[{"hash":"239482532169595861","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":17,"triangles":4,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0042273","count":7},{"id":"GO:0000463","count":7},{"id":"GO:0000472","count":7},{"id":"GO:0000480","count":7},{"id":"GO:0000466","count":7}]},{"hash":"2053737555427605503","title":"Proteostasis and cell-cycle processes","description":"Top GO terms indicate proteostasis and quality control (ubiquitin-dependent ERAD, chaperone-cofactor\u2013dependent refolding, proteasome assembly, oxidation-dependent protein catabolic process) and trafficking (ER to Golgi, intralumenal vesicle formation). The inclusion of DNA replication, cell division, and CENP-A\u2013containing chromatin assembly suggests coupling to the cell cycle. Together, this cluster seems to reflect proteins involved in maintaining protein homeostasis while coordinating cell-cycle events.","confidence":"Medium","size":29,"edges":84,"triangles":114,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":14},{"id":"GO:0070389","count":11},{"id":"GO:0006260","count":10},{"id":"GO:0051301","count":10},{"id":"GO:0006888","count":10}]},{"hash":"1846898590795006121","title":"Epigenetic Regulation and Chromatin Organization","description":"The cluster shows a strong representation of epigenetic-related terms (regulation of DNA methylation; histone H3-K9 acetylation; H3-K27 trimethylation) and chromosome organization, indicating a core theme around chromatin state and genome structure. A few transport-related terms (xenobiotic and vitamin transmembrane transport) appear present but are less central to the majority of terms, suggesting potential annotation noise or multi-function proteins. Overall, the dominant signal supports epigenetic regulation and chromatin organization as the cluster\u2019s main function.","confidence":"Medium","size":29,"edges":88,"triangles":0,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0044030","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0045857","count":2}]},{"hash":"69750108437774122","title":"Gene Expression and DNA Integration","description":"The top GO terms point to core gene expression processes (cytoplasmic and mitochondrial translation, DNA-templated transcription) and DNA-level events (DNA recombination, DNA integration). This suggests a cohesive cluster of proteins involved in both transcription/translation and genome modification/integration. A few terms related to viral latency or host\u2013pathogen interactions appear as minor outliers but do not override the central theme of gene expression and DNA-level processes.","confidence":"Medium","size":29,"edges":406,"triangles":3654,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006915","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0032543","count":2}]},{"hash":"48994580141236700","title":"Mitotic spindle assembly and ubiquitination","description":"The most represented GO terms are protein ubiquitination, spindle assembly, and cell cycle, pointing to roles in mitotic regulation and chromosome segregation. The presence of actin filament bundle assembly suggests cytoskeletal remodeling during division, while mRNA processing and telomere maintenance terms are present but less central. Overall, the cluster is best described by mitotic spindle assembly together with ubiquitin-mediated regulation.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016567","count":10},{"id":"GO:0051017","count":9},{"id":"GO:0051225","count":9},{"id":"GO:0090501","count":9},{"id":"GO:0032212","count":9}]},{"hash":"1488626851636007073","title":"Ribosome Biogenesis and Cell Division","description":"Based on the top GO terms, the cluster is dominated by ribosome biogenesis, translation, and related processes (ribosome biogenesis, translation, cytoplasmic translation, ribosomal subunit export), with supporting signals for cell growth and division (cell cycle, cell division, cell septum assembly). This suggests the proteins largely participate in assembling and using ribosomes while coordinating cell proliferation and cytokinesis, making a combined label appropriate and specific.","confidence":"High","size":29,"edges":8,"triangles":0,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":4},{"id":"GO:1903833","count":4},{"id":"GO:0006412","count":4}]},{"hash":"292645323405253422","title":"Ribosome biogenesis and translation initiation","description":"This cluster is enriched for GO terms tied to translation reinitiation, formation of the translation preinitiation complex, and both ribosome biogenesis and large subunit biogenesis, pointing to core protein synthesis machinery. Spliceosome-mediated mRNA splicing appears as RNA processing linked to gene expression, with a few terms touching on chromatin assembly and development. Overall, the dominant signal is ribosome- and translation-related processes, making this label representative.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":11},{"id":"GO:0001731","count":11},{"id":"GO:0000398","count":9},{"id":"GO:0071456","count":9},{"id":"GO:0042254","count":9}]},{"hash":"265576394113230597","title":"Unknown","description":"The top GO terms span membrane proteolysis linked to ER-to-cytosol transport, unfolded protein response, sphingolipid biosynthesis, and insect developmental fate decisions, with an additional immune-regulatory term. The terms point to several unrelated themes and there is no single cohesive function tying all proteins together. ","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904211","count":3},{"id":"GO:0032815","count":2},{"id":"GO:0048515","count":2},{"id":"GO:0034620","count":2},{"id":"GO:0042676","count":2}]},{"hash":"1503048494411072854","title":"Nuclear Transcription Regulation and Protein Modification","description":"The cluster\u2019s top GO terms are dominated by nuclear transcription processes (DNA-templated transcription and negative regulation of transcription by RNA polymerase II), indicating a core role in transcription control. Supporting this are post-translational modification and signaling terms (peptidyl-proline hydroxylation, I-kappaB phosphorylation), suggesting regulation of transcription factors via modifications. Other terms touch on stress responses (viral process, detoxification), but the central theme remains transcription regulation with linked protein modification.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0033158","count":3}]},{"hash":"1264715711499487085","title":"Transcriptional Regulation and Sensory Signaling cluster","description":"This cluster is dominated by transcription-related terms (miRNA metabolism, tRNA transcription by RNA polymerase III, DNA-templated transcription) but also includes signaling and sensory terms (GPCR signaling, pain and mechanical stimulus detection, synapse assembly) and a defense/kinase regulation term. The mix suggests proteins involved in gene expression management that also participate in signaling and sensory-response pathways, rather than a single, tight pathway. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010586","count":3},{"id":"GO:0042797","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007186","count":2},{"id":"GO:0050830","count":2}]},{"hash":"1920114593022859828","title":"Root hair cell wall biosynthesis","description":"The top terms cluster around plant cell wall organization and root hair development, including cell wall biosynthesis (RG-II) and actin filament bundle assembly, suggesting a shared function in root hair growth and cell wall construction. Some unrelated terms (e.g., heat response, NF-kappaB) appear, but the core signal points to cell wall formation and root hair morphogenesis in plants.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":1},{"id":"GO:0080147","count":1},{"id":"GO:0010306","count":1},{"id":"GO:0033345","count":1},{"id":"GO:0006517","count":1}]},{"hash":"1353510419714290930","title":"Dopaminergic Synaptic Signaling","description":"The cluster shows enrichment for GO terms tied to neuronal communication and dopamine response, notably regulation of synaptic vesicle exocytosis and excitatory postsynaptic potential, plus cellular response to dopamine, pointing to a role in dopaminergic neurotransmission. Some terms are obsolete or unrelated (e.g., mating projection growth, lysosomal pH), but the dominant signal aligns with synaptic signaling modulated by dopamine.","confidence":"Medium","size":29,"edges":95,"triangles":54,"max_degree":16,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000186","count":8},{"id":"GO:2000300","count":8},{"id":"GO:0031384","count":7},{"id":"GO:0060079","count":7},{"id":"GO:0035751","count":7}]},{"hash":"233754390425217456","title":"Nociception and Thermosensation","description":"The cluster\u2019s top GO terms center on sensing pain and temperature: thermoception, detection of chemical and mechanical stimuli involved in sensory perception of pain, and responses to cold and to pain. While a few terms (e.g., DNA replication, virus defense) are more general or unrelated, the dominant signal points to nociceptive and thermosensory functions, supporting a label focused on pain and temperature sensing.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0050955","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0048265","count":2}]},{"hash":"41052148040257692","title":"Chondrocyte Differentiation and Bone Morphogenesis","description":"The strongest signals are regulation of chondrocyte differentiation, bone morphogenesis, and TGF-beta signaling, pointing to skeletal development. Additional terms about cilium localization and endosomal sorting suggest related trafficking roles in signaling during cartilage formation. Overall, a skeletal development theme with supporting intracellular trafficking aspects.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032330","count":1},{"id":"GO:0030512","count":1},{"id":"GO:0010955","count":1},{"id":"GO:0060349","count":1},{"id":"GO:0032511","count":1}]},{"hash":"765097275377436278","title":"Cvt-mediated vacuolar targeting and ER-Golgi transport","description":"The top GO terms cluster around vesicle trafficking to the vacuole and between the ER and Golgi, including the Cvt pathway to the vacuole and endocytosis. This suggests the proteins function mainly in intracellular trafficking to the vacuole and ER-Golgi transport, with some housekeeping processes like ribosome biogenesis and rRNA transcription as broader context.","confidence":"High","size":28,"edges":7,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0006623","count":4},{"id":"GO:0032258","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0006888","count":4}]},{"hash":"1981928248213045691","title":"Ubiquitination and innate immune signaling","description":"The cluster is dominated by ubiquitin-related terms (ubiquitin-dependent protein catabolic process, protein ubiquitination, autoubiquitination, K6-linked ubiquitination) and includes innate immune terms (innate immune response, defense response to virus, TNF signaling regulation). The co-occurrence suggests a cohesive role in ubiquitin-mediated regulation of immune responses, potentially linking chromatin regulation (histone catabolic process) to antiviral signaling. Overall, these proteins appear to function together in ubiquitin-driven control of immunity and protein turnover.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0016567","count":8},{"id":"GO:0036205","count":8},{"id":"GO:1903265","count":7},{"id":"GO:0051865","count":7}]},{"hash":"1527007873479254412","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0045947","count":2}]},{"hash":"574681159397842711","title":"Neural development and ion-channel signaling","description":"This cluster shows a coherent emphasis on neural development and excitability, with terms for multicellular development, sensory perception of pain, and neural signaling routes (Purkinje to ventricular signaling) alongside ion transport through calcium and potassium channels. Transcription and protein oligomerization support neuronal differentiation and synaptic assembly, pointing to a module of proteins involved in nervous system development and ion-channel\u2013driven signaling. Some terms reflect broader developmental or behavioral aspects, but the dominant theme remains neural development and excitability.","confidence":"Medium","size":28,"edges":37,"triangles":40,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":12},{"id":"GO:0019233","count":11},{"id":"GO:0097623","count":9},{"id":"GO:1990573","count":9},{"id":"GO:0006351","count":8}]},{"hash":"1408549704928608505","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":7},{"id":"GO:1905639","count":7},{"id":"GO:1900865","count":7},{"id":"GO:0031426","count":7},{"id":"GO:0031425","count":7}]},{"hash":"2274845075186495685","title":"DNA replication checkpoints and cell cycle control","description":"Most of the prominent GO terms point to genome replication and cell-cycle regulation, including replication fork arrest, intra-S and DNA damage checkpoint signaling, and regulation of nuclear DNA replication and cohesin establishment during mitosis. A smaller subset includes spliceosome-related splicing and mating-type imprinting, which may reflect annotation noise or multifunctional proteins, but the dominant signal supports a theme of replication control and cell-cycle progression. Confidence: Medium","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0007049","count":1},{"id":"GO:0000076","count":1},{"id":"GO:0034087","count":1},{"id":"GO:0071515","count":1}]},{"hash":"187859537447919700","title":"Unknown","description":"The top terms span adipogenesis, heat response, immune signaling, cytoskeletal processes, cell migration, cardiac development and electrophysiology, neural synaptic regulation, and cell division. These represent disparate biological contexts with no single cohesive function, so a specific cluster label cannot be confidently assigned.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045444","count":9},{"id":"GO:0009408","count":8},{"id":"GO:0007253","count":8},{"id":"GO:0051017","count":8},{"id":"GO:0045083","count":8}]},{"hash":"109826128601373892","title":"Zinc Ion Transport and Homeostasis","description":"This cluster is dominated by GO terms about zinc handling: intracellular zinc ion homeostasis, zinc ion import across the plasma membrane, detoxification of zinc, and related metal transport (including cadmium). The occasional limb development term is likely incidental; overall the proteins appear connected by zinc uptake, distribution, and detoxification processes, supporting a zinc homeostasis/transport role.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0006882","count":1},{"id":"GO:0060173","count":1},{"id":"GO:0006830","count":1},{"id":"GO:1903615","count":1}]},{"hash":"1272323818977593908","title":"Heat- and Light-Stress Response with ROS Regulation","description":"The cluster\u2019s top GO terms cluster around response to heat, UV-A, and high light, together with protein stabilization and regulation of ROS metabolism, pointing to a proteostasis and oxidative-stress response program driven by environmental light/heat stress. The lens fiber morphogenesis term hints at eye-related contexts where such stress responses are important, while other terms like estradiol response or muscle contraction are broader and less central. Overall, the label captures the dominant theme of heat/light-induced stress response with antioxidant regulation.","confidence":"Medium","size":27,"edges":335,"triangles":2569,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0050821","count":8},{"id":"GO:0009408","count":7},{"id":"GO:2000378","count":7},{"id":"GO:0032355","count":7},{"id":"GO:0070141","count":7}]},{"hash":"823336771001915672","title":"Organelle ribosome biogenesis and RNA processing","description":"The top GO terms cluster around mitochondrial RNA processing, mitochondrial large ribosomal subunit assembly, and chloroplast rRNA processing, pointing to a core theme of ribosome biogenesis and RNA maturation in organelles. Additional terms touch on nuclear pore transport and kinetochore localization, which may reflect broader trafficking roles but do not override the organelle ribosome signal. Overall, the dominant pattern supports organelle ribosome assembly and RNA processing as the main function of this cluster.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000963","count":3},{"id":"GO:0045333","count":3},{"id":"GO:1902775","count":3},{"id":"GO:1901259","count":3},{"id":"GO:0043547","count":2}]},{"hash":"2257107070500435264","title":"Cytoskeleton remodeling and cell migration","description":"The top terms concentrate on cytoskeletal processes: actin filament bundle assembly, spindle assembly, and cell migration, suggesting a focus on cytoskeletal dynamics and movement. While other terms (RNA processing, telomere maintenance, signaling, immune regulation) appear as well, the strongest consistent signal is cytoskeletal organization and locomotion, justifying a label around these functions. This connection is present but moderate due to the diverse annotations.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":4},{"id":"GO:0051225","count":4},{"id":"GO:0090501","count":4},{"id":"GO:0032212","count":4},{"id":"GO:0006397","count":4}]},{"hash":"1742635404982989486","title":"Cell growth, division, and differentiation","description":"This cluster shows terms tied to cell proliferation and developmental processes, including mitotic cell cycle, regulation of cytokinesis, and differentiation events like lung epithelial differentiation and mesoderm morphogenesis. While there are some miscellaneous terms (ribosome maturation, vesicle size regulation), the dominant theme is coordination of cell growth/division with development, justifying this label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0060487","count":2},{"id":"GO:0032465","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000462","count":2}]},{"hash":"1571193190435375308","title":"DNA Damage Response and Ribosome Biogenesis","description":"The cluster combines DNA-damage/stress signals (nucleotide-excision repair, SOS response, antibiotic response) with ribosome biogenesis and rRNA maturation/translation initiation regulation, suggesting a theme of coordinating stress responses with protein synthesis. Some transport-related terms (taurine, fatty acid import, heme transport) are less clearly connected, likely background noise.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006289","count":5},{"id":"GO:0009432","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1427847419606873959","title":"Unknown","description":"The GO terms cover reproductive development, protein targeting and trafficking, cytoskeleton dynamics, RNA processing, mitochondrion inheritance, and immune signaling, with no single cohesive function linking most proteins; thus there is no clear common theme to assign a specific label.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0006463","count":1},{"id":"GO:0046661","count":1}]},{"hash":"1814758915688495799","title":"Unknown","description":"The top terms span heat response, RNA processing, telomere regulation, adipocyte differentiation, signaling, cytoskeletal assembly, and immune regulation, with no obvious shared pathway and no edges linking proteins, so a cohesive, specific label can't be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006397","count":3},{"id":"GO:1904357","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0035556","count":3}]},{"hash":"207180693625193755","title":"Gene Expression and Chromatin Dynamics in Development","description":"The GO terms cluster around nuclear processes\u2014DNA-templated transcription, CENP-A\u2013dependent chromatin assembly, and ribosome biogenesis\u2014along with developmental and growth-related signals (growth hormone, TGF-beta, prostate gland development), suggesting a cohesive theme of gene regulation and chromatin management linked to development.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071560","count":9},{"id":"GO:0006351","count":9},{"id":"GO:0007568","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0060528","count":8}]},{"hash":"1333683897596144401","title":"Cardiac development and signaling","description":"This cluster includes GO terms tied to heart biology, notably regulation of SA node action potential and Notch signaling in the heart field, plus migration and cytoskeletal assembly that support cardiac morphogenesis. Other terms (heat response, IL-12 regulation, synaptic localization) seem less connected, but the strongest recurring theme is cardiac development and signaling.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":8},{"id":"GO:0007205","count":8},{"id":"GO:0051225","count":8},{"id":"GO:0009408","count":7},{"id":"GO:0007253","count":7}]},{"hash":"776829608313278205","title":"Insect follicle epithelium morphogenesis and cytokinesis","description":"The top GO terms point to epithelial adhesion and polarity in the insect follicle, cytokinesis processes (contractile ring, septum site selection, and post-division septum digestion), and related structural biosynthesis (chitin/cell wall), all of which align with morphogenesis and cell division within insect follicle epithelium. Some terms (like accidental references to fungal chitin and eye development) are peripheral but do not override the central theme. Confidence: Medium","confidence":"","size":27,"edges":63,"triangles":41,"max_degree":14,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0007299","count":3},{"id":"GO:0042248","count":3},{"id":"GO:0000920","count":3},{"id":"GO:0034217","count":3},{"id":"GO:0071555","count":3}]},{"hash":"1041763301910617246","title":"Embryogenesis and Placental/Organ Development","description":"This cluster is driven by developmental processes across tissues\u2014placenta, heart, pancreas, cartilage\u2014with left-right patterning, EMT in endocardial cushion formation, and remodeling via apoptosis, reflecting embryogenesis and organogenesis.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":3},{"id":"GO:0060536","count":3},{"id":"GO:0035270","count":3},{"id":"GO:0060972","count":3},{"id":"GO:0003323","count":3}]},{"hash":"949788780912880043","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":4},{"id":"GO:1905639","count":4},{"id":"GO:1900865","count":4},{"id":"GO:0031426","count":4},{"id":"GO:0031425","count":4}]},{"hash":"1303518791855319418","title":"ECM remodeling in bone and lung development","description":"The cluster\u2019s top GO terms cluster around bone remodeling (bone resorption, intramembranous ossification, collagen catabolic process, basement membrane disassembly) and lung morphogenesis (epithelial tube branching, branching subdivisions), all pointing to extracellular matrix remodeling during skeletal and pulmonary development. Some terms like short-term memory and bradykinin catabolism are less directly tied, but the dominant signal fits ECM remodeling during development.","confidence":"Medium","size":26,"edges":13,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045453","count":4},{"id":"GO:0010815","count":4},{"id":"GO:0001957","count":3},{"id":"GO:0060441","count":3},{"id":"GO:0007614","count":3}]},{"hash":"2267172896424429971","title":"Neural development and synaptic signaling","description":"This cluster is enriched for neural-related processes: long-term synaptic potentiation and visual perception, plus Rho signaling and actin cytoskeleton dynamics that underlie synapse formation and plasticity. While there are broader developmental terms (myoblast fusion, multicellular development) and an apparently plant-specific ABA term, the dominant theme points to neural development and synaptic signaling.","confidence":"Medium","size":26,"edges":311,"triangles":2299,"max_degree":25,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0009738","count":21},{"id":"GO:0060291","count":21},{"id":"GO:0007601","count":21},{"id":"GO:0046827","count":21},{"id":"GO:0043065","count":21}]},{"hash":"144759098381880079","title":"Unknown","description":"The Top Terms span very diverse areas (brain development and branching morphogenesis; nitrogen utilization, starvation, zinc ion response; viral process; translation and tRNA modification; dephosphorylation; cyclooxygenase pathway). There isn\u2019t a single coherent function tying these together, so the cluster cannot be confidently assigned a specific biological theme. ","confidence":"","size":26,"edges":49,"triangles":1,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":4},{"id":"GO:0006808","count":4},{"id":"GO:0016311","count":4},{"id":"GO:0042594","count":3},{"id":"GO:0010043","count":3}]},{"hash":"732139521208527571","title":"Nuclear transcription and chromosome maintenance","description":"The cluster\u2019s top GO terms center on nuclear processes and chromosome dynamics: DNA-templated transcription and regulation of DNA replication, meiotic chromatid cohesion and spindle elongation, and centromeric cohesion, plus related processes like nuclear pore assembly. These together point to a group of proteins involved in nuclear gene expression and chromosome maintenance during cell division, with some additional regulatory signals (GTPase activity regulation, phosphatase activity, and stress responses) that fit into the broader nuclear/cell-cycle context.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":10},{"id":"GO:0043547","count":8},{"id":"GO:0051306","count":7},{"id":"GO:0071276","count":7},{"id":"GO:0051292","count":6}]},{"hash":"860022821022220598","title":"Mitochondrial Transport and Metabolism","description":"This cluster is characterized by multiple GO terms tied to mitochondrial transport and membrane processes (pyrimidine nucleotide import into mitochondrion, mitochondrial ATP and NAD transmembrane transport, mitochondrial L-ornithine and thiosulfate transport, heme transport, and regulation of mitochondrial membrane permeability), suggesting a cohesive theme of mitochondrial transport/metabolic functions. The liver regeneration and cell division terms appear as broader, context-dependent signals but do not override the central mitochondrial transport/metabolism pattern.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":3},{"id":"GO:0051301","count":3},{"id":"GO:1990519","count":2},{"id":"GO:1990544","count":2},{"id":"GO:0015886","count":2}]},{"hash":"1021880686532088275","title":"Developmental transcription and cell migration","description":"This cluster is enriched for DNA-templated transcription and its regulation, along with actin filament bundle assembly and cell migration, which together suggest a module coordinating gene expression with cytoskeletal remodeling during development. Notch signaling related to heart development and trophoblast giant cell differentiation further support a developmental differentiation theme. Some terms (immune regulation and heat response) are present but appear less central to the core function, so the primary theme is developmental transcriptional control coupled with cellular movement.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0008284","count":2},{"id":"GO:0060707","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1413911609901366683","title":"Cardiac signaling and calcium dynamics","description":"The top terms center on heart rate regulation, Notch signaling in cardiac development, and calcium signaling (calcium release and NFAT pathways), with supportive hints from cytoskeletal remodeling and stress responses. Together, they suggest a cluster focused on cardiac signaling/ development and calcium-dependent regulation of function. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0051209","count":4},{"id":"GO:0002027","count":3},{"id":"GO:0051533","count":3},{"id":"GO:0009408","count":3}]},{"hash":"303083385424957851","title":"Unknown","description":"The GO terms span antibiotic response, reticulophagy, neuronal development, touch sensation, hair follicle placode formation, Ras signaling, mating projection growth, cytokinesis, GABAergic synaptic transmission, and epithelial morphogenesis, with no common functional thread or single pathway linking them. Because there are no interactions (Edges 0) and only a heterogeneous mix of very different processes, there isn't a coherent biological theme to name beyond Unknown.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0061709","count":1},{"id":"GO:0016358","count":1},{"id":"GO:0050975","count":1},{"id":"GO:0060789","count":1}]},{"hash":"837320054685043196","title":"Signaling Pathway Regulation and Organelle Trafficking","description":"The terms point to broad regulatory control over signaling pathways (BMP, NF-kappaB, SMAD/TGF-beta), phosphorylation/dephosphorylation, and nuclear-cytoplasmic transport, along with processes tied to development (meristem identity) and organelle dynamics (vacuole fusion, photosystem regulation). This suggests a theme of coordinated regulation of signaling and intracellular trafficking across organelles rather than a single pathway, hence a multifaceted regulator cluster.","confidence":"Medium","size":25,"edges":20,"triangles":15,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010074","count":10},{"id":"GO:0030514","count":10},{"id":"GO:0042347","count":10},{"id":"GO:0080005","count":10},{"id":"GO:0035970","count":10}]},{"hash":"1013065434474978389","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":9,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006283","count":3},{"id":"GO:0000462","count":3},{"id":"GO:0014070","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000472","count":3}]},{"hash":"602207834729960425","title":"DNA replication and genome maintenance","description":"The cluster is dominated by DNA-related processes: DNA replication, mitotic cell cycle, DNA repair, and DNA-templated transcription, indicating a core theme of nuclear DNA metabolism and genome maintenance. While there are additional terms related to development and membrane processes (lens development, caveolin-mediated endocytosis), these appear less central and may reflect broader roles or annotation spillovers. Overall, the proteins likely function together in replication, transcription, repair, and cell-cycle control.","confidence":"High","size":25,"edges":57,"triangles":38,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":24},{"id":"GO:0048701","count":21},{"id":"GO:0000278","count":19},{"id":"GO:0006351","count":17},{"id":"GO:0006281","count":17}]},{"hash":"285357341831377744","title":"Proviral DNA Integration and Latency","description":"Based on the strongest GO signals (DNA recombination, DNA replication, DNA integration, and establishment of integrated proviral latency), the cluster centers on viral genome integration and latency within host cells. The \u201csymbiont entry into host cell\u201d term supports an infection context, while the remaining terms are likely ancillary annotations. Overall, the core theme is proviral integration/latency in host genomes.","confidence":"Medium","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006310","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0071555","count":4},{"id":"GO:0075713","count":3},{"id":"GO:0046718","count":3}]},{"hash":"690164197742396733","title":"Transcriptional Regulation of Nucleotide and Amino Acid Biosynthesis","description":"The top GO terms cluster around DNA-templated transcription and positive regulation of transcription from the RNA polymerase II promoter, plus several biosynthetic pathways (pyrimidine nucleotides, leucine, lysine, proline) and regulation of cellular respiration. This suggests a group of proteins that modulate transcriptional programs coordinating metabolism, rather than enzymes of a single biosynthetic route. The mix of transcription-related terms with diverse biosynthetic regulation points to regulation-centric roles rather than a defined catalytic complex.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0061429","count":5},{"id":"GO:1900399","count":5},{"id":"GO:0035959","count":5},{"id":"GO:1904741","count":5}]},{"hash":"1194806066732687310","title":"Unknown","description":"The cluster's GO terms cover diverse processes (urate catabolism, allantoin biosynthesis, retinol and purine metabolism, extracellular matrix organization, thyroid hormone transport, neutrophil degranulation, and general transport) with no dominant shared function. The network shows only a single edge and no triangles, indicating weak or incidental connections, so there isn't a clear, cohesive theme to name.","confidence":"","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0001560","count":1},{"id":"GO:0019628","count":1},{"id":"GO:0019428","count":1},{"id":"GO:0042572","count":1}]},{"hash":"489302322524989829","title":"Innate Immune Signaling and Cytoskeletal Remodeling","description":"This cluster centers on ubiquitination and immune signaling (NOD2 pathway, NF-kappaB regulation, IL-12 modulation) together with cytoskeletal dynamics (actin bundle assembly, cell migration) and stress responses (heat, mechanical stimulus). While Notch-related heart development terms appear, the dominant themes are innate immune signaling intertwined with cytoskeletal remodeling and cell movement.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":10},{"id":"GO:0070431","count":9},{"id":"GO:0032088","count":9},{"id":"GO:0071260","count":9},{"id":"GO:0009408","count":8}]},{"hash":"1788220658784691240","title":"Lipid metabolism and signaling","description":"This cluster's terms are dominated by lipid-related metabolic activities, including triglyceride and monoacylglycerol catabolism, phosphatidylserine catabolic processes, phospholipid dephosphorylation, and regulation of endocannabinoid signaling, with supporting mentions of biotin biosynthesis. The collection points to a cohesive lipid metabolism and lipid-derived signaling theme, despite a few unrelated biosynthetic terms. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":10},{"id":"GO:0017000","count":9},{"id":"GO:0019433","count":9},{"id":"GO:2000124","count":9},{"id":"GO:0006660","count":8}]},{"hash":"1708480025217970976","title":"Heat-stress response and immune signaling network","description":"Top terms converge on heat stress response and transcriptional regulation, along with innate immune signaling (NOD2 pathway, NF-kappaB regulation, IL-12 production), protein ubiquitination, mRNA processing, and cytoskeletal remodeling. This suggests a heat-induced stress response network that interfaces with immune signaling and cytoskeleton dynamics.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061408","count":3},{"id":"GO:0006397","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0032088","count":3}]},{"hash":"1574995943232627026","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:2000616","count":1},{"id":"GO:0051573","count":1},{"id":"GO:0008284","count":1},{"id":"GO:0031442","count":1}]},{"hash":"2224291502288103065","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by GO terms related to protein synthesis and ribosome assembly, notably translation (GO:0006412), ribosome biogenesis (GO:0042254), tRNA modification (GO:0006400), and ribosomal large subunit export from the nucleus (GO:0000055). These points indicate a cohesive group of proteins involved in ribosome construction and function, with a few auxiliary annotations (DNA-templated transcription, DNA replication) likely reflecting broader cellular co-regulation rather than core function. Confidence: High","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006260","count":2},{"id":"GO:0046677","count":1},{"id":"GO:0046898","count":1},{"id":"GO:0009408","count":1}]},{"hash":"267743271224903690","title":"Insulin processing and signaling","description":"This cluster\u2019s GO terms center on insulin processing and insulin receptor signaling, plus secretory pathway trafficking from ER to Golgi, which together point to peptide hormone maturation and secretion mechanisms. The inclusion of bradykinin catabolic process also reflects peptide hormone turnover, consistent with a theme of peptide hormone processing and trafficking.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010815","count":2},{"id":"GO:0006888","count":1},{"id":"GO:0030070","count":1},{"id":"GO:0007155","count":1},{"id":"GO:0071555","count":1}]},{"hash":"1770541881483959993","title":"Lipid Catabolism and Endocannabinoid Regulation","description":"GO terms are dominated by lipid catabolic processes (triglyceride, monoacylglycerol, diacylglycerol, phosphatidylserine catabolism) with related endocannabinoid signaling regulation and detoxification responses, suggesting a cohesive theme around lipid metabolism and signaling in stress/detox contexts.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0030245","count":6},{"id":"GO:2000124","count":6},{"id":"GO:0019433","count":6}]},{"hash":"1156360881553990880","title":"Ubiquitin-Dependent Protein Degradation","description":"Predominant ubiquitination signals: multiple GO terms describe ubiquitin conjugation, autoubiquitination, and specific ubiquitin linkages (K48, K6) tied to protein degradation. Additional terms cover histone catabolism and regulation of apoptosis, suggesting a core theme of ubiquitin-mediated protein turnover and related signaling pathways.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0016567","count":10},{"id":"GO:1903265","count":10},{"id":"GO:0051865","count":10},{"id":"GO:0036205","count":10}]},{"hash":"653641308123295293","title":"Unknown","description":"The top terms show a mix of metabolic, developmental, stress response, cell cycle, and ubiquitination processes with no single cohesive theme linking all proteins, so a specific functional label isn\u2019t justifiable.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0005978","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0009409","count":4},{"id":"GO:0006552","count":4},{"id":"GO:0007507","count":4}]},{"hash":"1808959184827800794","title":"DNA replication and cell cycle regulation","description":"The cluster's top GO terms cluster around DNA replication, centrosome cycle, transcription, and regulation of nuclear DNA replication, suggesting a core theme of genome duplication and cell cycle control. There are additional signals related to apoptosis, meiosis, and nutrient-stress signaling (TORC1) that often accompany cell-cycle processes, making the overarching theme genome maintenance with growth and stress regulation. Some terms (developmental morphogenesis and bacterial defense) are peripheral, but the dominant signal is DNA replication and cell cycle regulation.","confidence":"Medium","size":24,"edges":44,"triangles":23,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":15},{"id":"GO:0048701","count":15},{"id":"GO:0007098","count":15},{"id":"GO:0010571","count":15},{"id":"GO:0006915","count":13}]},{"hash":"1177743266723994626","title":"Cell growth signaling and ribosome biogenesis","description":"The cluster centers on processes linking cell growth and division (mitotic cell cycle) with protein synthesis capacity (ribosomal large subunit biogenesis and rRNA maturation). Regulatory signaling themes (positive regulation of GTPase activity and protein kinase autophosphorylation) plus mRNA transport and developmental processes suggest a coordinated program of growth, gene expression, and development, especially under stress such as hypoxia. This points to a cohesive label around growth control and ribosome assembly rather than a narrow single function.","confidence":"Medium","size":24,"edges":18,"triangles":7,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0051028","count":9},{"id":"GO:0071456","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0071902","count":9}]},{"hash":"2050285836737544292","title":"Unknown","description":"These proteins are annotated with a highly heterogeneous mix of GO terms (heat response, actin filament bundle and spindle assembly, cell migration, Notch signaling in cardiac development, regulation of SA node action potential, synaptic plasticity, immune signaling) and even include obsolete terms. There is no clear single function or pathway uniting them, suggesting the cluster represents diverse, loosely related regulators rather than a cohesive biological process.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000083","count":5},{"id":"GO:0009408","count":4},{"id":"GO:0007253","count":4},{"id":"GO:0051017","count":4},{"id":"GO:0045083","count":4}]},{"hash":"286657447851422290","title":"Developmental Regulation and Transcription","description":"The top GO terms converge on multicellular development, transcription (DNA-templated), and mRNA transport, with supporting signals in skin development and cell-cycle processes, suggesting a set of proteins involved in developmental programs and gene-expression control. Some terms are marked obsolete, and there are no reported edges in this cluster, but the repeated emphasis on development and transcriptional regulation supports a cohesive developmental-regulatory theme. Confidence: Medium","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":16},{"id":"GO:0000278","count":16},{"id":"GO:0043547","count":16},{"id":"GO:0006349","count":15},{"id":"GO:0001403","count":15}]},{"hash":"2061117647143336338","title":"Mitotic cell cycle and ribosome biogenesis","description":"This cluster is dominated by GO terms tied to cell division and mitosis (mitotic cell cycle, spindle orientation, cell division, cell population proliferation) and to core gene expression processes (ribosome biogenesis, mRNA splicing). The inclusion of SCF-dependent ubiquitin-proteasomal protein catabolic process aligns with regulated protein turnover during division, strengthening a theme of growth and division coupled to protein synthesis and degradation. A couple of stress- or condition-related terms appear but are secondary to the central cell-cycle/gene-expression motif.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090344","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0000132","count":2}]},{"hash":"2067220750804439590","title":"Embryonic development and organogenesis","description":"The top GO terms cluster around developmental processes across multiple tissues\u2014placental development, left-right patterning, cartilage morphogenesis, endocrine and pancreatic cell development, and EMT-related heart formation. Collectively, these terms point to early development and organogenesis rather than a single pathway. A couple of terms like antibiotic biosynthesis or an obsolete oxidation-reduction term appear as noise or misannotation, but the dominant signal supports embryonic development and organ formation as the cluster theme.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0060021","count":3},{"id":"GO:0060806","count":3},{"id":"GO:0060536","count":3},{"id":"GO:0035270","count":3}]},{"hash":"2107008166882250693","title":"Diverse specialized metabolite biosynthesis","description":"The GO terms point to multiple biosynthetic and catabolic processes for diverse metabolites (tropane alkaloids, phylloquinone, retinal, C21-steroid hormones, androgen metabolism, antibiotic biosynthesis, fatty acids, PHB), suggesting a shared theme of production and processing of specialized metabolites, with an ancillary note on transcriptional regulation. ","confidence":"Medium","size":24,"edges":183,"triangles":714,"max_degree":22,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":19},{"id":"GO:0042619","count":19},{"id":"GO:0030497","count":18},{"id":"GO:0009710","count":18},{"id":"GO:0006355","count":18}]},{"hash":"1112340958567202915","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":145,"triangles":475,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006564","count":7},{"id":"GO:0007219","count":7},{"id":"GO:0097053","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0034354","count":6}]},{"hash":"530333521241091728","title":"Cardiac development and electrophysiology with cytoskeleton remodeling","description":"This cluster shows terms tied to heart development and electrical activity, including Notch signaling in heart field, regulation of SA node action potential, and cell migration, plus actin filament bundle assembly, suggesting a cardiac development/electrophysiology theme with cytoskeletal remodeling. Some terms (e.g., ubiquitination, heat response) are more general, but the cardiac-focused terms are prominent enough to define the group.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":10},{"id":"GO:1904357","count":10},{"id":"GO:0016567","count":10},{"id":"GO:0009408","count":9},{"id":"GO:0007253","count":9}]},{"hash":"989377656374185082","title":"ER stress and proteostasis","description":"The cluster shows enrichment for ER-associated degradation (ERAD) and proteasomal degradation terms, plus an ER stress\u2013triggered apoptotic pathway, alongside translation initiation/ribosome biogenesis and transcription terms. This pattern suggests a coordinated ER stress response that balances protein folding, degradation, and synthesis (proteostasis), consistent with a stress-induced remodeling of protein homeostasis. Confidence is High.","confidence":"","size":23,"edges":95,"triangles":207,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0030433","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0002188","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0001731","count":4}]},{"hash":"135913970060965303","title":"Chromatin Regulation in Development","description":"This cluster centers on epigenetic regulators: chromatin remodeling and DNA methylation/histone modification terms, and an in utero embryonic development term, suggesting a shared role in epigenetic control during development. Additional terms related to corticosterone response and neurotransmitter turnover hint at neural and stress-related contexts, supporting a developmental epigenetic function with possible neural regulation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":5},{"id":"GO:0043044","count":4},{"id":"GO:0034720","count":4},{"id":"GO:0032496","count":4},{"id":"GO:0042135","count":4}]},{"hash":"442072785821702654","title":"DNA replication and chromatin remodeling","description":"This cluster is dominated by GO terms centered on DNA replication and associated chromatin dynamics: DNA replication, DNA unwinding during replication, primer synthesis, nucleosome mobilization, and histone exchange all point to replication machinery and chromatin remodeling activities. While there are fringe terms related to RNA decay and stress responses, the strongest signal is replication and chromatin remodeling, suggesting these proteins function together at replication forks and during chromatin reorganization. ","confidence":"High","size":23,"edges":78,"triangles":136,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0032508","count":10},{"id":"GO:0006260","count":9},{"id":"GO:0006268","count":9},{"id":"GO:0000184","count":9},{"id":"GO:0042766","count":8}]},{"hash":"1364700781691175421","title":"Transmembrane Transporters","description":"The GO terms converge on transmembrane transport of xenobiotics, vitamins, ions, and sugars, plus neurotransmitter loading into vesicles, indicating a group of membrane transporter proteins with diverse substrates.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0042891","count":3},{"id":"GO:0070634","count":2},{"id":"GO:0042493","count":2}]},{"hash":"1151597034048014185","title":"Unknown","description":"The terms span antibiotic response, lipid A biosynthesis, chitin/xylan/polysaccharide catabolism, lung development, transcription, and histone modifications/deubiquitination, with no clear shared pathway or interaction among the proteins. The lack of edges suggests there isn\u2019t a cohesive functional cluster to label beyond Unknown.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0009245","count":4},{"id":"GO:0006032","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0000272","count":3}]},{"hash":"1848784396853647663","title":"Unknown","description":"The GO terms in this cluster are highly diverse and cover disparate functions (GTPase activity regulation, antibiotic response, histone acetylation, ossification, smooth muscle relaxation, GPCR signaling modulation, centromere cohesion, NF-kappaB activation by symbionts, and heart field development). With no apparent unifying pathway or process and no edges linking proteins, there is no coherent functional theme to name the cluster with confidence.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0043970","count":2},{"id":"GO:0044154","count":2},{"id":"GO:0001957","count":1}]},{"hash":"1424147774544533383","title":"Lens development and developmental signaling","description":"This cluster is dominated by GO terms for lens development in the camera-type eye and broader multicellular development, with supporting signals such as negative regulation of calcineurin-NFAT signaling. Additional terms point to membrane trafficking and ER polarization (caveolin-mediated endocytosis, ER polarization) and general regulatory processes (translation, metabolism, metallopeptidase activity, cell migration). Together, these suggest a group of proteins involved in eye lens development coupled with developmental signaling and associated cellular logistics rather than a single housekeeping function.","confidence":"Medium","size":23,"edges":227,"triangles":1296,"max_degree":22,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0051534","count":23},{"id":"GO:0002088","count":23},{"id":"GO:0007275","count":23},{"id":"GO:0061167","count":23},{"id":"GO:0072584","count":23}]},{"hash":"916055582779636873","title":"Developmental transcription and organogenesis","description":"The cluster is enriched for developmental processes (multicellular organism development, forebrain development, neural tube closure, skeletal system development) and transcriptional regulation (DNA-templated transcription; imprinting-related regulation), suggesting proteins that coordinate developmental programs through transcriptional control. Some immune/stress terms (defense response to Gram-positive bacteria, cadmium response) appear but are likely secondary to the dominant developmental theme.","confidence":"Medium","size":23,"edges":38,"triangles":18,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0001403","count":6},{"id":"GO:0006351","count":6}]},{"hash":"204150597250118343","title":"Cell Cycle Regulation and Signaling","description":"The top GO terms cluster around mitotic cell cycle, cell division, and DNA-templated transcription, with strong indications of regulation through phosphorylation and GTPase signaling (positive regulation of GTPase activity, serine/threonine kinase activity, and autophosphorylation). There is also a note of ribosome biogenesis, which aligns with growth-related processes. Overall, the dominant theme is coordination of cell cycle progression via signaling and transcription control.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":8},{"id":"GO:0071902","count":8},{"id":"GO:0031954","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0006351","count":8}]},{"hash":"2030079993961569110","title":"Developmental RNA processing and chromatin assembly","description":"The cluster is enriched for RNA processing (mRNA splicing), ribosome biogenesis, and CENP-A\u2013related chromatin assembly, along with ubiquitination and broad development signals (multicellular development, tissue differentiation). This suggests a cohesive theme of core gene expression and chromatin maintenance that underlies developmental processes, hence a name centered on RNA processing and chromatin assembly in development.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0072520","count":5},{"id":"GO:0060528","count":4},{"id":"GO:0042273","count":4}]},{"hash":"195754327865982136","title":"Thermal Stress and Inflammatory Signaling","description":"This cluster includes GO terms for heat and cold response and thermoception, indicating a core theme of temperature sensing and stress response. It also includes positive regulation of chemokine production (CXCL1, CXCL5), pointing to inflammatory signaling. Additional terms point to neuroendocrine (vasopressin secretion) and calcium signaling related to cellular excitability (SA node action potential regulation, calcium import). Taken together, the proteins likely participate in temperature-stress signaling with accompanying inflammatory responses, though the lack of direct interactions (edges) suggests a broad, not tightly wired grouping.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0071642","count":2},{"id":"GO:0050955","count":2},{"id":"GO:2000340","count":2}]},{"hash":"1240337972247174486","title":"Unknown","description":"The Top Terms are extremely heterogeneous, spanning mitochondrial complex I assembly, T-cell immune processes, regulation of transcription and DNA methylation, thymus and thymocyte development, and even plant-specific anther morphogenesis. Several terms are obsolete and there is no clear shared pathway or function linking them, and the cluster has no interactions (edges/triangles). This suggests no coherent biological theme can be assigned to the group, supporting an Unknown label.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032981","count":1},{"id":"GO:0002458","count":1},{"id":"GO:2001040","count":1},{"id":"GO:1901097","count":1},{"id":"GO:2000410","count":1}]},{"hash":"2230962984651088526","title":"Immune signaling and ubiquitin regulation","description":"This cluster centers on immune-related processes, including B cell receptor signaling and positive regulation of dendritic cell differentiation, coupled with ubiquitin-related regulation such as ubiquitin-dependent protein catabolic processes and K33-linked ubiquitination. While a few terms like sarcomere organization and phototropism are less directly connected, the dominant theme is immune signaling modulated by ubiquitin-mediated protein turnover, suggesting a group of proteins involved in transmitting immune signals with regulated degradation. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045214","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0006749","count":1},{"id":"GO:0008216","count":1},{"id":"GO:2001200","count":1}]},{"hash":"597901497721291482","title":"Detox and redox metabolism with DNA repair","description":"This cluster is enriched for detox and redox-related GO terms (cellular oxidant detoxification, glutathione metabolic process) and DNA repair (nucleotide-excision repair), with supporting terms for prostaglandin biosynthesis and response to estradiol, indicating a core of detox/redox balance linked to signaling and genome maintenance. ","confidence":"Medium","size":22,"edges":227,"triangles":1462,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":17},{"id":"GO:0009072","count":13},{"id":"GO:0060316","count":13},{"id":"GO:0014810","count":13},{"id":"GO:0006749","count":13}]},{"hash":"911875736254963178","title":"Translation Machinery and Ribosome Biogenesis","description":"The cluster is dominated by GO terms tied to protein synthesis and ribosome construction (translation, cytoplasmic translation, translational initiation/termination, ribosome biogenesis, and ribosomal subunit assembly), with selenium incorporation highlighting specialized translation. The presence of an antibiotic response term further aligns with inhibition or modulation of translation, collectively pointing to a role in the translation apparatus and ribosome assembly.","confidence":"High","size":22,"edges":229,"triangles":1501,"max_degree":21,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":17},{"id":"GO:0046677","count":8},{"id":"GO:0042254","count":7},{"id":"GO:0002181","count":6},{"id":"GO:0000027","count":5}]},{"hash":"2159061287078548666","title":"Neuronal Development and Metabolic Signaling","description":"Most representative terms point to neural development and activity (dendrite morphogenesis, potassium ion transport, response to cocaine) along with core metabolism (glucose metabolic process) and transcriptional activity. While some terms indicate broader development or signaling (placenta development, GM-CSF stimulus), the dominant theme across the cluster is neural development paired with metabolic readiness.","confidence":"Medium","size":22,"edges":157,"triangles":548,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007100","count":15},{"id":"GO:0006351","count":12},{"id":"GO:0097011","count":10},{"id":"GO:0006006","count":10},{"id":"GO:0048813","count":10}]},{"hash":"1236549860142695452","title":"Lipid mediator biosynthesis and detoxification","description":"The cluster is enriched for prostaglandin biosynthesis and linoleic acid metabolism, with multiple terms related to detoxification and response to toxic substances, suggesting a group of proteins involved in lipid mediator production and chemical defense. Some annotations for translation and methylation appear, but the lipid/detox theme is the strongest overall.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001516","count":5},{"id":"GO:0009636","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0032259","count":4},{"id":"GO:0033280","count":4}]},{"hash":"2224411563324220046","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0071630","count":1},{"id":"GO:0000740","count":1},{"id":"GO:0010198","count":1}]},{"hash":"967170615301251372","title":"mRNA processing and translational regulation","description":"The cluster is dominated by GO terms related to post-transcriptional control, including mRNA splicing (spliceosome, splice site recognition, mRNA cis splicing), formation of translation preinitiation complexes and translation reinitiation, and regulation of translational initiation and mRNA stability in response to stress, indicating a cohesive theme of RNA processing and translation regulation.","confidence":"High","size":22,"edges":19,"triangles":4,"max_degree":6,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":14},{"id":"GO:0002188","count":13},{"id":"GO:0001731","count":13},{"id":"GO:0045292","count":13},{"id":"GO:1901407","count":12}]},{"hash":"1022291692322580058","title":"Transcription Regulation and Chromatin Remodeling","description":"This cluster is enriched for GO terms related to RNA polymerase II transcription regulation, promoter assembly, and transcriptional responses, as well as chromatin dynamics such as histone acetylation, nucleosome mobilization, and heterochromatin formation. The combination of transcription control and chromatin-modifying processes (including plant-specific processes like photomorphogenesis) points to proteins coordinating transcription with chromatin state rather than a single metabolic pathway. High confidence.","confidence":"High","size":22,"edges":57,"triangles":57,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":7},{"id":"GO:0043966","count":6},{"id":"GO:2000306","count":5},{"id":"GO:0000436","count":5},{"id":"GO:0042766","count":5}]},{"hash":"1067769424395569495","title":"ER-Golgi secretory transport and Ras signaling","description":"The core terms point to vesicle trafficking within the secretory pathway (ER to Golgi, Golgi to plasma membrane, ERAD-related processes) and small GTPase\u2013mediated signaling, including Ras and EGFR pathways, with related inputs from insulin signaling and intracellular transport regulation. This suggests a functional module where endomembrane transport is coordinated with growth factor\u2013related signaling networks.","confidence":"Medium","size":22,"edges":8,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007264","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0046579","count":2}]},{"hash":"711650214677308234","title":"Muscle development and cardiac function","description":"This cluster is dominated by GO terms pointing to muscle and heart biology: actin filament bundle assembly, skeletal muscle tissue regeneration, and SA node action potential regulation, plus Notch signaling in the heart field. Together these suggest roles in muscle formation/maintenance and cardiac function. Other terms like heat response and NF-kappaB sequestration are less central and may reflect broader cellular stress responses. Overall, the core themes link muscle development, regeneration, and heart physiology.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0045083","count":2},{"id":"GO:0016477","count":2}]},{"hash":"827481406753402907","title":"RNA splicing and nucleolar localization regulation","description":"This cluster is defined by GO terms centered on RNA splicing, spliceosome dynamics, and nucleolar localization (e.g., RNA splicing, spliceosomal disassembly, regulation of alternative splicing, and protein localization to the nucleolus), indicating a cohesive role in RNA processing within the nucleolus. A few telomere and EGFR-related terms exist but are not the main theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902570","count":1},{"id":"GO:0007175","count":1},{"id":"GO:0032211","count":1},{"id":"GO:0000390","count":1},{"id":"GO:0097309","count":1}]},{"hash":"1879843859110865010","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":70,"triangles":43,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0031425","count":3},{"id":"GO:0042793","count":3},{"id":"GO:0000961","count":3},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2}]},{"hash":"132071845457114363","title":"Mitochondrial Transporters and Metabolic Carriers","description":"The cluster is dominated by GO terms related to transport across mitochondrial membranes and mitochondrial metabolism (pyrimidine nucleotide import, NAD transport, heme transport, thiosulfate transport, ornithine transport, ATP transmembrane transport, and regulation of membrane permeability), suggesting the proteins function primarily as mitochondrial transporters or carriers. Developmental terms like heart development and liver regeneration may reflect tissue-specific expression but are less central to the core transport theme.","confidence":"High","size":22,"edges":9,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":3},{"id":"GO:0097421","count":3},{"id":"GO:0048387","count":2},{"id":"GO:1990519","count":2},{"id":"GO:1990544","count":2}]},{"hash":"1071164445311127353","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by ubiquitin-related processes: ubiquitin-dependent protein catabolic process and protein ubiquitination, indicating a group of proteins involved in tagging substrates for degradation. While there are a few peroxisomal and regulatory terms present, the strongest and most consistent signal centers on ubiquitin-mediated protein turnover, justifying a label centered on ubiquitination and degradation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0016558","count":9},{"id":"GO:0016567","count":9},{"id":"GO:2000620","count":8},{"id":"GO:0070512","count":8}]},{"hash":"1514650521528399057","title":"Ubiquitin-dependent innate antiviral signaling","description":"The terms cluster around ubiquitin-mediated protein turnover and innate immune pathways, including NOD2 signaling, NF-kappaB and TNF signaling, and defense against viruses. Autoubiquitination and K6-linked ubiquitination reinforce the idea that ubiquitin marks regulate immune signaling components in antiviral responses.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0070431","count":5},{"id":"GO:0032088","count":5},{"id":"GO:0045087","count":5},{"id":"GO:1903265","count":5}]},{"hash":"1507314828178893031","title":"Acetylation-focused metabolism and regulation","description":"This cluster is dominated by GO terms related to acetylation and acetyl-CoA\u2013dependent processes, including N-terminal acetylation, propionylation, putrescine acetylation, and N-acetylglucosamine metabolism, suggesting a unifying theme around acetyl transfer and related metabolism. A few terms (e.g., subtelomeric heterochromatin formation, leaf formation regulation, angiogenesis) appear as outliers or cross-species annotations, but the acetylation-centric signals are the strongest. ","confidence":"High","size":21,"edges":36,"triangles":14,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":13},{"id":"GO:0017198","count":12},{"id":"GO:0032920","count":12},{"id":"GO:0010125","count":12},{"id":"GO:0001525","count":12}]},{"hash":"28564310830729431","title":"Virus-host interaction and proviral latency","description":"The top GO terms point to immune functions (B cell homeostasis, innate immune response) alongside viral lifecycle processes (establishment of integrated proviral latency, RNA-templated DNA biosynthetic process, DNA integration, DNA recombination). This combination suggests a cluster centered on how host cells interact with viruses, including viral DNA integration and latency, with related immune modulation and cellular trafficking components. Confidence: Medium","confidence":"","size":21,"edges":21,"triangles":0,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0001782","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0048490","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0075713","count":2}]},{"hash":"2203114176694899874","title":"Epidermal development and pigmentation signaling","description":"The top GO terms cluster around skin development, multicellular organism development, and pigmentation, with supporting signals of cell proliferation (mitotic cell cycle) and signaling regulation (kinases, GTPases) and mRNA transport. This suggests a module involved in epidermal differentiation and pigment-related processes, coordinated by signaling and post-transcriptional regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0051028","count":6},{"id":"GO:0071456","count":6}]},{"hash":"2227919287669088857","title":"Calcium-Driven Developmental Differentiation","description":"Several terms point to calcium signaling (cellular response to calcium ion; cellular response to parathyroid hormone stimulus) and transcriptional regulation, along with various differentiation processes (skeletal muscle, nephron, floral meristem, inflorescence) and early development (primitive streak). This suggests a theme where calcium-responsive signaling interfaces with transcription to drive development across tissues and species.","confidence":"Medium","size":21,"edges":210,"triangles":1330,"max_degree":20,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071277","count":7},{"id":"GO:0006351","count":6},{"id":"GO:2001016","count":6},{"id":"GO:0010076","count":6},{"id":"GO:0090009","count":6}]},{"hash":"2043468824863862740","title":"Immune signaling and cytokine regulation","description":"Based on the top GO terms, many entries relate to immune signaling and cytokine production, including regulation of NF-kappaB, negative regulation of IL-12 production, and positive regulation of chemokine and MIP-1 alpha production, as well as cellular responses to salicylic acid. While terms like Wnt signaling, spindle assembly, and thermoception are present, they appear more peripheral to the core theme, suggesting the cluster is primarily about immune/inflammatory signaling and cytokine regulation.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016055","count":7},{"id":"GO:0048549","count":7},{"id":"GO:0007253","count":6},{"id":"GO:0045083","count":6},{"id":"GO:0098907","count":6}]},{"hash":"489691222055099344","title":"Unknown","description":"The terms span signaling (Wnt), cell division, ion transport, and various biosynthetic/catabolic processes with no unifying theme; there is no clear shared function to define this cluster, so the label is Unknown with no confidence.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044339","count":2},{"id":"GO:0000022","count":2},{"id":"GO:0035725","count":2},{"id":"GO:0034418","count":1},{"id":"GO:0019358","count":1}]},{"hash":"879221890768951243","title":"Nociception and Calcium Channel Signaling","description":"The cluster is dominated by GO terms tied to sensing pain and temperature (sensory perception of pain, detection of chemical stimuli involved in sensory perception of pain, thermoception) and by calcium-related processes (calcium ion import across the plasma membrane, calcium ion transmembrane transport via high voltage-gated calcium channels). This suggests a shared function in nociceptive signaling and calcium-mediated activity, with additional terms related to development and cardiac signaling likely reflecting broader expression contexts; overall, the motif centers on pain/temperature sensing linked to calcium channel activity.","confidence":"Medium","size":21,"edges":38,"triangles":15,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":12},{"id":"GO:0019233","count":12},{"id":"GO:0043931","count":10},{"id":"GO:0098703","count":10},{"id":"GO:0050968","count":10}]},{"hash":"1840041822607883474","title":"Cardiac Signaling and Contraction Regulation","description":"The top GO terms cluster around cardiac muscle contraction and heart development, with supporting signals from calcium handling (ryanodine receptor activity), GPCR signaling, and guanylate cyclase regulation, pointing to a core function in cardiac muscle function and its signaling pathways. Some terms like myelination and terminal web assembly appear less related and may reflect noise or multifunctional proteins in the set.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060048","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0022011","count":3},{"id":"GO:0007507","count":3}]},{"hash":"2140390298148908796","title":"Unknown","description":"The GO terms span diverse processes\u2014from bacterial secondary metabolism (antibiotic and menaquinone biosynthesis) to lipid catabolism, signaling regulation, transcription, and stress responses\u2014without a single clear, shared function tying the proteins together. The lack of network connectivity further supports the absence of a cohesive module, so no specific functional theme can be confidently assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0009234","count":3},{"id":"GO:2000124","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0052651","count":3}]},{"hash":"745272725254506787","title":"RNA and protein methylation machinery","description":"The top GO terms indicate methylation across RNA and proteins (rRNA methylation/modification; N-terminal peptidyl-glycine methylation; peptidyl-lysine dimethylation/trimethylation; peptidyl-arginine hydroxylation) and related chromatin effects (rDNA heterochromatin formation). While some biosynthetic terms appear, the shared theme is methylation/modification activities affecting RNA, proteins, and chromatin, justifying a methylation-focused label.","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":7},{"id":"GO:0031167","count":5},{"id":"GO:0018013","count":5},{"id":"GO:0018027","count":5}]},{"hash":"1329992380253617273","title":"Plant metabolism and growth processes","description":"The top GO terms point to broad metabolic activities (proteolysis; cellulose and other catabolic processes; phytochelatin and antibiotic biosynthesis) plus regulation of enzyme activity, alongside plant development signals (root meristem growth, cell growth) and cell division (spindle assembly). This suggests a cluster of proteins tied to general metabolism and growth regulation in plants rather than a single pathway.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":5},{"id":"GO:0030245","count":3},{"id":"GO:0050784","count":3},{"id":"GO:0046938","count":2},{"id":"GO:0043085","count":2}]},{"hash":"1437771450792076465","title":"RNA processing and ribosome biogenesis with translation control","description":"This cluster is enriched for GO terms related to ribosome biogenesis, regulation of translational initiation, spliceosome assembly, and mRNA export, which together point to the cellular machinery for RNA processing and protein synthesis. DNA replication appears as a secondary theme, but the dominant signal is gene-expression machinery in the nucleus and translation initiation control; a few terms indicate context-specific responses (antibiotic response, immune signaling) that do not override the core theme.","confidence":"Medium","size":20,"edges":178,"triangles":944,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006446","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000387","count":3},{"id":"GO:0045292","count":3}]},{"hash":"254799103360739214","title":"Cerebellar development and neural signaling","description":"This cluster highlights cerebellar-specific development: cerebellar cortex formation and Bergmann glial cell differentiation are prominent, suggesting a cerebellum-focused gene set. Other enriched terms like axon regeneration and calcineurin-NFAT signaling align with neuronal differentiation and activity-dependent pathways. While insulin- and T-cell\u2013related signaling appear in the list, the cerebellar development terms dominate, supporting a label centered on cerebellar neural development.","confidence":"Medium","size":20,"edges":80,"triangles":119,"max_degree":14,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0031647","count":15},{"id":"GO:0014850","count":15},{"id":"GO:0021697","count":15},{"id":"GO:2001275","count":15},{"id":"GO:0008286","count":15}]},{"hash":"1180642351620134333","title":"Unknown","description":"The top GO terms span unrelated processes (DNA replication, kinetochore localization, sporulation, meiotic transcription regulation, lipid A biosynthesis, excitatory synaptic potential, transcription termination, adenosine biosynthesis), including obsolete terms, which suggests no cohesive, single-function theme for this cluster.","confidence":"","size":20,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070940","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0009245","count":5},{"id":"GO:0034501","count":4},{"id":"GO:0030437","count":4}]},{"hash":"1192348079064347596","title":"Unknown","description":"The GO terms include inner-ear development (vestibular reflex, semicircular canal morphogenesis), RNA splicing (spliceosomal snRNP assembly, mRNA splicing), immune activation, and cell cycle, with no single cohesive function tying all terms together; a specific representative label is not apparent.","confidence":"","size":20,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0060005","count":1},{"id":"GO:1900625","count":1},{"id":"GO:0032765","count":1},{"id":"GO:0038097","count":1},{"id":"GO:0009444","count":1}]},{"hash":"2145513668283524372","title":"Spliceosome-driven mRNA processing and translation control","description":"This cluster centers on post-transcriptional gene expression regulation, dominated by mRNA splicing via the spliceosome, along with regulation of mRNA stability and translational initiation/reinitiation, and include regulatory ncRNA-mediated gene silencing. The strongest signals are spliceosome-mediated mRNA processing and related translational controls, justifying a label focused on splicing and translation regulation.","confidence":"High","size":20,"edges":173,"triangles":970,"max_degree":19,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":8},{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0000398","count":7},{"id":"GO:1901407","count":7}]},{"hash":"1809049229739517519","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":5},{"id":"GO:0006261","count":5},{"id":"GO:0000467","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0000738","count":4}]},{"hash":"2119427140927613826","title":"Neurovascular development and signaling","description":"This cluster shows GO terms centered on neural development and glial involvement (forebrain astrocyte development, reelin\u2013mediated signaling, and regulation of synapse structure) alongside vascular-related processes (blood vessel morphogenesis and VEGF receptor-2 signaling). A couple of outlier terms (hair follicle maturation, sugar transport) exist, but the dominant theme is neurovascular development and signaling.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048820","count":2},{"id":"GO:1904659","count":2},{"id":"GO:0015739","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0038026","count":1}]},{"hash":"1344444696910734660","title":"Nuclear transcription and DNA replication","description":"The top terms are dominated by nuclear processes: DNA-templated transcription and DNA replication, with additional terms touching on nuclear transport regulation. While some peripheral terms (metabolism, chemotaxis, development) appear, the strongest signal centers on nuclear gene expression and genome maintenance, justifying a label focused on nuclear processes. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0046826","count":11},{"id":"GO:0030517","count":10},{"id":"GO:0045793","count":10},{"id":"GO:0006006","count":10}]},{"hash":"542865705782617299","title":"Mitochondrial function and apoptosis regulation","description":"The top GO terms cluster around mitochondria-related processes: regulation of mitochondrial membrane potential, cytochrome c release, and cellular respiration, all central to mitochondrial function and intrinsic apoptosis pathways. The presence of apoptosis-related terms (T cell apoptotic process) and regulation of protein targeting to mitochondrion (even if obsolete) further supports a mitochondrial-centric theme. A few terms touch on membrane lipid biosynthesis and transport, which align with mitochondrial membranes, while a distant cell cycle term indicates broader energetic and proliferative context. Overall, the dominant signal is mitochondria-associated regulation and apoptosis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903955","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0010917","count":1},{"id":"GO:1901857","count":1},{"id":"GO:0070234","count":1}]},{"hash":"1113429976502565426","title":"DNA replication and chromatin remodeling","description":"This cluster\u2019s strongest signals are nuclear: telomeric D-loop disassembly, chromatin remodeling, and DNA replication, plus the G1/S cell cycle transition, pointing to genome maintenance and chromatin dynamics during replication. Peripheral terms like Rho and insulin signaling may reflect broader growth-related processes, but the core theme is DNA replication and chromatin regulation.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0061820","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0007266","count":3},{"id":"GO:0008286","count":3}]},{"hash":"887933582123396230","title":"Macromolecule Modification and Cofactor Biosynthesis","description":"The top GO terms point to both RNA and protein modification activities (tRNA wobble uridine modification, rRNA modification, peptidyl-arginine hydroxylation, N-terminal peptidyl-glycine methylation) and to biosynthesis of cofactors and related lipids (ubiquinone, menaquinone, phosphatidylcholine), with additional diverse biosynthetic and xenobiotic-responsive terms. The cluster spans modification and core biosynthetic pathways rather than a single specific process, so this label captures the common theme without overfitting. ","confidence":"Medium","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0002098","count":3},{"id":"GO:0006744","count":3},{"id":"GO:0000154","count":2},{"id":"GO:0030961","count":2},{"id":"GO:0006656","count":2}]},{"hash":"1071581506417048657","title":"Developmental and sensory signaling","description":"These terms cluster around developmental processes (multicellular development, heart development) and sensory functions (visual perception, pain perception, long-term synaptic potentiation), with supporting transcriptional regulation and signaling pathways (DNA-templated transcription, Rho signaling, ABA signaling). The mix suggests proteins involved in coordinating development and stimulus-related signaling rather than a single pathway. Confidence: Medium","confidence":"","size":20,"edges":82,"triangles":12,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007275","count":10},{"id":"GO:0019233","count":10},{"id":"GO:0006351","count":10},{"id":"GO:0046827","count":10},{"id":"GO:0007507","count":10}]},{"hash":"496283150780791684","title":"Spliceosome-Mediated mRNA Processing","description":"The top GO terms are dominated by spliceosome- and mRNA processing-related functions (positive regulation of mRNA splicing, mRNA export, regulation of alternative splicing, and spliceosome conformational changes). A smaller group pertains to actin filament dynamics, but the prevailing signal points to RNA splicing and mRNA maturation as the cluster\u2019s core function.","confidence":"Medium","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0006406","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0000388","count":2}]},{"hash":"1207443782689713578","title":"Mitotic cell cycle control and ubiquitination","description":"This cluster is dominated by GO terms related to cell division and mitosis (cell cycle, mitotic cell cycle, positive regulation of metaphase/anaphase transition) and a specific emphasis on K11-linked ubiquitination, which are key regulators of mitotic progression. While there are outliers referencing prostate development, male differentiation, interferon response, and unfolded protein response, they appear less central to the core theme. Therefore, a label focused on mitotic regulation best represents the cluster\u2019s primary functional coherence.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":8},{"id":"GO:0030850","count":7},{"id":"GO:0046661","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0071357","count":7}]},{"hash":"1266221478931442762","title":"Intracellular Signaling and Transport","description":"The top GO terms cluster around signaling (positive regulation of GTPase activity, GPCR signaling, TORC1 signaling) and cytoskeleton/transport processes (microtubule-based movement, mRNA transport) plus ribosome biogenesis, suggesting a core theme of intracellular signaling linked to cargo movement and growth. Although terms like spinal cord development and defense against Gram-positive bacteria appear, they are less central to the dominant functional group. Thus \"Intracellular Signaling and Transport\" captures the main shared function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0021510","count":3},{"id":"GO:0007018","count":3},{"id":"GO:0007200","count":3},{"id":"GO:0050830","count":3}]},{"hash":"1074013402091105126","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031425","count":6},{"id":"GO:0042793","count":6},{"id":"GO:0000961","count":6},{"id":"GO:0001682","count":5},{"id":"GO:0090502","count":5}]},{"hash":"1574820181518150621","title":"Actin cytoskeleton remodeling and vesicle trafficking","description":"Top GO terms indicate strong emphasis on actin dynamics: nucleation, polymerization, severing, and capping (both barbed- and pointed-end) leading to actin filament network formation. The presence of ER-to-Golgi vesicle transport suggests coupling of actin remodeling to membrane trafficking, with additional signals for apoptotic processes and mitochondrial fission reflecting cytoskeletal rearrangements during stress. Overall, the cluster centers on actin-mediated structural changes tied to vesicle transport.","confidence":"High","size":20,"edges":128,"triangles":426,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0045010","count":3},{"id":"GO:0051014","count":2},{"id":"GO:0030041","count":2},{"id":"GO:0051694","count":2},{"id":"GO:0006888","count":2}]},{"hash":"462353218249232436","title":"Unknown","description":"The GO terms show a wide mix of processes from cell division and apoptosis to signaling, eye/photoreceptor development, RNA processing, and neural transport. There isn\u2019t a single dominant function linking these proteins, so a meaningful, concise label is not evident.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0010018","count":2},{"id":"GO:0046061","count":1},{"id":"GO:0035176","count":1}]},{"hash":"17874780306972980","title":"Unknown","description":"The GO terms cover very diverse processes (lipopolysaccharide biosynthesis, serine biosynthesis, hormone response, various transport and muscle-related activities, and mineralization), with no clear common function linking the proteins. This suggests the cluster lacks a cohesive biological theme rather than a single, interpretable label.","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009103","count":9},{"id":"GO:0006564","count":8},{"id":"GO:0033574","count":6},{"id":"GO:0046839","count":6},{"id":"GO:0006825","count":6}]},{"hash":"2111661001767645082","title":"Multivesicular body trafficking and exosome biogenesis","description":"These terms cluster around endosomal sorting, intralumenal vesicle formation, MVB\u2013lysosome fusion, and exosomal secretion, with ubiquitin-dependent sorting indicating a coherent theme of endosome- and exosome-related trafficking and turnover. The occasional unrelated terms (lens maintenance, cell cycle, apoptosis) seem ancillary noise rather than core drivers of the cluster.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000920","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0043162","count":1},{"id":"GO:0070676","count":1},{"id":"GO:0061763","count":1}]},{"hash":"501844018011563985","title":"DNA Damage Response and Gene Expression Regulation","description":"The cluster\u2019s top GO terms cluster around DNA-templated transcription regulation, DNA repair, DNA damage\u2013induced apoptotic signaling, and RNA processing (mRNA poly(A) tail shortening, ribosome biogenesis), suggesting a group of nuclear proteins involved in genome maintenance and control of gene expression. Some terms (eye development, IL-4 response) are less directly connected and may reflect multifunctional proteins or annotation noise, but the dominant theme points to nuclear genome maintenance and transcriptional/RNA processing roles.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006298","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0007060","count":2},{"id":"GO:0000289","count":2}]},{"hash":"37309080276420806","title":"Ciliary/flagellar assembly and vesicle transport","description":"The top GO terms point to inner dynein arm assembly and spermatid development (ciliary/flagellar motility), alongside vesicle trafficking and intracellular transport (Golgi-associated vesicle fusion, transport). Additional terms on motor activity regulation and ubiquitin-related deubiquitination suggest coordinated motor function and proteostasis in these processes. Altogether, this cluster appears to integrate ciliary/flagellar assembly with vesicle transport and motor regulation, justifying the label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0007286","count":1},{"id":"GO:2000574","count":1}]},{"hash":"430318723416748394","title":"Unknown","description":"The top GO terms cover a mix of transcription, cell-cycle control, ER stress, protein oligomerization, metabolic signaling, and even symbiont/immune interactions, plus nitrogen fixation and a deprecated biosynthetic process. This diversity suggests there is no single cohesive function tying the cluster together, making a concise, specific label infeasible.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0045737","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0030968","count":3},{"id":"GO:0051301","count":3}]},{"hash":"493374434967042005","title":"Transcription, ribosome biogenesis, and cell cycle control","description":"This cluster centers on nuclear processes: DNA-templated transcription, ribosomal RNA maturation (ribosome biogenesis), and cell division/cell cycle terms, with supporting chromatin regulation and ubiquitination that are typical of cell-cycle control. The combination suggests a cohesive theme around gene expression and cell-cycle\u2013related nuclear activities, though the mix is broad rather than pointing to a single pathway.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0070979","count":2}]},{"hash":"1144197182332967842","title":"Cardiac signaling and cytoskeletal dynamics","description":"The cluster centers on intracellular signal transduction, actin filament assembly, and cell migration, with notable cardiac-specific terms like Notch signaling in heart field regulation and SA node action potential regulation, suggesting a cohesive theme of signaling and cytoskeletal processes shaping cardiac development and function. Peripheral terms such as fat cell differentiation and heat response appear less central to this core theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045444","count":4},{"id":"GO:0035556","count":4},{"id":"GO:0032088","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0007253","count":3}]},{"hash":"1958677396445437202","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":4},{"id":"GO:0016477","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0090617","count":2},{"id":"GO:1905639","count":2}]},{"hash":"42480202157165554","title":"GABAergic Synapse Cytoskeleton Remodeling","description":"This cluster combines a clear signal for GABAergic synaptic transmission with multiple actin-related processes (filopodium/stress fiber assembly, Rac signaling, TORC2 signaling) and endocytic recycling, pointing to coordinated synaptic signaling plus cytoskeletal dynamics at GABAergic synapses.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051932","count":3},{"id":"GO:1900026","count":3},{"id":"GO:0045792","count":3},{"id":"GO:0046847","count":3},{"id":"GO:0051489","count":3}]},{"hash":"1870692075937736637","title":"Drosophila development and proteostasis","description":"The terms cluster around developmental differentiation (wing cell fate specification, compound eye cone cell fate, spermatid differentiation) and signaling regulation, with additional proteostasis-related terms (unfolded protein response, ERAD) and redox homeostasis. Several terms are characteristic of Drosophila development, suggesting a unified theme of developmental differentiation intertwined with protein quality control and signaling. This supports a label that highlights development with proteostasis in a Drosophila context.","confidence":"Medium","size":19,"edges":25,"triangles":9,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":5},{"id":"GO:0038005","count":4},{"id":"GO:1904211","count":4},{"id":"GO:0048515","count":4},{"id":"GO:0034620","count":4}]},{"hash":"1698476068436047121","title":"Autophagy and Endolysosomal Trafficking","description":"This cluster is dominated by GO terms for autophagosome assembly regulation, multivesicular body sorting/assembly, lysosomal membrane organization, and vacuolar protein targeting, all pointing to endolysosomal trafficking and autophagy pathways. While some cell-cycle terms appear, the strongest signal ties to vesicle sorting, lysosome/vacuole targeting, and exocytosis, suggesting a cohesive role in degradation and vesicle trafficking processes.","confidence":"High","size":19,"edges":18,"triangles":0,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":5},{"id":"GO:0051301","count":5},{"id":"GO:1902902","count":5},{"id":"GO:0010458","count":4},{"id":"GO:0071985","count":4}]},{"hash":"337249482896200222","title":"Ubiquitin-dependent mitosis and antiviral defense","description":"This cluster highlights ubiquitin-related processes (K11-linked ubiquitination, ubiquitin-dependent ERAD) tied to mitotic regulation (APC-dependent catabolic process, spindle assembly) and antiviral/immune responses, suggesting a theme where ubiquitin controls both cell division and innate defense mechanisms.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070979","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0045842","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1068910157857497242","title":"Golgi trafficking and secretion regulation","description":"This cluster is dominated by GO terms tied to the Golgi apparatus and its transport network, including ER-to-Golgi vesicle transport, endosome-to-Golgi routing, vesicle fusion with the Golgi, and regulation of protein localization to the plasma membrane and exocytosis; mitochondrial dynamics and cell cycle terms are present but appear less central, making the Golgi/secretory pathway the defining theme.","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:1903358","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0045956","count":6},{"id":"GO:0000266","count":6},{"id":"GO:0007049","count":6}]},{"hash":"252305542948976579","title":"Quinone Biosynthesis and Central Metabolism","description":"This cluster centers on quinone biosynthesis (phylloquinone/menaquinone) and key energy pathways (glycolysis, TCA cycle, beta-oxidation) with amino acid/phenylacetate catabolism; plus antibiotic biosynthesis and xenobiotic response, hinting at broader secondary metabolism and detox mechanisms. Taken together, it reflects a metabolism-focused group tied to quinone production and energy generation.","confidence":"Medium","size":19,"edges":140,"triangles":566,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0042372","count":8},{"id":"GO:0009234","count":8},{"id":"GO:0006096","count":7},{"id":"GO:0006635","count":7},{"id":"GO:0017000","count":7}]},{"hash":"1633783090577610993","title":"Light Response and Endosomal Trafficking","description":"These proteins cluster around functions tied to light- and pheromone-related responses (visual perception, UV-B response) and membrane trafficking (receptor recycling, endosome size), with supporting roles for small GTPase regulation and growth signaling (Hippo pathway, mitotic cell cycle). The dominant pattern points to a module coordinating light-triggered signaling with endosomal trafficking and receptor recycling, hence the chosen label.","confidence":"Medium","size":19,"edges":169,"triangles":935,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":14},{"id":"GO:0007601","count":14},{"id":"GO:0043547","count":13},{"id":"GO:0019236","count":13},{"id":"GO:1905490","count":12}]},{"hash":"851438160760027933","title":"RNAPII Transcription Regulation & Chromatin Remodeling","description":"The cluster is dominated by GO terms tied to RNA polymerase II\u2013mediated transcription, including DNA-templated transcription, termination, start-site regulation, and chromatin remodeling with nucleosome positioning/density and histone modification, suggesting a cohesive group of factors that regulate transcription by altering chromatin state.","confidence":"High","size":19,"edges":115,"triangles":369,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0060303","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0006369","count":3},{"id":"GO:0016584","count":3}]},{"hash":"274817106762482374","title":"Chromatin Modification and Development","description":"The top GO terms cluster around chromatin and transcription regulation (DNA-templated transcription; histone methylation) and RNA processing (RNA (guanine-N7)-methylation; rRNA maturation). Developmental processes (multicellular organism development; forebrain and neural tube development) are also prominent, suggesting a nuclear program coordinating gene expression during development. An outlier defense-related term hints at possible condition-specific co-regulation or annotation noise.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0036265","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0051568","count":3},{"id":"GO:0034729","count":3}]},{"hash":"2129498364079430501","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is enriched for GO terms related to ribosome assembly and RNA maturation across organelles: ribosomal small subunit export from nucleus, mitochondrial RNA processing, mitochondrial large ribosomal subunit assembly, and chloroplast rRNA processing, indicating a shared function in ribosome biogenesis and RNA maturation. Some other terms (antibiotic response, osmotic stress, ion transport) may reflect broader cellular stress responses but do not overshadow the ribosome/RNA processing theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0071470","count":2},{"id":"GO:0009992","count":2}]},{"hash":"1346748651667883485","title":"Unknown","description":"The top GO terms span highly diverse processes (neuronal morphogenesis, transcription regulation, mitophagy, ubiquitin-mediated proteolysis, DNA repair, immune/antibiotic responses, splicing) with no clear single theme tying them together, and the cluster has no edges, suggesting there isn\u2019t a coherent shared function among these proteins. ","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060997","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0061734","count":3},{"id":"GO:0006511","count":3},{"id":"GO:0046677","count":3}]},{"hash":"1693124043699498331","title":"Mitotic Cell Cycle Regulation and Transcription","description":"The dominant GO terms point to mitotic control (G2/M transition, spindle pole separation, chromosome condensation via histone phosphorylation) and transcription regulation (DNA-templated transcription, Pol II regulation), with a meiosis chromosome pairing term linking to chromosome dynamics during division. Together these terms suggest a cluster of proteins involved in mitotic cell cycle control and associated transcriptional regulation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0060153","count":2},{"id":"GO:0007129","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0030968","count":2}]},{"hash":"2162129861574680541","title":"RNA Splicing and Translation Regulation","description":"The GO terms cluster around RNA processing and translation control: spliceosome-mediated mRNA splicing (cis splicing, splice site recognition, preinitiation complex formation) and regulation of translational initiation and translation reinitiation, plus stress-related mRNA stability. This points to a group of splicing factors and translation regulators. A couple terms appear tangential (blastocyst formation, obsolete NF-kappaB term) but do not change the core theme.","confidence":"High","size":19,"edges":16,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0031047","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0002188","count":1}]},{"hash":"902186556177555335","title":"Organelle protein import (mitochondria & chloroplasts)","description":"The GO terms are dominated by protein import into mitochondrial matrix and chloroplast stroma, along with mitochondrial inner membrane insertion and mitophagy regulation, indicating a shared role in targeting and processing proteins for organelle compartments.","confidence":"High","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030150","count":4},{"id":"GO:0000002","count":3},{"id":"GO:0045037","count":3},{"id":"GO:0045039","count":3},{"id":"GO:0032094","count":3}]},{"hash":"417304394180777516","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0032781","count":2},{"id":"GO:0045087","count":2}]},{"hash":"1118422384685453865","title":"Secretory and pigment granule transport","description":"The most represented GO terms point to vesicle transport along actin, secretory granule localization, and pigment granule transport, suggesting the proteins cluster around vesicular trafficking and granule movement. Other terms (rRNA maturation, hair follicle maturation) are less central and may be noise, but the dominant theme is intracellular transport and secretion.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0031585","count":1},{"id":"GO:0007339","count":1},{"id":"GO:0030050","count":1},{"id":"GO:0032252","count":1}]},{"hash":"2164466105730338985","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":6},{"id":"GO:0090617","count":5},{"id":"GO:1905639","count":5},{"id":"GO:1900865","count":5},{"id":"GO:0031426","count":5}]},{"hash":"538322713759561961","title":"Cardiac development and cytoskeletal dynamics","description":"The presence of SA node action potential regulation and Notch signaling related to heart field development, along with actin filament bundle assembly and cell migration, points to a theme of cardiac development and cytoskeletal remodeling. Other terms such as heat response or NF-kappaB regulation appear peripheral but do not override the central cardiac-focused signals.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0007253","count":3},{"id":"GO:0051017","count":3}]},{"hash":"2242711620568912368","title":"Ubiquitin-Dependent Protein Degradation and Apoptosis","description":"The cluster is dominated by ubiquitin-related GO terms (ubiquitin-dependent protein catabolic process and protein ubiquitination) with supporting links to apoptosis regulation and growth control, suggesting a core function in proteostasis via the ubiquitin\u2013proteasome system and its role in cell survival and size regulation. Obsolete histone modification and other terms appear less informative for current function, but do not override the main ubiquitination signal.","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0070512","count":7},{"id":"GO:2000620","count":7},{"id":"GO:0046621","count":7},{"id":"GO:0042981","count":7}]},{"hash":"1898057628410218384","title":"Ribosome biogenesis and translation machinery","description":"Top terms show a strong focus on translation and ribosome biogenesis (cytoplasmic translation, ribosome biogenesis, small subunit biogenesis, translation initiation/termination, tRNA modification). This indicates the cluster largely comprises proteins involved in ribosome production and protein synthesis, with a secondary signal from cell cycle and glial proliferation annotations. Confidence in this label is high because the dominant functions clearly converge on ribosome assembly and translation.","confidence":"High","size":18,"edges":44,"triangles":46,"max_degree":11,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0002181","count":5},{"id":"GO:0042254","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0042274","count":4}]},{"hash":"1738632745232546970","title":"RNA Splicing and Translational Regulation","description":"The top GO terms cluster around mRNA splicing and spliceosome activity (splice site recognition, cis splicing, preinitiation complex formation) as well as regulation of translation initiation and reinitiation, plus ncRNA-mediated gene silencing and stress-related mRNA stability. This suggests proteins in the cluster coordinate RNA processing and control of gene expression at both splicing and translation stages, with a possible link to development contexts. ","confidence":"High","size":18,"edges":20,"triangles":3,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006376","count":4},{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0006446","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1013603350499393161","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":21,"triangles":5,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006223","count":5},{"id":"GO:0006541","count":5},{"id":"GO:0016310","count":4},{"id":"GO:0046038","count":4},{"id":"GO:0032263","count":4}]},{"hash":"2286844083406803518","title":"Light-regulated transcription and growth in plants","description":"The top GO terms cluster around light-responsive transcription (DNA-templated transcription and its regulation) and phototransduction, with supporting signals for growth and metabolism (cell size regulation, glucose metabolism, secondary growth). While some terms appear noisy or cross-species (iron transport, complement regulation, obsolete nuclear transport), the dominant pattern points to light-driven transcriptional control linked to growth in plants.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0009585","count":3},{"id":"GO:0045793","count":3},{"id":"GO:0034757","count":3},{"id":"GO:0006355","count":3}]},{"hash":"2011289928159159916","title":"Ubiquitin-Dependent Degradation and NF-\u03baB Signaling","description":"The top GO terms cluster around ubiquitination and ubiquitin-mediated protein catabolism (including K48- and K6-linked ubiquitination, autoubiquitination, ERAD), plus links to inflammatory signaling (TNF and NF-\u03baB activation) and histone turnover. This suggests a cohesive group of proteins involved in ubiquitin-driven protein degradation and regulation of signaling pathways, rather than disparate functions. ","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051865","count":9},{"id":"GO:0070936","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0036205","count":8}]},{"hash":"1737873047223556205","title":"Epithelial differentiation and transcriptional regulation","description":"This cluster shows a theme of epithelial differentiation (skin development and prostate glandular epithelium) together with transcriptional activity and chromatin-related processes (DNA-templated transcription, CENP-A chromatin assembly). TGF-beta signaling response and GTPase regulation hint at coordinated signaling to drive cell fate, while ribosomal biogenesis and protein oligomerization reflect general cellular machinery supporting these programs.","confidence":"Medium","size":18,"edges":65,"triangles":101,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071560","count":7},{"id":"GO:0043547","count":7},{"id":"GO:0006351","count":6},{"id":"GO:0051260","count":6},{"id":"GO:0007568","count":6}]},{"hash":"1605430641490169011","title":"DNA Damage Response and Repair","description":"The cluster centers on DNA maintenance activities, with strong signals for DNA recombination, base-excision repair, and DNA catabolic processes. The presence of apoptotic processes and cell-cycle regulation (G1/S transition) suggests a coordinated response to DNA damage, while xenobiotic stimulus response reflects stress-related signaling. Together, these terms point to a DNA damage response and repair module.","confidence":"Medium","size":18,"edges":47,"triangles":40,"max_degree":11,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006310","count":9},{"id":"GO:0042493","count":7},{"id":"GO:0006284","count":7},{"id":"GO:0080111","count":6},{"id":"GO:0044179","count":6}]},{"hash":"524015215020199942","title":"TCA cycle and NADPH regeneration","description":"The cluster is dominated by central carbon metabolism terms, especially the TCA cycle and 2-oxoglutarate metabolism, with supporting signals from acetyl-CoA and amino acid biosynthesis, and redox-related processes (glutathione metabolism and PPP-related NADPH regeneration). This pattern suggests a cohesive group of proteins involved in energy production and redox balance, where TCA activity supplies carbon skeletons and NADPH is generated for antioxidant and reductive biosynthesis functions. High","confidence":"","size":18,"edges":65,"triangles":90,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":7},{"id":"GO:0019878","count":3},{"id":"GO:0009098","count":3},{"id":"GO:0006749","count":3},{"id":"GO:0006103","count":3}]},{"hash":"1944447736015362746","title":"Ribosome biogenesis and RNA methylation","description":"The cluster\u2019s terms are dominated by ribosome-related processes: rRNA base methylation, ribosome biogenesis, preribosome large subunit assembly, and cytosolic ribosome assembly, along with tRNA wobble base cytosine methylation. Additional RNA-processing terms (spliceosomal assembly) and cell-cycle related terms (meiotic division) appear but are secondary. Overall, the core theme is ribosome production and RNA modification.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070475","count":2},{"id":"GO:0006893","count":2},{"id":"GO:0000387","count":2},{"id":"GO:0007143","count":2},{"id":"GO:0070131","count":1}]},{"hash":"458079555070095881","title":"Yeast osmostress signaling and ER-Golgi trafficking","description":"The Top Terms point to yeast-specific stress and trafficking functions: osmosensory signaling via Sho1, responses to nutrient limitation, and invasiveGrowth under glucose restriction, along with vesicle transport between the ER and Golgi and regulation of GTPases. While some terms like nuclear mRNA surveillance and mitotic cell cycle appear, the strongest shared theme is a stress/nutrient adaptation program coupled to secretory transport. Thus, this label captures the core function linking these proteins.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071028","count":2},{"id":"GO:0071039","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0043473","count":2}]},{"hash":"1568596984396761768","title":"Mitosis and cell division cluster","description":"The top GO terms are dominated by mitotic cell cycle, kinetochore localization, and general cell division, with a G2/M transition term, pointing to a cohesive theme of mitotic progression and chromosome segregation. Some terms (ascospore formation, Purkinje signaling, calcium release regulation) are notes of broader or secondary roles, but they do not override the central mitotic signal. Thus, labeling as a mitosis/cell division-focused cluster captures the strongest common function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0034501","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000086","count":1},{"id":"GO:0030437","count":1}]},{"hash":"166838589428196613","title":"Signaling and transcriptional response cluster","description":"The top terms point to transcription (DNA-templated transcription), signaling (Rho protein signal transduction) and responses to stimuli (chemotaxis, response to cocaine), with supporting processes in metabolism, cell size, and development. While there is some noise (e.g., placenta and nervous system development), the common theme centers on regulation of gene expression and signal transduction across contexts. Note that one term is obsolete, but the overall pattern supports a signaling-transcription focus.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033160","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006006","count":3},{"id":"GO:0001890","count":3},{"id":"GO:0006935","count":3}]},{"hash":"674233199821918818","title":"Epithelial Polarity and Tight Junction Assembly","description":"The strongest GO signals are about establishing epithelial cell polarity and assembly/maintenance of tight junctions, including bicellular tight junction assembly and apical/basal polarity. While there are additional terms related to nervous system development and neuronal processes, the prominent theme across the cluster points to epithelial polarity and junction organization, with some secondary roles in cell cycle and xenobiotic response. ","confidence":"Medium","size":18,"edges":28,"triangles":10,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043524","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0035641","count":3},{"id":"GO:0070830","count":3},{"id":"GO:0090162","count":3}]},{"hash":"1015032599365826315","title":"Transcription Regulation and Chromatin Modification","description":"The terms cluster around controlling gene expression: DNA-templated transcription and its regulation, spliceosomal assembly for RNA processing, and various chromatin-modifying activities (histone methylation, deacetylation, and deubiquitination). While there are some broader or context-specific terms (neuronal morphogenesis, seed germination, collateral sprouting), the core theme is transcription control and chromatin state.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048668","count":2},{"id":"GO:0000245","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0060997","count":1},{"id":"GO:0071218","count":1}]},{"hash":"641687230857151478","title":"Golgi trafficking and mitosis proteins","description":"The top GO terms cluster around vesicle transport between the Golgi, plasma membrane, and ER and core mitotic processes (mitotic cell cycle, spindle assembly, cell division), indicating a functional link between intracellular trafficking and cell division machinery. Additional terms on ribosome biogenesis and organism growth fit the broad cellular growth context but do not overshadow the primary themes of vesicle transport and mitosis.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006893","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0000186","count":2}]},{"hash":"300619649778382095","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000055","count":2},{"id":"GO:0046020","count":1},{"id":"GO:0007492","count":1},{"id":"GO:0001892","count":1},{"id":"GO:0032968","count":1}]},{"hash":"1281179449268169426","title":"Sterol Biosynthesis Across Kingdoms","description":"The top GO terms include ergosterol biosynthetic process, cholesterol biosynthetic process, and brassinosteroid biosynthetic process, pointing to a cross-kingdom sterol biosynthesis theme. The other terms (chromatin localization, centriole regulation, actin severing, etc.) are sparse and may reflect annotation noise or multifunctional proteins, but sterol biosynthesis is the strongest shared signal.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071169","count":2},{"id":"GO:0046599","count":1},{"id":"GO:0006696","count":1},{"id":"GO:0016132","count":1},{"id":"GO:0006695","count":1}]},{"hash":"497793801692164423","title":"RNA Pol I Transcription Elongation & Ribosome Biogenesis","description":"This cluster\u2019s terms are dominated by transcription elongation by RNA polymerase I, DNA-templated transcription, and ribosomal large subunit biogenesis, suggesting a nucleolar/co-transcriptional role in ribosome production. The presence of translation regulation and DNA damage/repair-related terms may reflect broader nuclear coordination with transcription and ribosome assembly.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900364","count":1},{"id":"GO:0042273","count":1},{"id":"GO:2001208","count":1},{"id":"GO:0006351","count":1},{"id":"GO:2001209","count":1}]},{"hash":"809106125813807190","title":"Peroxisome Biogenesis and Inheritance","description":"These proteins cluster around peroxisome biology, including inheritance, membrane biogenesis, protein import into the peroxisome membrane, peroxisome fission, and ER-dependent organization, suggesting a cohesive module devoted to peroxisome formation and maintenance. The presence of multiple peroxisome-related terms indicates a shared functional theme rather than unrelated processes. Some minor terms (e.g., protein stabilization) may reflect ancillary roles but do not override the primary theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045033","count":1},{"id":"GO:1900131","count":1},{"id":"GO:0016557","count":1},{"id":"GO:0045046","count":1},{"id":"GO:0016559","count":1}]},{"hash":"1121584105898301311","title":"Steroid and Lipid Metabolism","description":"The cluster shows enrichment for steroid hormone and lipid metabolic processes (androgen metabolism, C21-steroid hormone metabolism, fatty acid elongation) and regulation of transcription, suggesting a core function in steroid/lipid metabolism and signaling, with some unrelated antibiotic-related terms likely due to annotation noise.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0046677","count":4},{"id":"GO:0055007","count":4},{"id":"GO:0030497","count":3},{"id":"GO:0008209","count":3}]},{"hash":"937945270457919243","title":"Unknown","description":"The enriched GO terms span diverse areas, including immune signaling (lipopolysaccharide response), cyclic nucleotide signaling (cAMP/cGMP), calcium handling and vascular permeability regulation, and even retinal cone development and cardiac hypertrophy. There isn\u2019t a single dominant function linking most proteins in this cluster, so a precise, representative label isn\u2019t supported by the shared terms. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":3},{"id":"GO:0006198","count":3},{"id":"GO:0010446","count":2},{"id":"GO:0046549","count":2},{"id":"GO:0010880","count":2}]},{"hash":"1379383866667205638","title":"Ubiquitin-Dependent Degradation and Antiviral Immunity","description":"The cluster shows strong enrichment for ubiquitin-related processes (protein ubiquitination, autoubiquitination, ERAD, K63-linked ubiquitination) and innate immune/virus defense (innate immune response, defense response to virus, TNF signaling), suggesting a cohesive role in ubiquitin-regulated protein turnover linked to antiviral and inflammatory signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0033280","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0030433","count":4}]},{"hash":"1368067267183790290","title":"RNA processing and translation regulation","description":"The cluster features frequent GO terms for mRNA splicing via the spliceosome, splice site recognition, and regulation of translation initiation/reinitiation, as well as stress-related mRNA stability, indicating coordinated control of RNA processing and translation.","confidence":"High","size":17,"edges":134,"triangles":650,"max_degree":16,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":12},{"id":"GO:0048026","count":12},{"id":"GO:0006378","count":12},{"id":"GO:0045292","count":11},{"id":"GO:1901407","count":11}]},{"hash":"1231679812226071244","title":"Golgi nucleotide-sugar transport and fucosylation","description":"The dominant GO terms point to transport of sugar nucleotides into the Golgi lumen (UDP-glucose, GDP-fucose) and fucosylation-related glycosylation events (N- and O-linked). Several entries explicitly mention Golgi lumen transport, supporting a cohesive module of Golgi sugar-nucleotide transporters tied to glycosylation steps. While broader membrane transport terms appear, the Golgi-specific sugar-nucleotide transport and fucosylation terms anchor the cluster\u2019s function.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":2},{"id":"GO:0015992","count":2},{"id":"GO:1990034","count":1},{"id":"GO:1990536","count":1},{"id":"GO:0036066","count":1}]},{"hash":"813004199275269798","title":"MVB/Exosome Biogenesis and Secretory Trafficking","description":"The GO terms show strong enrichment for intralumenal vesicle formation, multivesicular body (MVB) sorting and fusion with lysosomes, and regulation of exosomal secretion, along with Golgi/ER trafficking signals (protein retention in Golgi, ER membrane targeting). This points to a cohesive functional theme around MVB/exosome biogenesis and the secretory pathway, with vesicle formation and trafficking events, and a secondary association to cytokinetic abscission. ","confidence":"High","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070676","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0045053","count":4},{"id":"GO:0000920","count":3},{"id":"GO:0006620","count":3}]},{"hash":"1284647121387490505","title":"Chromatin silencing and transcription regulation","description":"Based on the GO terms, several entries involve chromatin silencing and heterochromatin regulation (telomeres, rDNA, silent mating-type cassette) and transcriptional control (RNA polymerase I and II). While a few terms pertain to development or ECM remodeling, the strongest recurring theme is chromatin state and transcription regulation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000219","count":2},{"id":"GO:0007141","count":2},{"id":"GO:0031939","count":1},{"id":"GO:0061188","count":1},{"id":"GO:0035914","count":1}]},{"hash":"2070832672650960753","title":"Mitotic progression and APC/C-mediated ubiquitination","description":"This cluster is strongly enriched for cell-division and mitosis-related GO terms (cell division, mitotic cell cycle, APC/C-dependent catabolic process) and for K11-linked ubiquitination, indicating regulation of mitosis through ubiquitin-mediated proteolysis. While transport and hypoxia-related terms appear, the core signal points to mitotic control and proteolysis of mitotic regulators by the APC/C complex.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":9},{"id":"GO:0000278","count":8},{"id":"GO:0008284","count":7},{"id":"GO:0070979","count":7},{"id":"GO:0031145","count":7}]},{"hash":"1601071392052160703","title":"RNA processing and translational regulation","description":"The top GO terms cluster around translation initiation and its regulation (translation reinitiation, formation of translation preinitiation complex, regulation of translational initiation) together with RNA processing/splicing (spliceosome-mediated splicing, splice site recognition, cis splicing) and regulatory ncRNA\u2013mediated gene silencing, plus mRNA stability under stress. This pattern points to a functionally cohesive group of proteins coordinating RNA metabolism with control of translation, rather than a random mix of unrelated processes. Blastocyst formation appears but is not central to the dominant RNA-processing and translational-regulatory theme.","confidence":"High","size":17,"edges":19,"triangles":4,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0002188","count":6},{"id":"GO:0001731","count":6},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0006446","count":5}]},{"hash":"1923526866125094495","title":"Cardiac development and skeletal morphogenesis","description":"The top GO terms cluster around heart development (including secondary heart field specification and vascular smooth muscle relaxation) and skeletal differentiation (intramembranous ossification and chondrocyte differentiation), suggesting a developmental program coordinating cardiac morphogenesis with bone/cartilage formation. Supporting terms on GTPase regulation and signaling pathways (MAPK, adenylate cyclase-inhibiting adrenergic signaling) may reflect broader regulatory roles in these processes, while a related host NF-kappaB term could be incidental. Overall, the cluster appears to represent cardiac development linked with skeletal morphogenesis.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0001957","count":2},{"id":"GO:0060087","count":2},{"id":"GO:0071877","count":2}]},{"hash":"1860748707233858854","title":"Redox Homeostasis and Oxidative Stress Response","description":"The cluster is characterized by multiple GO terms tied to redox biology (oxidation-reduction, NADPH oxidation, cell redox homeostasis) and stress responses (cellular response to hyperoxia, response to lipopolysaccharide). While there are some unrelated terms related to transcription and development, the dominant theme is maintaining redox balance and responding to oxidative stress, with associated metabolic adjustments.","confidence":"Medium","size":17,"edges":126,"triangles":550,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042853","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0071455","count":4},{"id":"GO:0070995","count":4}]},{"hash":"1057351374943886270","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":135,"triangles":665,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0031425","count":2}]},{"hash":"565587595827237390","title":"Unknown","description":"The terms include both intracellular membrane trafficking (endosome localization, ER exit, phospholipid translocation, vacuole regulation, xenobiotic transport) and developmental processes (limb development, anterior/posterior axis specification, neuroblast proliferation) with no obvious single function or pathway tying them together, and each term appears only once. This scattered enrichment makes a cohesive, specific label inappropriate.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0036010","count":1},{"id":"GO:0045332","count":1},{"id":"GO:0010570","count":1},{"id":"GO:0070863","count":1}]},{"hash":"2166328150933008661","title":"Unknown","description":"The terms span both nuclear processes (DNA-templated transcription, DNA replication, CENP-A chromatin assembly, mRNA export) and ER/secretory pathway processes (unfolded protein response, ER polarization, intralumenal vesicle formation, insulin response, mitochondrial inner membrane insertion). There isn\u2019t a single cohesive function that ties these together, suggesting a heterogeneous cluster; thus Unknown with no confidence.","confidence":"","size":17,"edges":126,"triangles":547,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0032869","count":6},{"id":"GO:0032979","count":6},{"id":"GO:0061641","count":6},{"id":"GO:0070676","count":6}]},{"hash":"296161901057158929","title":"Embryonic development and tissue differentiation","description":"This cluster\u2019s top GO terms cluster around development of diverse tissues and organs (placenta, cartilage, endocrine system, pancreatic cells, left\u2013right patterning, endocardial cushion formation) and include general gene expression processes (splicing, translation, negative regulation of translation). The common theme is embryonic development and differentiation across multiple lineages, despite sparse connectivity.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060806","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0003323","count":1}]},{"hash":"344990050646695768","title":"Mitochondrial transport and membrane potential regulation","description":"The top GO terms describe transmembrane transport of various substrates (pyrimidine nucleotides, ATP, NAD, citrate, heme, ornithine, thiosulfate) into or across the mitochondrion, and regulation of mitochondrial membrane permeability and potential. This repeated emphasis on mitochondrial transport and energetic regulation supports a cohesive theme of mitochondrial membrane transport.","confidence":"High","size":17,"edges":95,"triangles":255,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:1990519","count":14},{"id":"GO:1990544","count":14},{"id":"GO:0015886","count":14},{"id":"GO:0000066","count":14},{"id":"GO:0015709","count":14}]},{"hash":"1359572882551194982","title":"Chromatin assembly and histone modification","description":"This cluster is centered on chromatin biology, with terms for CENP-A chromatin assembly and histone H3-K27 methylation regulation, plus imprinting-related regulation, indicating a focus on chromatin organization and gene expression control. Some ribosome biogenesis and signaling terms appear as peripheral connections rather than defining the core function.","confidence":"Medium","size":17,"edges":25,"triangles":6,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":2},{"id":"GO:0060528","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0006349","count":1},{"id":"GO:0030157","count":1}]},{"hash":"825401892047340791","title":"Vacuolar trafficking and ion homeostasis","description":"The top GO terms lean strongly toward vacuole-related processes (vacuole organization, protein/vacuole targeting, vacuolar acidification) and ion transport (proton, sodium, copper), suggesting a coherent theme around vacuolar function and associated transport mechanisms. Some terms like light sensing or taste perception appear incidental, but do not override the dominant vacuolar signal.","confidence":"High","size":17,"edges":29,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0006626","count":1},{"id":"GO:0006878","count":1}]},{"hash":"1945543860233115917","title":"Mitotic spindle assembly and microtubule organization","description":"The top GO terms cluster around spindle assembly and microtubule-focused processes\u2014mitotic spindle assembly, microtubule nucleation, centrosome duplication, cortical microtubule organization, and meiotic cell cycle\u2014indicating a cohesive role in organizing the spindle and cytoskeleton during cell division (including meiosis II).","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007058","count":1},{"id":"GO:0030472","count":1},{"id":"GO:0071963","count":1},{"id":"GO:0043622","count":1},{"id":"GO:1990734","count":1}]},{"hash":"1760906586045663704","title":"Cytoskeletal dynamics and transcriptional regulation","description":"This cluster highlights both transcriptional activity (DNA-templated transcription) and cytoskeletal remodeling (microtubule severing, actin filament bundle assembly) with associated processes like cell migration and Notch signaling, plus heat response and immune modulation terms, suggesting a cohesive theme of coordinating gene expression with cytoskeletal dynamics and signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0032504","count":2},{"id":"GO:0009408","count":2}]},{"hash":"1701127913628746941","title":"Signaling and cytoskeletal remodeling","description":"The top GO terms span signaling events (Notch signaling in heart development, NF-kappaB-related sequestration, receptor localization to synapses, regulation of IL-12 production, SA node action potential regulation) together with cytoskeletal processes (actin filament bundle assembly, cell migration, spindle assembly, response to mechanical stimulus, heat response), suggesting a theme of signaling pathways coordinating cytoskeletal dynamics rather than a single specific function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0045083","count":1}]},{"hash":"2177394968928167812","title":"Redox Balance and Oxidative Stress Response","description":"Based on the top GO terms, the cluster is dominated by oxidation-reduction processes and cellular responses to oxidative stress (redox homeostasis, oxidative stress response, oxidant detoxification), with a few metabolic and transport-related terms that appear secondary. The strongest shared function appears to be redox regulation and detoxification, suggesting these proteins participate in maintaining cellular redox balance. An outlier term related to neural crest cell migration in heart formation may reflect multifunctionality but does not define the core theme.","confidence":"High","size":16,"edges":75,"triangles":171,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0045454","count":4},{"id":"GO:0098869","count":3},{"id":"GO:0009263","count":3},{"id":"GO:0003147","count":3}]},{"hash":"30359642582382160","title":"Mitotic cell cycle regulation","description":"This cluster is dominated by terms related to cell cycle progression (G1/S and G2/M transitions, mitotic re-entry, and spindle pole separation) and cyclin-dependent kinase regulation, with a transcriptional component consistent with cell-cycle\u2013associated gene expression; collectively, they point to mitotic control as the core theme.","confidence":"High","size":16,"edges":43,"triangles":23,"max_degree":13,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0045737","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0010696","count":7},{"id":"GO:0000320","count":7}]},{"hash":"117754938593917624","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":96,"triangles":287,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006541","count":5},{"id":"GO:0006508","count":5},{"id":"GO:0044344","count":4},{"id":"GO:0044210","count":4},{"id":"GO:0001889","count":4}]},{"hash":"448378424534260416","title":"ER Stress and Apoptosis with Developmental Signals","description":"GO terms center on ER stress response and multiple apoptotic processes, with ubiquitination and cell cycle regulation indicating stress-related protein turnover and proliferation control. Additional terms on epithelial polarity, mechanical stimulus response, and neural development (dendrite regulation, radial glial differentiation) suggest a broad interplay between cellular stress, programmed cell death, and developmental signaling rather than a single narrowly defined function.","confidence":"Medium","size":16,"edges":21,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0034976","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0033028","count":3},{"id":"GO:2000171","count":3},{"id":"GO:0007049","count":3}]},{"hash":"402373583204283821","title":"Protein dephosphorylation and cell cycle signaling","description":"This cluster centers on dephosphorylation events (peptidyl-tyrosine and general protein dephosphorylation) and cell cycle control (G2/M transition and mitotic cell cycle), indicating regulation of signaling through phosphorylation state. Supporting GO terms touch on signaling in muscle and neural contexts, development, and apoptosis, suggesting a broad signaling network linked to cell cycle progression.","confidence":"High","size":16,"edges":69,"triangles":121,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035335","count":8},{"id":"GO:0014850","count":7},{"id":"GO:0030948","count":7},{"id":"GO:0000086","count":6},{"id":"GO:0060079","count":6}]},{"hash":"2169166397621544126","title":"Sugar transport and carbohydrate metabolism","description":"The GO terms are dominated by sugar transport and metabolism (glucose import in response to insulin, galactose transmembrane transport, trehalose transport, fructose stimulus response, fucose metabolic process). A few other terms (mitotic processes, nitrate assimilation) appear less representative and may reflect noise.","confidence":"Medium","size":16,"edges":8,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045907","count":2},{"id":"GO:0007080","count":1},{"id":"GO:0000070","count":1},{"id":"GO:0071332","count":1},{"id":"GO:0042128","count":1}]},{"hash":"2002213377896681844","title":"Ubiquitin-Driven Protein Degradation and Cell Cycle","description":"The cluster is dominated by ubiquitination-related processes (ubiquitination, autoubiquitination, ubiquitin-dependent proteolysis, K6-linked ubiquitination) and protein catabolic pathways, with supporting terms for histone turnover and poly-ADP-ribosylation, plus cell cycle and stress-response aspects (response to heat, TNF signaling). This points to a cohesive theme around regulated protein degradation and its links to cell-cycle control and stress signaling.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":7},{"id":"GO:0042787","count":6},{"id":"GO:0070212","count":6},{"id":"GO:1903265","count":6},{"id":"GO:0051865","count":6}]},{"hash":"1323457285715529971","title":"Nuclear transcription regulation and proteostasis","description":"The top GO terms cluster around RNA polymerase II\u2013mediated transcription regulation and elongation, circadian regulation of gene expression, and androgen receptor signaling, together with proteostasis processes (proteasomal degradation, aggresome assembly, ERAD) and ribosome biogenesis. The mix also includes stress/DNA damage responses (UV-C, translesion synthesis), suggesting a nuclear network that coordinates gene expression with protein quality control and stress resilience. This combination supports a label focused on transcription control linked to proteostasis.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032436","count":2},{"id":"GO:0032922","count":2},{"id":"GO:0006357","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0070842","count":2}]},{"hash":"1142055871660577788","title":"Ribosome Biogenesis and Translation Machinery","description":"Strong enrichment for ribosome biogenesis and rRNA processing terms (GO:0042254, GO:0042273, GO:0000463) and translation reinitiation (GO:0002188) points to a core function in ribosome assembly and protein synthesis. Secondary terms related to transcription and cell cycle appear contextual. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0007275","count":4}]},{"hash":"2075762188128722372","title":"Zinc Ion Homeostasis and Cadmium Detox","description":"The GO terms converge on zinc ion handling: intracellular zinc homeostasis, zinc/cadmium transport, and detoxification related to zinc and cadmium, including negative regulation of zinc import. While iron and cobalt ion terms appear, the dominant theme is zinc/cadmium metal ion homeostasis and detoxification.","confidence":"High","size":16,"edges":20,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006882","count":5},{"id":"GO:0070574","count":5},{"id":"GO:0010312","count":5},{"id":"GO:0071584","count":4},{"id":"GO:0071577","count":4}]},{"hash":"560302683108966929","title":"Negative Regulation of Inflammatory Signaling","description":"The top terms point to suppression of innate immune pathways: negative regulation of NF-kappaB activity, TLR signaling, and cytokine production (IL-1, IL-8, TNF, IFN-\u03b2) in response to LPS, with ubiquitination as a common regulatory mechanism. A few terms related to development or mechanical stimulus appear, but the dominant theme is negative regulation of inflammatory signaling.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071260","count":2},{"id":"GO:0032717","count":1}]},{"hash":"1732951651479269314","title":"Gene Expression and Translation Machinery","description":"This cluster\u2019s top GO terms center on transcription (DNA-templated) and its regulation, ribosome biogenesis, and translation-related processes (translation initiation and reinitiation), indicating a core theme of gene expression from transcription through translation. Additional terms about microtubule organization and development reflect broader cellular and developmental roles that can accompany expression machinery, but the dominant signal is gene expression and translation assembly. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0030953","count":2}]},{"hash":"113355754960583745","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0009240","count":2}]},{"hash":"351149241135371393","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0000470","count":1},{"id":"GO:1990022","count":1},{"id":"GO:0007064","count":1}]},{"hash":"23036331230739125","title":"Mitotic spindle and chromatin assembly","description":"This cluster is dominated by mitosis-related terms: spindle assembly, CENP-A-containing chromatin assembly, cell division, and microtubule severing, pointing to chromosome segregation and spindle dynamics. Some ER-related and proteasome-related terms may reflect general protein turnover during cell division, with heat response being a minor co-occurrence. Overall, the common theme is mitotic machinery and chromatin organization.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051225","count":3},{"id":"GO:0070682","count":3},{"id":"GO:0061641","count":2},{"id":"GO:0030433","count":2}]},{"hash":"2019324313072402352","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0060733","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0043547","count":2}]},{"hash":"670583477057730937","title":"Immune signaling and transcription regulation","description":"The term list is dominated by immune-related processes (innate immune response, T cell receptor signaling, lipopolysaccharide signaling) and signaling/transcription control (DNA-templated transcription, JUN kinase regulation, response to TGF-beta and nitric oxide). This points to proteins involved in immune signaling and transcriptional regulation rather than metabolism or structural roles, even though a couple terms touch development (neural tube closure, social behavior).","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0031666","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0045087","count":2}]},{"hash":"2023057911346625977","title":"Ubiquitin-Mediated Proteolysis and Cell Cycle","description":"This cluster is dominated by GO terms related to ubiquitination and proteasome-dependent degradation, including K11- and K48-linked ubiquitination, SCF-dependent proteolysis, ERAD, and protein autoubiquitination, which point to a core theme of ubiquitin-mediated protein turnover. The presence of cell-cycle\u2013related terms like anaphase-promoting complex\u2013dependent catabolic process and cell division further links these proteolysis pathways to cell-cycle regulation. Some terms (viral process, peroxisomal import) may be peripheral, but the central signal is clear: ubiquitin signaling driving protein degradation and cell-cycle control.","confidence":"High","size":15,"edges":81,"triangles":216,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0070979","count":9},{"id":"GO:0031146","count":9},{"id":"GO:0030433","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0016558","count":8}]},{"hash":"1217725968374135630","title":"Ribosome Biogenesis and Translational Fidelity","description":"The top GO terms center on ribosome assembly and function\u2014translation, ribosome biogenesis, small subunit biogenesis, and SSU rRNA maturation\u2014plus tRNA modification and rRNA pseudouridine synthesis, all pointing to ribosome quality control and maintained translational accuracy, with an accompanying antibiotic-response signal likely related to translation-targeting antibiotics. Overall, the cluster appears to group proteins involved in ribosome construction and ensuring accurate protein synthesis.","confidence":"High","size":15,"edges":104,"triangles":442,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0042254","count":8},{"id":"GO:0046677","count":4},{"id":"GO:0000462","count":4},{"id":"GO:0042274","count":4}]},{"hash":"679100337699583832","title":"Ribosome Biogenesis and Cell Division","description":"The cluster shows strong representation of ribosome-related processes (ribosome biogenesis, cytoplasmic translation, tRNA modification, ribosomal large subunit export) along with cell-cycle and division terms (cell cycle, cell division, cell septum assembly), suggesting a theme of coordinating protein synthesis capacity with cell growth and division.","confidence":"High","size":15,"edges":17,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0046475","count":2},{"id":"GO:0090529","count":1},{"id":"GO:0000747","count":1},{"id":"GO:0042254","count":1}]},{"hash":"669674329630731771","title":"Proteostasis and ER Stress Response","description":"The cluster's top GO terms center on protein folding quality control (ER unfolded protein response, ERAD, proteasome-mediated degradation, and related catabolic processes), indicating a cohesive theme of maintaining protein homeostasis and handling misfolded or damaged proteins, with additional hints from mitochondrial insertion and vesicle formation that fit into broader protein quality control networks.","confidence":"Medium","size":15,"edges":9,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0070389","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0032979","count":5},{"id":"GO:0061641","count":5}]},{"hash":"1745157153571497328","title":"Amino acid and lipid transporters","description":"This cluster is dominated by GO terms for transport of small molecules and lipids across membranes (glycine betaine, taurine, methionine, heme, phosphorus/phospholipid translocation, and long-chain fatty acid import into peroxisomes) and a related lipid catabolic process, indicating a coherent group of proteins involved in nutrient and lipid transport and metabolism. A few terms like stem cell proliferation or endoribonuclease regulation appear as potential noise, but the overall signal is transport and lipid-related functions.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0045332","count":5},{"id":"GO:0031460","count":5},{"id":"GO:0015734","count":4},{"id":"GO:0015910","count":4},{"id":"GO:0015886","count":4}]},{"hash":"1414699327080596492","title":"Peroxisome Biogenesis and Import","description":"Most frequent terms center on peroxisome biogenesis and import\u2014peroxisome inheritance, membrane biogenesis, protein import into peroxisome membrane, and ER-dependent organization\u2014indicating a cluster of proteins involved in peroxisome assembly and maintenance. Other terms reflect broader metabolic regulation (e.g., ceramide biosynthesis, sugar transport), which might reflect secondary roles or annotation noise. Overall, the core theme is peroxisome formation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032483","count":2},{"id":"GO:0045033","count":1},{"id":"GO:0016557","count":1},{"id":"GO:0045046","count":1},{"id":"GO:0032581","count":1}]},{"hash":"1578734534317636126","title":"Neural signaling and sensory development","description":"The dominant GO terms point to neuronal activity and sensory functions (glutamate receptor signaling, action potential, taste perception, dendritic spine development), with supporting cellular processes like Golgi localization and lysosomal organization relevant to neurons. While some terms relate to general development (ascospore formation, digit morphogenesis, hair placode formation), the core theme is neural signaling and sensory perception.","confidence":"Medium","size":15,"edges":82,"triangles":227,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":15},{"id":"GO:0042733","count":15},{"id":"GO:0007215","count":15},{"id":"GO:0060789","count":15},{"id":"GO:0001508","count":15}]},{"hash":"265476071943128298","title":"TORC1-Driven Growth and Protein Synthesis Regulation","description":"This cluster is dominated by GO terms related to growth signaling and protein production: positive regulation of TORC1 signaling, ribosomal large subunit biogenesis, translation reinitiation, and regulation of the cell cycle with growth hormone response. Together these indicate a coordinated theme of cell growth, metabolism, and protein synthesis, despite a few tissue-specific or obsolete annotations that are less representative of the core function.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:1904263","count":6},{"id":"GO:0060528","count":5},{"id":"GO:0042273","count":5},{"id":"GO:0006349","count":5},{"id":"GO:0061641","count":5}]},{"hash":"456487732694537062","title":"Root Hair Growth and Cell Wall Biosynthesis","description":"The cluster is dominated by plant-specific processes: root hair cell development, cell wall organization, and rhamnogalacturonan II (RG-II) biosynthesis, all tying to polarized growth and cell wall remodeling in root hairs. The inclusion of actin filament bundle assembly supports cytoskeletal changes needed for tip growth. Some terms like Notch signaling or NF-kappaB sequestering may reflect broader or cross-species annotations but do not override the plant-root-hair theme.","confidence":"High","size":15,"edges":16,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0043488","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0010306","count":2},{"id":"GO:0009408","count":1}]},{"hash":"1059559196465014695","title":"Developmental Transcription Regulation","description":"This cluster centers on transcriptional regulation during development: terms for DNA-templated transcription and RNA Pol II\u2013mediated repression, plus several development-related terms (cardiac ventricle formation, cardiac cell fate specification, hindgut morphogenesis, lens epithelial cell proliferation). A few terms (mitochondrial chromosome packaging, TNF production) are peripheral. The lack of edges suggests these proteins share GO annotations rather than direct interactions but collectively point to regulators of developmental gene expression.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0007129","count":3},{"id":"GO:0003211","count":2},{"id":"GO:0090139","count":2}]},{"hash":"1155515613467448076","title":"Cytoskeletal dynamics and endosomal trafficking","description":"The top GO terms are dominated by actin remodeling (Arp2/3-mediated nucleation, filopodium assembly), microtubule-based movement, and endosomal transport, with involvement of Rho signaling and substrate adhesion-dependent cell spreading. Together, they point to coordinated regulation of the cytoskeleton and vesicle trafficking, underlying cell movement and morphology changes. Some developmental terms appear, but the core theme centers on cytoskeletal dynamics and trafficking.","confidence":"Medium","size":15,"edges":17,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0034314","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0021510","count":2},{"id":"GO:0007018","count":2}]},{"hash":"586029782816620176","title":"Neural development and synapse formation","description":"The top GO terms point to neural development processes (cortical layer formation, lens development, multicellular development) and synaptic organization (protein localization to synapse, positive regulation of synapse assembly). Sensory perception of pain and response to cocaine highlight neural signaling, while ER polarization and caveolin-mediated endocytosis reflect membrane trafficking relevant to neurons. Together, these terms suggest a cluster of proteins involved in neural development and synaptic assembly/localization.","confidence":"High","size":15,"edges":19,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0035418","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0021819","count":3},{"id":"GO:0042220","count":3}]},{"hash":"1984062951111213842","title":"RNA Pol II Transcription Regulation & Splicing","description":"This cluster is dominated by GO terms tied to transcription control by RNA Polymerase II (DNA-templated transcription, Pol II promoter\u2013driven transcription, and negative regulation of transcription by Pol II) and RNA processing (alternative mRNA splicing via spliceosome). Together, these signals point to functions in transcriptional regulation and mRNA processing.","confidence":"High","size":15,"edges":32,"triangles":26,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0016049","count":3},{"id":"GO:0010735","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0000122","count":3}]},{"hash":"1018492131991162356","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0006398","count":1},{"id":"GO:0033260","count":1},{"id":"GO:0045038","count":1},{"id":"GO:0044030","count":1}]},{"hash":"1282928808134273091","title":"Glycosylation-Linked Developmental Proteins","description":"The top GO terms cluster around protein glycosylation (O-linked mannose and O-GlcNAcylation) and developmental processes (larval cuticle development, embryonic development), suggesting these proteins function in glycosylation-modulated development. Additional terms indicate broader stress and signaling roles, but the strongest signal ties to PTM-related development.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008363","count":2},{"id":"GO:0035269","count":2},{"id":"GO:0097370","count":2},{"id":"GO:0043278","count":2},{"id":"GO:0035994","count":2}]},{"hash":"1316325128904185845","title":"Innate immune signaling and bacterial sensing","description":"The top GO terms are dominated by innate immune response, regulation of IFN-\u03b3 signaling, and cellular response to muramyl dipeptide, pointing to an immune-focused cluster. While there are a few metabolic and iron-sulfur related terms, the strongest and most representative theme is innate immunity and bacterial sensing.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0060335","count":2},{"id":"GO:0071225","count":2},{"id":"GO:0030011","count":2},{"id":"GO:0009399","count":1}]},{"hash":"332746827444103022","title":"Ubiquitination-linked stress signaling and cytoskeletal remodeling","description":"This cluster is enriched for protein ubiquitination, response to mechanical stimulus, and actin filament bundle assembly, pointing to a theme of ubiquitin-mediated signaling driving cytoskeletal remodeling and mechanotransduction; cell migration supports a motility-related function. Some heart- and synaptic-related GO terms appear but do not define a single cohesive pathway, so the primary signal is stress-response signaling linked to the cytoskeleton.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":7},{"id":"GO:0071260","count":7},{"id":"GO:0009408","count":5},{"id":"GO:0007253","count":5},{"id":"GO:0051017","count":5}]},{"hash":"980566112526148800","title":"Cell proliferation and survival pathways","description":"The cluster includes terms tied to cell growth and division (mitotic spindle assembly; CENP-A chromatin assembly), ribosome biogenesis, protein ubiquitination, and TORC1 signaling, along with apoptosis-related processes. Although there are some tissue-specific annotations (pancreatic juice secretion; prostate gland development) that may reflect contextual roles, the dominant theme is regulation of cell cycle progression, protein synthesis/turnover, and cell survival. Therefore, the label highlights core proliferative and survival pathways.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":3},{"id":"GO:0034349","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0051402","count":3},{"id":"GO:1904263","count":3}]},{"hash":"825955237498789088","title":"Unknown","description":"The terms include ozone response, androgen metabolism, cholesterol catabolism, ecdysone biosynthesis, obsolete oxidative deethylation, prostaglandin biosynthesis, sex differentiation, omega-hydroxylase P450 pathway, carbazole catabolic process, and retina vasculature development. They span environmental response and multiple distinct metabolic routes, with no single dominant theme. Because of this fragmentation, there is no clear, representative function for the cluster beyond broad metabolism, so Unknown with confidence None. ","confidence":"","size":14,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010193","count":1},{"id":"GO:0008209","count":1},{"id":"GO:0006707","count":1},{"id":"GO:0006697","count":1},{"id":"GO:0071615","count":1}]},{"hash":"35961583588686033","title":"Golgi-ER vesicle trafficking and SNARE-mediated synaptic exocytosis","description":"This cluster centers on ER-to-Golgi and intra-Golgi vesicle transport, SNARE complex assembly, and Golgi organization, plus exocytic delivery of neurotransmitter receptors and synaptic potentiation. The combined GO terms point to a cohesive role for Golgi- and SNARE-driven vesicle trafficking in neuronal receptor trafficking and synaptic plasticity.","confidence":"High","size":14,"edges":51,"triangles":53,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0048280","count":7},{"id":"GO:0006888","count":7},{"id":"GO:0098967","count":7},{"id":"GO:0006891","count":7},{"id":"GO:0060291","count":7}]},{"hash":"112507224941132642","title":"Embryonic development and cardiac morphogenesis","description":"The cluster shows GO terms centered on early development and heart formation (inner cell mass morphogenesis, cardiac ventricle formation, regulation of cardiac cell fate specification, embryonic hindgut morphogenesis) along with DNA-templated transcription, suggesting a developmental/programmatic theme tied to embryogenesis and heart organogenesis. A few metabolism-related terms appear but are likely noise relative to the main developmental signal.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0001828","count":2},{"id":"GO:0042413","count":1},{"id":"GO:0043427","count":1},{"id":"GO:0033611","count":1}]},{"hash":"1672315075183308256","title":"Central Carbon Metabolism and Signaling","description":"The top GO terms point to core energy pathways (glycolysis, TCA cycle, gluconeogenesis) and amino-acid catabolism with lipid biosynthesis via malonyl-CoA, plus some signaling (Notch, cAMP) and ion transport. This pattern suggests a cluster of metabolic enzymes with regulatory signaling relationships rather than a single specialized function.","confidence":"Medium","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":9},{"id":"GO:0033512","count":6},{"id":"GO:0006096","count":6},{"id":"GO:0051591","count":4},{"id":"GO:0007219","count":4}]},{"hash":"559235881361879274","title":"Cardiac and skeletal muscle development with cytoskeletal remodeling","description":"Several top GO terms center on heart development and function (secondary heart field cardioblast proliferation, SA node action potential regulation), along with skeletal muscle regeneration and actin filament bundle assembly, indicating a shared focus on muscle development and cytoskeletal dynamics. Spindle assembly and cell migration reflect broader cytoskeletal remodeling required for tissue growth, while a couple of terms pertain to stress or immune responses that are less central to the core theme. Overall, the dominant signal ties muscle development and cardiac function with cytoskeletal organization.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":9},{"id":"GO:0009408","count":8},{"id":"GO:0007253","count":8},{"id":"GO:0051017","count":8},{"id":"GO:0045083","count":8}]},{"hash":"1041037113190224018","title":"Neural signaling and actin remodeling","description":"This cluster is driven by terms for GABAergic synaptic transmission, filopodium assembly/regulation, and vesicle trafficking, all pointing to neuronal signaling intertwined with actin-driven cytoskeletal dynamics. Additional terms touch on neuromuscular balance and endothelial signaling, suggesting broader cellular communication roles. The yeast mating projection term appears as an outlier and does not define the cluster. Overall, the dominant pattern is neural signaling coupled to actin remodeling.","confidence":"Medium","size":14,"edges":14,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0031384","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0010796","count":2},{"id":"GO:1900026","count":2},{"id":"GO:0050885","count":2}]},{"hash":"698746470572446358","title":"Lipid biosynthesis and immune regulation","description":"The top GO terms cluster around lipid metabolism and biosynthesis, including triglyceride, phosphatidylcholine, cardiolipin, and ether lipid pathways, as well as CDP-diacylglycerol biosynthesis and platelet activating factor production, suggesting a core function in lipid biosynthesis and signaling. The presence of immune-related terms such as interleukin-2 production and negative regulation of activation-induced T cell death indicates a link to immune modulation, possibly through lipid mediators. There is one plant-specific term (cutin biosynthetic process) that may reflect an outlier or misannotation, but the predominant theme centers on lipid metabolism with immune signaling. ","confidence":"Medium","size":14,"edges":40,"triangles":59,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0019432","count":7},{"id":"GO:0036151","count":6},{"id":"GO:0006663","count":6},{"id":"GO:0035965","count":6},{"id":"GO:0016024","count":6}]},{"hash":"441697437687748167","title":"Endosomal trafficking and endocytosis regulation","description":"Most terms describe intracellular transport between Golgi and endosomes, including endosome maturation and receptor-mediated endocytosis, plus regulation of related signaling and cytoskeletal processes. A few terms are peripheral (ion homeostasis, pregnancy), but the core theme is membrane trafficking and endocytic pathways.","confidence":"Medium","size":14,"edges":35,"triangles":30,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:1902961","count":1},{"id":"GO:0032511","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0034316","count":1}]},{"hash":"2088735383682632315","title":"Drosophila cell fate specification and differentiation","description":"The top GO terms cluster around developmental differentiation and tissue fate decisions in Drosophila, notably eye cone cell fate and wing cell fate specification, plus spermatid differentiation and EGFR ligand maturation, suggesting a developmental signaling/differentiation theme. Some terms pertain to protein processing (glycosylation, co-translational modification, ER-associated proteolysis), which may reflect general biogenesis rather than a single cohesive function. Overall, the cluster seems best described as developmental differentiation and signaling in Drosophila, with annotation noise.","confidence":"Medium","size":14,"edges":16,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0032815","count":2},{"id":"GO:0048515","count":2},{"id":"GO:0034620","count":2},{"id":"GO:0042676","count":2},{"id":"GO:0035311","count":2}]},{"hash":"2225278620333351057","title":"Membrane Biogenesis and Envelope Assembly","description":"The top GO terms cluster around membrane-related biosynthetic and assembly processes: GPI anchor biosynthesis, protein insertion into membranes, cristae formation, Gram-negative outer membrane assembly, V-type ATPase complex assembly, and biosynthesis of envelope components like colanic acid and sporopollenin/phenylpropanoid. This suggests a shared theme of building or assembling membrane- or envelope-associated structures across organisms.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0043165","count":1},{"id":"GO:0051205","count":1},{"id":"GO:0070072","count":1}]},{"hash":"258702005413002287","title":"Stress-Responsive Translation Regulation","description":"This cluster centers on cellular stress responses (starvation, UV, ER stress, hypoxia) that regulate protein synthesis, including translational initiation and eIF2\u03b1 phosphorylation, suggesting a common theme of stress-induced control of translation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071264","count":1},{"id":"GO:0072755","count":1},{"id":"GO:0031333","count":1},{"id":"GO:0033235","count":1},{"id":"GO:0042149","count":1}]},{"hash":"1025039980490947353","title":"Neurodevelopmental cell cycle regulation","description":"The top GO terms reveal neural development (spinal cord development, forebrain development) alongside core cell cycle and transcription-related processes (DNA-templated transcription, mitotic cell cycle, cell division, RNA methylation). The mix of neural development with growth, cytoskeletal movement, and TORC1 signaling suggests these proteins coordinate neurodevelopment with proliferation and growth control, making this a coherent neurodevelopment + cell cycle cluster.","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:0021510","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0051301","count":2}]},{"hash":"1399409088221151304","title":"Chromatin Assembly and Ribosome Biogenesis","description":"Based on GO terms, the cluster is dominated by nuclear processes: nucleosome assembly, chromosome condensation, CENP-A\u2013containing chromatin assembly, and ribosomal large subunit biogenesis. A few terms describe tissue-specific differentiation and development, which are likely incidental annotations. Overall, the shared theme points to chromatin organization and ribosome production in the nucleus.","confidence":"Medium","size":14,"edges":14,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":1},{"id":"GO:0030261","count":1},{"id":"GO:0060528","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0006349","count":1}]},{"hash":"1901695284935342842","title":"Developmental Signaling and Tissue Patterning","description":"This cluster is dominated by nervous system development and key signaling pathways (Roundabout/Slit and Smoothened/Hedgehog) along with organogenesis terms like kidney development and sensory perception, suggesting a cohesive theme of signaling-driven tissue formation across multiple organs, with additional hints from cytoskeletal remodeling and epidermal differentiation.","confidence":"Medium","size":14,"edges":23,"triangles":8,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007399","count":7},{"id":"GO:0035385","count":7},{"id":"GO:0007224","count":7},{"id":"GO:0050852","count":7},{"id":"GO:0001822","count":7}]},{"hash":"1284842244791252152","title":"Unknown","description":"This cluster's GO terms span diverse processes from Hedgehog signaling and renal angiotensin regulation to plant biosynthesis (lignin, cutin, flavonoids) and a few miscellaneous terms; there is no single coherent function tying all terms together, so a specific label is not justifiable.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":1},{"id":"GO:0002001","count":1},{"id":"GO:0051220","count":1},{"id":"GO:0060271","count":1},{"id":"GO:0002019","count":1}]},{"hash":"1733983192812549167","title":"Unknown","description":"The top GO terms are spread across mitochondrial processes, oxidative stress response, and plant-specific cell wall activities, with no single function dominating. This lack of a cohesive theme suggests the cluster may reflect a mixed or non-specific set of annotations rather than a distinct biological module.","confidence":"","size":14,"edges":53,"triangles":67,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0099132","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0033615","count":1},{"id":"GO:0008203","count":1}]},{"hash":"1864893201207705810","title":"GTPase signaling and neuronal cytoskeleton remodeling","description":"The cluster is enriched for small GTPase\u2013mediated signaling, actin-based cytoskeletal dynamics (filopodium assembly and its regulation), and neuronal signaling components (GABAergic transmission and acetylcholine receptor pathways), along with nervous system and heart development terms. This combination suggests proteins coordinating GTPase-driven signaling with cytoskeletal remodeling in neuronal contexts, rather than a single narrow function.","confidence":"Medium","size":14,"edges":26,"triangles":10,"max_degree":11,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0007264","count":11},{"id":"GO:0000266","count":11},{"id":"GO:0046847","count":10},{"id":"GO:0051489","count":10},{"id":"GO:0051932","count":10}]},{"hash":"922539588648325472","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":4},{"id":"GO:1905639","count":4},{"id":"GO:1900865","count":4},{"id":"GO:0031426","count":4},{"id":"GO:0031425","count":4}]},{"hash":"773520108694024347","title":"Prenyl diphosphate biosynthesis","description":"The top GO terms point to the production of isoprenoid precursors (IPP, FPP, and DMAPP), suggesting a shared function in prenyl diphosphate biosynthesis. Some unrelated or obsolete terms appear, but the strongest cohesive signal across terms is isoprenoid/terpenoid biosynthesis, supporting a labeling as a prenyl biosynthesis cluster.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006308","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0009240","count":1}]},{"hash":"915059455941044664","title":"Ubiquitin-Proteasome Regulation and Wnt Signaling","description":"The top terms emphasize protein turnover (deubiquitination, proteasome assembly, ubiquitin ligase activity) and modulation of Wnt pathways (canonical and PCP), suggesting a functional cluster centered on ubiquitin-proteasome control of signaling. Immune/defense terms appear but do not define the core theme; they may reflect annotation diversity rather than a separate function.","confidence":"Medium","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":8},{"id":"GO:0080129","count":7},{"id":"GO:0090263","count":7},{"id":"GO:0010950","count":7},{"id":"GO:0010363","count":7}]},{"hash":"445102625913410636","title":"Ribosome Biogenesis and Protein Translation","description":"The top terms are dominated by translation, ribosome biogenesis, and translational initiation/termination, pointing to a cluster centered on the protein synthesis machinery. Minor signals related to MAPK pathways and mRNA decay appear but do not define the primary function.","confidence":"High","size":13,"edges":45,"triangles":74,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0042254","count":4},{"id":"GO:0006413","count":4},{"id":"GO:0006415","count":3},{"id":"GO:0042273","count":2}]},{"hash":"2012873537451110178","title":"DNA Damage Response and Translation Regulation","description":"The cluster is enriched for translation-related terms (translation, positive regulation of translation, ribosomal biogenesis) alongside DNA damage/stress-response terms (p53-mediated signaling, gamma radiation, UV response, transcription elongation), suggesting a coherent theme where protein synthesis control is tied to DNA damage response pathways.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:1904803","count":3},{"id":"GO:1902167","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0031564","count":3}]},{"hash":"896339339736730428","title":"Gonadal steroidogenesis and sex differentiation","description":"The top GO terms cluster around steroid hormone production and gonadal development (female gonad development, sex differentiation, androgen metabolic process, ecdyson biosynthetic process, cholesterol catabolic process, prostaglandin biosynthetic process) with P450-related pathways (omega-hydroxylase P450). This points to a cohesive theme of steroidogenesis and sexual development, with a few peripheral terms that may reflect broader developmental or detoxification roles.","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008585","count":6},{"id":"GO:0010193","count":5},{"id":"GO:0008209","count":5},{"id":"GO:0006707","count":5},{"id":"GO:0006697","count":5}]},{"hash":"911992424637590313","title":"Ubiquitin-regulated inflammatory signaling","description":"The top GO terms cluster around innate and adaptive immune signaling (innate immune response, IL-1-mediated signaling, LPS response, T cell receptor signaling) and ubiquitination processes (K63-linked ubiquitination, autoubiquitination) with NF-kB-related regulation. This suggests a module of proteins involved in inflammatory signaling that is modulated by ubiquitin chains. The presence of neural tube closure and Hippo signaling hints at broader developmental signaling roles or annotation overlap, but the dominant theme is immune signaling controlled by ubiquitination.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0045087","count":2},{"id":"GO:0070498","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0070534","count":2}]},{"hash":"1395811690836449280","title":"Embryonic Development and Gene Regulation","description":"This cluster is enriched for vertebrate developmental terms (multicellular organism development, skeletal system development, neural tube closure) and transcription-related processes (DNA-templated transcription, mitotic cell cycle), suggesting a core theme of embryogenesis with gene expression control. The presence of cadmium response and defense to Gram-positive bacteria may reflect broader stress response roles or annotation noise, but the dominant signal points to development and transcriptional regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0006351","count":5},{"id":"GO:0000209","count":4},{"id":"GO:0006349","count":4}]},{"hash":"1182564203627858943","title":"Developmental Growth and Morphogenesis Regulation","description":"These proteins cluster around processes that control how cells proliferate, migrate, and shape tissues during development. The presence of negative regulation of canonical Wnt signaling and hair follicle placode formation suggests involvement in skin appendage development, while DNA replication and cytokinesis relate to cell division, and anisotropic growth and cell migration point to morphogenesis. Taken together, this cluster seems best described as a developmental growth and morphogenesis regulator.","confidence":"Medium","size":13,"edges":11,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000011","count":4},{"id":"GO:0043065","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0008285","count":4},{"id":"GO:0090090","count":4}]},{"hash":"404934999140201393","title":"Cell Cycle and Division Regulation","description":"Based on the prominent GO terms, especially regulation of the cell cycle, positive regulation of cytokinesis, and regulation of centromeric sister chromatid cohesion, the cluster appears to center on controls of cell division and chromosome dynamics. Additional terms point to broader regulatory roles in apoptosis, development, and physiology, but the core theme ties to proliferative control and division processes, suggesting a cohesive module of division-regulatory proteins.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0007050","count":7},{"id":"GO:0051211","count":6},{"id":"GO:0060789","count":6},{"id":"GO:0032467","count":6},{"id":"GO:0032471","count":6}]},{"hash":"1665687629966442682","title":"Ribosome Assembly and Translation Initiation","description":"The top GO terms are strongly skewed toward translation machinery: formation of the translation preinitiation complex, cytosolic ribosome assembly, and positive regulation of eIF4F complex assembly, plus a regulator of translational initiation. A few terms about energy homeostasis and unrelated processes appear, but the dominant signal points to protein synthesis machinery and its initiation control.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":2},{"id":"GO:2000507","count":2},{"id":"GO:0042256","count":1},{"id":"GO:1905537","count":1},{"id":"GO:0043547","count":1}]},{"hash":"348350567079284593","title":"mRNA processing and translation regulation","description":"This cluster is enriched for splicing and post-transcriptional control processes: regulatory ncRNA-mediated gene silencing, spliceosome-mediated mRNA splicing (including snoRNA splicing and splice site recognition), mRNA stability in stress, and regulation of translational initiation and reinitiation, plus preinitiation complex formation. Together these terms point to a coherent module governing post-transcriptional gene expression.","confidence":"High","size":13,"edges":70,"triangles":207,"max_degree":12,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0006378","count":6},{"id":"GO:0010610","count":5},{"id":"GO:0045292","count":5}]},{"hash":"1536024310755064483","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0090617","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2},{"id":"GO:0031426","count":2}]},{"hash":"295504046064376012","title":"Phosphatase-regulated mitosis and spindle dynamics","description":"The cluster is enriched for dephosphorylation (tyrosine and serine/threonine), negative regulation of CDK activity, kinetochore localization, and meiotic spindle disassembly, which together point to phosphatase-driven control of cell cycle progression and spindle function during mitosis/meiosis. While some terms touch on signaling and RNA processing, the core theme centers on phosphatase-mediated regulation of mitotic machinery.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":10},{"id":"GO:0034501","count":7},{"id":"GO:0045736","count":7},{"id":"GO:0051229","count":6},{"id":"GO:0060266","count":6}]},{"hash":"2074621125693429929","title":"Metabolic Regulation and Aging Signaling","description":"This cluster shows enrichment in GO terms tied to metabolism and energy signaling (insulin receptor signaling pathway, aerobic respiration, pyrroloquinoline quinone biosynthesis), plus aging-related processes (determination of adult lifespan) and protein homeostasis (negative regulation of proteolysis, positive regulation of protein oligomerization). Together, the proteins appear to function in coordinating metabolic signaling with lifespan regulation and protein maintenance. Some terms (viral process, obsolete pheromone maturation) are less cohesive, but may reflect broader functional annotations in this dataset.","confidence":"Medium","size":13,"edges":6,"triangles":0,"max_degree":4,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0018189","count":5},{"id":"GO:1901143","count":5},{"id":"GO:0010815","count":5},{"id":"GO:0045861","count":5},{"id":"GO:0008286","count":5}]},{"hash":"2161018111461815674","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"The proteins in this cluster are enriched for transmembrane transport of mitochondrial metabolites (nucleotides, ATP, NAD, citrate, heme, ornithine, thiosulfate) and for regulation of mitochondrial membrane permeability and membrane potential, pointing to a cohesive role in mitochondrial transport and maintenance of membrane potential.","confidence":"High","size":13,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1990519","count":12},{"id":"GO:1990544","count":12},{"id":"GO:0015886","count":12},{"id":"GO:0000066","count":12},{"id":"GO:0015709","count":12}]},{"hash":"1461889755482257684","title":"Histone Lysine Methylation","description":"The cluster\u2019s top GO terms are dominated by lysine methylation modifications: histone H3-K36 methylation and the three forms of peptidyl-lysine methylation (monomethylation, dimethylation, trimethylation). This points to a shared theme of lysine methylation, a key post-translational modification affecting chromatin and protein function. Some plastid-related terms and differentiation processes appear, which may reflect annotation noise or multi-functional proteins, but the lysine methylation signature remains the strongest indicator of a common function.","confidence":"Medium","size":13,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010452","count":1},{"id":"GO:0048863","count":1},{"id":"GO:0010027","count":1},{"id":"GO:0018023","count":1},{"id":"GO:0042793","count":1}]},{"hash":"1117415379937232850","title":"Gene Expression and Microtubule Dynamics","description":"The top GO terms point to transcriptional regulation (DNA-templated transcription, RNA polymerase II transcription) alongside cytoskeletal/mitotic processes (mitotic spindle elongation, plus-end directed microtubule sliding, mitotic metaphase chromosome recapture). Calcium signaling and developmental terms (flower meristem identity, primitive streak formation) suggest broader regulatory roles, but the recurrent theme is a link between transcription control and cytoskeletal dynamics during cell division. Confidence: Medium","confidence":"","size":12,"edges":52,"triangles":129,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0071277","count":4},{"id":"GO:0006366","count":3},{"id":"GO:0010076","count":3},{"id":"GO:0090009","count":3}]},{"hash":"350356506262061277","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0003203","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0042254","count":1}]},{"hash":"2091746134068519603","title":"Co-translational targeting and secretion","description":"This cluster is dominated by translation-related terms and membrane-targeting/secretion processes: translation, regulation of translation, SRP-dependent cotranslational targeting to membrane, Sec complex\u2013mediated transport, and general protein targeting. These together point to a module involved in producing proteins and directing them to membranes or the secretory pathway. A few outliers (DNA repair, substantia nigra development, dexamethasone response) are less representative of the central theme.","confidence":"Medium","size":12,"edges":65,"triangles":210,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006417","count":2},{"id":"GO:0006281","count":1},{"id":"GO:0071549","count":1},{"id":"GO:0009306","count":1}]},{"hash":"1925339939435467612","title":"Unknown","description":"The GO terms are highly diverse, ranging from ubiquitination to piRNA processing, photoreceptor differentiation, cell migration, and social behavior, with no single dominant shared function to anchor a meaningful cluster label. Only a lone ubiquitination term hints at a possible thread, but overall the set appears heterogeneous.","confidence":"","size":12,"edges":7,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046061","count":1},{"id":"GO:0070979","count":1},{"id":"GO:0035176","count":1},{"id":"GO:1903744","count":1},{"id":"GO:0051497","count":1}]},{"hash":"1786743302725324983","title":"Steroid signaling, development, and mitosis","description":"The cluster centers on developmental processes linked to steroid signaling, including prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly, with a core emphasis on cell proliferation as shown by mitotic cell cycle and cell division terms. While there are stress-response terms (interferon response, unfolded protein response) present, they are less central to the cluster\u2019s primary theme, which appears to fuse hormone-driven development with cell cycle regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030850","count":3},{"id":"GO:0051348","count":3},{"id":"GO:0006463","count":3},{"id":"GO:0046661","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1918655264159320689","title":"Unknown","description":"The top GO terms cover a highly diverse set of functions (transcription, metabolism, various stimulus responses, development) with little unifying function across the cluster. There isn\u2019t a clear, cohesive theme tying these proteins into a single intuitive label, so an Unknown designation with None confidence is most appropriate.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0045793","count":8},{"id":"GO:0006006","count":8},{"id":"GO:0033160","count":8},{"id":"GO:0006935","count":8}]},{"hash":"2142716610918492616","title":"Epigenetic transcription regulation","description":"The cluster is dominated by GO terms linked to chromatin organization and transcription control (DNA-templated transcription, nucleosome assembly, CENP-A chromatin assembly, and histone modification-related terms). This points to an epigenetic regulatory module governing gene expression. A few tissue-specific or ribosome-related terms appear but are less central and may reflect annotation noise. ","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0061087","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0060528","count":1}]},{"hash":"1723133016290065898","title":"Membrane Transporters","description":"The top GO terms are dominated by diverse transmembrane transport activities (nitrite, nitrate, sodium, phosphate, arabinose, xenobiotics, vitamins, and related compounds), plus a vesicular transport step for neurotransmitter loading. This pattern points to a cohesive set of proteins involved in moving ions and small molecules across membranes, rather than a single substrate or pathway. Therefore, labeling the cluster as Membrane Transporters captures the shared function.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":3},{"id":"GO:0035725","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0006855","count":2}]},{"hash":"1487269307288930160","title":"Ribosome Biogenesis and rRNA Processing","description":"Dominated by GO terms for large ribosomal subunit assembly, export from the nucleus, preribosome assembly, and maturation of 5.8S and LSU rRNA, pointing to ribosome biogenesis and rRNA processing as the core theme. A few unrelated terms (aerobic respiration, DNA replication) appear as outliers.","confidence":"High","size":12,"edges":11,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0000055","count":1}]},{"hash":"97458985124939372","title":"Neuronal plasticity and cytoskeletal regulation","description":"Top GO terms emphasize neuronal signals (positive regulation of synaptic plasticity; regulation of dendrite development) and cytoskeletal dynamics (barbed-end actin filament capping; mitotic spindle assembly), with ubiquitin-related regulation also present. An exocrine pancreatic secretion term appears as an outlier, and several terms are obsolete, but the dominant theme points to neuronal development/plasticity linked to cytoskeletal remodeling and protein turnover.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030157","count":3},{"id":"GO:0070979","count":3},{"id":"GO:0031915","count":3},{"id":"GO:0090344","count":3},{"id":"GO:1905705","count":3}]},{"hash":"721528094566391314","title":"Neural development and glutamatergic synapse signaling","description":"This cluster is driven by terms about nervous system development, regulation of synapse structure or activity, and ionotropic glutamate receptor signaling, indicating a core theme around neural development and glutamatergic neurotransmission. While there are a few morphogenesis and calcium homeostasis terms present, the dominant representation points to neural development and synaptic signaling.","confidence":"High","size":12,"edges":14,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007399","count":1},{"id":"GO:0050803","count":1},{"id":"GO:0035235","count":1},{"id":"GO:0010951","count":1},{"id":"GO:0048669","count":1}]},{"hash":"145543800446898159","title":"Growth signaling and developmental regulation","description":"This cluster centers on positive regulation of signaling activities (GTPase regulation, kinase activity, and autophosphorylation) and development-related processes (multicellular development, growth hormone response, and prostate gland development), with additional links to ribosome biogenesis and chromatin assembly. Together these terms suggest a cohesive theme of growth-related signaling coordinating development and cellular biogenesis, despite some annotation noise from obsolete terms.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0043547","count":5},{"id":"GO:0071902","count":5},{"id":"GO:0031954","count":5},{"id":"GO:0060528","count":4},{"id":"GO:0042273","count":4}]},{"hash":"1546781768812443150","title":"Unknown","description":"The GO terms in this cluster are highly diverse, spanning bacterial envelope biosynthesis (lipopolysaccharide and lipid A), biofilm formation, drug response, allantoin/xylan metabolism, spore wall processes, and an outlier term (synaptic vesicle exocytosis). No single, cohesive biological function ties these annotations together, so a meaningful, specific label cannot be assigned with confidence.","confidence":"","size":12,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0042710","count":1},{"id":"GO:0019428","count":1},{"id":"GO:0045493","count":1}]},{"hash":"136533031405124819","title":"Metabolic and Membrane Lipid Processing","description":"The top GO terms point to a range of metabolic activities (serine biosynthesis, antibiotic biosynthesis, stilbene catabolism) alongside membrane-associated processes (phospholipid dephosphorylation, dephosphorylation, and maintenance of transmembrane electrochemical gradients) and a P450 epoxygenase pathway. This suggests a broad but cohesive theme of metabolism intertwined with membrane lipid remodeling, rather than a single specific function, hence this label.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0046839","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0046272","count":3}]},{"hash":"661217992577541406","title":"Unknown","description":"The GO terms cover cell-cycle progression, fungal development, synaptic signaling, calcium release, immune signaling, toxin response, astrocyte activation, autophagy, and cAMP signaling, with no unifying function across the cluster; thus a single representative label is not evident.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":1},{"id":"GO:0030437","count":1},{"id":"GO:0060079","count":1},{"id":"GO:0051281","count":1},{"id":"GO:0000742","count":1}]},{"hash":"502762777261362412","title":"Plant metabolic biosynthesis and SA defense signaling","description":"This cluster includes multiple biosynthetic and catabolic metabolic processes (valine catabolism, fatty acid beta-oxidation, phenylacetate catabolism, phylloquinone and menaquinone biosynthesis, protoporphyrinogen IX biosynthesis, antibiotic biosynthesis) along with a plant-specific defense term (systemic acquired resistance, salicylic acid\u2013mediated signaling). The common theme is metabolic pathway activity with a possible link to plant defense signaling, so the label emphasizes plant metabolism paired with SA-mediated defense.","confidence":"Medium","size":12,"edges":14,"triangles":3,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006574","count":1},{"id":"GO:0006635","count":1},{"id":"GO:0042372","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0009234","count":1}]},{"hash":"45036162351198917","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033615","count":1},{"id":"GO:0008203","count":1},{"id":"GO:0090617","count":1},{"id":"GO:1905639","count":1},{"id":"GO:1900865","count":1}]},{"hash":"428898821380724656","title":"Neuronal GPCR Signaling and Perception","description":"The dominant GO terms point to neural signaling and sensory processing, with multiple GPCR signaling pathways (general GPCR signaling, AC-inhibiting GPCR signaling) and neurotransmitter-related pathways (GABA), along with sensory perception (vision, taste) and related behaviors (short-term memory, locomotion). Some terms (mitotic spindle assembly, peptidoglycan catabolic process, electron transport chain) appear unrelated, suggesting mixed annotations or background proteins. Overall, the strongest coherent theme is neuronal signaling linked to perception and behavior.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":3},{"id":"GO:0050908","count":3},{"id":"GO:0050917","count":3},{"id":"GO:0007614","count":3},{"id":"GO:0038042","count":3}]},{"hash":"1847762597999632520","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090617","count":2},{"id":"GO:1905639","count":2},{"id":"GO:1900865","count":2},{"id":"GO:0031426","count":2},{"id":"GO:0031425","count":2}]},{"hash":"990304064833061121","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to ribosome production and protein synthesis\u2014translation, cytoplasmic translation, ribosome biogenesis, SSU rRNA maturation, and ribosomal subunit assembly\u2014indicating a cohesive role in ribosome assembly and function. A couple of outlier terms exist but do not define the cluster\u2019s main function.","confidence":"High","size":11,"edges":47,"triangles":106,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":11},{"id":"GO:0000462","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006415","count":2},{"id":"GO:0002181","count":2}]},{"hash":"1609674057056158040","title":"Microtubule Dynamics in Mitosis and Neuronal Transport","description":"The top terms emphasize microtubule-based processes (spindle elongation, plus/minus-end sliding, mitotic chromosome recapture) and cytoskeletal regulation (actomyosin ring assembly), plus related transport in neurons (anterograde dendritic transport) with a cerebellar context, suggesting a cohesive theme of dynamic microtubule regulation in both cell division and neuronal transport.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":11},{"id":"GO:0031535","count":11},{"id":"GO:0021693","count":11},{"id":"GO:1990942","count":11},{"id":"GO:0001560","count":11}]},{"hash":"215169267810343567","title":"Leukocyte adhesion and T cell activation signaling","description":"This cluster is enriched for immune-related terms: leukocyte cell-cell adhesion (GO:0007159) and T cell activation via TCR contact with antigen (GO:0002291), along with regulation of integrin activation (GO:0033623) and filopodium assembly (GO:0046847). These collectively point to leukocyte adhesion and activation with actin remodeling. Other terms reflect broader growth factor/hormone signaling and cross-talk (e.g., IGF receptor signaling, thyroid hormone response), while the neuronal synaptic depression term is likely incidental. Overall, the dominant theme is immune cell adhesion and activation signaling.","confidence":"Medium","size":11,"edges":12,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0060292","count":2},{"id":"GO:0051660","count":2},{"id":"GO:0033623","count":2},{"id":"GO:0097067","count":2},{"id":"GO:0032485","count":2}]},{"hash":"1887156160583119112","title":"RNA splicing and translation initiation regulation","description":"The cluster is enriched for mRNA splicing (via spliceosome) and splice site recognition, plus regulation of translational initiation and translation reinitiation, and regulatory ncRNA-mediated gene silencing, indicating a cohesive theme of post-transcriptional control at RNA processing and translation levels (with a developmental note in blastocyst formation).","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":8},{"id":"GO:0048026","count":8},{"id":"GO:0010610","count":7},{"id":"GO:0000398","count":6},{"id":"GO:0006446","count":5}]},{"hash":"1809781031643806379","title":"Ribosome Biogenesis and Metabolite Transport","description":"This cluster shows strong signals for ribosome biogenesis and cytoplasmic translation, pointing to protein synthesis machinery. It also features multiple transporter-related terms for taurine, methionine, heme, and long-chain fatty acids into peroxisomes, plus fatty acid catabolism and endoribonuclease activity regulation, suggesting a theme around translation components linked with nutrient/metabolite transport. Some terms like bacteriocin transport and stem cell proliferation are less clearly connected, so the label remains cautious and representative of the main theme.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0002181","count":3},{"id":"GO:0015734","count":3},{"id":"GO:0015910","count":3},{"id":"GO:0015886","count":3}]},{"hash":"669180695390496023","title":"Epigenetic Gene Regulation","description":"The cluster's GO terms center on transcription and chromatin modification, notably DNA-templated transcription and histone methylation (H3K4 and H3K79), suggesting regulation of gene expression at the chromatin level. Additional terms touch on gene expression regulation and some differentiation/secretion processes, but the dominant theme across the proteins appears to be epigenetic control of transcription.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0035264","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0034729","count":2}]},{"hash":"2090929082959191863","title":"Development and Cytoskeletal Remodeling","description":"The top GO terms cluster around cellular growth and development (cell division, multicellular organism growth) with cytoskeletal dynamics (actin filament branching, keratinization) and tissue-specific development (hippocampus development, sensory perception of touch). There are also general housekeeping processes (ribosomal large subunit export, phospholipid homeostasis) that support these programs, suggesting a broad theme of growth and structural remodeling across tissues rather than a single, cohesive pathway.","confidence":"Medium","size":11,"edges":24,"triangles":19,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0035264","count":4},{"id":"GO:0000055","count":4},{"id":"GO:0050975","count":3},{"id":"GO:0090135","count":3}]},{"hash":"731896202673036469","title":"Unknown","description":"GO terms across plant hormone synthesis, neural tissue structure, cell cycle regulation, transcription control, and NF-kappaB signaling show no coherent shared function for all proteins. The diverse annotations suggest either heterogeneous individual roles or inconsistent labeling, making a reliable, representative cluster label impossible to assign.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0009688","count":3},{"id":"GO:0021693","count":3},{"id":"GO:0044810","count":3},{"id":"GO:1990705","count":3},{"id":"GO:0007249","count":3}]},{"hash":"699752143278645426","title":"Ribosome biogenesis and RNA modification","description":"Top terms show RNA processing and ribosome biogenesis (rRNA modification; ribosomal large subunit biogenesis; tRNA wobble uridine modification and methylation), pointing to a core function in ribosome assembly and RNA modification; the other terms suggest related stress responses rather than defining the primary activity.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000154","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0030961","count":1},{"id":"GO:0072332","count":1},{"id":"GO:0006656","count":1}]},{"hash":"2095613227100328919","title":"Zinc Ion Homeostasis and Transport","description":"Most terms are about zinc handling: import of zinc across membranes, intracellular zinc ion homeostasis, and detoxification of zinc ions, with additional related metal ion transport (e.g., cadmium) and zinc starvation response. A couple of development terms (limb and prostate gland development) may reflect zinc\u2019s broad role in development but do not dominate the signal. Overall, the cluster is best described by zinc ion uptake, balance, and detoxification.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006882","count":1},{"id":"GO:0060173","count":1},{"id":"GO:0006830","count":1},{"id":"GO:1903615","count":1},{"id":"GO:0044749","count":1}]},{"hash":"2255475121680983913","title":"Unknown","description":"The term set combines fungal development (ascospore formation, pseudohyphal growth) with vertebrate development (digit morphogenesis, hair follicle placode formation) and diverse signaling/sensory activities (glutamate receptor signaling, action potential, taste perception). Because the GO terms span very distinct biological contexts with no clear shared pathway or process, there isn't a single cohesive function to label this cluster beyond Unknown.","confidence":"","size":11,"edges":19,"triangles":4,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030437","count":4},{"id":"GO:0042733","count":4},{"id":"GO:0007215","count":4},{"id":"GO:0060789","count":4},{"id":"GO:0001508","count":4}]},{"hash":"397993713868966888","title":"Mitochondrial Protein Import and p53-Regulated Apoptosis","description":"This cluster centers on processes related to mitochondria, including protein targeting to the mitochondrion, inner membrane insertion, and assembly of mitochondrial respiratory chain components, along with GO terms describing p53-mediated DNA damage response and regulation of cytochrome c release\u2014key aspects of the mitochondrial pathway of apoptosis. The combination suggests a module linking mitochondrial protein handling with p53-dependent stress responses and apoptotic control. Some terms about tubulin folding are less central but may reflect chaperone-related connections; overall, the mitochondrial function and apoptosis linkage best explains the group.","confidence":"Medium","size":11,"edges":28,"triangles":36,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":4},{"id":"GO:0045039","count":3},{"id":"GO:0072321","count":3},{"id":"GO:0033617","count":1},{"id":"GO:0007023","count":1}]},{"hash":"62304613410654280","title":"Viral entry and replication","description":"The GO terms point to core steps of viral infection and replication, including uncoating and membrane fusion of the virus, the viral life cycle, and RNA-templated DNA synthesis (reverse transcription), as well as host entry by symbionts and related immune responses (leukocyte migration) and general processes like protein secretion and folding that can be involved in host\u2013virus interactions. This cluster is best described as viral entry/replication-related functions.","confidence":"High","size":11,"edges":13,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0050900","count":1},{"id":"GO:0019061","count":1},{"id":"GO:0019064","count":1},{"id":"GO:0050714","count":1},{"id":"GO:0010849","count":1}]},{"hash":"1787518390732618463","title":"Unknown","description":"The GO terms cover disparate areas, including post-translational modifications (N-terminal acetylation and propionylation), amino-sugar metabolism (glucosamine/N-acetylglucosamine), and species-specific processes like mycothiol biosynthesis, plus unrelated developmental and chromatin-related terms (angiogenesis, leaf formation, subtelomeric heterochromatin). No single unifying function emerges, so a concise, representative label cannot be inferred. ","confidence":"","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0017198","count":10},{"id":"GO:0032920","count":10},{"id":"GO:0010125","count":10},{"id":"GO:0001525","count":10},{"id":"GO:0009447","count":10}]},{"hash":"852313975102994348","title":"Protein modification and autophagy","description":"The cluster's proteins are enriched for post-translational modifications (sumoylation, ubiquitination, lipidation) and autophagy-related processes (macroautophagy and piecemeal microautophagy of the nucleus), suggesting a role in protein quality control and turnover. Some terms are less clearly connected (amygdala development, molybdopterin biosynthesis), but the dominant signal points to coordinated protein regulation and degradation pathways.","confidence":"High","size":10,"edges":32,"triangles":44,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0018192","count":4},{"id":"GO:0061504","count":4},{"id":"GO:0021764","count":4}]},{"hash":"475293588500945438","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0045444","count":2},{"id":"GO:0035556","count":2},{"id":"GO:2001275","count":2}]},{"hash":"31932703011797388","title":"Retinoid and lipid metabolism","description":"The top terms converge on metabolism of retinoids (retinal, retinol) and lipids (cholesterol, prostaglandins, androgen metabolism) with supporting carbohydrate metabolism (fructose) and a touch of signaling (JAK-STAT). This suggests a cluster centered on metabolic pathways, particularly vitamin A and lipid/hormone-related processes, rather than a single narrow pathway.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":10},{"id":"GO:0042572","count":10},{"id":"GO:0046427","count":5},{"id":"GO:0001894","count":5},{"id":"GO:1901653","count":5}]},{"hash":"1196311998349250950","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":32,"triangles":51,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0042273","count":9},{"id":"GO:0000463","count":9},{"id":"GO:0000398","count":9},{"id":"GO:0000462","count":9},{"id":"GO:0031047","count":9}]},{"hash":"671415455843690131","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is clearly centered on ubiquitin-related protein turnover: autoubiquitination, K48-linked ubiquitination, and ubiquitin-dependent proteolysis are all represented. The presence of Wnt receptor catabolic process and negative regulation of organ growth aligns with ubiquitin-proteasome\u2013mediated receptor turnover and growth control, while peroxisomal import and ERAD-related terms can be tied to ubiquitin-based quality control across organelles. Overall, the common theme is ubiquitin-mediated degradation and protein turnover.","confidence":"High","size":10,"edges":10,"triangles":1,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:1900095","count":2},{"id":"GO:0070936","count":2},{"id":"GO:0038018","count":2},{"id":"GO:0046621","count":2}]},{"hash":"698909425912277956","title":"Mitochondrial and Cytoplasmic Translation","description":"The cluster is driven by translation-associated GO terms, including mitochondrial translation, cytoplasmic translation, and general translation, indicating a core translation machinery function. The presence of translation-stress related terms (response to antibiotic, response to cycloheximide) supports a translation-centric context, while a few other terms (chromatin organization, collagen catabolic process) appear as minor, likely incidental associations.","confidence":"Medium","size":10,"edges":31,"triangles":57,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0002181","count":1},{"id":"GO:1990090","count":1}]},{"hash":"1455123530023535533","title":"RNA Transcription and Ribosome Biogenesis","description":"This cluster centers on transcription by RNA polymerases I, II, and III, ribosome biogenesis, and translation initiation, with additional RNA processing/splicing terms. The convergence on RNA synthesis and ribosome assembly suggests a cohesive set of factors coordinating transcription, RNA processing, and ribosomal biogenesis.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0048025","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006360","count":2}]},{"hash":"915848051859904035","title":"RNA Processing and Ribosome Biogenesis","description":"The cluster is dominated by terms for ribosome assembly and RNA processing, including large subunit biogenesis, ITS1 cleavage, and spliceosomal rearrangements, with additional signals for regulatory ncRNA\u2013mediated gene silencing. These repeatedly point to RNA metabolism as the core theme, making \"RNA Processing and Ribosome Biogenesis\" a concise, representative label. Some terms are obsolete or broader, but they do not override the main pattern.","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":10},{"id":"GO:0031047","count":10},{"id":"GO:0008306","count":10},{"id":"GO:0000464","count":10},{"id":"GO:0045003","count":10}]},{"hash":"1834286686186913478","title":"Unknown","description":"The top GO terms cover highly diverse areas (immune regulation, ion transport, growth factor response, RNA localization, development, and even obsolete histone modification terms), with no single dominant function or pathway linking the proteins. This heterogeneity suggests there isn\u2019t a clear, coherent biological theme for this cluster, so a specific, representative label cannot be confidently assigned.","confidence":"","size":10,"edges":19,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043029","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0044344","count":1},{"id":"GO:1904246","count":1},{"id":"GO:0002635","count":1}]},{"hash":"1717134158740239393","title":"Prostate development and cell cycle regulation","description":"Top GO terms point to reproductive/hormonal context (prostate gland development, male sex differentiation, steroid hormone receptor complex assembly) alongside core cell-cycle and transcription processes (mitotic cell cycle, cell division, DNA-templated transcription). Some stress-related terms appear but are not dominant. This suggests a theme where reproductive development intersects with cell proliferation signals. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":2},{"id":"GO:0051348","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1458032839243528645","title":"Neuronal signaling and protein turnover","description":"The terms point to neuronal signaling and development (dopamine response, regulation of neuron maturation, postsynaptic potential, Wnt signaling) intertwined with protein homeostasis (ubiquitin-proteasome\u2013dependent degradation, endosome-Golgi transport). This suggests a cluster focused on how neurons regulate signaling pathways while controlling protein turnover and trafficking.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035751","count":2},{"id":"GO:1902499","count":2},{"id":"GO:0030011","count":2},{"id":"GO:1903125","count":2},{"id":"GO:1903351","count":2}]},{"hash":"2245121550172389353","title":"Ubiquitin-regulated immune signaling","description":"The cluster is dominated by immune-related terms (adaptive immune response, T cell homeostasis, regulation of RIG-I signaling) and ubiquitination (K11-linked, linear polyubiquitination), suggesting a core role in ubiquitin-dependent control of immune signaling. Supporting terms for ER-Golgi transport and cytoskeletal organization imply involvement of trafficking and cytoskeletal dynamics in these pathways. Overall, this set likely reflects ubiquitin-mediated regulation of immune signaling processes.","confidence":"Medium","size":10,"edges":17,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":2},{"id":"GO:0007026","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070979","count":1}]},{"hash":"625437641717561810","title":"GPCR-Mediated Innate Immunity and Pain Signaling","description":"The cluster centers on GPCR signaling as a major theme, with multiple terms pointing to innate immune recognition (detection of LPS, defense response to Gram-negative bacteria) and nociceptive/pain-related responses (formalin-induced pain). While a few terms are peripheral (chromatin localization, water homeostasis or obsolete terms), the dominant signals describe GPCR-driven signaling connected to immune sensing and pain. ","confidence":"Medium","size":10,"edges":13,"triangles":4,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006469","count":8},{"id":"GO:0050829","count":7},{"id":"GO:0060007","count":7},{"id":"GO:0014068","count":7},{"id":"GO:0061368","count":7}]},{"hash":"500361693168579719","title":"RNA Processing and Translation Machinery","description":"The cluster\u2019s top GO terms center on RNA processing (mRNA splicing, RNA methylation) and translation initiation/elongation (translation reinitiation, preinitiation complex formation, ribosomal subunit biogenesis). These suggest a cohesive RNA processing and ribosome-related function, despite a few broader development-related terms that may reflect pleiotropy or annotation noise. Overall, the dominant signal points to RNA processing and translation machinery.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0031175","count":3},{"id":"GO:0000398","count":3}]},{"hash":"22918110907077658","title":"Vesicle trafficking and exosome secretion","description":"The terms cluster around vesicle transport, lysosome targeting, Golgi retention, and exosome assembly/secretion, indicating involvement in the secretory/lysosomal trafficking pathway rather than a single enzymatic activity. Some outliers (sporulation, ATP export) may be noise, but the core signal supports vesicle/exosome dynamics.","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006622","count":1},{"id":"GO:0016192","count":1},{"id":"GO:0031954","count":1},{"id":"GO:1901998","count":1},{"id":"GO:0045743","count":1}]},{"hash":"814562815863329140","title":"Cell Proliferation and Development","description":"The cluster centers on mitotic cell cycle and DNA replication, with several terms tied to multicellular development (including lens development), pointing to cell division accompanying organismal growth. Additional terms like ER polarization, caveolin-mediated endocytosis, and metabolism likely reflect cellular infrastructure and energy needs in proliferating cells. While some terms are peripheral, the dominant theme is proliferation linked to development.","confidence":"Medium","size":10,"edges":27,"triangles":28,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0051534","count":8},{"id":"GO:0002088","count":8},{"id":"GO:0007275","count":8}]},{"hash":"1860448961184443533","title":"Neuronal spine morphogenesis and intracellular transport","description":"The top GO terms converge on neuronal development and spine remodeling (regulation and development of dendritic spines, hippocampus development) with substantial intracellular transport activity (ER-Golgi vesicle transport, nuclear import, and general protein transport). This suggests a functional theme around how neurons shape their synaptic structures via targeted trafficking, making a label centered on neuronal spine formation and vesicle transport appropriate.","confidence":"Medium","size":10,"edges":34,"triangles":58,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0035735","count":3},{"id":"GO:0030836","count":2},{"id":"GO:0000060","count":2},{"id":"GO:0006606","count":2}]},{"hash":"365351541126565767","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes\u2014mesoderm development and signaling, immune regulation, hormone signaling, metabolism, epigenetic modification, endosomal trafficking, and even yeast mating projection growth. The lack of a coherent, shared function across these terms (and several obsolete entries) makes it hard to assign a specific, meaningful theme to this cluster. ","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048332","count":1},{"id":"GO:0031384","count":1},{"id":"GO:0097676","count":1},{"id":"GO:0010796","count":1},{"id":"GO:1902459","count":1}]},{"hash":"1519477661160592559","title":"Actin cytoskeleton remodeling and cell adhesion","description":"This cluster is dominated by GO terms for actin filament organization and assembly (stress fibers, filopodium, actin branching) and Rac signaling, plus positive regulation of cell spreading/adhesion, pointing to actin-driven cytoskeletal remodeling and adhesion/motility. A few peripheral terms (mitotic spindle assembly, keratinization) are less central. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051496","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0046847","count":2},{"id":"GO:0016601","count":2},{"id":"GO:1900026","count":2}]},{"hash":"1368659219190095450","title":"Unknown","description":"No GO terms are provided for this cluster (Top Terms list is empty), and there is no clear shared biological function or process among the proteins based on the available data. Without functional terms to anchor a label, a meaningful high-level name cannot be inferred.","confidence":"","size":10,"edges":11,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[]},{"hash":"1792065995454397212","title":"Mitochondrial energy metabolism and nucleotide catabolism","description":"The top GO terms point to mitochondrial inner membrane functions, including proton motive force-driven ATP synthesis and cristae formation, alongside several dNTP catabolic processes (dUTP, dATP, dGTP, TTP). This combination suggests a cluster tied to mitochondrial energy production and nucleotide turnover, with additional terms like protein complex oligomerization and DNA protection fitting mitochondrial protein assembly and genome maintenance. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":1},{"id":"GO:0042407","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0035786","count":1},{"id":"GO:0046081","count":1}]},{"hash":"168690611713348638","title":"Developmental transcriptional regulation","description":"The terms cluster around gene expression control (DNA-templated transcription, Notch signaling modulation) and development-related processes (vasculogenesis, myoblast differentiation), suggesting a group of proteins involved in regulating transcription during muscle and blood vessel development. Some terms (stress granule assembly, certain hydroxylation processes) are less central but reflect broader regulation of RNA/protein function. Overall, the theme is transcriptional control in development, with emphasis on differentiation signaling pathways.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:2001214","count":2},{"id":"GO:0061428","count":2},{"id":"GO:0042264","count":2},{"id":"GO:0042265","count":2}]},{"hash":"2153110200746749608","title":"Nuclear gene expression and cell cycle","description":"This cluster is enriched for GO terms tied to nuclear processes: mRNA splicing via spliceosome, transcription termination of RNA Pol II, DNA replication, and kinetochore localization, plus meiotic/sporulation terms. These point to functions governing gene expression and chromosome segregation during cell division and meiosis. Some terms are peripheral (mesoderm development, adenosine biosynthesis), but the core theme centers on nuclear gene expression and cell cycle events.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007498","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0034501","count":2},{"id":"GO:0030437","count":2},{"id":"GO:0060079","count":2}]},{"hash":"2300011206378795791","title":"Nucleotide-sugar and polysaccharide biosynthesis","description":"The top GO terms are dominated by nucleotide-sugar and sugar biosynthesis (e.g., UDP-D-xylose, dTDP-rhamnose, galacturonate, galactose metabolism, ADP-L-glycero-beta-D-manno-heptose), which points to carbohydrate biosynthesis and the formation of polysaccharide constituents. Some outliers like hair follicle and labyrinthine layer development appear less connected, but the central theme clearly centers on carbohydrate/nucleotide-sugar biosynthetic processes.","confidence":"Medium","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0033320","count":4},{"id":"GO:0009699","count":4},{"id":"GO:0019305","count":4},{"id":"GO:0033481","count":4}]},{"hash":"1155047961996360271","title":"Ribosome Biogenesis and Translational Regulation","description":"The cluster is dominated by GO terms for ribosome biogenesis and translation initiation/regulation (ribosome assembly, preinitiation complex formation, translation reinitiation, and IRES-dependent initiation), with additional signals of ribosome disassembly and translational fidelity. This suggests a coherent module of proteins involved in ribosome production and control of protein synthesis, rather than disparate functions; the remaining terms (developmental and dosage compensation) appear more as incidental annotations rather than core cluster themes.","confidence":"High","size":9,"edges":23,"triangles":24,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0001701","count":2}]},{"hash":"348383261323330051","title":"Negative regulation of autophagy and endocytosis","description":"Several GO terms emphasize negative regulation of trafficking and degradation pathways (clathrin-dependent endocytosis, autophagosome maturation, GPCR internalization) along with related quality-control processes like aggrephagy and deglycosylation. This suggests the cluster functions as a module that dampens protein clearance and trafficking rather than promoting them. A nucleotide-excision repair term is present but less cohesive with the main theme.","confidence":"High","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1900186","count":7},{"id":"GO:1901097","count":7},{"id":"GO:1901340","count":7},{"id":"GO:1904021","count":7},{"id":"GO:0006517","count":7}]},{"hash":"1780023718273636762","title":"Microtubule dynamics and cytoskeleton organization","description":"These proteins cluster around microtubule-based processes: spindle dynamics (elongation, plus-/minus-end sliding, mitotic chromosome recapture) and regulation of microtubule-based processes, along with neuronal structural organization in cerebellar layers and anterograde transport of receptor complexes. The overarching theme is cytoskeletal/microtubule machinery underpinning both cell division and neuronal transport/architecture, making this label representative of the cluster\u2019s function.","confidence":"High","size":9,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000022","count":8},{"id":"GO:0031535","count":8},{"id":"GO:0021693","count":8},{"id":"GO:1990942","count":8},{"id":"GO:0001560","count":8}]},{"hash":"770483622394111657","title":"DNA Replication and Genome Maintenance","description":"This cluster centers on DNA metabolism: replication, recombination, primer synthesis, and double-strand break repair, suggesting a genome maintenance theme. A few RNA-processing and ribosome biogenesis terms are present but appear secondary.","confidence":"Medium","size":9,"edges":9,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006310","count":4},{"id":"GO:0006268","count":4},{"id":"GO:0006269","count":4},{"id":"GO:0019079","count":4}]},{"hash":"1171738439121672362","title":"Translation initiation and ribosome biogenesis","description":"The cluster is defined by strong enrichment for translation-related processes: translation reinitiation, formation of translation preinitiation complex, and ribosomal large subunit biogenesis, indicating a group of proteins tied to protein synthesis. Some unrelated terms (chromatin assembly, metal homeostasis, development) appear but do not override the core translation-focused signal.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0030433","count":3},{"id":"GO:2000011","count":3}]},{"hash":"1868715519375125984","title":"Genome maintenance and protein homeostasis","description":"The cluster centers on genome maintenance with DNA replication and CENP-A\u2013-containing chromatin assembly terms, while also showing strong signals for protein quality control and homeostasis across organelles (ER UPR, proteasomal regulation, oxidative proteolysis, mitochondrial protein import, vesicle formation). This suggests a broad connection between genome maintenance processes and cellular protein quality control mechanisms.","confidence":"Medium","size":9,"edges":19,"triangles":17,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0071897","count":5},{"id":"GO:0032979","count":3},{"id":"GO:0061641","count":3}]},{"hash":"479905074943350745","title":"Gene expression and cytoskeleton remodeling in development","description":"This cluster mixes RNA processing and protein synthesis machinery (spliceosome, ribosome biogenesis, translation initiation/reinitiation) with actin cytoskeleton dynamics (Arp2/3 nucleation, GTPase regulation, barbed-end capping) and development-associated processes (neuron projection development, TGF-beta response, prostate glandular differentiation). Such co-occurrence suggests a coordinated program where gene expression machinery supports cytoskeletal remodeling during developmental events like neurite outgrowth and epithelial differentiation.","confidence":"Medium","size":9,"edges":34,"triangles":70,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":3},{"id":"GO:0002188","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0031175","count":2}]},{"hash":"2064215691603307350","title":"Neuronal actin dynamics and filopodium signaling","description":"The cluster is dominated by actin-related processes (filopodium assembly, actin filament branching, actin polymerization regulation) and small GTPase signaling, which together point to actin-driven morphogenesis and protrusion formation. The inclusion of neuronal terms (GABAergic synaptic transmission, substantia nigra development) suggests a neural context for these cytoskeletal and adhesion processes, while adhesion and Wnt pathway terms tie into broader cell-adhesion and signaling mechanisms that shape neuronal connectivity. Overall, this constellation best fits coordinated actin remodeling in neurons and filopodium-mediated connectivity.","confidence":"Medium","size":9,"edges":9,"triangles":1,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046847","count":4},{"id":"GO:0007264","count":4},{"id":"GO:1900026","count":4},{"id":"GO:0090135","count":3},{"id":"GO:0030838","count":3}]},{"hash":"1629156583738528631","title":"DNA repair and telomere maintenance","description":"This cluster is dominated by GO terms related to DNA damage response, homologous recombination, nucleotide-excision repair, DNA replication, and telomere maintenance, indicating a theme of genome integrity maintenance. A couple of tRNA aminoacylation terms appear but do not override the core link to DNA repair and chromosome stability.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000724","count":2},{"id":"GO:0006430","count":1},{"id":"GO:0034502","count":1},{"id":"GO:0000722","count":1},{"id":"GO:0006293","count":1}]},{"hash":"476116544216162643","title":"Ion transport and osmotic homeostasis","description":"The cluster is enriched in terms related to osmotic stress response, water homeostasis, and transmembrane transport of ions (Na+, K+, Cu), along with maintaining electrochemical gradients, indicating a core function in membrane ion transport and osmoregulation. ATP biosynthesis likely supports these energy-demanding processes, reinforcing the transport/homeostasis theme.","confidence":"High","size":9,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0071470","count":3},{"id":"GO:0009992","count":3},{"id":"GO:0034220","count":3},{"id":"GO:0010248","count":2},{"id":"GO:1903249","count":2}]},{"hash":"1245853076957481478","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":9,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0016320","count":1},{"id":"GO:0048280","count":1},{"id":"GO:0048279","count":1},{"id":"GO:0006564","count":1},{"id":"GO:0034354","count":1}]},{"hash":"786032534542931006","title":"Unknown","description":"The terms span cell adhesion, GPCR signaling, several developmental patterning cues (spinal cord ventral patterning, Smoothened pathway), sensory stimulus detection (pain, maltose), vascular development (aorta), vitamin K response, and cell proliferation. No clear common function emerges, so a single, representative label cannot be assigned; thus Unknown with confidence None.","confidence":"","size":9,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0007155","count":1},{"id":"GO:0008283","count":1},{"id":"GO:1904209","count":1},{"id":"GO:0071307","count":1},{"id":"GO:0021775","count":1}]},{"hash":"2236518781945458855","title":"Unknown","description":"The GO terms include DNA-templated transcription, calcium signaling, hormone response, and plant-specific development terms, which are highly heterogeneous across species. There is no single coherent function or pathway that clearly ties these terms together, so a confident, specific label cannot be assigned.","confidence":"","size":9,"edges":32,"triangles":59,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0072160","count":3},{"id":"GO:1900466","count":3},{"id":"GO:0048283","count":3},{"id":"GO:0071277","count":3}]},{"hash":"860700170864290801","title":"Diverse stimulus-response signaling","description":"The proteins are linked to cellular responses and signaling across a range of stimuli\u2014xenobiotic exposure, pH changes, cGMP signaling, calcium handling in muscle/secretory systems, and immune/vascular modulation\u2014with one term touching retinal development. This points to a broad theme of signaling in response to diverse cues rather than a single, precise function, though several terms center on calcium, vascular regulation, and cardiac signaling. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":3},{"id":"GO:0010446","count":2},{"id":"GO:0046549","count":2},{"id":"GO:0010880","count":2},{"id":"GO:0043116","count":2}]},{"hash":"506256617249153006","title":"Unknown","description":"The top GO terms span diverse processes\u2014from nuclear transport and mitosis-related localization to spermatid development, lipid biosynthesis, and proteasome assembly\u2014showing no single cohesive function for the cluster. Because there is no clear common theme, there is no reliable label beyond Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033674","count":2},{"id":"GO:0007286","count":1},{"id":"GO:0051292","count":1},{"id":"GO:0034501","count":1},{"id":"GO:0000055","count":1}]},{"hash":"1475554093688160565","title":"Steroid signaling and mitochondrial membrane organization","description":"The cluster includes mitochondrial outer membrane organization and translocase assembly terms, pointing to mitochondrial membrane dynamics, along with steroid hormone receptor complex assembly and male development terms (prostate gland development, male sex differentiation), suggesting a link between steroid signaling and mitochondrial functions. A cellular response to type I interferon term is present but less central. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0070096","count":1},{"id":"GO:0007008","count":1},{"id":"GO:0030850","count":1},{"id":"GO:0006463","count":1}]},{"hash":"291599914618078791","title":"Carbohydrate Catabolism and Sugar Metabolism","description":"The cluster's GO terms are dominated by sugar catabolic and carbohydrate metabolic processes, including D-xylose, L-arabinose, L-fucose, D-glucuronate, glycerol-3-phosphate biosynthesis, and related pathways. These recurring themes point to carbohydrate metabolism as the core function of this cluster, with a few outliers (interleukin-13 response, antibiotic biosynthesis) that may reflect annotation noise.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0046167","count":1},{"id":"GO:0019563","count":1},{"id":"GO:0019569","count":1}]},{"hash":"29295359152012779","title":"Chitin biosynthesis and septum formation","description":"The GO terms are dominated by chitin biosynthetic process, cell wall organization, division septum site selection, and actomyosin contractile ring contraction, which together point to a module dedicated to cell wall construction and cytokinesis/septation. Some insect epithelial terms appear but the core signal is septum formation and chitin synthesis, suggesting a fungal-like cytokinesis theme with related processes.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007299","count":2},{"id":"GO:0042248","count":2},{"id":"GO:0000920","count":2},{"id":"GO:0034217","count":2},{"id":"GO:0071555","count":2}]},{"hash":"1398178103174978285","title":"Ribosome Biogenesis and Translation Regulation","description":"The cluster shows multiple GO terms centered on ribosome function and translation: translation, ribosome biogenesis, tyrosyl-tRNA aminoacylation, and rRNA modification, plus regulation of translational initiation and translational fidelity. The antibiotic response term aligns with ribosome-targeted drugs, and the heat response can modulate translation. While some transcription terms appear, the dominant theme is ribosome assembly and translational control.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0045947","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000455","count":2}]},{"hash":"1900517664695014276","title":"Ion Transport and Gradient Maintenance","description":"GO terms show a clear pattern of ion export (sodium, potassium, copper) and establishing/maintaining transmembrane electrochemical gradients, pointing to a core function in membrane ion transport and gradient regulation. ATP biosynthesis aligns with energy needs for transport, while a few terms related to amino acid biosynthesis and hormone response appear as minor outliers. Overall, the cluster is best described by its ion transport/homeostasis theme.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010248","count":5},{"id":"GO:1903249","count":5},{"id":"GO:0036376","count":5},{"id":"GO:0030007","count":5},{"id":"GO:0060003","count":5}]},{"hash":"1749719646910186317","title":"Virus Entry and Life Cycle","description":"These proteins show GO terms strongly linked to viral infection steps: entry (symbiont/virus entry into host, membrane fusion, uncoating), genome replication (RNA-templated DNA biosynthetic process, viral life cycle), and related host responses (leukocyte migration). The core theme appears to be viral entry and replication processes, with some host interaction signals.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein folding","top_go_terms":[{"id":"GO:0050900","count":3},{"id":"GO:0019061","count":3},{"id":"GO:0019064","count":3},{"id":"GO:0050714","count":3},{"id":"GO:0010849","count":3}]},{"hash":"1176550370456855199","title":"Zinc ion transport and homeostasis","description":"The top terms are dominated by zinc-related processes\u2014zinc ion import across the plasma membrane, intracellular zinc ion homeostasis, detoxification, and response to zinc ion starvation\u2014indicating the cluster mainly contains zinc transporters and homeostasis regulators. A couple of terms on limb development and CNS myelin maintenance could reflect broader zinc roles in development and neural maintenance, but they do not change the central theme.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006882","count":2},{"id":"GO:0060173","count":2},{"id":"GO:0006830","count":2},{"id":"GO:1903615","count":2},{"id":"GO:0044749","count":2}]},{"hash":"624421451706796504","title":"Mitotic spindle dynamics","description":"This cluster is dominated by mitosis- and microtubule-related processes: mitotic metaphase chromosome alignment, spindle elongation, plus- and minus-end directed microtubule sliding, and regulation of microtubule-based processes, indicating a cohesive group of proteins involved in spindle dynamics and chromosome segregation. Some terms like stress granule disassembly and cerebellar structure are less central to this core theme, but do not override the main signal of microtubule regulation during cell division.","confidence":"High","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007080","count":5},{"id":"GO:0035617","count":5},{"id":"GO:0000022","count":3},{"id":"GO:0031535","count":3},{"id":"GO:0021693","count":3}]},{"hash":"384631107452629078","title":"Ribosome Biogenesis and RNA Processing","description":"The cluster\u2019s terms heavily point to ribosome production and RNA handling, with ribosome biogenesis, ribosomal large subunit export from nucleus, and tRNA modification as prominent signals. Other terms appear more peripheral (e.g., liver development, copper homeostasis, autophagy regulation), likely reflecting annotation breadth rather than a cohesive alternate function. Overall, the central theme is ribosome assembly and RNA processing.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:1990386","count":1},{"id":"GO:0034379","count":1},{"id":"GO:0046909","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006400","count":1}]},{"hash":"1614203820929355443","title":"Fatty acid biosynthesis and catabolism cluster","description":"This cluster is dominated by GO terms for fatty acid metabolism, including medium- and long-chain fatty-acyl-CoA biosynthesis and catabolic processes, palmitic acid biosynthesis, and negative regulation of fatty acid biosynthesis, suggesting a lipid metabolism module. Additional terms like enterobactin biosynthesis and phenylacetate catabolism are present but less central to the core theme.","confidence":"High","size":8,"edges":8,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051792","count":3},{"id":"GO:0045892","count":3},{"id":"GO:0035338","count":3},{"id":"GO:0036116","count":3},{"id":"GO:1900535","count":3}]},{"hash":"565226087543917200","title":"Ribosome and Translation Machinery","description":"The cluster is dominated by GO terms related to translation and ribosome function, including cytoplasmic translation, translation, translational termination, ribosome biogenesis, and ribosomal subunit export from the nucleus, with supporting terms for mitochondrial translation. These together point to a group of proteins involved in ribosome assembly and protein synthesis across cytosolic and organellar contexts; the few outliers (cell cycle, salt-stress regulation, conjugation) are likely peripheral or secondary roles. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006415","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006400","count":1},{"id":"GO:0000055","count":1}]},{"hash":"699628759842527748","title":"Endosomal trafficking and receptor-mediated endocytosis","description":"The top GO terms cluster around endosomal transport routes (early endosome to Golgi, Golgi to endosome, endosome to vacuole) and overall vesicle trafficking, plus regulation of actin dynamics involved in endocytosis and regulation of receptor-mediated endocytosis and even EGFR signaling, all pointing to a shared role in endosome/vesicle trafficking and endocytosis. A few terms (iron import, pregnancy, storage protein import) are likely annotations or background noise, but the core theme remains vesicular trafficking and endocytic regulation.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902961","count":1},{"id":"GO:0032511","count":1},{"id":"GO:0034498","count":1},{"id":"GO:0034316","count":1},{"id":"GO:0045742","count":1}]},{"hash":"304576429252193982","title":"miRNA Processing and Transcription Regulation","description":"The cluster is dominated by RNA metabolism and transcription control terms, notably miRNA processing (GO:0031054) and miRNA catabolic process (GO:0010587), along with CRD-mediated mRNA stabilization. Additional links to transcription regulation (GO:0060567), DNA-templated transcription (GO:0006351), and transcription antitermination (GO:0031564) reinforce a coherent theme of RNA processing linked to transcriptional control. A single term related to kidney development is peripheral to the main signal. ","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070934","count":3},{"id":"GO:0010587","count":3},{"id":"GO:1901724","count":3},{"id":"GO:0060567","count":3},{"id":"GO:0031054","count":3}]},{"hash":"318219041326051667","title":"Central metabolism and Fe-S cluster biogenesis","description":"Top GO terms cluster around central carbon metabolism (TCA cycle, oxaloacetate, acetyl-CoA) and biosynthesis (biotin, porphyrinogen IX), together with iron-sulfur (Fe-S) cluster assembly and maturation. This points to a functional module focused on core metabolism supported by Fe-S biogenesis. Transcription-related terms appear incidental.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0019551","count":2},{"id":"GO:0006782","count":2},{"id":"GO:0009102","count":2}]},{"hash":"216772568627190233","title":"Unknown","description":"The terms span cellulose degradation, cell proliferation control, neural/behavioral traits, immune signaling, and detoxification, with no clear shared function or pathway linking the proteins. The heterogeneous GO terms and lack of network connections suggest there is no coherent cluster-level function to label beyond Unknown.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":4},{"id":"GO:0008284","count":3},{"id":"GO:0060244","count":2},{"id":"GO:0036343","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1856415266071466610","title":"Radial glial development and neuronal trafficking","description":"This cluster is characterized by neural development terms, notably forebrain radial glial cell differentiation and formation of radial glial scaffolds, suggesting a role in neural progenitor development. It also includes endocytosis and neurotransmitter receptor transport, pointing to membrane trafficking and receptor localization in neurons, alongside cell polarity maintenance. Chromatin remodeling and heterochromatin formation imply gene regulation during differentiation, tying together development and membrane trafficking in a neural context.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006348","count":3},{"id":"GO:0071963","count":3},{"id":"GO:0006897","count":3}]},{"hash":"184392382614538606","title":"Calcium signaling and phosphorylation pathways","description":"Most terms center on calcium dynamics (calcium release into cytosol, calcium transport) and signaling regulation via phosphorylation (protein phosphorylation/dephosphorylation, inositol phosphate metabolism) and receptor-mediated signaling (Fc-epsilon receptor pathway). While one term points to cell cycle (G2/M) and another to muscle fate specification, the dominant theme across the cluster is calcium-dependent signal transduction modulated by kinases.","confidence":"Medium","size":8,"edges":9,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0051281","count":2},{"id":"GO:0038095","count":2},{"id":"GO:0007190","count":2},{"id":"GO:0043647","count":2}]},{"hash":"1849196277244895313","title":"Signaling Regulation and Proteostasis","description":"The cluster features GO terms focused on positive regulation of various signaling pathways (NF-kappaB/I-kappaB, intracellular estrogen receptor signaling, and cell surface receptor signaling) alongside processes related to protein turnover (proteasomal ubiquitin-dependent degradation and ufmylation) and protein localization to the ER. This suggests a theme of coordinated modulation of signaling activities with proteostasis mechanisms, rather than a single enzyme or pathway. Therefore, a label capturing both signaling regulation and proteostasis is appropriate.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051092","count":1},{"id":"GO:1990592","count":1},{"id":"GO:0033146","count":1},{"id":"GO:1905636","count":1},{"id":"GO:1905552","count":1}]},{"hash":"410512032508047344","title":"Bacterial energy metabolism and secretion","description":"The terms cluster around membrane-associated energy production (proton motive force-driven ATP synthesis, proton transmembrane transport) and lipid metabolism, plus components for bacterial secretion and flagellum assembly, suggesting a group of proteins tied to bacterial energetic and motility/secretion machinery. Some eukaryotic-related terms (angiogenesis, transcription regulation) are outliers, but the dominant theme remains bacterial energy and secretion systems.","confidence":"Medium","size":8,"edges":8,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042776","count":2},{"id":"GO:0006933","count":2},{"id":"GO:0001525","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0015991","count":2}]},{"hash":"1296554983357409884","title":"GPI anchor biosynthesis and protein glycosylation","description":"This cluster is dominated by GO terms tied to GPI anchor biosynthesis and related glycosylation steps (GO:0006506, GO:0006488, GO:0016255), suggesting a shared function in attaching and assembling GPI anchors on proteins. The remaining terms appear as diverse or unrelated processes (e.g., histone methylation, thylakoid or fungal cell wall organization), likely representing noise or multifunctionality rather than core cluster themes.","confidence":"Medium","size":8,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006506","count":3},{"id":"GO:0006488","count":2},{"id":"GO:0046425","count":1},{"id":"GO:0016255","count":1},{"id":"GO:0050976","count":1}]},{"hash":"1118860936227316476","title":"Rab-Mediated Neuronal Signaling and Development","description":"The top terms center on neuronal morphogenesis and signaling: regulation of axonogenesis, substantia nigra development, sensory perception, and actin filament branching\u2014all key to neuronal connectivity and growth. The Rab protein signal transduction term reinforces vesicle trafficking crucial for neuronal communication, supporting a coherent theme of neuronal development and signaling. Some terms relate to stress responses or epithelial processes, but these are less representative of the core cluster.","confidence":"Medium","size":8,"edges":13,"triangles":7,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0050771","count":3},{"id":"GO:0032482","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0042493","count":3}]},{"hash":"2118997855925149670","title":"Ubiquitin-Mediated Proteolysis","description":"The Top Terms are dominated by ubiquitination-related processes (ubiquitin-dependent ERAD pathway, autoubiquitination, and K63-linked ubiquitination) and ubiquitin-dependent protein catabolic process, pointing to a cluster centered on tagging proteins for degradation via ubiquitin signaling. Some peripheral terms like peroxisome import may reflect broader protein quality control, but the core theme is ubiquitin-mediated degradation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0051865","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0016558","count":3},{"id":"GO:0002635","count":2}]},{"hash":"894955194959872171","title":"Calcium-signaling and nuclear transport mediators","description":"The cluster shows strong hints of calcium signaling (regulation of calcium release from the sarcoplasmic reticulum, excitatory postsynaptic potential, and cardiac signaling) combined with RNA/nuclear transport (mRNA transport and NLS-bearing protein import). This suggests a group of proteins that coordinate calcium-dependent signaling with intracellular transport processes, with additional, broader links to development. Confidence: Medium","confidence":"","size":7,"edges":8,"triangles":2,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051028","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006607","count":4},{"id":"GO:0000086","count":3},{"id":"GO:0030437","count":3}]},{"hash":"1321909670410421562","title":"Redox Signaling and Immune Response","description":"The set highlights redox-related processes (oxidation-reduction, hydrogen peroxide catabolic, peptidyl-cysteine oxidation, cellular oxidant detoxification) and signaling events (I-kappaB phosphorylation, regulation of stress-activated MAPK cascade) that underpin NF-\u03baB/MAPK pathways, with an additional note of NK cell cytotoxicity suggesting immune activity. A few terms like lipoprotein biosynthetic process and spermatogenesis appear as outliers and may reflect broader functional annotations, but the core theme is oxidative stress response coupled with immune signaling.","confidence":"Medium","size":7,"edges":10,"triangles":4,"max_degree":6,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0042158","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0007283","count":4},{"id":"GO:0032872","count":4},{"id":"GO:0030416","count":4}]},{"hash":"2062168170368093039","title":"Nucleotide Metabolism and Cofactor Biosynthesis","description":"The top GO terms are dominated by nucleotide salvage, phosphorylation, and biosynthetic processes (AMP salvage, ADP biosynthesis, CDP biosynthesis, ITP metabolism, nucleoside monophosphate phosphorylation) plus coenzyme A biosynthetic process. A few development terms (brain, liver) and translesion synthesis appear less central, likely reflecting incidental annotations for some members. Overall, the cluster seems to group proteins involved in nucleotide metabolism and cofactor biosynthesis.","confidence":"Medium","size":7,"edges":15,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0044209","count":4},{"id":"GO:0046705","count":3},{"id":"GO:0046041","count":3},{"id":"GO:0046940","count":3},{"id":"GO:0015937","count":3}]},{"hash":"478393913265953914","title":"Inflammatory signaling and angiogenesis regulation","description":"The cluster\u2019s top terms center on I-kappaB phosphorylation (NF-kB pathway), defense against Gram-negative bacteria (LPS detection), and negative regulation of VEGF signaling/angiogenesis, suggesting a core theme of immune-triggered signaling intertwined with vascular growth control. A few terms about synapse assembly and vestibulo-ocular reflex appear, but the dominant signal is inflammatory signaling and angiogenesis regulation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007252","count":2},{"id":"GO:0016525","count":2},{"id":"GO:0051965","count":2},{"id":"GO:1900747","count":2},{"id":"GO:0050829","count":1}]},{"hash":"127280897079633195","title":"Ubiquitin-regulated mitotic progression","description":"The dominant GO terms point to ubiquitin-related protein turnover (K11-linked ubiquitination; ubiquitin-dependent protein catabolic process) and control of mitotic progression (metaphase/anaphase transition), suggesting proteins in this cluster function in tagging substrates for degradation to regulate mitosis. While terms related to innate immunity and reproductive development appear, they are secondary and do not redefine the core theme. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0045842","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0046661","count":2}]},{"hash":"577064393818208403","title":"Gene Expression and RNA Processing","description":"This cluster is enriched for GO terms tied to gene expression and RNA biogenesis, including DNA-templated transcription, translation, regulation of translation, maturation of SSU rRNA, and tRNA modification. These converge on core transcription/translation machinery and RNA processing steps, suggesting the proteins function in gene expression control. A couple of terms (telomere maintenance and lipopolysaccharide biosynthesis) appear as outliers, likely noise or species-specific annotations, but the dominant theme remains expression and RNA processing.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006468","count":1},{"id":"GO:0070525","count":1},{"id":"GO:0000722","count":1}]},{"hash":"2299554690462201537","title":"Multi-Pathway Metabolism and Systemic Physiology","description":"The top GO terms point to diverse metabolic activities (fatty acid biosynthesis, fructose and galactose metabolism, D-xylulose 5-phosphate biosynthesis, and retinoic acid metabolism), suggesting a metabolism-centric cluster. The inclusion of systemic physiological terms (respiratory system process, positive regulation of blood pressure) and a drug-response term indicates broader physiological regulation beyond a single pathway. This combination supports labeling the cluster as metabolism with systemic regulatory roles.","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0006633","count":6},{"id":"GO:0006069","count":6},{"id":"GO:0018119","count":6},{"id":"GO:0046370","count":6},{"id":"GO:0033498","count":6}]},{"hash":"1393777953028536705","title":"Sugar transport and glucose metabolism","description":"This cluster is dominated by GO terms related to carbohydrate transport and glucose handling, including D-glucose transmembrane transport, galactose and trehalose transport, glucose starvation response, and glucose import in response to insulin, indicating a cohesive theme of sugar uptake and metabolism. A few terms like nitrate assimilation or chromate response appear, but the primary signal centers on sugar transport/metabolism.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046687","count":1},{"id":"GO:0071332","count":1},{"id":"GO:0042128","count":1},{"id":"GO:0044381","count":1},{"id":"GO:0015771","count":1}]},{"hash":"1838511933802507209","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are focused on ubiquitination\u2014ubiquitin-dependent protein catabolic process, autoubiquitination, and polyubiquitination\u2014indicating these proteins primarily participate in tagging and degrading proteins via the ubiquitin-proteasome system. Some distant terms (e.g., peroxisome import, certain obsolete/regulatory terms) are less representative and do not override the main ubiquitination theme.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":4},{"id":"GO:0000209","count":3},{"id":"GO:0070512","count":3},{"id":"GO:2000620","count":3}]},{"hash":"1444029540674234478","title":"Unknown","description":"The terms cover heat response, cytoskeletal organization, immune signaling, cell migration, cardiac development and electrophysiology, synaptic regulation, spindle assembly, and muscle regeneration, with no single coherent function tying them all together.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0007253","count":3},{"id":"GO:0051017","count":3},{"id":"GO:0045083","count":3},{"id":"GO:0016477","count":3}]},{"hash":"643303403541651205","title":"Unknown","description":"The GO terms are heterogeneous, including photosynthesis-related terms (photosynthesis, nonphotochemical quenching, proton transmembrane transport) alongside xenobiotic catabolic processes, apoptosis regulation, and a meiosis term, with no edges or cohesive functional theme linking the proteins. This lack of a shared, interpretable function makes a specific label Uncertain, so Unknown is appropriate.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1902600","count":1},{"id":"GO:0010196","count":1},{"id":"GO:0046232","count":1},{"id":"GO:0015979","count":1}]},{"hash":"2304108853954875628","title":"Unknown","description":"The GO terms are diverse, spanning plant development, immune regulation, iron metabolism, ER quality control, and post-translational processing, with no single unifying function evident. Because the terms do not converge on a shared pathway or process, a specific, representative label cannot be confidently assigned.","confidence":"","size":7,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010103","count":1},{"id":"GO:0042135","count":1},{"id":"GO:0006879","count":1},{"id":"GO:0045830","count":1},{"id":"GO:0033572","count":1}]},{"hash":"1194708608331658569","title":"Mitochondrial fatty acid oxidation and apoptosis regulation","description":"The top terms cluster around mitochondrial function, especially regulation of mitochondrial membrane permeability in apoptotic signaling, along with fatty acid metabolism (beta-oxidation, acetyl-CoA catabolic processes, ketone body biosynthesis). This points to a group of proteins involved in mitochondrial energy metabolism coupled with control of cell survival. Some development-related terms appear but do not define the core function of the cluster. ","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:1902109","count":5},{"id":"GO:0006635","count":5},{"id":"GO:0014070","count":5},{"id":"GO:0046951","count":5},{"id":"GO:0001889","count":5}]},{"hash":"1078715742428908040","title":"Kinetochore Assembly and Spindle Organization","description":"The top GO terms are dominated by kinetochore- and spindle-related processes, such as mitotic spindle organization, attachment of spindle microtubules to the kinetochore, kinetochore assembly, and meiosis I kinetochore attachment, indicating a shared function in chromosome segregation. A few terms related to transcription or other processes appear, but the core theme centers on kinetochore-spindle dynamics.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030472","count":1},{"id":"GO:0051315","count":1},{"id":"GO:0051382","count":1},{"id":"GO:0051455","count":1},{"id":"GO:1903394","count":1}]},{"hash":"786320603119466005","title":"Transsulfuration and H2S biosynthesis","description":"The top GO terms converge on sulfur-containing amino acid metabolism: L-serine catabolic to pyruvate, transsulfuration with cysteine biosynthesis via cystathionine, and hydrogen sulfide production. Together these indicate a module focused on flux through sulfur amino acids and H2S biosynthesis, with related sulfur pathways (e.g., 2-oxobutyrate and cyanide metabolism) as supporting connections. This cohesive theme supports labeling the cluster as Transsulfuration and H2S biosynthesis.","confidence":"High","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006565","count":5},{"id":"GO:0019346","count":4},{"id":"GO:0019343","count":4},{"id":"GO:0070814","count":4},{"id":"GO:0051289","count":3}]},{"hash":"1054670818463705902","title":"Cardiac and skeletal muscle signaling and cytoskeleton","description":"These terms point to muscle and heart development/function (actin bundle assembly, skeletal muscle regeneration, SA node regulation, Notch signaling in heart field) and cytoskeletal processes (cell migration, spindle assembly). While there are a few unrelated terms, the dominant theme is muscle/heart signaling and cytoskeletal dynamics.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0045083","count":1},{"id":"GO:0016477","count":1}]},{"hash":"780469685045218741","title":"DNA Metabolism and Cell Cycle Regulation","description":"This cluster centers on nuclear nucleic acid processes and cell fate control, with terms like DNA catabolic process, DNA recombination, and positive regulation of G1/S transition, alongside apoptotic processes. Although there are some unrelated or obsolete terms present, the core theme appears to be DNA metabolism linked to proliferation and apoptosis, suggesting a cohesive functional group around nuclear DNA processing and cell cycle control.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":1},{"id":"GO:0080111","count":1},{"id":"GO:0044179","count":1},{"id":"GO:0006308","count":1},{"id":"GO:1900087","count":1}]},{"hash":"88662486685963862","title":"ER Protein Folding and Oxidative Stress Response","description":"The cluster is dominated by GO terms for managing oxidative stress and redox homeostasis (cellular oxidant detoxification, cellular response to oxidative stress, redox homeostasis) along with endoplasmic reticulum\u2013related processes (response to ER stress, protein folding in ER). This points to a cohesive theme of maintaining protein folding and redox balance under ER stress. A few transcription-related terms are present but appear secondary to the core ER folding and redox functions. ","confidence":"Medium","size":7,"edges":12,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0033158","count":1},{"id":"GO:0055114","count":1}]},{"hash":"686653798815862815","title":"Redox-linked metabolism and nutrient response","description":"The terms cluster around redox biology (oxidation-reduction processes, nitric oxide metabolism, S-nitrosylation) and metabolic pathways (triglyceride catabolism, cholesterol biosynthesis regulation, nitrate assimilation), with an additional note of nutrient response and a small signal of IL-6 production. This points to a theme where cellular redox state intersects with metabolic and nutrient signaling, with a minor inflammatory component. Some GO terms are obsolete, but the core pattern supports a redox-metabolism-nutrient axis.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009636","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0018119","count":2}]},{"hash":"387875681930198193","title":"Cell Cycle, Chromatin Regulation, and Proteostasis","description":"The terms center on G2/M transition, protein ubiquitination, histone modification/heterochromatin formation, and cytoplasmic protein quality control, indicating a module that links cell cycle progression with chromatin state and proteostasis. Immune signaling terms appear but are less representative of the cluster\u2019s main function.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000086","count":6},{"id":"GO:0070979","count":6},{"id":"GO:0061186","count":6},{"id":"GO:0070076","count":6},{"id":"GO:0071455","count":6}]},{"hash":"1076840463331142777","title":"Translation and Ribosome Biogenesis","description":"The cluster\u2019s top GO terms are centered on protein synthesis, with translation (GO:0006412) and cytoplasmic translation (GO:0002181) plus ribosome biogenesis (GO:0042254) indicating a core involvement in the translation machinery. The remaining terms (immune responses, globoside biosynthesis, amino acid starvation response, plant development, and hemidesmosome assembly) seem less related to this theme, suggesting some annotation noise or multifunctional proteins. Overall, the group most likely represents proteins involved in the translation apparatus and ribosome assembly.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":1},{"id":"GO:0019731","count":1},{"id":"GO:0002227","count":1},{"id":"GO:0002181","count":1}]},{"hash":"1399456755470843657","title":"Ribosome biogenesis and translation regulation","description":"GO terms indicate translation and ribosome assembly/regulation, including large subunit preribosome assembly and initiation complex regulation, with a peripheral link to mitochondrial translation termination. This suggests a cohesive group of proteins involved in ribosome biogenesis and control of protein synthesis.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0070126","count":2},{"id":"GO:0090070","count":1},{"id":"GO:1902626","count":1},{"id":"GO:1901194","count":1}]},{"hash":"1953487777191490077","title":"Nuclear RNA Processing and Splicing Machinery","description":"The Top Terms point to RNA maturation and surveillance processes, including nuclear import, spliceosome/snRNP assembly, tRNA processing, P-body assembly, and deadenylation-dependent decapping of mRNA, indicating a cluster focused on RNA processing and metabolism in the nucleus and related surveillance pathways. ","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":6},{"id":"GO:1990141","count":6},{"id":"GO:0000245","count":6},{"id":"GO:0008033","count":6},{"id":"GO:0042633","count":6}]},{"hash":"1138726849115652452","title":"Ubiquitin-Dependent Protein Degradation and Cell Cycle","description":"The GO terms co-occurring are strongly centered on ubiquitin-mediated proteolysis (ERAD, protein polyubiquitination, and catabolic processes) and cell cycle processes (mitotic cell cycle, cell division). While some terms touch on splicing or translation initiation, the dominant theme is ubiquitin-dependent degradation linked to cell-cycle control, suggesting a cluster of proteins involved in protein turnover regulating proliferation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0000278","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2077511612669924692","title":"Bacterial cell wall biosynthesis and morphogenesis","description":"Based on GO terms such as peptidoglycan biosynthetic process, cell wall organization, regulation of cell shape, and regulation of bipolar cell growth, the cluster appears to center on bacterial cell wall biogenesis and morphogenesis. Translation and various biosynthesis terms are more general background, and SOS response suggests stress signaling that can accompany envelope perturbations, but the core signals point to cell wall construction and shape control.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0009252","count":1},{"id":"GO:0008360","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0009432","count":1}]},{"hash":"1569339190005362610","title":"ER Targeting and Unfolded Protein Response","description":"Dominant GO terms point to SRP-dependent cotranslational protein targeting to the membrane (ER targeting), cellular response to unfolded protein, and chaperone-assisted protein refolding, along with regulation of ER-stress\u2013related apoptosis. This pattern suggests the cluster reflects ER quality-control pathways and the unfolded protein response rather than core DNA replication or morphogenesis functions, despite a few more general terms present.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006616","count":5},{"id":"GO:0000742","count":5},{"id":"GO:1903751","count":5},{"id":"GO:1903382","count":5},{"id":"GO:0006260","count":5}]},{"hash":"2189882072189672790","title":"Unknown","description":"The listed terms span several unrelated cellular processes (ribosome biogenesis, cell division, chromatin organization, proteolysis, collagen catabolism, kidney filtration), with no single pathway linking the proteins and no interactions observed (edges 0). Therefore there isn't a clear shared function to name; label Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000747","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030574","count":1},{"id":"GO:0034724","count":1}]},{"hash":"1088392806662347808","title":"Tissue Development and Differentiation","description":"The top GO terms indicate morphogenesis and differentiation across multiple tissues (neural, cardiac, kidney, seed, etc.), along with general cell organization. While there are no interactions among proteins, the common thread is developmental programs rather than a single pathway, suggesting the cluster reflects broad tissue development and differentiation processes.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072284","count":1},{"id":"GO:0045805","count":1},{"id":"GO:0021702","count":1},{"id":"GO:0045216","count":1},{"id":"GO:0048317","count":1}]},{"hash":"971184461519865610","title":"Unknown","description":"The cluster shows several distinct themes\u2014ion and water homeostasis, riboflavin biosynthesis, neuromuscular processes and motor neuron differentiation, and post-transcriptional regulation\u2014without a common dominant function. The sparse connectivity (one edge, no triangles) and only a few shared terms suggest there isn\u2019t a cohesive biological role tying these proteins together. Therefore Unknown.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009992","count":2},{"id":"GO:0034220","count":2},{"id":"GO:0009231","count":2},{"id":"GO:0050885","count":1},{"id":"GO:0048009","count":1}]},{"hash":"62762808939028776","title":"Immune response regulation and transcriptional control","description":"The cluster shows strong representation of innate and adaptive immune responses, chemokine production, and NOS regulation, with accompanying transcriptional regulation and ubiquitin-dependent protein turnover, suggesting proteins that modulate immune signaling and gene expression. Some terms are obsolete, but the immune-related terms are most representative of the cluster\u2019s function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0002635","count":1},{"id":"GO:0070512","count":1},{"id":"GO:2000620","count":1},{"id":"GO:1903886","count":1}]},{"hash":"2299593494171551013","title":"Unknown","description":"The top GO terms span plant development (meristem identity) and photosystem adjustment, as well as animal signaling (BMP/TGF-\u03b2/SMAD, NF-\u03baB) and cellular processes like dephosphorylation and nuclear export, with no clear, shared function tying the proteins together. There are no interactions (edges) to suggest a cohesive pathway or complex, so a single interpretable label isn\u2019t supported.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010074","count":1},{"id":"GO:0030514","count":1},{"id":"GO:0042347","count":1},{"id":"GO:0080005","count":1},{"id":"GO:0035970","count":1}]},{"hash":"1416775668999599331","title":"RNA transcription and ribosome biogenesis","description":"The GO terms cluster around RNA synthesis (Pol I/II/III transcription, RNA-templated transcription, elongation, termination), mRNA export, and ribosome biogenesis, suggesting a coherent group of proteins involved in transcriptional activity and ribosome assembly.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0006360","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0070893","count":1},{"id":"GO:0042254","count":1}]},{"hash":"370174660004410143","title":"Innate immune signaling and cell fate regulation","description":"TheTop GO terms cluster around innate immune pathways (regulation of Toll-like receptor signaling; defense response to fungus) and downstream cell fate outcomes (regulation of necroptotic process, negative regulation of apoptotic process, and regulation of cell cycle), with ubiquitination as a regulatory mechanism. While a few catabolic terms (chitin, polysaccharide) appear, the dominant theme ties innate immune signaling to cell survival/death decisions, justifying a label focused on innate immunity and cell fate control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034121","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060544","count":1}]},{"hash":"2293915545719590063","title":"Spindle Assembly and Chromosome Segregation","description":"The top GO terms cluster around mitotic spindle dynamics: positive regulation of microtubule polymerization, attachment of spindle microtubules to kinetochores, and mitotic sister chromatid biorientation. Together these point to roles in spindle assembly and accurate chromosome segregation during mitosis. Some terms relate to broader ubiquitin/nuclear processes, but the dominant signal is mitotic spindle function.","confidence":"Medium","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0035987","count":1},{"id":"GO:0051987","count":1},{"id":"GO:0031116","count":1},{"id":"GO:1990758","count":1},{"id":"GO:2000203","count":1}]},{"hash":"1812406398024413950","title":"DNA Replication and Meiotic Cell Cycle","description":"The top GO terms are dominated by DNA replication and cell cycle processes, including mitotic and premeiotic replication, along with female gamete generation, which together point to replication-linked events during meiosis/oogenesis. Subtelomeric heterochromatin formation and eggshell chorion gene amplification further support replication-associated chromatin remodeling in germ-line contexts. A few outliers (e.g., bacteriochlorophyll biosynthetic process) may be noise, but the core signal centers on DNA replication and meiosis-related cell-cycle activity.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006268","count":6},{"id":"GO:1902969","count":5},{"id":"GO:0006279","count":5},{"id":"GO:0006348","count":5}]},{"hash":"1950458783362504493","title":"Lipid Catabolism and Mobilization","description":"The proteins are enriched for triglyceride catabolic processes, triglyceride mobilization, and phospholipid catabolic processes (PE and PC), plus triglyceride acyl-chain remodeling, indicating a lipid breakdown/remodeling role. A smaller signal for transport and a regulatory hint from negative regulation of PKA activity does not outweigh the lipid-centric terms, supporting a cohesive lipid metabolism cluster.","confidence":"High","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":3},{"id":"GO:0036153","count":3},{"id":"GO:0019433","count":3},{"id":"GO:0046338","count":3},{"id":"GO:0034638","count":3}]},{"hash":"780887471444288465","title":"Unknown","description":"The terms span diverse processes including thiamine biosynthesis, various catabolic pathways (thymidine, leucine, camphor), redox homeostasis, membrane potential regulation, immune response to lipopolysaccharide, and gastrulation, with several obsolete GO terms. This wide diversity does not point to a single coherent function for the six proteins, so a specific label is not supported.","confidence":"","size":6,"edges":13,"triangles":12,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0032496","count":3},{"id":"GO:0007369","count":3},{"id":"GO:0042135","count":3}]},{"hash":"1349240991519787166","title":"Mitochondrial ROS-Linked Apoptosis Regulation","description":"Proteins in this cluster are enriched for mitochondrial-related processes (respiratory chain complex IV assembly, respirasome assembly, inner membrane insertion) and apoptosis signaling (extrinsic pathway, regulation of intrinsic pathway), with a notable emphasis on ROS metabolism and stress responses, suggesting a mitochondria-centered role in apoptosis and oxidative stress signaling.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097191","count":1},{"id":"GO:0072593","count":1},{"id":"GO:0045732","count":1},{"id":"GO:0071300","count":1},{"id":"GO:0035458","count":1}]},{"hash":"13524467049339809","title":"Chromatin Regulation and Ubiquitin-Proteasome Proteostasis","description":"The cluster centers on chromatin-related processes (heterochromatin formation, silencing regulation, histone demethylation) and proteostasis via the ubiquitin-proteasome system (K11-linked ubiquitination, cytoplasmic protein quality control), with a notable link to cell-cycle control (G2/M transition) through ubiquitin signaling. Some immune/stress responses appear (hyperoxia, Fc-epsilon receptor, interferon signaling) but are less central, making the core theme chromatin regulation together with ubiquitin-mediated proteolysis.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0000086","count":5},{"id":"GO:0070979","count":5},{"id":"GO:0061186","count":5},{"id":"GO:0070076","count":5},{"id":"GO:0071455","count":5}]},{"hash":"1988872208585249828","title":"Ribosome Biogenesis and Translational Fidelity","description":"The cluster centers on translation-related processes: translation, ribosome biogenesis, tyrosyl-tRNA aminoacylation, and rRNA pseudouridine synthesis, with explicit terms on translational fidelity and its maintenance/regulation. These together point to ribosome assembly and the accuracy of protein synthesis as the core theme; other terms about transcription or stress responses are supportive rather than central.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0006437","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1996949800655342736","title":"Nuclear RNA processing and splicing","description":"The cluster shows strong representation of RNA-related processes: import into nucleus, spliceosome and snRNP assembly, tRNA processing, and mRNA decay/P-body dynamics, plus links to chromatin-related RNA regulation (pericentric heterochromatin formation). This constellation points to a cohesive function in RNA maturation and splicing within the nucleus, with related post-transcriptional regulation mechanisms likely coordinated among the proteins.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":4},{"id":"GO:1990141","count":4},{"id":"GO:0000245","count":4},{"id":"GO:0008033","count":4},{"id":"GO:0042633","count":4}]},{"hash":"535139899918435830","title":"Developmental signaling and membrane trafficking","description":"The proteins appear linked to development and signaling (lens development, multicellular organism development, regulation of calcineurin-NFAT signaling) as well as membrane trafficking and polarity (caveolin-mediated endocytosis, ER polarization), with additional roles spanning migration, translation regulation, metabolism, and protease activity that may reflect growth/remodeling contexts. Overall, a developmental/remodeling theme with emphasis on signaling and membrane dynamics.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0051534","count":5},{"id":"GO:0002088","count":5},{"id":"GO:0007275","count":5},{"id":"GO:0061167","count":5},{"id":"GO:0072584","count":5}]},{"hash":"1133606251947371075","title":"Innate and Adaptive Immune Response","description":"The top terms are dominated by innate immune response and adaptive immune response, indicating this cluster centers on immune-related proteins. Additional terms such as ubiquitin-dependent protein catabolic process, chemokine production, and microtubule-associated localization suggest roles in intracellular immune signaling and regulation. Together, these features point to a cohesive immune-function cluster rather than a single narrow pathway.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0035372","count":2},{"id":"GO:0051092","count":2},{"id":"GO:0002635","count":1},{"id":"GO:0070512","count":1}]},{"hash":"1790197657311115103","title":"Unknown","description":"Top GO terms span cell migration, telomere maintenance, mRNA processing, fat cell differentiation, stress responses, and CDK activity regulation, without a single cohesive function tying them together. The diversity suggests no clear, interpretable cluster theme, so a specific label cannot be confidently assigned.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0006397","count":2},{"id":"GO:0045444","count":2},{"id":"GO:2001275","count":2}]},{"hash":"861008092391494836","title":"Unknown","description":"The top GO terms cover highly diverse processes (redox response, plant hormone signaling, elastin metabolism, iron transport regulation, maternal reproductive processes, glucose metabolism, muscle differentiation, circadian rhythm, ethylene signaling, and autophosphorylation). This lack of a single cohesive function or pathway indicates no clear common theme, suggesting a heterogeneous or noisy cluster rather than a unified module.","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051775","count":4},{"id":"GO:0009736","count":4},{"id":"GO:0051541","count":3},{"id":"GO:0034757","count":3},{"id":"GO:0060137","count":3}]},{"hash":"1284790385012889619","title":"Regulation of signaling, cell cycle, and death","description":"The cluster's GO terms cluster around regulatory roles across diverse processes: regulation of Toll-like receptor signaling, protein ubiquitination, control of cell cycle, transcription regulation by RNA Pol II, regulation of necroptosis and apoptosis, kinetochores localization, mitotic ring maturation, and habituation. The shared theme is regulatory control rather than a single specific pathway, so a label emphasizing regulation across signaling, division, and cell fate is most representative.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034121","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0071157","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0060544","count":1}]},{"hash":"2003132072528243829","title":"Homologous recombination and DNA repair","description":"This cluster is defined by a strong representation of homologous recombination and DNA damage response terms (reciprocal meiotic recombination, DNA recombination, synthesis-dependent strand annealing, heteroduplex formation, telomere maintenance via recombination) along with core DNA replication/repair processes (DNA replication, double-strand break repair). This points to a cohesive set of proteins involved in recombination-driven repair and telomere maintenance; peripheral terms like viral genome replication are less central. ","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007131","count":3},{"id":"GO:0006268","count":3},{"id":"GO:0045003","count":3},{"id":"GO:0030491","count":3},{"id":"GO:0000722","count":3}]},{"hash":"695810624757393661","title":"Unknown","description":"The terms cluster around metabolism (fatty acid, carbohydrate, GTP biosynthesis), signaling (activation of protein kinase activity), cell cycle regulation, immune proliferation, and ion transport, but no single coherent function ties all five proteins together.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0006633","count":5},{"id":"GO:0030071","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0006183","count":5},{"id":"GO:0032147","count":5}]},{"hash":"786632448282191202","title":"Unknown","description":"The terms span stress response, signaling pathways, cytoskeletal organization, and growth processes with no obvious unifying function across the five proteins, and several terms are obsolete or not connected. Because there is no coherent theme and no interactions, I cannot assign a meaningful label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0031384","count":1},{"id":"GO:0090085","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0051017","count":1}]},{"hash":"2293938190302884846","title":"Unknown","description":"The GO terms across this cluster are highly diverse (mesoderm development, mating projection growth, histone modification, actin movement, stem cell maintenance, Hippo signaling, fatty acid biosynthesis, T cell anergy). With no coherent, shared function and no edges linking members, there isn\u2019t a clear biological theme to assign a specific label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048332","count":1},{"id":"GO:0031384","count":1},{"id":"GO:0097676","count":1},{"id":"GO:0010796","count":1},{"id":"GO:0030048","count":1}]},{"hash":"1742225720947425250","title":"Mitochondrial Lipid Regulation and Proteolysis Control","description":"Based on the top GO terms, the cluster centers on mitochondrial lipid metabolism (cardiolipin metabolism, lipid localization, cholesterol biosynthesis regulation) and control of proteolysis (positive/negative regulation of peptidase activity), with an extra note of dopaminergic synaptic transmission. This pattern suggests a module where mitochondrial lipid homeostasis and proteolytic regulation intersect within neuronal (dopaminergic) signaling contexts.","confidence":"Medium","size":5,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032226","count":2},{"id":"GO:0052547","count":2},{"id":"GO:1900210","count":2},{"id":"GO:1990046","count":2},{"id":"GO:0045861","count":2}]},{"hash":"1491799171686397564","title":"Unknown","description":"The top GO terms span diverse biological contexts, including microbial secondary metabolism (phenazine biosynthesis), various catabolic and nitrogen metabolism processes, detoxification, and even dopamine uptake, with no single coherent function tying them together. Therefore a clear, representative label cannot be assigned.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0002047","count":2},{"id":"GO:0006769","count":2},{"id":"GO:0019358","count":2},{"id":"GO:1904524","count":2},{"id":"GO:0006212","count":2}]},{"hash":"606097107066140593","title":"Mitochondrial translation and tRNA charging","description":"This cluster is dominated by GO terms for mitochondrial tRNA aminoacylation (lysyl-, aspartyl-, asparaginyl-tRNA) and general translation, indicating proteins involved in mitochondrial protein synthesis and charging of tRNAs. A few terms related to telomere capping and DNA recombination are present but not central to the main theme.","confidence":"High","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0071915","count":5},{"id":"GO:0070145","count":5},{"id":"GO:0072581","count":5},{"id":"GO:0070146","count":5}]},{"hash":"739523702407463760","title":"Unknown","description":"The top GO terms cover a broad and unrelated mix of responses (pain/heat), signaling and transcriptional regulation (NF-kappaB, Notch), cytoskeletal processes (actin, migration, spindle assembly), cardiac function, and neural/synaptic regulation, with no single clear function linking all proteins.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048265","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0051017","count":1},{"id":"GO:0045083","count":1}]},{"hash":"665617598338541549","title":"Unknown","description":"The GO terms cover diverse processes, including spliceosomal complex assembly, transcription regulation, multiple forms of deubiquitination, and even behavioral response to ethanol, defense response, and differentiation, with no single cohesive function uniting the proteins. This makes it hard to assign a specific, representative name to the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900425","count":1},{"id":"GO:0048149","count":1},{"id":"GO:0000245","count":1},{"id":"GO:1990108","count":1},{"id":"GO:0006351","count":1}]},{"hash":"1258822533389904870","title":"Endosomal MVB/Exosome Trafficking","description":"The top GO terms cluster strongly around multivesicular body formation, intralumenal vesicle formation, MVB-lysosome fusion, and regulation of exosomal secretion, pointing to endosomal-lysosomal trafficking and exosome biology. Ubiquitin-dependent degradation via the MVB sorting pathway also supports this theme, with a few broader terms (cell cycle, abscission) likely reflecting more general cellular processes. Overall, the endosomal/MVB-exosome trafficking axis best explains the cluster\u2019s functional signals.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0000920","count":1},{"id":"GO:0006620","count":1},{"id":"GO:0043162","count":1},{"id":"GO:0070676","count":1}]},{"hash":"222691915082205257","title":"Fungal actin cytoskeleton and cytokinesis","description":"The cluster is dominated by GO terms related to actin dynamics (actin filament polymerization, actin cortical patch localization, actin filament bundle assembly) and cell division processes (mitotic cytokinesis, vacuole inheritance), pointing to a cohesive role in actin-driven cytokinesis in fungi. Sporulation-related terms like ascospore wall assembly further support a fungal-specific developmental context, while some chromatin-related terms appear historical but do not override the cytoskeletal/division theme.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030476","count":4},{"id":"GO:0021762","count":4},{"id":"GO:0043981","count":4},{"id":"GO:0043486","count":4},{"id":"GO:0000281","count":4}]},{"hash":"1726704481306963677","title":"SUMOylation and ubiquitination in innate immunity","description":"The top GO terms cluster around SUMOylation and ubiquitin-dependent protein turnover, together with innate immune processes (innate immune response, LPS signaling, chemokine production) and immune regulation. This suggests a cohesive theme: ubiquitin/SUMO pathways modulate immune signaling, with additional transport-related terms possibly reflecting immune cell function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":2},{"id":"GO:0002635","count":2},{"id":"GO:1903886","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0046621","count":2}]},{"hash":"136291243714734091","title":"Ubiquitin-Proteasome Protein Quality Control","description":"The top terms center on ubiquitin-dependent proteolysis across cellular compartments\u2014ERAD, ribosome-associated and mitochondria-associated degradation, retrograde ER-to-cytosol transport, and cytoplasmic protein quality control\u2014indicating a cohesive theme of proteostasis managed by the ubiquitin-proteasome system.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0039536","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0070651","count":1},{"id":"GO:1990116","count":1}]},{"hash":"666063651068280959","title":"Mitotic division and ER-Golgi transport","description":"The top GO terms show a clear emphasis on mitosis (mitotic cell cycle, mitotic spindle assembly, cell division) and vesicle transport between the ER and Golgi, suggesting a cluster tied to cell division coupled with secretory pathway remodeling. The other terms (brain development, ribosome biogenesis) likely reflect general growth programs, but the dominant signal is mitosis with ER-Golgi trafficking.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000278","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0007420","count":3}]},{"hash":"902080736780173332","title":"Kinetochore-Associated Cell Cycle and Meiosis","description":"The cluster is dominated by terms tied to chromosome segregation and DNA replication, notably protein localization to the kinetochore, DNA replication, and mitotic DNA damage checkpoint signaling, with ascospore formation pointing to meiosis. These together suggest a core function in kinetochore-mediated cell cycle control during meiosis/mitosis, with some peripheral metabolic terms annotated to general growth processes.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034501","count":4},{"id":"GO:0030437","count":4},{"id":"GO:0060079","count":4},{"id":"GO:0030846","count":4},{"id":"GO:0051037","count":4}]},{"hash":"792067859836194413","title":"Skeletal muscle development and differentiation","description":"The cluster includes several GO terms tied to skeletal muscle formation, fiber development, and muscle tissue differentiation (skeletal muscle tissue development; skeletal muscle cell differentiation; skeletal muscle fiber development). While some terms appear as noise (nervous system development, B cell signaling, ubiquitin-related processes), the dominant muscle-related terms suggest a muscle development/differentiation theme.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":1},{"id":"GO:0050853","count":1},{"id":"GO:1990390","count":1},{"id":"GO:0036268","count":1},{"id":"GO:0051260","count":1}]},{"hash":"2039789196828740685","title":"Cajal body-associated telomere maintenance","description":"The dominant terms are about scaRNA and telomerase RNA localization to Cajal bodies and telomere maintenance via telomerase, indicating a nuclear RNA-processing/telomere biology theme. Other terms like heat response, mitochondrial import, and sperm binding appear but are peripheral, so the label reflects the core telomere-related function with moderate confidence.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090666","count":4},{"id":"GO:1904874","count":4},{"id":"GO:0009408","count":4},{"id":"GO:0007339","count":4},{"id":"GO:0052212","count":4}]},{"hash":"399908702455090701","title":"Negative regulation of vesicle trafficking and secretion","description":"The top GO terms point to suppression of membrane-trafficking processes, including negative regulation of clathrin-dependent endocytosis and negative regulation of autophagosome maturation, along with reduced spontaneous neurotransmitter release and membrane protein insertion into the ER. These collectively suggest a theme of dampened vesicle dynamics and secretion related to membrane trafficking, with some weaker signals (e.g., insecticide response, GnRH neuron development) that are less informative for the cluster\u2019s core function. Thus, a concise label is \u201cNegative regulation of vesicle trafficking and secretion.\u201d","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1900186","count":1},{"id":"GO:1901097","count":1},{"id":"GO:0014070","count":1},{"id":"GO:0021888","count":1},{"id":"GO:0017085","count":1}]},{"hash":"1078445108827816898","title":"Calcium-Dependent Signaling and Phosphorylation","description":"This cluster centers on calcium signaling and phosphorylation-related processes: calcium release into the cytosol, calcium transmembrane transport, inositol phosphate metabolism, and protein phosphorylation/dephosphorylation, with related pathways such as adenylate cyclase activation and Fc-epsilon receptor signaling. While there are also cell-cycle and muscle-development terms, they can be connected through calcium- and phosphorylation-driven signaling cascades. Confidence: Medium","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000086","count":4},{"id":"GO:0051281","count":4},{"id":"GO:0038095","count":4},{"id":"GO:0007190","count":4},{"id":"GO:0043647","count":4}]},{"hash":"410624418695724134","title":"Membrane ion transport and gradient maintenance","description":"This cluster is dominated by GO terms related to establishing/maintaining transmembrane electrochemical gradients and exporting various ions (sodium, potassium, copper), plus ATP biosynthesis, which together point to membrane transport and ion homeostasis as the core theme. A few terms about hormone response and metabolism appear, but the strongest signal is ion transport and gradient maintenance, suggesting a small group of transport-related proteins. ","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010248","count":2},{"id":"GO:1903249","count":2},{"id":"GO:0036376","count":2},{"id":"GO:0030007","count":2},{"id":"GO:0060003","count":2}]},{"hash":"537142125349399395","title":"SCF/Ubiquitin-Dependent Mitosis Regulation","description":"The cluster is dominated by GO terms tied to ubiquitin-dependent proteolysis and to the G2/M transition of the mitotic cell cycle (SCF-dependent proteasomal ubiquitination, K11-linked ubiquitination, and mitotic DNA replication initiation). This points to a core function in regulating mitosis via targeted protein degradation, with additional development-related terms (embryonic cleavage, egg chamber growth) likely reflecting cell-cycle\u2013linked developmental processes. Overall, the shared theme is ubiquitin-proteasome\u2013mediated control of mitotic progression.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0007295","count":1},{"id":"GO:0070979","count":1}]},{"hash":"1584803036295412409","title":"DNA Damage Response and Repair","description":"The GO terms cluster around DNA repair and damage signaling: base-excision repair, nonhomologous end joining, gamma radiation response, and apoptotic signaling in response to DNA damage, with supporting roles for deubiquitination. Some immune-related terms (somatic hypermutation, spleen development) relate to DNA modification contexts, but the shared theme is sensing, repairing DNA damage and mediating cell fate decisions. ","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061674","count":1},{"id":"GO:0006287","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0010332","count":1},{"id":"GO:0071897","count":1}]},{"hash":"1592344063699323424","title":"Membrane Ion Transport and Homeostasis","description":"The top GO terms point to processes that maintain transmembrane electrochemical gradients and move ions across membranes (sodium export, potassium homeostasis, copper export, gradient establishment), which together define a membrane transport/ion homeostasis theme. Some terms appear tangential (serine biosynthesis, testosterone response), but the dominant signal is ion transport and gradient maintenance.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010248","count":4},{"id":"GO:1903249","count":4},{"id":"GO:0036376","count":4},{"id":"GO:0030007","count":4},{"id":"GO:0060003","count":4}]},{"hash":"1854768877890319256","title":"Branched-chain amino acid biosynthesis and metabolism","description":"This cluster's top GO terms are dominated by L-leucine, L-valine, and L-isoleucine biosynthetic processes and related amino acid metabolism, with additional signals from D-amino acid pathways and central carbon metabolism, suggesting a cohesive focus on amino acid biosynthesis and turnover rather than a single narrow function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009098","count":2},{"id":"GO:0019478","count":1},{"id":"GO:0046437","count":1},{"id":"GO:0009099","count":1},{"id":"GO:0009097","count":1}]},{"hash":"1201470623856465295","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1990603","count":1},{"id":"GO:0071031","count":1},{"id":"GO:0031664","count":1},{"id":"GO:0036450","count":1},{"id":"GO:0007344","count":1}]},{"hash":"2091634194452407282","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070911","count":1},{"id":"GO:0002031","count":1},{"id":"GO:0006363","count":1},{"id":"GO:0006366","count":1},{"id":"GO:0006296","count":1}]},{"hash":"930673543206878302","title":"Diverse biosynthesis pathways","description":"The top GO terms show several distinct biosynthetic processes (fatty acid biosynthesis and metabolism, siderophore biosynthesis, menaquinone biosynthesis, and NRPS-related peptide biosynthesis) along with some plant-specific seed development terms. There isn't a single dominant function that ties all proteins together, so a broad label like diverse biosynthesis best represents the cluster.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":1},{"id":"GO:0019290","count":1},{"id":"GO:0010214","count":1},{"id":"GO:0009234","count":1},{"id":"GO:0000038","count":1}]},{"hash":"1069177126829006534","title":"Chromosome maintenance and mitosis","description":"The cluster is dominated by nuclear functions: CENP-A chromatin assembly, mitotic sister chromatid cohesion, DNA repair by homologous recombination, cell division, and microtubule severing, all pointing to chromosome maintenance and mitotic processes. A few terms (ER-Golgi transport, secretory differentiation) appear as outliers or annotation noise, but do not override the central nuclear theme.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0000724","count":2}]},{"hash":"1851078522811314440","title":"RNA Polymerase III transcription machinery","description":"The top GO terms are dominated by RNA polymerase III\u2013related processes (preinitiation complex assembly, transcription by RNA polymerase III, and 5S rRNA transcription by RNA Pol III), indicating these proteins function together in Pol III transcription. A few other terms (cilium assembly, renal filtration, adipocyte development) appear only once, likely peripheral annotations. Overall, the strongest shared theme is Pol III transcription machinery.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001021","count":1},{"id":"GO:0001041","count":1},{"id":"GO:0042791","count":1},{"id":"GO:0000999","count":1},{"id":"GO:0001009","count":1}]},{"hash":"1985552065376300168","title":"Unknown","description":"There are no shared GO terms or interactions (edges 0, triangles 0, no top terms), so a clear functional theme cannot be determined.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1600529356448315512","title":"Developmental signaling and morphogenesis","description":"The top GO terms cluster around developmental signaling pathways and morphogenesis, including positive regulation of canonical Wnt signaling, Hippo signaling, embryonic cranial skeleton morphogenesis, and growth hormone receptor signaling, plus transcription regulation and apoptosis. This suggests proteins in this cluster coordinate growth, tissue patterning, and organ development, with some involvement in DNA replication and cytoskeletal dynamics (stress fiber regulation).","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0035329","count":2},{"id":"GO:0060044","count":2}]},{"hash":"153480697371611380","title":"Eye Lens Development","description":"This cluster is most strongly associated with lens development in a camera-type eye and multicellular organism development, suggesting its proteins may participate in ocular morphogenesis. While there are additional terms related to cellular trafficking and metabolism (ER polarization, caveolin-mediated endocytosis, translation, migration), the developmental themes\u2014especially lens development\u2014provide the most coherent core. Confidence: Medium.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0051534","count":4},{"id":"GO:0002088","count":4},{"id":"GO:0007275","count":4},{"id":"GO:0061167","count":4},{"id":"GO:0072584","count":4}]},{"hash":"3069976275113379","title":"Co-translational targeting and protein quality control","description":"The GO terms are dominated by SRP-dependent cotranslational targeting to membranes, coupled with protein folding and cytoplasmic protein quality control (ubiquitin-proteasome system and chaperone assembly), suggesting a functional theme around nascent protein handling during translation and membrane targeting, with quality control.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0045900","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1950884509654637294","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0022900","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0048542","count":1},{"id":"GO:0000461","count":1},{"id":"GO:0042274","count":1}]},{"hash":"941506793609104031","title":"Golgi-endosome vesicle trafficking","description":"This cluster is dominated by GO terms related to intracellular transport within the endomembrane system, including endocytic recycling, retrograde transport from endosomes to the Golgi, Golgi vesicle transport, vesicle docking and fusion, and endosome organization, plus Golgi ribbon formation. Two terms (transcription and nucleotide-excision repair) appear incidental. The clear common theme is vesicle trafficking between endosomes and the Golgi apparatus.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":1},{"id":"GO:0032456","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0048193","count":1},{"id":"GO:0048278","count":1}]},{"hash":"1280286361311551389","title":"Fatty acid oxidation and energy metabolism","description":"The terms are dominated by fatty acid catabolic processes (long-chain and medium-chain), carnitine biosynthesis (essential for mitochondrial FA transport), and pathways that feed into energy production (regulation of gluconeogenesis, steroid biosynthesis). While some terms touch on development, the strongest common theme across the cluster is lipid metabolism and energy generation, suggesting these proteins function in fatty acid oxidation\u2013related pathways and lipid-derived metabolite production.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0006552","count":2},{"id":"GO:0001701","count":2},{"id":"GO:0006694","count":1}]},{"hash":"709682117191751975","title":"Unknown","description":"The four proteins show a mix of immune signaling (interleukin-4 response, chemotaxis, regulation of complement-dependent cytotoxicity), transcription regulation, basic metabolism, and even phototransduction, with no single cohesive function tying them together. So a precise, representative label cannot be assigned.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":2},{"id":"GO:0009585","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0034757","count":1}]},{"hash":"813996830692197792","title":"Unknown","description":"The Top Terms span adipose development, seed growth, cilium assembly regulation, meiotic recombination, mitosis, DNA repair, and chromatin formation, which do not reveal a single coherent function for the cluster. With only four proteins and no observed edges, there is no clear shared biological theme to name a specific function. Therefore, this cluster is best described as Unknown with no confidence.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060613","count":2},{"id":"GO:0070979","count":1},{"id":"GO:1903070","count":1},{"id":"GO:0007091","count":1},{"id":"GO:0080113","count":1}]},{"hash":"2282706931385411391","title":"Bacterial cell wall polysaccharide biosynthesis and glycosylation","description":"This cluster centers on polysaccharide biosynthesis for the cell wall (capsule, teichoic acid, mycolate layer) and associated glycosylation processes, supported by UDP-sugar metabolism terms, indicating a cohesive role in cell wall assembly and modification.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015774","count":1},{"id":"GO:0052573","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0071769","count":1}]},{"hash":"1597569403342700378","title":"Unknown","description":"The GO terms are scattered across distinct biological processes (glutamate signaling, bitter taste perception, antibiotic response, apoptosis, cytoskeleton localization), with no clear common function linking the four proteins. Hence no coherent cluster label beyond Unknown.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000560","count":1},{"id":"GO:0031384","count":1},{"id":"GO:0007215","count":1},{"id":"GO:2000438","count":1},{"id":"GO:0071236","count":1}]},{"hash":"1810760641802087037","title":"Unknown","description":"The top GO terms span many unrelated processes, including ER stress-induced apoptosis regulation, nucleotide-excision repair, neuronal development, endocytosis and autophagy regulation, and nuclear pore localization. There is no single cohesive function or pathway that ties these proteins together, so a meaningful, specific label cannot be assigned.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902236","count":3},{"id":"GO:0070911","count":3},{"id":"GO:0045759","count":3},{"id":"GO:1900186","count":3},{"id":"GO:1901097","count":3}]},{"hash":"1729673918189099147","title":"Cajal body RNA localization and telomere maintenance","description":"This cluster is driven by GO terms for scaRNA localization to Cajal bodies and for positive regulation of telomerase RNA localization to Cajal bodies, plus positive regulation of telomere maintenance via telomerase, suggesting a shared role in nuclear RNA processing and telomere biology. The remaining terms (heat response, mitochondrial import, pore complex assembly, protein refolding) are less central to this core theme.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090666","count":3},{"id":"GO:1904874","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0007339","count":3},{"id":"GO:0052212","count":3}]},{"hash":"807263666132806515","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0030517","count":2},{"id":"GO:0042273","count":1},{"id":"GO:0009650","count":1}]},{"hash":"518048511504039245","title":"Ribosome-ER Targeting and Cell Cycle Control","description":"Top GO terms point to translation and SRP-dependent cotranslational targeting to the membrane, indicating ribosome-associated protein synthesis and entry into the ER. Additional terms about cell cycle regulation and ubiquitin-related protein stability suggest a broader coordination between protein production, processing, and cell division. This combination supports a label capturing both translation machinery and cell-cycle\u2013related regulation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006614","count":2},{"id":"GO:0051301","count":2},{"id":"GO:1901798","count":1},{"id":"GO:0072717","count":1}]},{"hash":"806501818873979234","title":"DNA replication and chromatin assembly","description":"The top terms include DNA replication, DNA-templated transcription, and CENP-A\u2013containing chromatin assembly, indicating a clear focus on chromatin maintenance and DNA synthesis. A few vesicle transport terms are present but appear ancillary; overall the cluster centers on nuclear chromatin-related processes.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0032979","count":1},{"id":"GO:0061641","count":1}]},{"hash":"2032365767497005723","title":"RNA processing and spliceosome assembly","description":"The cluster shows strong enrichment for RNA metabolism processes: spliceosomal complex and snRNP assembly, tRNA processing, mRNA decapping/decay, and P-body assembly, plus nuclear import. This points to a set of proteins involved in RNA maturation, splicing, and turnover, with some outliers likely representing background noise. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":3},{"id":"GO:1990141","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0042633","count":3}]},{"hash":"2101641436337390609","title":"Spliceosome Assembly and RNA Processing","description":"The terms point to nuclear RNA metabolism, including spliceosome/snRNP assembly, RNA processing (tRNA), and mRNA turnover with P-body involvement; a few items are less directly related, but the core signal is RNA splicing and processing.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051170","count":3},{"id":"GO:1990141","count":3},{"id":"GO:0000245","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0042633","count":3}]},{"hash":"465896717756011099","title":"Membrane trafficking and cytoskeletal dynamics","description":"The top GO terms point to Golgi COPI vesicle coating, membrane tubulation, and regulation of GTPase activity, all of which tie to membrane trafficking and cytoskeletal remodeling. Additional terms about cytokinesis and actin reorganization support a broader theme where vesicle trafficking and cytoskeletal dynamics intersect across processes like cell division and abscission, with some terms citing neuronal structures. Overall, these terms converge on membrane remodeling and cytoskeletal control as a common function of the cluster.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048205","count":3},{"id":"GO:1990386","count":3},{"id":"GO:0010227","count":3},{"id":"GO:0030037","count":3},{"id":"GO:0035021","count":3}]},{"hash":"861038305967589051","title":"Ubiquitin-mediated ERAD and autophagy regulation","description":"The panel is dominated by ubiquitin-related processes: protein autoubiquitination and the ubiquitin-dependent ERAD pathway, plus connections to ER stress-induced apoptotic signaling and autophagosome maturation. While some terms touch on broader trafficking or signaling (nuclear pore localization, TNF pathways), the central theme is regulation of protein quality control and degradation via ubiquitin pathways, encompassing ERAD and autophagy. This supports labeling the cluster as a ubiquitin-driven protein homeostasis module.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1902236","count":1},{"id":"GO:0070911","count":1}]},{"hash":"837987003862977651","title":"Unknown","description":"The cluster's top GO terms span mitotic cell cycle, heat response, development, NF-kappaB regulation, actin filament assembly, IL-12 regulation, cell migration, Notch signaling in heart field development, DNA recombination regulation, and SA node electrophysiology. The functions are highly diverse with no clear, shared biological process or pathway tying all members together, and there are no edges connecting the proteins, so a single, coherent label cannot be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0007275","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0051017","count":1}]},{"hash":"963381794485665936","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070131","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0039694","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0042256","count":1}]},{"hash":"99170648683611050","title":"Organelle protein import and quality control","description":"The terms cluster around protein import into mitochondria and peroxisomes, ER unfolded protein response, cellular response to misfolded protein, proteasomal protein catabolic processes, and vesicle formation, pointing to a shared theme of organelle protein trafficking and proteostasis. A single term on CENP-A chromatin assembly is outliers but does not negate the overall pattern of protein handling across compartments.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032979","count":1},{"id":"GO:0061641","count":1},{"id":"GO:0070407","count":1},{"id":"GO:0070676","count":1},{"id":"GO:0030420","count":1}]},{"hash":"629452902043421453","title":"Developmental Regulation and Gene Expression","description":"The GO terms center on developmental processes (spinal cord development, multicellular organism development) and on gene expression/assembly mechanisms (ribosomal biogenesis, CENP-A chromatin assembly, translation reinitiation), suggesting a cluster tied to development with regulation of gene expression and protein synthesis rather than a single enzymatic function.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":3},{"id":"GO:0060528","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0061641","count":2}]},{"hash":"1684643977984687215","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035665","count":1},{"id":"GO:0045410","count":1},{"id":"GO:0032738","count":1},{"id":"GO:0090073","count":1},{"id":"GO:0002781","count":1}]},{"hash":"978526069744309413","title":"SRP-dependent cotranslational protein targeting to membrane","description":"Three proteins share GO terms GO:0006616 and GO:0006614, both describing SRP-dependent cotranslational protein targeting to the membrane. This indicates a common function in directing nascent polypeptides to the ER membrane during translation, supporting a cohesive cluster despite no observed interaction edges.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006616","count":1},{"id":"GO:0006614","count":1}]},{"hash":"1306197511803477072","title":"Proteostasis and ER stress response","description":"The top GO terms cluster around protein quality control, including unfolded protein response in the ER, cellular response to misfolded proteins, and positive regulation of proteasomal degradation, all central to maintaining proteostasis under stress. Some terms (mitochondrial membrane insertion, chromatin assembly) are less directly tied, but the dominant themes are protein folding/refolding, misfolding stress responses, and degradation pathways.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0070389","count":3},{"id":"GO:0032979","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0070407","count":2}]},{"hash":"122111411410823119","title":"Cardiac muscle development and regeneration","description":"Based on the terms, the cluster centers on heart-related development and muscle biology: Notch signaling in heart field, regulation of SA node action potential, skeletal muscle regeneration, and actin cytoskeleton dynamics (actin bundle assembly, cell migration), with spindle assembly indicating cell division during tissue growth. Some terms reflect generic stress or signaling, but the muscle/heart theme appears most coherent overall.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0045083","count":2},{"id":"GO:0016477","count":2}]},{"hash":"1314949813165562635","title":"Gene Expression Regulation (Transcription & RNA Metabolism)","description":"The cluster centers on DNA-templated transcription and regulation of transcription elongation, with additional GO terms tied to mRNA processing, decapping, deadenylation, and translational control, plus P-body assembly. This indicates a coherent theme of regulating gene expression at both transcriptional and post-transcriptional levels, with a few differentiation-related terms that appear secondary. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0032968","count":1},{"id":"GO:0001829","count":1},{"id":"GO:2000036","count":1},{"id":"GO:0031087","count":1}]},{"hash":"222861057953988328","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0071630","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0006458","count":2}]},{"hash":"2184405154545088839","title":"Unknown","description":"No interactions (Edges 0, Max Degree 0, Triangles 0) and no GO terms are reported, so there is no clear shared function among the proteins. ReCIPE added 20 proteins but still shows no connections, so a reliable label cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1223546573950267557","title":"Chromatin organization and histone modification","description":"These proteins cluster around chromatin-related processes: nucleosome assembly, heterochromatin organization, and histone methylation (including H3K27 and H3K4). The GO terms indicate chromatin packaging, nucleosome dynamics, and chromatin localization, supporting a shared role in chromatin maintenance and epigenetic regulation.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098532","count":1},{"id":"GO:0080182","count":1},{"id":"GO:0097298","count":1},{"id":"GO:0006334","count":1},{"id":"GO:0070828","count":1}]},{"hash":"1852345770348578331","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0071630","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0036494","count":1},{"id":"GO:0006260","count":1}]},{"hash":"2265314502117792440","title":"K11-ubiquitination\u2013mediated mitotic control","description":"The cluster\u2019s top GO terms strongly point to regulation of mitotic transitions (metaphase/anaphase) and specifically to K11-linked ubiquitination, suggesting proteins here act in ubiquitin-dependent control of the cell cycle. Some other terms (e.g., prostate development, chlorophyll biosynthesis) appear incidental or cross-species noise given the small cluster size, but the core signal centers on ubiquitin-mediated mitotic regulation.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":2},{"id":"GO:0045842","count":2},{"id":"GO:0070979","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0046661","count":2}]},{"hash":"1858245308312594825","title":"Developmental patterning and nutrient signaling","description":"The top terms include hindbrain development, pancreas development, and proximal/distal pattern formation, pointing to developmental patterning. Additionally, responses to nutrient and signaling cues (e.g., cAMP) suggest regulation by metabolic signals. Some catabolic terms are obsolete, so the theme centers on development intertwined with nutrient signaling rather than a single metabolic pathway.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030902","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0031016","count":3},{"id":"GO:0006069","count":3},{"id":"GO:0006537","count":3}]},{"hash":"467941711354304515","title":"Unknown","description":"There are no GO terms available to define a shared function for these proteins, and the small network without cohesive functional signals offers no basis for a specific label.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[]},{"hash":"2046018603934964130","title":"Phytochrome signaling and transcriptional growth control","description":"This cluster centers on red/far-red light phototransduction, i.e., phytochrome signaling, coupled with regulation of transcription (DNA-templated transcription, regulation of transcription) and growth-related processes (secondary growth, positive/negative regulation of cell size, metabolism), which together suggest a plant light-sensing pathway that controls gene expression and growth. The terms point to a coherent functional theme rather than unrelated processes.","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009585","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0045793","count":1},{"id":"GO:0034757","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1974032778413081137","title":"RNA Surveillance and Nuclear Transport","description":"The cluster shows strong signals for RNA quality control, including nonsense-mediated decay and RNase MRP-dependent decay, plus a term for positive regulation of protein import into the nucleus, pointing to a core theme of RNA processing and nuclear transport. The other terms (plant development, morphogenesis, immune-related) are sparse and likely incidental in this small cluster, so the dominant interpretation centers on RNA surveillance and nuclear import functions.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":2},{"id":"GO:2000024","count":1},{"id":"GO:0030335","count":1},{"id":"GO:0031538","count":1},{"id":"GO:0035011","count":1}]},{"hash":"942797082769504290","title":"Unknown","description":"Reason: The GO terms cover a wide range of unrelated processes (prostate development, male sex differentiation, ciliary motility, innate immunity, ubiquitination, and mitotic cell cycle transitions). There is no clear, single functional theme tying these proteins together, so a cohesive label is not supported.","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030850","count":2},{"id":"GO:0045842","count":2},{"id":"GO:0070979","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0046661","count":2}]},{"hash":"896060079450023230","title":"Unknown","description":"The terms are highly heterogeneous, spanning immune defense (defense response to Gram-negative bacteria, detection of lipopolysaccharide), GPCR signaling, neural reflexes, chromatin localization, water homeostasis, and kidney development. There isn\u2019t a single clear function that ties the cluster together, so a concise, representative label cannot be determined with confidence.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050829","count":1},{"id":"GO:0060007","count":1},{"id":"GO:0014068","count":1},{"id":"GO:0061368","count":1},{"id":"GO:0007186","count":1}]},{"hash":"1546817446552854042","title":"Bacterial cell wall polysaccharide biosynthesis and glycosylation","description":"These GO terms cluster around bacterial cell wall carbohydrate biosynthesis: multiple polysaccharide biosynthetic processes (capsule, teichoic acid, cell wall polysaccharide), transport and glycosylation pathways (O-linked and N-acetyl-galactosamine), and related UDP-sugar metabolism. The proteins are likely involved in assembling and modifying cell wall polysaccharides, including capsule and teichoic acids.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015774","count":1},{"id":"GO:0052573","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0071769","count":1}]}]