signaling mechanisms.","confidence":"Medium","size":6,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0035502","count":3},{"id":"GO:0033234","count":3},{"id":"GO:0097264","count":3},{"id":"GO:0003151","count":3}]},{"hash":"895716704150979222","title":"Phytochelatin-metal detox and proteostasis","description":"The four top GO terms suggest a stress-response module combining metal detox (phytochelatin biosynthesis) with protein quality control processes (proteolysis, regulation of catalytic activity, and autophagy regulation). This points to a theme of maintaining proteostasis under metal stress, aligning phytochelatin-mediated detox with protein turnover and autophagy regulation. Given the sparse term counts, the connection is plausible but not strongly supported.","confidence":"Medium","size":6,"edges":9,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0046938","count":1},{"id":"GO:1904715","count":1}]},{"hash":"82253160191087116","title":"Unknown","description":"There are no GO terms listed for this cluster, and no clear shared function emerges from the limited interaction data (6 proteins, 8 edges, 3 triangles). Without functional signals, a specific label cannot be confidently assigned.","confidence":"","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[]},{"hash":"1504004197175498100","title":"Vesicle trafficking and organelle maintenance","description":"The GO terms cluster around intracellular transport and organelle maintenance, including ER-to-Golgi and inter-Golgi vesicle transport, SNARE disassembly, and mitochondrial inner membrane protein insertion, plus protein turnover and cytoskeletal dynamics that support trafficking. Additional terms related to stress responses (heat acclimation, UV repair) further tie into maintaining organelle function and proteome integrity under stress. Overall, a cohesive theme of vesicle trafficking and organelle quality control fits best, with some stress-related maintenance aspects.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0001319","count":1},{"id":"GO:0070914","count":1}]},{"hash":"1099670265317986540","title":"Cellular Stress Response and Protein Modification","description":"The cluster\u2019s GO terms converge on stress-handling and proteostasis processes: mitochondrial fusion regulation, heat acclimation, and cellular responses to toxins suggest a focus on stress adaptation; nucleotide-excision repair and post-translational modifications (sumoylation and deubiquitination) point to damage sensing and protein quality control. While a few terms touch on development or ion transport, the dominant pattern is cellular stress response and regulation of protein function. ","confidence":"Medium","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010636","count":4},{"id":"GO:0006289","count":3},{"id":"GO:0016925","count":3},{"id":"GO:0097237","count":3},{"id":"GO:0016579","count":3}]},{"hash":"1798821981102459559","title":"Nuclear DNA replication, repair, and transcription","description":"The cluster centers on nuclear processes: DNA replication and nucleotide-excision repair, plus transcription initiation and RNA processing. While a couple terms hint at development or stress responses, the core shared activity is DNA metabolism and RNA maturation in the nucleus.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0006289","count":1},{"id":"GO:0001113","count":1},{"id":"GO:0000464","count":1}]},{"hash":"379738899414087127","title":"Embryonic and Multicellular Development","description":"The GO terms center on embryonic and multicellular development (forebrain development, neural tube closure, skeletal system development, multicellular organism development) and a broad transcriptional component, suggesting these proteins function as regulators of developmental programs. While some terms refer to cell cycle or stress responses, the dominant theme is developmental regulation and gene expression during early development.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0007275","count":2}]},{"hash":"302086530334603389","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010390","count":1},{"id":"GO:0019827","count":1},{"id":"GO:2001173","count":1},{"id":"GO:0021529","count":1},{"id":"GO:0001711","count":1}]},{"hash":"2171481692771524194","title":"Developmental transcriptional regulation","description":"This cluster is enriched for terms tied to regulation of gene expression during development (male gonad development; DNA-templated transcription; transcription factor localization) and developmental morphogenesis (skeletal system morphogenesis; cardiac muscle cell apoptotic process). The presence of cell-cycle and ubiquitin ligase activity regulation further supports a broad developmental regulatory program, rather than a single straightforward pathway. Overall, a label centered on developmental transcriptional regulation best captures the shared theme.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008584","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007064","count":1},{"id":"GO:0070317","count":1},{"id":"GO:1904668","count":1}]},{"hash":"1697262748181623626","title":"Neural development and epigenetic regulation","description":"The GO terms point to neural development processes (cerebellar cortex development, regulation of gliogenesis, neural development-related transcription) coupled with epigenetic control via histone H3K36 methylation/dimethylation and transcriptional regulation. This combination suggests a cohesive theme of chromatin-mediated gene regulation during neural differentiation, with the drug-response terms being ancillary. ","confidence":"Medium","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0097198","count":1},{"id":"GO:0071314","count":1},{"id":"GO:2001040","count":1},{"id":"GO:0051154","count":1}]},{"hash":"877658594228312616","title":"APC/C-Mediated Mitotic Progression","description":"The top GO terms cluster around mitosis and ubiquitin-dependent regulation: mitotic cell cycle, anaphase-promoting complex\u2013dependent catabolic process, mitotic sister chromatid cohesion, and K11-linked ubiquitination. The presence of positive regulation of ubiquitin ligase activity and regulation of G0 to G1 transition supports a core function in ubiquitin-mediated control of mitotic progression, likely centered on APC/C activity. Some RNA and histone methylation terms may reflect broader regulatory connections but do not override the dominant mitotic ubiquitin theme.","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":5},{"id":"GO:0000278","count":5},{"id":"GO:2001162","count":5},{"id":"GO:0031145","count":5},{"id":"GO:0051301","count":5}]},{"hash":"825026986513671078","title":"Oxidative stress response and redox metabolism","description":"This cluster is dominated by GO terms related to reactive oxygen species (superoxide, hydrogen peroxide) generation and detoxification (glutathione metabolism), indicating a core theme of redox balance and oxidative stress response. Some peripheral terms (platelet degranulation, heart development, amphetamine response) may reflect physiological contexts where ROS signaling is relevant, but the central pattern is ROS production and antioxidant pathways.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042554","count":2},{"id":"GO:0002576","count":2},{"id":"GO:0050665","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0001975","count":2}]},{"hash":"555674416870526572","title":"Nucleotide Phosphorylation and Cofactor Biosynthesis","description":"This cluster is enriched for GO terms about phosphorylation of nucleotides and biosynthesis of energy-related cofactors (NAD+ and CoA), with additional nucleotide interconversion and dephosphorylation terms. The common theme appears to be nucleotide metabolism and energy metabolism, potentially linked to cell division.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":3},{"id":"GO:0015937","count":2},{"id":"GO:0046940","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0009435","count":2}]},{"hash":"377043569435407857","title":"Bacterial lipid and teichoic acid biosynthesis","description":"This cluster shows strong enrichment for lipid and teichoic acid biosynthetic processes (lipoteichoic acid biosynthesis, teichoic acid D-alanylation, fatty acid and lipid A biosynthesis) and related antibiotic biosynthesis, suggesting proteins function together in building the bacterial cell envelope lipids and teichoic acids. Translation appears incidental rather than central.","confidence":"High","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0009245","count":1},{"id":"GO:0043041","count":1},{"id":"GO:0070395","count":1},{"id":"GO:0017000","count":1}]},{"hash":"2291394001687130544","title":"Glycolysis and TCA Cycle","description":"The top GO terms cluster tightly around central carbon metabolism: glycolytic process, the tricarboxylic acid cycle, pyruvate decarboxylation to acetyl-CoA, and related carbon flow through 2-oxoglutarate, pointing to energy production. Additional terms for nucleotide metabolism and minor stress/translation hints are secondary and do not outweigh the core metabolic theme. ","confidence":"High","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0006086","count":2},{"id":"GO:0033512","count":2},{"id":"GO:0006213","count":2}]},{"hash":"810228161704410183","title":"Nucleotide and cofactor salvage","description":"The cluster is mainly characterized by GO terms tied to salvage and interconversion of nucleotides and related cofactors (purine nucleotide salvage, purine nucleoside interconversion, nucleotide catabolic process, deoxyguanosine catabolic process, NAD biosynthesis via salvage). While there are a couple of outliers (methionine salvage and menaquinone biosynthesis), the dominant theme points to nucleotide and cofactor salvage/metabolism. Confidence: Medium","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":2},{"id":"GO:0019284","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0046638","count":1},{"id":"GO:0019358","count":1}]},{"hash":"491361818541431551","title":"Unknown","description":"The terms are diverse and do not point to a single cohesive function: redox/detoxification, multiple catabolic metabolism processes, and a few unrelated functions like cytoplasmic microtubule organization and chromatin binding regulation. There is no clear common theme tying all proteins together. ","confidence":"","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0031122","count":2},{"id":"GO:0006096","count":1},{"id":"GO:0046168","count":1}]},{"hash":"1616426393891466596","title":"Immune receptor signaling and antigen processing","description":"This cluster includes T cell receptor signaling, MHC I antigen processing/presentation, and Fc\u03b5 receptor signaling, along with regulatory pathways like non-canonical NF-kappaB signaling, deubiquitination, and mRNA stability control. The combination points to a cohesive module of immune receptor signaling linked to antigen processing/presentation, with additional transcriptional and post-translational regulation.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0002479","count":5},{"id":"GO:0038095","count":5},{"id":"GO:0043488","count":5}]},{"hash":"832017626811127305","title":"DNA Damage Response and Apoptosis","description":"The cluster shows enrichment for DNA repair, apoptotic process, and oxidative stress response (cellular response to menadione), plus transcription-related activity and mRNA decay, which together point to genome maintenance and stress-triggered cell fate pathways. The presence of multiple single-term connections suggests a broad but stress-linked function rather than a single enzymatic activity.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:2000757","count":1},{"id":"GO:0044240","count":1},{"id":"GO:0009154","count":1},{"id":"GO:1901919","count":1}]},{"hash":"1064382584738690107","title":"Vesicle trafficking and receptor recycling","description":"The GO terms cluster around intracellular vesicle transport (ER\u2013Golgi, intra-Golgi, retrograde endosome-to-Golgi), exocytic insertion and recycling of receptors, and related processes like long-term synaptic potentiation, reflecting a common function in vesicle trafficking and exocytosis across neurons and other cells.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0098967","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0060291","count":2}]},{"hash":"1211358527638025957","title":"Glycerophospholipid Biosynthesis","description":"These proteins show strong GO terms for biosynthesis of major phospholipids (phosphatidylethanolamine, phosphatidylserine, phosphatidylglycerol) and related lipid metabolism (platelet activating factor biosynthesis), with additional related regulatory terms. This indicates a cohesive lipid biosynthesis function for the cluster.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1905711","count":2},{"id":"GO:0006663","count":2},{"id":"GO:0006659","count":2},{"id":"GO:0006646","count":2},{"id":"GO:0070317","count":2}]},{"hash":"1383235773967371167","title":"Unknown","description":"The GO terms are highly diverse (cell division, sex development, hormone signaling, immune response, and trafficking) with no single shared function for this cluster, so a cohesive label cannot be inferred.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0071357","count":2}]},{"hash":"407331959376877549","title":"Neural crest migration and axonogenesis","description":"The terms strongly indicate neural crest\u2013derived processes, including neural crest cell migration and melanocyte migration, along with axonogenesis and related neural development (e.g., mammillary axonal development, positive regulation of axonogenesis). Supporting terms like Wnt receptor catabolic process and ubiquitination may regulate these developmental pathways, reinforcing a cohesive theme of neural crest\u2013driven neural and pigment cell development.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002250","count":1},{"id":"GO:0038018","count":1},{"id":"GO:0060816","count":1},{"id":"GO:0046621","count":1},{"id":"GO:0061373","count":1}]},{"hash":"933822692010763362","title":"DNA Replication and Repair","description":"The GO terms collectively point to DNA metabolism: replication of the genome during mitosis (leading and lagging strand elongation), nucleotide-excision repair including UV-damage excision repair, and translesion synthesis (both error-free and error-prone), plus proofreading. This suggests the cluster comprises proteins involved in DNA replication and damage-tolerance/repair.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903460","count":1},{"id":"GO:0006297","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0039693","count":1},{"id":"GO:0070987","count":1}]},{"hash":"1594284107832011194","title":"Unknown","description":"The proteins are annotated with a wide mix of GO terms ranging from histidyl diphthamide modification and SAM metabolism to antibiotic response, lipid A and UDP-GlcNAc biosynthesis, GDP-mannose biosynthesis, cell shape regulation, fungal-type cell wall biogenesis, and several obsolete biosynthesis terms. There is no clear, shared functional theme or pathway linking these terms, and the cluster has minimal connectivity, so a coherent label is not supported.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017183","count":1},{"id":"GO:0050843","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0009298","count":1}]},{"hash":"1059620162114137320","title":"Stress-Responsive Cytoskeleton and Transport","description":"The cluster combines multiple stress-response GO terms (heat, UV-A, gamma radiation) with cytoskeletal and transport-related terms (microtubule polymerization/depolymerization, anterograde axonal transport, lens fiber morphogenesis), suggesting a theme of stress-induced cytoskeletal remodeling and transport processes. ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":5},{"id":"GO:0099641","count":5},{"id":"GO:0030308","count":5},{"id":"GO:0070141","count":5},{"id":"GO:0031109","count":5}]},{"hash":"2139990899391495872","title":"Innate immune signaling and cytokine production","description":"The top GO terms concentrate on toll-like receptor 3 signaling and interleukin-2 production, pointing to innate immune activation and cytokine regulation. Supporting terms about protease activity and stress-related processes fit a broader inflammatory and cellular response context. A couple of terms (podocyte development, mitochondrial fusion) are less directly related and may reflect annotation breadth or pleiotropy, but the immune-focused terms dominate the cluster\u2019s theme.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0018279","count":2},{"id":"GO:0009826","count":1},{"id":"GO:0006613","count":1},{"id":"GO:0045861","count":1},{"id":"GO:0060355","count":1}]},{"hash":"1156105169117718380","title":"Unknown","description":"Top GO terms cover immune signaling, protease regulation, podocyte development, and mitochondrial dynamics without a single unifying function, implying the cluster is functionally heterogeneous rather than cohesive.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0045861","count":3},{"id":"GO:0060355","count":3},{"id":"GO:0034141","count":3},{"id":"GO:0072249","count":3},{"id":"GO:1990046","count":3}]},{"hash":"1169019817199956426","title":"Ion Transport and Osmotic Stress Response","description":"The top GO terms cluster around transmembrane transport of ions (potassium, methylammonium) and cellular/osmotic stress responses (salt stress, hyperosmotic response), suggesting a membrane transport/oosmoregulation function for the group. A few terms related to secretion or development appear as minor outliers, but the dominant theme aligns with membrane transport and osmotic adaptation.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":1},{"id":"GO:0044241","count":1},{"id":"GO:0071472","count":1},{"id":"GO:0030950","count":1},{"id":"GO:0072220","count":1}]},{"hash":"1986205806794218609","title":"Meiotic DNA Repair and Germline Development","description":"The top GO terms cluster around double-strand break repair and replication-associated repair in meiosis (meiotic recombination, joint molecule formation, replication-born repair), alongside DNA damage responses (X-ray, camptothecin). This points to meiotic DNA repair processes with germline development context, supported by terms like spermatid development and early embryonic growth. The combination suggests a cohesive theme of meiotic repair linked to germline development and DDR.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990918","count":2},{"id":"GO:1990414","count":1},{"id":"GO:0000709","count":1},{"id":"GO:0010165","count":1},{"id":"GO:2000269","count":1}]},{"hash":"1600013197722092474","title":"Heterochromatin Formation and Boundary Maintenance","description":"This cluster is driven by GO terms centered on heterochromatin formation, boundary formation, centromere-related assembly, and rDNA heterochromatin, indicating proteins involved in chromatin organization and maintenance of heterochromatin; a few terms are obsolete, but the core theme remains chromatin regulation and heterochromatin maintenance.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031453","count":1},{"id":"GO:0034508","count":1},{"id":"GO:0006354","count":1},{"id":"GO:0033696","count":1},{"id":"GO:0043984","count":1}]},{"hash":"1979880644420833413","title":"Transcription Regulation & Chromatin Modification","description":"These proteins cluster around core gene expression regulation: DNA-templated transcription, transcription factor localization, and histone/H3-K27 methylation, plus RNA guanine-N7 methylation and ubiquitin ligase activity regulation, all indicating transcriptional control and chromatin state influences. Some non-core terms like taste and skeletal morphogenesis may reflect broader annotations or secondary roles, but the dominant signal is transcriptional regulation and epigenetic modification with links to cell-cycle processes such as mitotic cohesion and G0\u2192G1 transitions.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0007064","count":2},{"id":"GO:0070317","count":2},{"id":"GO:1904668","count":2},{"id":"GO:0036265","count":2}]},{"hash":"45899642706354367","title":"DNA replication and transcription regulation","description":"The strongest signals are DNA replication and transcription elongation regulation, with chromatin-related hints from histone acetylation and estradiol response, suggesting a nuclear regulatory module. Vesicle transport terms appear ancillary.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0043968","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0032968","count":3},{"id":"GO:0071392","count":3}]},{"hash":"814772624990297492","title":"Toxic stress response and proteostasis","description":"This cluster centers on responses to toxic stress (cadmium ion, general toxic substances) and the maintenance of protein homeostasis, highlighted by ubiquitin/ERAD-related processes (ubiquitin-dependent ERAD, deubiquitination) and protein modification (sumoylation). Nucleotide-excision repair and heat acclimation also appear, suggesting a broader stress-defense program. Some terms related to development (axonogenesis, erythrocyte differentiation) may be ancillary or reflective of pleiotropic annotations.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006289","count":1},{"id":"GO:0016925","count":1},{"id":"GO:0097237","count":1}]},{"hash":"783235435335511471","title":"Cell cycle regulation and growth signaling","description":"The top GO terms center on controlling core cell cycle processes (regulation of DNA replication, mitotic nuclear membrane reassembly, meiotic cell cycle regulation) and growth signaling pathways (TORC1 signaling, lipid kinase regulation, amino acid response). Additional terms related to protein turnover and RNA transport fit into a broader theme of coordinating cellular growth with division and protein homeostasis, with a hint of ciliogenesis via basal body docking. This combination suggests a cohesive functional cluster around cell cycle control linked to growth signaling.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043550","count":3},{"id":"GO:0097711","count":3},{"id":"GO:0031030","count":3},{"id":"GO:0007084","count":3},{"id":"GO:1903538","count":3}]},{"hash":"581461382167219069","title":"Mitotic spindle assembly and microtubule dynamics","description":"The top GO terms cluster around mitosis and microtubule dynamics, including plus-end microtubule activities, spindle midzone assembly, centrosome separation, and metaphase chromosome alignment, which together point to spindle organization and microtubule polarity during cell division. A couple of terms (e.g., chloroplast movement) are outliers but do not override the dominant mitotic theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990942","count":3},{"id":"GO:0070462","count":3},{"id":"GO:0001560","count":3},{"id":"GO:0030951","count":3},{"id":"GO:0031535","count":3}]},{"hash":"666951859161346009","title":"Metabolic Diversity and Stress Response","description":"These proteins show a mix of metabolic activities (aerobic respiration; sorbitol catabolism; D-xylulose-5-phosphate biosynthesis; fatty acid omega-oxidation; formaldehyde catabolism) and stress/interaction signals (response to copper ion; response to lipopolysaccharide; symbiont entry into host cell). The shared GO terms point to a broad metabolic toolkit with ancillary stress-response roles rather than a single, tightly defined function, so a name reflecting general metabolism with stress responsiveness is most representative.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":2},{"id":"GO:0046718","count":2},{"id":"GO:0046688","count":1},{"id":"GO:0006062","count":1},{"id":"GO:0010430","count":1}]},{"hash":"1318795297613763884","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0046101","count":1},{"id":"GO:0006189","count":1},{"id":"GO:0046651","count":1}]},{"hash":"1410264115864786651","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031573","count":1},{"id":"GO:0009650","count":1},{"id":"GO:0051097","count":1},{"id":"GO:0006296","count":1},{"id":"GO:0000736","count":1}]},{"hash":"1159789630458532825","title":"RNA splicing and translation regulation","description":"Based on the most frequent GO terms, the proteins appear to be involved in post-transcriptional gene regulation: both positive and negative regulation of mRNA splicing via the spliceosome, and steps in translation initiation including formation of the preinitiation complex and miRNA-mediated translational repression. A few terms mention viral or host interactions (IRES-dependent initiation, viral release, symbiont entry), but the common thread is RNA processing and control of translation, rather than a single metabolic or signaling pathway.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0000381","count":2}]},{"hash":"1130353425661907471","title":"Ubiquitin-Dependent Regulation and DNA Repair","description":"Proteins in this cluster are linked by GO terms centered on ubiquitination and ubiquitin-like modifications (autoubiquitination, ubiquitin-protein transferase activity, K11-linked ubiquitination, ISG15 conjugation), as well as pathways related to protein quality control (ER-associated degradation) and innate immune signaling (type I interferon). In addition, DNA damage response terms such as global genome nucleotide-excision repair and error-free postreplication repair indicate a connection to DNA repair processes. Together, these terms suggest a cluster of proteins involved in ubiquitin-mediated signaling that coordinates DNA repair with immune-related regulation.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0070911","count":4},{"id":"GO:0042275","count":3},{"id":"GO:0060340","count":3}]},{"hash":"2085300488093156322","title":"Isoprenoid and Sterol Biosynthesis","description":"The top GO terms cluster around terpenoid/isoprenoid biosynthesis (geranyl, farnesyl, and geranylgeranyl diphosphate biosynthesis, monoterpene biosynthesis) and cholesterol biosynthesis, indicating these proteins are involved in lipid/isoprenoid pathway metabolism. Other terms like protein transport or regulation of serotonin secretion are present but do not define the core theme of this cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033384","count":1},{"id":"GO:1901663","count":1},{"id":"GO:0051290","count":1},{"id":"GO:0043693","count":1},{"id":"GO:0006695","count":1}]},{"hash":"1163351444569811790","title":"Nucleotide metabolism and RNA editing","description":"The top GO terms cluster around metabolic processing of nucleotides (guanine, uridine, cytidine, deoxycytidine, and UMP salvage) and tRNA wobble adenosine to inosine editing, pointing to nucleotide metabolism and RNA modification as a unifying theme. Additional terms like riboflavin biosynthesis and ribosome-associated protein turnover appear as ancillary metabolic/process links, but the core signal is nucleotide metabolism and RNA editing. Confidence: Medium","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006147","count":2},{"id":"GO:0002100","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0046109","count":2},{"id":"GO:0009972","count":2}]},{"hash":"2069964708759177046","title":"Cell Cycle Regulation and Growth Signaling","description":"Based on the Top Terms, the cluster centers on cell cycle control and growth signaling: mitotic G1 DNA damage checkpoint signaling and negative regulation of cell population proliferation, plus ERBB signaling pathway. While there are also terms related to stress responses (cadmium/arsenic) and circadian regulation, these can reflect cellular stress integration with growth control. Overall, the dominant theme is regulation of cell proliferation and growth signaling, making this a coherent cluster describing cell-cycle and growth pathways.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031571","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0051436","count":2},{"id":"GO:0038127","count":2}]},{"hash":"2010396245118447181","title":"Unknown","description":"The Top Terms span diverse cellular processes (cytoskeleton remodeling, heat acclimation, vesicle trafficking, DNA repair, transcription, ribosome assembly, protein catabolism, and SOS response). There is no clear, single unifying function tying these terms together, so a cohesive label is not evident. None","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":1},{"id":"GO:0070370","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0001319","count":1},{"id":"GO:0006351","count":1}]},{"hash":"627904857554809629","title":"Biosynthesis and Metabolism","description":"This cluster is enriched for multiple biosynthetic processes (lipoprotein, NAD+ biosynthesis, oxaloacetate metabolism, polyamine and wybutosine biosynthesis) and related metabolic activity; these shared functions point to core biosynthesis pathways. A few terms about circadian regulation and kidney development appear as outliers, but the dominant theme remains metabolic biosynthesis. ","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":2},{"id":"GO:0042158","count":1},{"id":"GO:0009435","count":1},{"id":"GO:0006107","count":1},{"id":"GO:0006596","count":1}]},{"hash":"2229367970368366226","title":"Carbohydrate and isoprenoid metabolism cluster","description":"The terms point to metabolism across multiple sugar-related pathways (galactose, galactitol, galacturonate) and isoprenoid/lipid biosynthesis (mevalonate pathway, IPP, farnesyl diphosphate, cholesterol). While there are a couple outliers (methylation, iron-sulfur cluster assembly), the strongest shared theme is involvement in diverse metabolic routes spanning carbohydrate processing and lipid/isoprenoid biosynthesis. This suggests a broad metabolic role rather than a single specific function for the cluster. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0042352","count":1},{"id":"GO:0061623","count":1},{"id":"GO:0010142","count":1}]},{"hash":"2013560519328589705","title":"Ubiquitination and Immune Signaling Regulation","description":"This cluster's top GO term is protein ubiquitination, pointing to a core role in tagging proteins for modification or degradation. The accompanying terms repeatedly describe negative regulation of signaling and immune-related processes (e.g., NF-kappaB activity, interleukin-12 production, NK cell cytotoxicity), suggesting these proteins collectively participate in dampening or modulating immune signaling pathways. While some terms are obsolete or less directly connected (e.g., certain hormone signaling pathways), the prevailing pattern centers on ubiquitin-mediated regulation of signaling in an immune context.","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":"intracellular protein transport","top_go_terms":[{"id":"GO:0016567","count":4},{"id":"GO:0032088","count":4},{"id":"GO:0016998","count":3},{"id":"GO:0032695","count":3},{"id":"GO:0044252","count":3}]},{"hash":"569808184255357424","title":"Thiamine and molybdenum cofactor biosynthesis","description":"The GO terms are dominated by thiamine biosynthetic processes and molybdenum cofactor biosynthesis and incorporation, indicating a shared function in cofactor assembly. Autophagy-related terms are present but appear secondary, suggesting primary relevance to cofactor biosynthesis with a possible auxiliary link to turnover pathways.","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0009229","count":2},{"id":"GO:0006777","count":2},{"id":"GO:0018315","count":1},{"id":"GO:0032258","count":1}]},{"hash":"1255779356275591517","title":"Ethylene and gibberellin ripening biosynthesis","description":"This cluster is driven by GO terms related to ethylene biosynthesis, fruit ripening, and gibberellin biosynthesis/catabolism, which are central to fruit maturation and hormonal control. Additional terms for proanthocyanidin biosynthesis and stress responses (hydrogen peroxide\u2013mediated PCD, SA catabolism) reflect related secondary metabolism and defense signaling that can accompany ripening, but the core theme appears to be hormone-driven fruit ripening.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009693","count":1},{"id":"GO:0009835","count":1},{"id":"GO:0045487","count":1},{"id":"GO:0009686","count":1},{"id":"GO:0010023","count":1}]},{"hash":"1185225287349551805","title":"Plant telomere and chromatin maintenance","description":"The top GO terms emphasize telomere-related processes (negative regulation of RNA localization to telomeres, protection from NHEJ at telomeres, subtelomeric heterochromatin formation) and replication-associated DNA repair along with chromatin regulation (histone acetylation). Plant hormone responses appear but the strongest signal is telomere maintenance and chromatin state in plants.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:1904911","count":4},{"id":"GO:0035066","count":4},{"id":"GO:0009739","count":4},{"id":"GO:1990414","count":4},{"id":"GO:1901347","count":4}]},{"hash":"1974654550970085766","title":"Unknown","description":"The GO terms show a mix of host\u2013microbe interaction (symbiont entry into host cell; viral process), hormone catabolism (insulin, bradykinin), and general cellular processes (proteolysis regulation, protein oligomerization, proton transport, aerobic respiration). There isn\u2019t a single coherent function tying all four proteins together, so a specific, intuitive label isn\u2019t supported. ","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0046718","count":4},{"id":"GO:0045861","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0051289","count":3},{"id":"GO:0042447","count":3}]},{"hash":"1810905787677072465","title":"Membrane transport of vitamins, lipids, and ions","description":"The GO terms cluster around transmembrane transport of diverse substrates: lipoprotein transport, vitamin and thiamine transport, potassium and cobalt ion transport, phospholipid translocation, and related cysteine/phytochelatin import. DNA repair terms (SOS response, nucleotide-excision repair) are present but appear incidental; the dominant theme is membrane transport of nutrients and lipids.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042953","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0071805","count":2},{"id":"GO:0045332","count":2},{"id":"GO:0009432","count":2}]},{"hash":"2249617554828843370","title":"RNA splicing and translation regulation","description":"This cluster centers on spliceosome-mediated mRNA splicing control (positive and negative) and translation initiation regulation, including formation of the preinitiation complex, IRES-driven initiation, and miRNA/ncRNA\u2013mediated silencing, with related poly(A) tail regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0035278","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0000381","count":2}]},{"hash":"1255226828061767258","title":"Metabolic Energy and Ion Transport Under Stress","description":"The terms cluster around energy metabolism (NAD+/NADP+ metabolism, phosphorylation, polyphosphate metabolism), membrane transport (proton transmembrane transport) and ion/homeostasis (potassium ion homeostasis), plus stress responses (salt stress, methylglyoxal). These together point to cellular energy management linked to ion transport and stress adaptation; an outlier term about cardiac conduction appears incidental. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019674","count":1},{"id":"GO:0006797","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0006741","count":1},{"id":"GO:0030007","count":1}]},{"hash":"254898367607571702","title":"Jasmonic acid/oxylipin biosynthesis and stress response","description":"This cluster is dominated by GO terms for jasmonic acid biosynthesis, oxylipin biosynthesis, and fatty acid beta-oxidation steps feeding JA production, plus multiple stress-related terms (response to ozone, toxic substances, cold) and a developmental link via stamen development. The common theme is plant lipid-derived signaling and stress responses centered on jasmonate/oxylipin pathways.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033543","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0048443","count":2},{"id":"GO:0031408","count":2},{"id":"GO:0010193","count":2}]},{"hash":"1373263893064259731","title":"Ribosome biogenesis and cell division","description":"The top GO terms point to ribosome biogenesis and translation-related processes (ribosome biogenesis, ribosomal small subunit biogenesis, tRNA modification) alongside cell cycle and cell division terms, suggesting a cluster centered on growth and protein synthesis machinery necessary for cell proliferation. Some terms also hint at bacterial division features (cell septum assembly, cellular fusion), but the predominant theme is ribosome-related assembly coupled to division. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0045087","count":2},{"id":"GO:1903833","count":1},{"id":"GO:0042274","count":1},{"id":"GO:0090529","count":1}]},{"hash":"924362988084781627","title":"Motor neuron and muscle development with adhesion","description":"These terms cluster around neuromuscular development and adhesion: motor neuron axon guidance and visceral motor neuron differentiation point to nervous system development, while skeletal muscle tissue development and cardiac muscle differentiation touch on muscle formation. Cell adhesion and cell-matrix adhesion further tie these processes together, with signaling such as calcineurin\u2013NFAT and growth hormone pathways supporting neuromuscular remodeling. A few outlier terms (e.g., B cell receptor signaling) are present but do not redefine the main theme.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008045","count":2},{"id":"GO:0060396","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0031532","count":2},{"id":"GO:0007160","count":2}]},{"hash":"1992819048654296029","title":"Innate immune signaling and mitochondrial stress","description":"This cluster is dominated by terms linked to innate immune signaling (TLR3 pathway, IL-2 production, regulation of cell adhesion molecule production) and cellular stress responses involving mitochondria (stress-induced mitochondrial fusion, mitochondrial membrane potential regulation). While there is a peripheral term about metanephric podocyte development, the majority of terms point to immune signaling and mitochondrial dynamics as the unifying theme. ","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045861","count":1},{"id":"GO:0060355","count":1},{"id":"GO:0034141","count":1},{"id":"GO:0072249","count":1},{"id":"GO:1990046","count":1}]},{"hash":"1472831547601226248","title":"Mitochondrial metabolism and transport","description":"The top GO terms cluster around mitochondrial energy production and metabolite/ion transport (malate-aspartate shuttle, adaptive thermogenesis, thiamine pyrophosphate and thiosulfate transport, magnesium export), membrane potential regulation, and related apoptotic/necroptotic signaling, indicating a coherent mitochondrial function theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060546","count":3},{"id":"GO:0036233","count":3},{"id":"GO:0000303","count":3},{"id":"GO:1990845","count":3},{"id":"GO:0008637","count":3}]},{"hash":"586926640428652282","title":"DNA replication and recombination factors","description":"The top GO terms indicate core DNA metabolism: replication, recombination, chromatid cohesion, and multiple DNA repair pathways (nucleotide-excision repair and meiotic DSB processing, HR regulation). This suggests the proteins function together as DNA maintenance and recombination factors; a couple of extracellular matrix terms seem incidental noise. Therefore the label reflects the cluster's primary theme.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0010705","count":2}]},{"hash":"1498606152820895026","title":"Endosome and cytoskeleton dynamics","description":"The prominent GO terms center on endosome/phagosome organization and actin-dependent motility, with supporting terms on cell polarity maintenance, suggesting a shared theme of vesicle trafficking and cytoskeletal regulation. Some terms related to meiosis or immune cell differentiation appear as outliers, but the dominant signal points to endosome dynamics and cytoskeleton. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044655","count":2},{"id":"GO:0001556","count":1},{"id":"GO:0040038","count":1},{"id":"GO:0090306","count":1},{"id":"GO:0007032","count":1}]},{"hash":"263472754046997394","title":"Protein quality control and trafficking","description":"The dominant terms point to handling misfolded proteins and their degradation (aggresome assembly, ubiquitin-dependent ERAD, protein catabolic process) and their transport within the cell (ER-to-Golgi vesicle transport), supported by microtubule severing which can facilitate cargo movement. These together define protein homeostasis under cellular stress. Some DNA-related terms appear, but they seem less central to the primary theme of quality control. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0006351","count":1}]},{"hash":"1497962114598664561","title":"Cofactor and Vitamin Biosynthesis","description":"The top GO terms cluster around biosynthetic processes for essential cofactors and vitamins (lipoate, biotin, molybdopterin, menaquinone) and related prosthetic group formation, with a peripheral note on porphyrin/heme precursor synthesis. This suggests the proteins share a common role in assembling or supplying cofactors for enzymes, rather than a single specific enzyme type. ","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009249","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0019475","count":1},{"id":"GO:0018339","count":1},{"id":"GO:0006782","count":1}]},{"hash":"69044522037985322","title":"Nucleotide Metabolism and RNA Editing","description":"The top GO terms cluster around nucleotide metabolism and RNA modification/editing: guanine catabolic process, UMP salvage, cytidine deamination, cytosine metabolic process, deoxycytidine catabolic process, and tRNA wobble adenosine to inosine editing. This suggests the proteins are involved in nucleotide turnover and RNA editing/modification, with a few broader metabolic terms (e.g., riboflavin biosynthesis) that are ancillary. Overall, a coherent theme of nucleotide metabolism and RNA editing best explains the cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006147","count":2},{"id":"GO:0002100","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0046109","count":2},{"id":"GO:0009972","count":2}]},{"hash":"2083633220870085955","title":"Unknown","description":"The terms span diverse functions (cell division, nucleotide-excision repair, multiple transport processes, antigen processing, and stem cell proliferation) with no single cohesive theme tying the proteins together. Because there isn\u2019t a clear, dominant shared function, a confident, specific label cannot be assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006289","count":2},{"id":"GO:0042883","count":2},{"id":"GO:0015803","count":2},{"id":"GO:0019885","count":2}]},{"hash":"665807349470214081","title":"Nuclear RNA processing and chromatin regulation","description":"The cluster\u2019s top GO terms emphasize RNA processing and splicing (RNA exon ligation, spliceosome regulation, transcription start site selection) alongside chromatin-related regulation (heterochromatin formation, histone acetylation) and rRNA processing, all pointing to nuclear control of gene expression; a few terms (e.g., cellular response to cold, excitatory synaptic potential regulation) may reflect broader or incidental stress signals but do not override the core theme.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090394","count":3},{"id":"GO:0000464","count":2},{"id":"GO:0031453","count":2},{"id":"GO:0070417","count":2},{"id":"GO:0048026","count":2}]},{"hash":"1513304158328207572","title":"Cardiac metabolism and development","description":"The cluster centers on energy and metabolic processes (fatty-acyl-CoA biosynthesis, carnitine and glycogen metabolism) with explicit heart-related development terms (cardiac muscle cell differentiation, heart development), suggesting proteins involved in cardiac energy metabolism and cardiac formation. A cold-response term appears but is less central; the metabolic-heart connection is the strongest signal.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009409","count":3},{"id":"GO:0046949","count":2},{"id":"GO:0019254","count":2},{"id":"GO:0009791","count":2},{"id":"GO:0006111","count":2}]},{"hash":"2214951163758394507","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006398","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0072684","count":1},{"id":"GO:0009395","count":1},{"id":"GO:0016180","count":1}]},{"hash":"1587783129725044079","title":"Neuronal Polarity and Cytoskeletal Regulation","description":"The terms cluster around establishing and maintaining cell polarity and cytoskeletal dynamics, including stress fiber and filopodium assembly, tight junction components, and neuronal growth/development. This points to a role in shaping neuronal cells and guiding polarity during neural development, with related processes like protein ubiquitination and regulation of secretion that can modulate signaling and trafficking.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021762","count":3},{"id":"GO:0010628","count":3},{"id":"GO:0071963","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0070830","count":2}]},{"hash":"1842720076925000989","title":"Chromatin-modifying Regulators of Development","description":"The GO terms cluster around histone modification/dna-templated transcription and embryonic patterning processes (somite axis specification, notochord morphogenesis, brain ventricle development) with Notch signaling regulation, indicating a group of chromatin-modifying factors that steer developmental gene expression.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033169","count":2},{"id":"GO:0021678","count":2},{"id":"GO:0061188","count":2},{"id":"GO:1901726","count":2},{"id":"GO:0006351","count":2}]},{"hash":"2180684292724436805","title":"Neural development and signaling","description":"Reason: The prominent terms cluster around neural development and signaling, including forebrain development, motor neuron axon guidance, peptide hormone signaling, and PI3K/AKT pathway activity. Transcription-related terms and chemotaxis fit within this broader neuronal development context, though a few entries are more general stress responses. Overall, the cluster appears to reflect neural differentiation and signaling processes.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0008045","count":1},{"id":"GO:0045736","count":1}]},{"hash":"1241803162740833417","title":"Unknown","description":"The GO terms listed are diverse, spanning cell cycle control, ubiquitin ligase regulation, RNA methylation, transcription factor localization, development (skeletal morphogenesis, cardiac apoptosis), chromatin modification, TORC1 signaling, and even taste perception. With only three proteins and no clear shared function or pathway, there isn't a single cohesive theme to describe this cluster.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007064","count":3},{"id":"GO:0070317","count":3},{"id":"GO:1904668","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0050909","count":3}]},{"hash":"1520382462392653198","title":"Developmental cytoskeletal remodeling and cell adhesion","description":"The cluster\u2019s top GO terms cluster around cytoskeletal and adhesion processes (stress fiber and filopodium assembly, bicellular tight junction assembly) and broad developmental roles (exocrine system development, multicellular growth, neuronal differentiation). This points to proteins involved in shaping cell morphology and epithelial junctions during development, with additional hints from ubiquitination and exosomal regulation that support broader cellular regulation. ","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070830","count":2},{"id":"GO:0051496","count":2},{"id":"GO:0051489","count":2},{"id":"GO:1903542","count":2},{"id":"GO:0016567","count":2}]},{"hash":"2246241798522323276","title":"Nucleotide and cofactor catabolism","description":"These proteins show GO terms focused on catabolic processes for nucleotides and cofactors (NAD+, CoA, diadenosine derivatives) and RNA-related turnover (snoRNA, RNA editing). While there are a few biosynthetic terms present, the overarching theme is breakdown/turnover of nucleotides and cofactors, suggesting a nucleotide/cofactor catabolic role. Confidence: Medium.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":1},{"id":"GO:0006382","count":1},{"id":"GO:0034656","count":1},{"id":"GO:0046057","count":1},{"id":"GO:1901909","count":1}]},{"hash":"1999560450574576138","title":"Heterochromatin Formation and Histone Modification","description":"The top GO terms cluster around chromatin state regulation, especially heterochromatin formation, pericentric heterochromatin, and histone modifications (e.g., H3K9 and H3K27 methylation and related silencing). Even though several terms are labeled obsolete, the remaining annotations consistently point to chromatin silencing and maintenance of repressive chromatin, suggesting the proteins function in chromatin state regulation. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060123","count":1},{"id":"GO:0010425","count":1},{"id":"GO:0021553","count":1},{"id":"GO:0031507","count":1},{"id":"GO:0098532","count":1}]},{"hash":"2141246364457877451","title":"Unknown","description":"The top GO terms are highly diverse (iron homeostasis, mitochondrial targeting-related processing, muscle differentiation, fatty acid metabolism/transport, seed coat development, bioluminescence) with no clear shared function or interaction pattern among the proteins (no edges). This suggests no coherent cluster function can be assigned beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006879","count":1},{"id":"GO:0006627","count":1},{"id":"GO:1902809","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0006465","count":1}]},{"hash":"1074299435772181545","title":"Immune signaling and cyclic nucleotide signaling cluster","description":"This small cluster prominently features immune-related signaling terms such as T cell receptor signaling and cellular response to lipopolysaccharide, alongside terms related to cyclic nucleotide signaling (cGMP and cAMP pathways). The combination suggests a theme around immune signal transduction that uses cyclic nucleotides as second messengers. Given the limited protein set, the connection is plausible but not deeply supported by many terms, hence a moderate confidence.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033159","count":3},{"id":"GO:0010753","count":3},{"id":"GO:0050852","count":3},{"id":"GO:0019933","count":3},{"id":"GO:0050995","count":3}]},{"hash":"2164188846337538129","title":"Unknown","description":"The top GO terms are highly diverse, including tRNA wobble modification (uridine thiolation and lysidine biosynthesis), urmylation, ERBB signaling and modulation of tyrosine kinase activity, plus developmental/learning terms. With only 3 proteins and a single edge, there isn\u2019t a single shared process or pathway that coherently ties these terms together, so a specific functional label cannot be confidently assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010098","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0032447","count":1},{"id":"GO:0002136","count":1},{"id":"GO:0038127","count":1}]},{"hash":"1613016137695740526","title":"Epidermal development and wound healing","description":"These GO terms converge on skin/epidermal biology and repair: wound healing and epidermal cell spreading, nail development, calcium signaling in keratinocytes, and lipid barrier processes (lipid storage/transport and HDL clearance) that are key to the skin barrier. The combination suggests a functional theme around epidermal development and wound response rather than unrelated processes.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010888","count":1},{"id":"GO:0035313","count":1},{"id":"GO:0007204","count":1},{"id":"GO:0035640","count":1},{"id":"GO:0010983","count":1}]},{"hash":"1969979954143812829","title":"Protein ubiquitination and SUMOylation","description":"This cluster is dominated by post-translational modification pathways, especially ubiquitination (including autoubiquitination and deubiquitination) and SUMOylation, with related processes like ERAD. The presence of terms regulating TNF signaling and TLR3 signaling suggests these proteins modulate immune pathways via ubiquitin/SUMO modifications, indicating a cohesive theme around ubiquitin/SUMO-mediated protein regulation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:1903265","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0034140","count":2},{"id":"GO:0051865","count":2}]},{"hash":"524291656587298032","title":"ECM remodeling and cell adhesion","description":"The cluster is enriched for terms related to extracellular matrix assembly/disassembly, cell-matrix adhesion, and integrin signaling (e.g., integrin-mediated signaling, calcium-independent adhesion, negative regulation of ECM assembly), plus supporting proteostasis processes that can regulate adhesion receptors or ECM components, suggesting a cohesive theme of ECM remodeling and adhesion rather than a single tissue-specific function.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031104","count":3},{"id":"GO:0006511","count":3},{"id":"GO:0006929","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0007229","count":3}]},{"hash":"2040121215673556238","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000957","count":1},{"id":"GO:0000964","count":1},{"id":"GO:0016049","count":1},{"id":"GO:0006656","count":1},{"id":"GO:0000154","count":1}]},{"hash":"1459745902953541428","title":"Unknown","description":"The GO terms are a mix of various biosynthetic processes (lipoprotein, NAD+, GMP, L-glutamine, oxaloacetate, cysteine, polyamine) plus sporulation and a cadmium response. With no edges or co-occurring theme beyond broad biosynthesis, there isn\u2019t a single coherent function tying these proteins together, so a specific label is not defensible from the data.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042158","count":1},{"id":"GO:0006541","count":1},{"id":"GO:0009435","count":1},{"id":"GO:0030436","count":1},{"id":"GO:0006107","count":1}]},{"hash":"47959461784369882","title":"Neural sensory perception signaling","description":"The top GO terms point to sensory perception and neural signaling, including light/visual perception, regulation of pain perception, short-term memory, and an adenylate cyclase-inhibiting GPCR pathway, suggesting a sensory-neural processing theme. Some terms appear unrelated (cell wall catabolic processes, viral release, cytolysis, gastrulation-related cytoskeleton polarity), indicating annotation noise or mixed functions in this small cluster. Overall, the dominant signal supports labeling this cluster as neural sensory perception signaling.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016998","count":2},{"id":"GO:0007614","count":2},{"id":"GO:0001661","count":2},{"id":"GO:0071257","count":2},{"id":"GO:0051930","count":2}]},{"hash":"911931399539038631","title":"Developmental Signaling Regulators","description":"The GO terms cluster around regulation and response to growth factor signaling (EGF, VEGF), small GTPase pathways (Rho, Ras), and development-related processes in neural and vascular contexts, suggesting a group of proteins that modulate signaling during development rather than a single pathway.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021764","count":2},{"id":"GO:0070493","count":2},{"id":"GO:0035924","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0043314","count":2}]},{"hash":"661335130882303968","title":"Nuclear RNA Surveillance and Decay","description":"This cluster is dominated by GO terms for nuclear RNA quality control and decay pathways, including nuclear mRNA surveillance and catabolic processes for snoRNA, snRNA, and histone mRNA, plus related post-transcriptional RNA handling at the nuclear periphery. The remaining terms are less cohesive with this theme, but the core signal points to nuclear RNA turnover mechanisms.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071048","count":1},{"id":"GO:0071036","count":1},{"id":"GO:0040009","count":1},{"id":"GO:0033259","count":1},{"id":"GO:0071044","count":1}]},{"hash":"438592688622103202","title":"SRP-dependent membrane targeting","description":"The top GO terms point to SRP-dependent cotranslational protein targeting to membrane, which reflects a shared function of guiding nascent proteins to the endoplasmic reticulum membrane during translation. The other terms (adipose development, organism growth, selenium response, corticosterone secretion) appear less connected to this core function and may be incidental. With only a single-edge cluster and low connectivity, the strongest common thread is the SRP-mediated targeting pathway, making this a concise and representative label.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0006617","count":1},{"id":"GO:0060612","count":1},{"id":"GO:0035264","count":1}]},{"hash":"1374487406134440922","title":"Fucosylation/Glycosylation in neural and immune development","description":"The cluster centers on fucosylation and glycosylation processes (L-fucose catabolism, Lewis a epitope biosynthesis, N-glycan fucosylation) and includes neural development terms (neuronal stem cell maintenance, cortical neuron migration) along with immune-related migration and T cell differentiation, suggesting a cohesive role for glycosylation in both neural and immune development.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097150","count":3},{"id":"GO:0042355","count":3},{"id":"GO:0006486","count":3},{"id":"GO:0010493","count":3},{"id":"GO:0021799","count":3}]},{"hash":"930302420133193681","title":"Unknown","description":"The top GO terms are highly heterogeneous, covering calcium transport, pinocytosis, epithelial polarity, ubiquitination, spindle assembly, and differentiation, with no single dominant function linking the proteins. No network edges and only three proteins, so there isn't a coherent functional theme to label beyond Unknown.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098703","count":1},{"id":"GO:0048549","count":1},{"id":"GO:0090162","count":1},{"id":"GO:0090501","count":1},{"id":"GO:0016567","count":1}]},{"hash":"29325311485878191","title":"Synaptic vesicle trafficking and neurotransmitter secretion","description":"The GO terms converge on vesicle transport between organelles (ER to Golgi, intra-Golgi, CVT/vacuole targeting) and on processes linked to neurotransmitter release and synaptic function (spontaneous secretion, vesicle priming, receptor insertion, long-term potentiation). This suggests the proteins participate in general vesicle trafficking with a strong emphasis on synaptic vesicle handling and neurotransmitter release. Therefore, the label reflects both their trafficking role and neuronal synaptic functions.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032258","count":2},{"id":"GO:0010811","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0061669","count":2},{"id":"GO:0010807","count":2}]}]