[{"hash":"2043906567227570401","title":"Nuclear Gene Expression and Cell Cycle","description":"Top GO terms are dominated by core nuclear processes: DNA-templated transcription, cell division, and ribosome biogenesis, along with transcriptional regulation and chromatin-related activity. A couple terms reference brain development and axon guidance, which may reflect cross-annotation noise or multifunctional proteins rather than a single neural-function theme. Overall, the set best fits a theme of fundamental gene expression and cell-cycle machinery.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0001662","count":3},{"id":"GO:0007420","count":2}]},{"hash":"1711961219115942800","title":"Mitochondrial metabolism and membrane transport","description":"Reasoning: The top GO terms cluster around mitochondrial processes, notably transport of NAD and coenzyme A across mitochondrial membranes, regulation of mitochondrial membrane potential, and apoptotic mitochondrial changes, indicating a focus on mitochondrial energy metabolism and membrane transport. While there are a few general nuclear processes (translation initiation and transcription) in the mix, the mitochondrial-related terms dominate, supporting a mitochondrial energy/metabolism theme.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0097421","count":5},{"id":"GO:0001731","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051881","count":4},{"id":"GO:0007565","count":4}]},{"hash":"145437810456123263","title":"Gene Expression and Stress Response","description":"The top GO terms are dominated by core gene expression processes (translation; DNA-templated transcription) plus cellular stress and maintenance (cellular response to ethanol and hydrogen peroxide; protein repair). While there are a couple broader developmental terms (skeletal system development; meiotic cell cycle), the combination still points to a cluster of proteins involved in basic expression machinery and responses to cellular stress rather than a single cohesive pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0001501","count":2},{"id":"GO:0071361","count":2},{"id":"GO:0046826","count":2},{"id":"GO:0055114","count":2}]},{"hash":"82248563995296524","title":"DNA replication and cell cycle regulation","description":"This cluster shows strong enrichment for DNA replication, DNA-templated transcription, and cell division, along with chromatin assembly (CENP-A) and telomere maintenance, pointing to chromosome maintenance and progression through the cell cycle. Additional terms related to oxidative stress response and nuclear export appear ancillary, but the core theme is cell-cycle\u2013/chromosome-associated processes.","confidence":"High","size":29,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0034599","count":3},{"id":"GO:0046827","count":3}]},{"hash":"563231555358356003","title":"Unknown","description":"The listed GO terms span a broad mix of processes\u2014cell division, viral processes, RNA splicing, Rab signaling, various developmental processes (axonogenesis, pseudopodium assembly, hair follicle placode formation, dopaminergic neuron differentiation) and an obsolete protein import/oxidoreduction term. There is no clear, common function or pathway that unites these terms, suggesting the cluster reflects a heterogeneous set of proteins without a single shared biology.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0032482","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1813847273872963004","title":"Protein and histone acetylation","description":"The top GO terms are dominated by acetylation-related processes (N-terminal acetylation, peptidyl-lysine acetylation, histone H4 acetylation), suggesting a shared role in acetylation and chromatin regulation. Some terms (angiogenesis, leaf formation) are less directly connected and may reflect broader annotations, but the strongest signal points to acetylation/modification of proteins and histones.","confidence":"High","size":28,"edges":76,"triangles":225,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":11},{"id":"GO:0061606","count":10},{"id":"GO:0060358","count":10},{"id":"GO:2000025","count":10},{"id":"GO:0006526","count":10}]},{"hash":"185055901342973629","title":"Signaling regulation and nuclear transport","description":"The GO terms cluster around regulation of signaling and phosphorylation dynamics (positive regulation of GTPase activity, protein dephosphorylation, and regulation of kinase activity) and signaling pathways such as canonical NF-kappaB and NFAT. In addition, there are terms related to nuclear processes (NLS-bearing protein import into nucleus, mRNA transport), suggesting a link to nuclear trafficking, with a few outliers (meiotic cohesion, lung differentiation, cytokinesis) that may reflect broader multifunctionality. Overall, this cluster appears to group proteins involved in regulating signaling with a component of nuclear localization/transport.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006470","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0051531","count":3}]},{"hash":"1557371833763344352","title":"Mitotic cell cycle and DNA replication","description":"The top GO terms center on mitosis, sister chromatid cohesion, APC-dependent protein turnover, and Okazaki fragment processing during mitotic replication, plus regulation of meiotic nuclear division and DNA-templated transcription. Nuclear pore localization and TORC1 signaling appear as supportive growth and nuclear transport aspects linked to cell division. Collectively, these terms point to a cluster enriched in cell-cycle progression, chromosome segregation, and DNA replication machinery. The presence of many mitosis-related terms with a few growth-related terms suggests a coherent cell division\u2013DNA replication theme.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007064","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0031145","count":6},{"id":"GO:0030433","count":6}]},{"hash":"1602351391318771823","title":"Ribosome Biogenesis and Cell Division","description":"The strongest GO signals center on ribosome assembly and export (ribosome biogenesis, ribosomal large subunit export from nucleus, tRNA modification) together with cell-cycle-related processes (cell division, cell cycle, cell septum assembly). This pattern points to a functional module where ribosome production and maturation are linked to cell proliferation, with some stress-response ties. I therefore label this cluster as Ribosome Biogenesis and Cell Division.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0000055","count":3},{"id":"GO:0006400","count":2},{"id":"GO:0000747","count":2}]},{"hash":"776726379046873594","title":"Genome maintenance and stress-response protein homeostasis","description":"The top GO terms cluster around genome maintenance (DNA replication, CENP-A chromatin assembly, translesion synthesis) and stress-related protein quality control (chaperone-dependent refolding, stress granule disassembly, aggrosome assembly). Additional terms about mitochondrial protein targeting and vesicle formation suggest broader organelle maintenance under stress. Overall, the proteins appear to coordinate genome integrity with proteostasis and cellular stress responses, making this a cohesive functional theme.","confidence":"Medium","size":27,"edges":10,"triangles":1,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0035617","count":4},{"id":"GO:0070987","count":3},{"id":"GO:0034551","count":3}]},{"hash":"1805680304201769606","title":"RNA processing and ribosome biogenesis","description":"This cluster is dominated by RNA-centric functions: mRNA splicing via the spliceosome, regulatory ncRNA\u2013mediated gene silencing, and multiple rRNA maturation steps (including 5.8S and ITS1 processing), with additional chromatin remodeling and a translation term. The strongest signal is RNA processing with ribosome biogenesis, suggesting proteins work together in RNA maturation and ribosome assembly, with translation reflecting downstream output. ","confidence":"High","size":27,"edges":28,"triangles":9,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0006412","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0000466","count":4}]},{"hash":"1047446293212335571","title":"Endomembrane trafficking and endosome transport","description":"The top GO terms cluster around intracellular transport within the endomembrane system: endosome-to-Golgi and endosome-to-lysosome routes, intracellular protein transport, endocytic recycling, and vacuole fusion regulation, all of which point to vesicle trafficking dynamics. Supporting signals such as phosphatidylinositol-mediated signaling and GTPase activity regulation reinforce the trafficking theme. A couple of terms (ascospore membrane formation, mitotic cell cycle) are less central but do not override the dominant endomembrane transport pattern. Overall, the proteins seem tied to vesicle trafficking and endomembrane organization. ","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032889","count":2},{"id":"GO:0034499","count":2},{"id":"GO:0006886","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0008333","count":2}]},{"hash":"27877076522245082","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":21,"triangles":8,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0048701","count":7},{"id":"GO:0009432","count":6},{"id":"GO:0070417","count":6},{"id":"GO:0048026","count":6}]},{"hash":"1488308311847815980","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":7,"triangles":0,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0000480","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0000472","count":3},{"id":"GO:0043547","count":3}]},{"hash":"938539569365391206","title":"Protein homeostasis and cell cycle","description":"It centers on protein synthesis and quality control (translation initiation, ribosome biogenesis, ubiquitination/ERAD) with cell division and DNA repair processes, suggesting a protein homeostasis theme tied to the cell cycle.","confidence":"Medium","size":27,"edges":6,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0060041","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000209","count":3}]},{"hash":"487005876797354812","title":"RNA Processing and Translation Control","description":"The cluster is dominated by RNA-centric terms: translation (GO:0006412) and box C/D snoRNP assembly, plus associated RNA maturation processes like pre-mRNA cleavage for polyadenylation. Other linked terms touch on transcriptional and chromatin regulation, suggesting the proteins function in broader gene-expression control beyond translation. Overall, the common thread appears to be RNA processing and regulation of gene expression, with translation acting as a core activity.","confidence":"Medium","size":27,"edges":8,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000492","count":2},{"id":"GO:0030579","count":2},{"id":"GO:0098789","count":2},{"id":"GO:1901726","count":1}]},{"hash":"1506674588102237128","title":"Nucleocytoplasmic transport and ER-Golgi trafficking","description":"The GO terms point to nuclear-cytoplasmic movement such as mRNA export and DNA-templated transcription, plus vesicle trafficking from the ER to the Golgi and regulation of GTPase activity, which governs vesicle transport. Together these indicate a cluster centered on transport and trafficking processes, bridging nucleus-to-cytoplasm and secretory pathway functions, with some broader developmental and xenobiotic response notes. ","confidence":"High","size":26,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009103","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0006351","count":3}]},{"hash":"532469846081695440","title":"Ubiquitin-Linked Trafficking and DUB Regulation","description":"The cluster\u2019s top GO terms center on deubiquitination across multiple ubiquitin linkages (K11, K29, K48, K6) together with protein retention in the Golgi and endosomal transport, pointing to a shared theme of ubiquitin-dependent control of protein localization and turnover within trafficking pathways. While a few terms touch on immune signaling or myelin assembly, these do not define a cohesive core beyond the trafficking/ubiquitination axis. Therefore, the label reflects the strongest common thread among the functions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":2},{"id":"GO:0015886","count":2},{"id":"GO:0035871","count":2},{"id":"GO:0035523","count":2},{"id":"GO:0071108","count":2}]},{"hash":"757091170020164664","title":"Wnt Pathway Regulation and Cell Migration","description":"Proteins in this cluster revolve around regulation of the canonical Wnt pathway, including negative regulation of Wnt signaling and terms linked to EMT and apoptotic control, which aligns with roles in controlling cell movement and survival. Additional terms like cell division, DNA repair, IL-4 response, and viral process may reflect broader cellular stress and proliferation contexts but do not override the central Wnt-related theme.","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0090090","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0071353","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1468431365205405153","title":"Ubiquitin-dependent NF-kB/TNF/JNK signaling","description":"The cluster is dominated by ubiquitin-related processes (autoubiquitination, ubiquitin-dependent protein catabolic process, ERAD) and signaling components of NF-kB and TNF pathways, with regulation of the JNK cascade suggesting a cohesive role in inflammatory signaling. Some terms touch chromatin remodeling and immune gene rearrangement (histone catabolic process, V(D)J recombination), but the core theme centers on ubiquitin-mediated regulation of inflammatory signaling.","confidence":"Medium","size":26,"edges":5,"triangles":0,"max_degree":4,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:0007250","count":7},{"id":"GO:1903265","count":7},{"id":"GO:0036205","count":7},{"id":"GO:0042787","count":7}]},{"hash":"2090119249860802571","title":"Nucleocytoplasmic Transport and Mitotic Reassembly","description":"The top GO terms show a strong emphasis on nuclear transport processes (NLS-bearing import, nuclear pore complex assembly) and mitotic nuclear membrane reassembly, suggesting a cohesive cluster centered on nucleocytoplasmic transport and cell cycle reorganization. Additional terms point to growth signaling and apoptosis-regulatory pathways that may accompany these core processes, but the nuclear transport/mitosis theme is most representative.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0007084","count":5},{"id":"GO:0051292","count":5},{"id":"GO:0045945","count":5},{"id":"GO:0071230","count":5},{"id":"GO:2001241","count":5}]},{"hash":"1145444168935662197","title":"Neural development and cell-cycle regulation","description":"Based on the top GO terms, the cluster combines core cellular processes (DNA-templated transcription, DNA replication, mitotic re-entry, spindle separation, apoptosis) with neural development signals (cerebral cortex development, visual perception) and cranial skeleton morphogenesis. This suggests proteins that coordinate gene expression and cell-cycle control within neural development and morphogenesis, rather than a single narrow function.","confidence":"Medium","size":25,"edges":8,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":7},{"id":"GO:0048701","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0014850","count":5}]},{"hash":"1560898996965060066","title":"Actin-Rho Signaling and Membrane Remodeling in Development","description":"Top GO terms center on actin filament organization, Rho GTPase signaling, and membrane tubulation, with developmental themes like neuron projection development and heart development. This suggests the proteins jointly drive actin-Rho\u2013mediated cytoskeletal remodeling and membrane shaping that guide neuronal and cardiac morphogenesis. Minor signals like corticosterone response are peripheral to the main pattern.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010976","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0051412","count":2},{"id":"GO:0060990","count":2},{"id":"GO:0043547","count":2}]},{"hash":"1597626838553114488","title":"Gene Expression and Protein Synthesis Machinery","description":"Top GO terms point to transcription control, translation, and ribosome biogenesis, suggesting a gene expression/protein synthesis theme. Additional terms like ER protein folding and detoxification relate to protein quality control and cellular stress responses. Some terms (e.g., single fertilization) seem incidental, but overall the cluster aligns with gene expression and protein synthesis machinery.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0046826","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0046330","count":2},{"id":"GO:0042254","count":2}]},{"hash":"289670995158039260","title":"Membrane transport and vesicle trafficking","description":"This cluster is dominated by GO terms for various transmembrane transports (sodium, potassium, nitrite, sugars like arabinose and galactose, sialic acid, vitamins) plus vesicle-related processes (ER-to-Golgi transport and neurotransmitter loading into synaptic vesicles). The shared theme is membrane transport and vesicle trafficking across diverse substrates, making this a coherent label despite the absence of network edges in the cluster.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0035461","count":3}]},{"hash":"1083291915143450669","title":"DNA Damage Response and Apoptotic Signaling","description":"The top GO terms center on sensing and transducing DNA damage (DNA-templated transcription, DNA damage response with p53 mediator) and triggering programmed cell death (intrinsic apoptotic signaling, anoikis, lens fiber cell apoptotic process). A cell-cycle term (mitosis without cytokinesis) and other tissue-specific terms appear as noise, but the core cluster seems to reflect DDR-driven apoptosis. Based on that pattern, the label captures DDR and apoptosis processes.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0008015","count":2},{"id":"GO:0070345","count":2},{"id":"GO:0030330","count":2},{"id":"GO:1990086","count":2}]},{"hash":"217005909348236403","title":"Synaptic Vesicle Trafficking and Dopamine Response","description":"The cluster features clear links to synaptic vesicle processes, with terms for synaptic vesicle maturation and presynaptic dense core vesicle exocytosis, as well as dopamine responsiveness, which together suggest a vesicle trafficking and neurotransmitter signaling theme in neurons. Rho signaling supports cytoskeletal changes needed for vesicle movement, while other terms point to general proteostasis and gene regulation that are less specific to the core vesicle/dopamine function.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030242","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0007266","count":2},{"id":"GO:0016188","count":2}]},{"hash":"1127104944227435821","title":"Mitotic division and vesicle trafficking","description":"This cluster is enriched for mitosis-related terms (mitotic spindle assembly, mitotic cell cycle, cell division) indicating a primary focus on cell division. It also includes vesicle trafficking signals (COPII-coated vesicle budding, calcium-dependent exocytosis) and growth-related signaling (TORC1), suggesting coordination between proliferation and membrane trafficking. The developmental and immune terms appear as broader context themes but do not dominate the core function. Overall, the dominant theme is mitotic progression with associated vesicle trafficking.","confidence":"Medium","size":24,"edges":9,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":6},{"id":"GO:0001501","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":4},{"id":"GO:1904263","count":4}]},{"hash":"1250033132894598618","title":"Bacterial LPS biosynthesis and metabolism","description":"The strongest signal in this set is lipopolysaccharide biosynthetic processes (including ADP-L-glycero-beta-D-manno-heptose and LPS core region synthesis), pointing to enzymes involved in bacterial outer-m membrane assembly. Additional terms indicate broader carbohydrate metabolism and core cellular processes (translation, transcription regulation, and cell cycle), suggesting a cluster that centers on LPS envelope biosynthesis within a general metabolic context. Some terms may reflect mixed annotations or cross-species data, but the LPS-related terms provide the clearest cohesive theme.","confidence":"Medium","size":24,"edges":12,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":4},{"id":"GO:0006412","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000390","count":2}]},{"hash":"1510482582587937218","title":"RNA processing and translation","description":"This cluster is enriched for RNA-related processes: translation (GO:0006412), various tRNA aminoacylation activities (lysyl-, aspartyl-, mitochondrial), and mRNA splicing via spliceosome. Together these indicate RNA metabolism and protein synthesis machinery. Other terms like DNA recombination and mitotic checkpoint are present but represent a smaller fraction and do not define the main theme.","confidence":"Medium","size":24,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0030007","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0007093","count":2},{"id":"GO:0006430","count":2}]},{"hash":"1915406924304141909","title":"ER protein folding and quality control","description":"The cluster\u2019s top GO terms cluster around protein homeostasis: unfolded protein response, chaperone/cofactor-dependent refolding, SRP-dependent cotranslational targeting to the ER, and general protein quality control (including responses to unfolded proteins and stress). While a few terms (DNA replication, karyogamy, Fe-S cluster assembly) are more divergent, the dominant signal is ER-associated protein folding and trafficking, justifying this label.","confidence":"High","size":24,"edges":52,"triangles":93,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":9},{"id":"GO:0006260","count":9},{"id":"GO:1903382","count":8},{"id":"GO:0006616","count":8},{"id":"GO:0000742","count":8}]},{"hash":"2068952696065101044","title":"RNA processing and ER-stress translation regulation","description":"The top GO terms cluster around mRNA processing (splicing, export from the nucleus, and regulation of splicing) and translational control, particularly in response to ER stress and unfolded protein response. This points to a cohesive theme of RNA processing coupled with stress-responsive regulation of translation, with additional signals for nuclear export and ncRNA-mediated regulation. Thus, the label captures both RNA maturation and stress-linked translation control.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":3},{"id":"GO:0045292","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1900363","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1685585903704626238","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":8,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006289","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1226219499921096391","title":"Gene Expression Regulation and RNA Processing","description":"This cluster is enriched for transcriptional regulation (positive regulation of transcription by RNA polymerase II), RNA splicing via the spliceosome, chromatin modification (histone acetylation), and ncRNA-mediated gene silencing, with additional links to ribosomal biogenesis and cell division. Together, these terms point to a cohesive theme of coordinating gene expression at transcriptional and post-transcriptional levels rather than a single, narrow pathway.","confidence":"Medium","size":23,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:2000616","count":2},{"id":"GO:0048026","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0031047","count":2}]},{"hash":"1635548678575512911","title":"RNA Processing and Splicing Machinery","description":"The top GO terms cluster around RNA biology: transcription termination by RNA Pol II, tRNA and rRNA maturation, spliceosome-mediated splicing, and mRNA decapping. This points to a coherent module of RNA processing and splicing machinery, with chromatin-related and stress-response terms appearing as secondary associations.","confidence":"High","size":23,"edges":96,"triangles":224,"max_degree":18,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006369","count":8},{"id":"GO:0008033","count":6},{"id":"GO:0042633","count":5},{"id":"GO:0009414","count":5},{"id":"GO:1990141","count":5}]},{"hash":"460897062564459099","title":"Mitotic cell cycle and signaling proteins","description":"The cluster centers on mitotic cell cycle, DNA replication, and multiple signaling pathways (JNK cascade, Wnt signaling, T cell receptor signaling) along with related vesicle transport and exocytosis processes, suggesting a core theme of cell-cycle regulation coupled with signaling/cargo trafficking. A few terms (hippocampus development, amino acid starvation response) appear broader or outliers, but do not override the main theme.","confidence":"Medium","size":23,"edges":9,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":7},{"id":"GO:0051301","count":5},{"id":"GO:0046330","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0090263","count":5}]},{"hash":"1899678465843209374","title":"Ribosome Biogenesis and rRNA Processing","description":"The top GO terms are dominated by ribosome-related processes\u2014ribosome biogenesis, small subunit biogenesis, and maturation/processing of rRNA (including box C/D snoRNP assembly and snoRNP-related steps). A related term, proteasome assembly, appears but less prominently. Given the strength and coherence of ribosome/RNA-processing terms vs. a few lone plant-specific terms, the cluster seems centered on ribosome production and RNA maturation rather than broader plant development. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052324","count":1},{"id":"GO:2001009","count":1},{"id":"GO:0009553","count":1},{"id":"GO:0043248","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1902894162162761138","title":"Translation initiation and ribosome recruitment","description":"The top GO terms cluster strongly around translation initiation, preinitiation complex formation, translation reinitiation, and IRES-dependent viral translation, indicating a coherent role in initiating and coordinating protein synthesis on ribosomes. While DNA replication, mRNA export, and sumoylation appear, they are secondary to the dominant initiation/translation signal.","confidence":"High","size":23,"edges":22,"triangles":10,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006406","count":3},{"id":"GO:0016925","count":3},{"id":"GO:0075522","count":3}]},{"hash":"1638684414577573687","title":"Microbial energy metabolism and motility","description":"The top GO terms cluster around energy production pathways (aerobic respiration, TCA cycle, electron transport chain, fermentation, methanogenesis) and motility/flagellar components (bacterial-type flagellum assembly and motility), with an additional note on photosynthesis-related processes. This mix points to proteins involved in energy generation in microbes and their ability to move, rather than a single narrow function. Therefore, a concise label capturing both energy metabolism and flagellar motility is appropriate.","confidence":"High","size":23,"edges":217,"triangles":1339,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0009060","count":6},{"id":"GO:0071973","count":5},{"id":"GO:0006099","count":5},{"id":"GO:0019516","count":5}]},{"hash":"1967270629311537523","title":"Unknown","description":"The GO terms are highly heterogeneous, covering translation fidelity regulation, DNA replication, hormone signaling responses, developmental pathways, and detoxification/stress responses, with no dominant shared function or pathway. There isn\u2019t a cohesive theme linking these proteins, so a single interpretable label cannot be assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006450","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1539549127362705717","title":"Nuclear import and RNA processing","description":"Proteins in this cluster are enriched for nuclear functions, notably import of NLS-bearing proteins into the nucleus and RNA processing steps such as splicing (with supporting polyadenylation term that is marked obsolete). This points to a coherent theme of nuclear trafficking and RNA maturation, although detoxification and lipid metabolism terms are present but less directly connected and may reflect broader multifunctionality or annotation noise.","confidence":"Medium","size":23,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":3},{"id":"GO:0042994","count":3},{"id":"GO:0006607","count":3},{"id":"GO:0000060","count":3},{"id":"GO:0006378","count":3}]},{"hash":"175179782845000621","title":"Unknown","description":"Unknown","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0072332","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0007595","count":2},{"id":"GO:0006362","count":2}]},{"hash":"459619282363363505","title":"Nuclear DNA replication, repair, and transcription during cell cycle","description":"The GO terms point to core nuclear processes: DNA-templated transcription, DNA replication and repair, centromeric chromatin assembly (CENP-A), chromatin dynamics (microtubule severing during mitosis), and mRNA export, all tied to cell division. A minor association with cellular response to oxidative stress fits a broader stress-linked genome maintenance context, but the dominant theme is genome maintenance and transcriptional regulation during the cell cycle.","confidence":"High","size":22,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0034599","count":3},{"id":"GO:0032508","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0061641","count":2}]},{"hash":"1271041795461558160","title":"Mitochondrial import and membrane regulation","description":"The top GO terms point to mitochondrial-specific processes, including protein import into the mitochondrial matrix and regulation of mitochondrial membrane permeability, with another related term on triglyceride biosynthesis (lipid metabolism) tied to mitochondria. While a few terms concern nuclear RNA processing or cell cycle regulation, the mitochondrial-focused terms dominate, supporting a cluster centered on mitochondrial function and lipid metabolism.","confidence":"Medium","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":4},{"id":"GO:1903740","count":4},{"id":"GO:0046902","count":4},{"id":"GO:0010867","count":4},{"id":"GO:0030150","count":4}]},{"hash":"2138791666929362434","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The top GO terms point strongly to ubiquitin-dependent proteolysis, including SCF-dependent and general ubiquitin-proteasome\u2013mediated protein degradation, with supporting signals around ERAD. Other terms (DNA replication, development, budding, septum digestion) may reflect secondary roles or shared components in growth and cell cycle, but the dominant pattern is proteasome/ubiquitin\u2013related turnover. Thus the cluster likely centers on proteostasis machinery and its regulation.","confidence":"High","size":22,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0042787","count":3}]},{"hash":"1059035753752349895","title":"Macromolecular assembly and processing","description":"This cluster centers on diverse but related macromolecular events: translation and mRNA export; DNA replication and chromatin assembly; RNA splicing regulation; DNA damage tolerance; mitochondrial protein insertion and respiratory complex assembly; aggresome formation; microtubule dynamics. Together these terms imply broad roles in the production, processing, and assembly of macromolecules and complexes across cellular compartments, rather than a single precise pathway.","confidence":"Medium","size":22,"edges":90,"triangles":292,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0006406","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0048025","count":3},{"id":"GO:0070987","count":2}]},{"hash":"1223471576844350048","title":"Cytoskeletal Dynamics and Chromatin Remodeling in Division","description":"The cluster shows strong signals for actin-related processes (Arp2/3-mediated nucleation, actin filament bundle assembly, mesenchyme migration, muscle development) and also chromatin remodeling (nucleosome mobilization, histone exchange) together with chromosome movements in meiosis/mitosis. This suggests a cohesive theme where cytoskeletal remodeling and chromatin dynamics coordinate during cell division and developmental processes. Some terms are obsolete, but the remaining GO terms point to a shared focus on structural reorganization and chromosome movement in dividing or developing cells.","confidence":"Medium","size":22,"edges":43,"triangles":47,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0042766","count":5},{"id":"GO:0043486","count":5},{"id":"GO:0051654","count":4},{"id":"GO:0016344","count":4},{"id":"GO:0048741","count":4}]},{"hash":"1187055194718376096","title":"Golgi-ER vesicle trafficking and synaptic exocytosis","description":"Proteins in this cluster are enriched for SNARE complex assembly, ER-to-Golgi and intra-Golgi vesicle transport, Golgi ribbon formation, vesicle fusion with Golgi, and exocytic insertion of neurotransmitter receptors at the postsynaptic membrane, as well as synaptic potentiation, indicating a cohesive role in secretory vesicle trafficking and synaptic membrane delivery.","confidence":"High","size":22,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035493","count":2},{"id":"GO:0090161","count":2},{"id":"GO:0006891","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0048280","count":2}]},{"hash":"1714309950263425352","title":"Mitotic Cell Cycle and DNA Replication","description":"The cluster is dominated by terms related to cell division and DNA synthesis (cell division, mitotic cell cycle, DNA replication, DNA-templated transcription), indicating a core set of proteins involved in cell-cycle progression and genome replication. Additional terms about nuclear export and intracellular trafficking (positive regulation of protein export from nucleus, endosome organization, vacuolar protein processing) suggest related functions in nuclear-cytoplasmic transport and vesicle handling, supporting a cohesive theme around cell-cycle\u2013coupled processes with some trafficking roles.","confidence":"High","size":21,"edges":3,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0007032","count":3},{"id":"GO:0006624","count":3}]},{"hash":"1007591250847714014","title":"Lipid Biosynthesis and Related Metabolic Pathways","description":"The top GO terms are dominated by fatty acid biosynthetic and fatty-acyl-CoA metabolic processes (short, medium, and long-chain), along with lipoteichoic acid and menaquinone biosynthesis, indicating a core focus on lipid metabolism and bacterial envelope-related biosynthesis. The presence of seed germination and seed coat development terms appears out of place and may reflect cross-species annotation noise, but the overall pattern centers on lipid-related metabolic activities. ","confidence":"Medium","size":21,"edges":50,"triangles":49,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006633","count":5},{"id":"GO:0009234","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0010030","count":4},{"id":"GO:0008218","count":4}]},{"hash":"2266571495714232911","title":"Nuclear transcription and chromatin regulation","description":"Top GO terms indicate a core of DNA-templated transcription and chromatin organization, pointing to a gene expression regulation function in the nucleus. However, several outlier terms (mitochondrial membrane organization, collagen catabolic, nitroglycerin metabolism) suggest added diversity, making the transcription/chromatin theme only partially representative. Confidence: Low","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030574","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0035551","count":1}]},{"hash":"1885863734294968018","title":"ER-Golgi trafficking and RNA processing","description":"The top terms show strong signals for vesicle transport between the ER and Golgi (and related retrograde transport), GTPase activity regulation, and TORC1 signaling, indicating a trafficking/growth control module. In addition, RNA-related processes (RNA methylation and rRNA processing) along with mRNA transport suggest coordinated RNA maturation or trafficking activities. Together, these point to a cohesive cluster centered on protein trafficking with concurrent RNA processing/transport roles.","confidence":"Medium","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0035948","count":3},{"id":"GO:0036265","count":3},{"id":"GO:0000447","count":3},{"id":"GO:0001501","count":3}]},{"hash":"869409106843068006","title":"Neural development and transcription regulation","description":"Based on the GO terms, the cluster centers on DNA-templated transcription and nervous system development (Schwann cell, forebrain, hippocampus), with neural signaling (response to cocaine) suggesting a group of proteins involved in neural development and transcriptional control.","confidence":"High","size":21,"edges":42,"triangles":58,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":14},{"id":"GO:0014044","count":14},{"id":"GO:0021766","count":13},{"id":"GO:0042220","count":13},{"id":"GO:0006977","count":13}]},{"hash":"965492399665073222","title":"Embryonic and neural development","description":"This cluster is dominated by GO terms tied to developmental processes across tissues (embryonic cranial skeleton morphogenesis; cerebellum and hippocampus development; transitional B cell differentiation), with additional terms pointing to fundamental cellular activities (DNA replication and DNA-templated transcription) and signaling contexts (cellular response to nitric oxide, death-inducing signaling complex assembly). The combination suggests a theme of broad developmental programs and cell fate decisions, with a notable emphasis on neural development alongside other tissue development; thus the label emphasizes embryonic/neural development as the core shared function.","confidence":"Medium","size":21,"edges":55,"triangles":85,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":19},{"id":"GO:0048701","count":16},{"id":"GO:0048240","count":15},{"id":"GO:0006351","count":14},{"id":"GO:0071550","count":13}]},{"hash":"1621030455719613791","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0019835","count":3},{"id":"GO:0045226","count":2},{"id":"GO:0019305","count":2},{"id":"GO:0006556","count":2}]},{"hash":"2271948986564972266","title":"Unknown","description":"The top GO terms span stress responses (cadmium ion response, SOS response), basic cellular processes (cell division, ribosome biogenesis), and various transport/trafficking pathways (doxorubicin transport, teichoic acid transport, ER to Golgi transport, ERAD). This broad and heterogeneous mix lacks a single cohesive function to define the cluster, so a focused label cannot be confidently assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0009432","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":2},{"id":"GO:1900753","count":2}]},{"hash":"1039784525697424896","title":"Transcription Regulation and Cell Cycle Control","description":"The cluster shows enrichment for DNA-templated transcription and negative regulation of transcription by RNA polymerase II, together with APC/C- and SCF-dependent ubiquitin-proteasome\u2013mediated catabolic processes and cell division, suggesting a core role in transcriptional control and cell-cycle progression. The presence of ribosome biogenesis and maturation of SSU-rRNA indicates coordination with growth and protein synthesis, while TGF-beta signaling points to upstream regulation of these processes. Overall, the proteins appear to cluster around transcription regulation coupled to cell-cycle and proteostasis machinery.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0061087","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":2}]},{"hash":"1295336544501010689","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000183","count":2},{"id":"GO:1990414","count":2},{"id":"GO:0060303","count":2},{"id":"GO:0000447","count":2}]},{"hash":"60832153525299523","title":"AGP glycosylation and plant cell wall development","description":"The cluster centers on arabinogalactan protein metabolism, hydroxyproline O-glycosylation, and mucilage/seed coat-related biosynthesis, all classic Plant cell wall glycoprotein processes. Though a few terms touch insect development, the dominant signals point to AGP-associated glycosylation and extracellular matrix formation in plant development.","confidence":"High","size":20,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0080147","count":2},{"id":"GO:0018258","count":2},{"id":"GO:0010493","count":2},{"id":"GO:0010405","count":2},{"id":"GO:0007299","count":2}]},{"hash":"1028679150298616914","title":"Mitotic cell cycle control","description":"The proteins in this cluster are enriched for GO terms tied to DNA replication, the G1/S transition, kinetochore localization, and regulation of chromosome condensation and DNA damage checkpoints, all central to mitosis and cell cycle progression. This suggests the cluster represents proteins involved in coordinating DNA synthesis and chromosome segregation during cell division. Some terms like lymphangiogenesis, ascospore formation, and response to cocaine appear as secondary or species-specific associations but do not override the core mitotic signal. Therefore, the label emphasizes mitotic cell cycle control.","confidence":"High","size":20,"edges":73,"triangles":151,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0000082","count":8},{"id":"GO:0001946","count":7},{"id":"GO:0034501","count":7},{"id":"GO:0032516","count":7}]},{"hash":"1951795368996221248","title":"Proteostasis, chaperone regulation, and mitophagy","description":"This cluster centers on protein quality control and cellular stress responses: multiple GO terms reference chaperone activity, deacetylation of chaperones like Hsp90, removal/transport of misfolded proteins into aggresomes, and selective autophagy of mitochondria (mitophagy). Oxidative stress\u2013related programmed cell death also appears, supporting a proteostasis- and stress-focused theme. Some transcription/heterochromatin terms are present but appear less central to the core proteostasis signal. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0030466","count":2},{"id":"GO:0070845","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0061734","count":2}]},{"hash":"1831157351274017395","title":"Ubiquitination-driven proteostasis and ERAD","description":"The top GO terms are dominated by ubiquitination-related processes: autoubiquitination, ubiquitin-dependent ERAD, general protein ubiquitination, and specific ubiquitin linkages (K6, K48), along with sumoylation. The presence of peroxisomal protein import also aligns with ubiquitin-regulated quality control in other compartments, reinforcing a proteostasis/degradation theme. While a few terms relate to repair or signaling, the central pattern is ubiquitin-mediated protein quality control and degradation pathways.","confidence":"High","size":20,"edges":72,"triangles":162,"max_degree":14,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":11},{"id":"GO:0030433","count":11},{"id":"GO:1903265","count":10},{"id":"GO:0016567","count":7},{"id":"GO:0016925","count":7}]},{"hash":"124595887663270238","title":"mRNA Processing and Splicing Regulation","description":"The cluster is dominated by GO terms about mRNA processing, modification, and splicing (polyadenylation, spliceosome-mediated splicing, mRNA modification), with supporting signals of transcriptional regulation via RNA polymerase II CTD phosphorylation, and a related note on translation initiation, indicating general RNA-level gene expression control.","confidence":"Medium","size":20,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":3},{"id":"GO:1901407","count":2},{"id":"GO:1905663","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0001825","count":2}]},{"hash":"736735630397315700","title":"Golgi UDP-sugar transport and pollen wall formation","description":"These proteins show enrichment for transport of sugar nucleotides into the Golgi (UDP-galactose, UDP-GlcNAc) and related sugar transport terms, along with plant-specific processes like pollen exine formation and shoot apical meristem development. The combination suggests a module focused on Golgi-mediated sugar nucleotide transport supporting cell wall and pollen wall biosynthesis, with actin nucleation and polarity regulation potentially facilitating vesicle trafficking. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":3},{"id":"GO:0045010","count":2},{"id":"GO:1903857","count":2},{"id":"GO:0097624","count":2},{"id":"GO:1990569","count":2}]},{"hash":"191518700052660779","title":"Neural Development and Behavior","description":"Based on the top terms, the cluster is anchored by nervous system functions such as CNS morphogenesis, adult feeding behavior, and the righting reflex. While a subset of terms relates to protein homeostasis (ubiquitin-mediated degradation and ERAD), these processes often support neural development and maintenance. Overall, the dominant theme points to neural development and behavioral function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008583","count":1},{"id":"GO:0034729","count":1},{"id":"GO:1901026","count":1},{"id":"GO:0008343","count":1},{"id":"GO:1904378","count":1}]},{"hash":"2281601521996892436","title":"Immune signaling regulation by protein tyrosine phosphatases","description":"The cluster is dominated by terms about dephosphorylation and negative regulation of signaling\u2014especially peptidyl-tyrosine dephosphorylation, negative regulation of T cell receptor signaling, and the ERK/MAPK cascade. This points to phosphatases dampening immune and related signaling pathways, with additional terms touching B cell differentiation, interferon production, and adhesion, suggesting a broader regulatory role in immune signaling networks.","confidence":"Medium","size":20,"edges":46,"triangles":90,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0070373","count":5},{"id":"GO:0000200","count":5},{"id":"GO:0050852","count":5},{"id":"GO:0050860","count":5},{"id":"GO:0035335","count":5}]},{"hash":"1604892316099275211","title":"Mitotic spindle and cell division machinery","description":"Enriched terms point to the core microtubule-based cell division machinery: spindle assembly/elongation, spindle orientation, midzone formation, and contractile ring assembly; with supporting references to karyogamy and meiosis, these together indicate components of the mitotic/cytokinetic apparatus. The chloroplast movement term suggests cytoskeletal transport roles in plants, but the dominant signal is spindle dynamics and division.","confidence":"High","size":19,"edges":36,"triangles":38,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":5},{"id":"GO:0000742","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0009904","count":3},{"id":"GO:0060404","count":3}]},{"hash":"2217194486859141913","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":110,"triangles":328,"max_degree":18,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":11},{"id":"GO:0031047","count":11},{"id":"GO:0071038","count":9},{"id":"GO:0000467","count":9},{"id":"GO:0071042","count":9}]},{"hash":"538799625772710754","title":"DNA replication and repair machinery","description":"The cluster is dominated by GO terms for DNA replication, DNA repair, and the mitotic cell cycle, indicating a core genome maintenance function. The other terms, such as development and sterol import, likely reflect broader gene annotations or secondary roles and do not define the primary theme of the cluster.","confidence":"High","size":19,"edges":66,"triangles":103,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":17},{"id":"GO:0006281","count":15},{"id":"GO:0000278","count":15},{"id":"GO:0071550","count":13},{"id":"GO:0021549","count":13}]},{"hash":"845989670787514664","title":"RNA Processing and Pol II Termination","description":"This cluster is centered on RNA biology, with multiple terms for RNA Pol II transcription termination (exosome-dependent and poly(A)-coupled) and RNA processing/decay; translation is also represented, suggesting involvement in gene expression regulation at the RNA level. Some stress-related terms (unfolded protein response) and signaling annotations are present but appear secondary to RNA processing/termination themes.","confidence":"High","size":19,"edges":64,"triangles":130,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0010288","count":3},{"id":"GO:0016576","count":3},{"id":"GO:2000324","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0043278","count":3}]},{"hash":"335687767003876040","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":122,"triangles":399,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0042273","count":6},{"id":"GO:0000467","count":4},{"id":"GO:0071038","count":4},{"id":"GO:0006369","count":4}]},{"hash":"86983559455963577","title":"Protein synthesis and proteostasis","description":"The top GO terms point to general protein production and maturation: translation; protein processing and autoprocessing; and ubiquitin-proteasome\u2013mediated quality control, with a few terms hinting at mitochondria-associated lipid metabolism and dynamics (phospholipid biosynthesis and mitochondrial fusion). This suggests a cohesive theme around how cells synthesize and mature proteins and maintain proteostasis, including mitonuclear and organelle-level regulation, rather than a single tightly defined pathway.","confidence":"Medium","size":19,"edges":138,"triangles":681,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0097428","count":2},{"id":"GO:0006646","count":1},{"id":"GO:0010636","count":1},{"id":"GO:0016540","count":1}]},{"hash":"1438987989827334431","title":"Ribosome and translation machinery","description":"The cluster is dominated by GO terms for translation and ribosome-related processes (translation, ribosomal large subunit assembly, ribosome disassembly, translational termination, mitochondrial translation, translational fidelity, cytoplasmic translation). Additional terms link mRNA decay with translation regulation, suggesting coordinated post-transcriptional control of protein synthesis. A single unrelated term (glial cell proliferation) is present but does not define the core function. Overall, this set best represents a module of ribosome function and translation regulation.","confidence":"High","size":19,"edges":48,"triangles":72,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0000027","count":3},{"id":"GO:0006415","count":2},{"id":"GO:0070125","count":2},{"id":"GO:0006449","count":2}]},{"hash":"1282314623232586769","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071035","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0000467","count":2},{"id":"GO:0071038","count":2}]},{"hash":"1040059626691949070","title":"RNA splicing and post-transcriptional regulation","description":"The cluster is dominated by terms about spliceosome-mediated mRNA splicing, regulation of mRNA stability, and mRNA modification, indicating a core theme of post-transcriptional control. A few terms such as IRES-dependent viral translational initiation and ncRNA-mediated gene silencing suggest broader RNA-level regulation, but the main signal centers on RNA processing and splicing regulation. Obsolete terms are present but do not override the core theme.","confidence":"High","size":19,"edges":109,"triangles":328,"max_degree":17,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":11},{"id":"GO:0031047","count":11},{"id":"GO:0010610","count":10},{"id":"GO:0006378","count":9},{"id":"GO:0045292","count":9}]},{"hash":"553832779244494934","title":"Cell division and vesicle trafficking","description":"The cluster\u2019s top GO terms reflect both cell division processes (mitotic and meiotic chromosome condensation) and intracellular transport (Golgi to lysosome, retrograde Golgi-ER, and clathrin-coated vesicle cargo loading), suggesting a dual thematic connection to chromosome dynamics and vesicle trafficking. Some terms like tRNA processing and microsporogenesis are less connected, but the dominant signals point to roles in cell division and membrane trafficking machinery.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0008033","count":2},{"id":"GO:0035652","count":2},{"id":"GO:0009556","count":2},{"id":"GO:0051138","count":2}]},{"hash":"408658154545566050","title":"Neuronal development and gene expression","description":"Based on the top GO terms, the cluster combines neural development signals (CNS neuron development, dendrite morphogenesis) with core gene expression processes (DNA replication, transcription, translation, tRNA processing, DNA repair) and some stimulus responses (response to cocaine, parathyroid hormone). This suggests proteins involved in neural differentiation alongside fundamental transcription/translation machinery, with ancillary signaling responsiveness. Therefore, the label Neuronal development and gene expression captures the prominent neural development terms while acknowledging the accompanying gene expression processes.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006412","count":3},{"id":"GO:0008033","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0042220","count":2}]},{"hash":"621532245473063383","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006458","count":2}]},{"hash":"1529497525222478252","title":"Proteostasis and Protein Targeting Machinery","description":"The cluster is enriched for protein quality control and targeting processes, including cellular response to unfolded protein, SRP-dependent cotranslational targeting to membrane, and chaperone-assisted protein refolding, plus iron-sulfur cluster assembly that ties to maturation of many proteins. These findings point to a coherent theme of proteostasis and trafficking to membranes, with a few terms (DNA replication, karyogamy) likely reflecting broader cellular roles or annotation overlap. Confidence: Medium","confidence":"","size":18,"edges":110,"triangles":344,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":12},{"id":"GO:0006260","count":11},{"id":"GO:0070389","count":10},{"id":"GO:1903382","count":9},{"id":"GO:0006616","count":9}]},{"hash":"595089597903224923","title":"Developmental Regulation and DNA Replication","description":"The top GO terms point to development (forebrain and skeletal system development, multicellular organism development) and core DNA processes (mitotic cell cycle, DNA replication, DNA-templated transcription), suggesting a cluster centered on coordinating development with cell cycle progression and gene expression. A couple of outlier terms (immune defense, ER-stress\u2013related apoptosis) may reflect annotation noise or broader stress responses but do not define the main theme. Overall, the label captures the prominent developmental and DNA-processing functions.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0030900","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0006260","count":3}]},{"hash":"1631503834997159989","title":"Ribosome Biogenesis and Translation","description":"The top GO terms converge on ribosome assembly and function: cytoplasmic translation, translation initiation/termination, ribosome biogenesis, SSU-rRNA maturation, and ribosomal subunit export, indicating a cluster of ribosome-related proteins; auxiliary terms like response to antibiotic and cell division may reflect broader cellular contexts but do not alter the core theme.","confidence":"High","size":18,"edges":36,"triangles":28,"max_degree":10,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":10},{"id":"GO:0000462","count":3},{"id":"GO:0006415","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0046677","count":3}]},{"hash":"1602276623985621110","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":19,"triangles":3,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070317","count":4},{"id":"GO:0000245","count":3},{"id":"GO:0006369","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3}]},{"hash":"1767133481844962754","title":"Vesicle Transport and Cell Division","description":"The dominant signals are ER-Golgi vesicle transport and retrograde Golgi-to-ER transport, indicating a core of intracellular trafficking. In addition, cell division and sister chromatid cohesion terms suggest involvement in the cell cycle. A few terms (pigmentation, defense response to Gram-positive bacteria, histone methylation) appear less connected to the main theme, but do not overshadow the central trafficking and division signals. Overall, the cluster seems to group proteins associated with membrane trafficking plus cell cycle processes rather than a single, uniform function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":4},{"id":"GO:0006890","count":4},{"id":"GO:0043473","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0031954","count":3}]},{"hash":"2082093294956615353","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":50,"triangles":120,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0009432","count":9},{"id":"GO:0048026","count":9},{"id":"GO:0000467","count":8},{"id":"GO:0006306","count":8},{"id":"GO:0014070","count":8}]},{"hash":"785117972349662613","title":"Nuclear chromatin remodeling and DNA repair","description":"The top GO terms are dominated by chromatin remodeling (including transcription-coupled remodeling) and heterochromatin regulation, plus localization to the nucleolus and a replication-associated DNA repair term, pointing to a nucleus-centric theme of chromatin dynamics and genome maintenance. A few terms related to ER stress or Golgi localization are present but far less represented, suggesting they are less central to the cluster. Overall, this set most coherently reflects proteins involved in chromatin structure modulation and DNA repair in the nucleus.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":4},{"id":"GO:1990414","count":3},{"id":"GO:0090394","count":2},{"id":"GO:1903206","count":2},{"id":"GO:1902570","count":2}]},{"hash":"841581913266614674","title":"Plant chromatin remodeling and autophagy regulation","description":"The cluster is dominated by GO terms for chromatin dynamics (rDNA heterochromatin formation, chromatin remodeling) and autophagy-related processes (autophagosome maturation, mitophagy regulation), with additional plant-specific metabolism terms (anthocyanin/flavonoid pathways) suggesting a plant context where chromatin state and autophagy intersect with secondary metabolism. This combination points to a cohesive theme around chromatin regulation and autophagy in plants, with some peripheral metabolic links.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0001300","count":2},{"id":"GO:0006613","count":2},{"id":"GO:0009718","count":1}]},{"hash":"1380044996428353656","title":"Ribosome biogenesis and translation machinery","description":"The cluster is strongly enriched for translation (GO:0006412) and ribosome biogenesis terms (GO:0042254, GO:0042273), indicating involvement in ribosome assembly and protein synthesis. Additional signals for transcription regulation and DNA damage response (p53 pathway, gamma radiation, UV) suggest coordination of gene expression and stress responses under DNA damage, but the core theme centers on ribosome production and translation. Confidence: High","confidence":"","size":17,"edges":136,"triangles":680,"max_degree":16,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":14},{"id":"GO:0042254","count":4},{"id":"GO:0032784","count":3},{"id":"GO:1902167","count":3},{"id":"GO:0071480","count":3}]},{"hash":"1428145283155911075","title":"Ribosome and mitochondrial translation","description":"Top terms are dominated by translation-related processes: cytosolic translation, various tRNA aminoacylation activities (valyl-, tyrosyl-, tryptophanyl-), and ribosomal small subunit assembly, with additional hints of mitochondrial translation. While other GO terms (angiogenesis, vasculogenesis, cuticle development, glycosylation) appear, the strongest signal centers on protein synthesis machinery, including mitochondrial translation, justifying this label.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006438","count":3},{"id":"GO:0000028","count":2},{"id":"GO:0070184","count":2},{"id":"GO:0001525","count":2}]},{"hash":"1083995331703377717","title":"RNA Processing and Cell-Cycle Machinery","description":"Top GO terms indicate RNA processing (spliceosome-mediated splicing), translation initiation (preinitiation complex formation and translation reinitiation), and cell division (mitotic cohesion, cell division) with additional signals from chromatin modification and apoptosis regulation. The combination points to core cellular processes rather than a single specialized function, justifying a broad label of RNA processing and cell-cycle machinery.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060271","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0031954","count":1}]},{"hash":"1923344774960567440","title":"Secretory vesicle trafficking","description":"The cluster shows strong representation of GO terms for vesicle transport along the secretory pathway: Golgi to plasma membrane, ER to Golgi and Golgi to ER (retrograde), and vesicle docking during exocytosis, along with regulation of synaptic vesicle endocytosis. This points to a shared role in moving and fusing vesicles between the endomembrane system and the cell surface. While terms like ribosome biogenesis and mitochondrion inheritance appear, they likely reflect generic cellular maintenance rather than defining the cluster\u2019s primary function.","confidence":"High","size":16,"edges":16,"triangles":0,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006904","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0006893","count":3},{"id":"GO:0006890","count":3}]},{"hash":"2067927991699385356","title":"Rab-regulated endosome-to-Golgi trafficking","description":"The terms cluster around vesicle transport connecting endosomal compartments with the Golgi, including plasma membrane-to-endosome, late endosome-to-Golgi, recycling endosome-to-Golgi, and COPII vesicle cargo loading, with Rab GTPase activation and signaling regulation. This points to a cohesive set of proteins governing Rab-dependent endosomal trafficking to the Golgi rather than other pathways.","confidence":"High","size":16,"edges":29,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0048227","count":2},{"id":"GO:0090630","count":2},{"id":"GO:0035526","count":2},{"id":"GO:0090110","count":2},{"id":"GO:0032889","count":2}]},{"hash":"1256795172649477389","title":"Retinoid and steroid lipid metabolism in lung development","description":"The top GO terms cluster around retinoid metabolism (retinol, retinal, retinoic acid) and steroid/lipid biosynthesis (testosterone, androgen, fatty acid elongation, sphingolipids), with lung development relevance. This points to a co-regulated lipid metabolism module involving retinoids and steroid lipids, including its role in lung morphogenesis via retinoic acid signaling.","confidence":"High","size":16,"edges":5,"triangles":2,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0061370","count":4},{"id":"GO:0042572","count":4},{"id":"GO:0008209","count":4},{"id":"GO:0042574","count":4}]},{"hash":"1693276093954810101","title":"Embryonic neural and placental development","description":"This cluster is dominated by developmental GO terms related to neural tissues (forebrain development, Schwann cell development) and placental formation (maternal placenta development, glycogen cell differentiation in placenta), suggesting a shared role in embryonic development across neural and placental lineages. Some terms (DNA replication, meiotic cell cycle, immune defense, insulin signaling) are broader or less tightly connected, indicating the core theme is developmental programs rather than a single unified pathway. Confidence: Medium.","confidence":"","size":16,"edges":18,"triangles":7,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0030900","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0001893","count":3},{"id":"GO:0010765","count":3}]},{"hash":"145617924993045064","title":"Unknown","description":"The terms cover ribosomal RNA processing, estrogen receptor signaling regulation, ufmylation, DNA replication/transcription, T cell apoptosis regulation, various lipid biosynthesis processes, and epithelial maturation\u2014none point to a single coherent function or pathway for the cluster, suggesting heterogeneous or unrelated roles.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":2},{"id":"GO:0033146","count":2},{"id":"GO:1990592","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006351","count":2}]},{"hash":"1668496367262801482","title":"Transcription regulation and ribosome biogenesis","description":"This cluster shows enrichment for both transcription-related GO terms (DNA-templated transcription, negative regulation of transcription by RNA Pol II) and ribosome-associated processes (ribosome biogenesis, ribosomal subunit export, rRNA maturation, and translation initiation/termination). The mix suggests a broad gene-expression\u2013level cluster spanning transcriptional control and ribosome assembly/translation; thus the label reflects the shared theme of coordinating gene expression from transcription to ribosome function.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0032790","count":1},{"id":"GO:0042273","count":1}]},{"hash":"2240673344602583308","title":"Protein Folding and ER Stress Response","description":"The top GO terms cluster around chaperone-assisted refolding, unfolded protein response, ER-targeted translocation, and quality control of protein aggregation, pointing to a theme of proteostasis in the secretory/ER pathway. While a few terms (DNA replication, iron-sulfur cluster assembly, karyogamy) are less clearly connected and may reflect housekeeping or shared components, the dominant signal is protein folding and ER stress management.","confidence":"Medium","size":15,"edges":24,"triangles":16,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":6},{"id":"GO:0006260","count":6},{"id":"GO:0043547","count":5},{"id":"GO:1903382","count":5},{"id":"GO:0006616","count":5}]},{"hash":"901370515973093965","title":"Rho GTPase\u2013driven actin remodeling and cell migration","description":"The listed GO terms center on small GTPase signaling, regulation of GTPase activity, and assembly of actin-based structures (filopodia and ruffles), which drive cell spreading, polarity, and shape changes. This points to coordinated actin cytoskeleton remodeling and cell movement, with EGFR signaling as an upstream contributor and osteoclast-related bone resorption reflecting motility-related cytoskeletal dynamics. Thus, a cohesive label is actin remodeling and cell migration governed by Rho-family GTPases.","confidence":"High","size":15,"edges":17,"triangles":4,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007264","count":6},{"id":"GO:1900026","count":6},{"id":"GO:0046847","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0007173","count":5}]},{"hash":"860870594892484624","title":"Bacterial Translation and Circadian Signaling","description":"The cluster is dominated by translation-related GO terms (GO:0006412), indicating core protein synthesis activity. The presence of circadian-related terms (entrainment of circadian clock, circadian rhythm) and regulation of phosphorelay signal transduction suggests co-occurrence of signaling/regulatory components with translation, possibly reflecting a bacterial system where translation is linked to circadian cues and two-component signaling. Overall, the theme centers on translation machinery with circadian and signaling context, though some terms seem less tightly connected.","confidence":"Medium","size":15,"edges":47,"triangles":91,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":3},{"id":"GO:0009649","count":2},{"id":"GO:0042754","count":2},{"id":"GO:0070297","count":2}]},{"hash":"2278183342947190835","title":"DNA-level gene regulation and drug responses","description":"The cluster includes DNA-templated transcription and DNA replication, indicating core gene expression and genome maintenance. It also references responses to antibiotics and cocaine, chemotaxis, and glucose metabolism, suggesting a mix of regulatory and stress-related processes rather than a single pathway. This supports naming the cluster as broadly focused on gene regulation with general cellular response to stimuli.","confidence":"Medium","size":15,"edges":19,"triangles":3,"max_degree":11,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006261","count":2},{"id":"GO:0032092","count":2},{"id":"GO:0042220","count":2}]},{"hash":"561750592805923751","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":42,"triangles":99,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":8},{"id":"GO:0000398","count":8},{"id":"GO:0031047","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0090394","count":6}]},{"hash":"877113029018611369","title":"Wnt Signaling Regulation and Proteasome-Mediated Degradation","description":"The cluster centers on regulation of the canonical Wnt pathway (both positive and negative) and on proteasomal/ubiquitin-dependent or -independent protein catabolism, with supporting terms for GTPase activity regulation and inflammatory response control. Together these suggest a coherent theme of signaling modulation via targeted protein turnover, with Wnt signaling as the core anchor, despite some peripheral terms reflecting broader ubiquitin-related processes across contexts.","confidence":"Medium","size":15,"edges":35,"triangles":34,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0090090","count":4},{"id":"GO:0000742","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0031146","count":3},{"id":"GO:0002862","count":3}]},{"hash":"474612330557294442","title":"Zinc Ion Homeostasis and Transport","description":"The top GO terms cluster tightly around zinc biology: zinc ion homeostasis, response to zinc, zinc transmembrane transport, detoxification, and regulation of import. While some iron/cobalt terms appear, zinc-related processes dominate, so the label Zinc Ion Homeostasis and Transport best reflects the group's shared function.","confidence":"High","size":15,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0006882","count":1},{"id":"GO:0010043","count":1},{"id":"GO:0071577","count":1},{"id":"GO:0071584","count":1}]},{"hash":"163049666345800634","title":"Ribosome Biogenesis and RNA Processing","description":"Dominant themes are ribosomal large subunit biogenesis and rRNA maturation (5.8S/LSU, export) and mRNA splicing, indicating RNA metabolism and ribosome assembly as the core function; a few trafficking terms appear but are secondary.","confidence":"Medium","size":15,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0090394","count":2}]},{"hash":"1326369796651673602","title":"Multicellular development and cell adhesion","description":"These proteins are enriched for multicellular development terms (including neuron projection and skeletal system development) and for homophilic cell\u2013cell adhesion, with supporting roles in transcription and mRNA transport. Together, the set points to roles in developmental patterning and cell interactions, justifying the label Multicellular development and cell adhesion.","confidence":"Medium","size":15,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0007156","count":2},{"id":"GO:0007120","count":2},{"id":"GO:0031954","count":2},{"id":"GO:0043547","count":2}]},{"hash":"923265880624845033","title":"Broad cellular stress and signaling responses","description":"The GO terms indicate responses to xenobiotics, hydrogen peroxide, and cAMP, plus regulation of cell cycle, metabolism, and development, suggesting a broad, stimulus-responsive regulatory cluster rather than a single pathway.","confidence":"Medium","size":14,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000466","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0046856","count":2},{"id":"GO:0042493","count":2},{"id":"GO:1900087","count":2}]},{"hash":"283688799629434139","title":"Developmental Transcription Regulators","description":"The cluster is driven by transcription-related GO terms (DNA-templated transcription and transcription termination) and several development-related terms across different tissues (neural and forebrain development, dendrite morphogenesis, root hair development), suggesting a shared role in regulating development through transcription. While a few plant- or tissue-specific terms appear, they are infrequent, so the overarching theme points to transcriptional regulation in developmental contexts.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0080147","count":2},{"id":"GO:0021954","count":2},{"id":"GO:0048813","count":2},{"id":"GO:0030900","count":2}]},{"hash":"284402854795981656","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":8,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0048568","count":2}]},{"hash":"905053188134572542","title":"Neuronal development and synaptic exocytosis","description":"The top GO terms point to brain and nervous system development, regulation of synaptic vesicle exocytosis, Rac signaling, and axon extension, all pointing to neuronal differentiation and synaptic trafficking. While a ribophagy term appears, the dominant signal is neuronal development and synaptic function, suggesting this cluster comprises proteins involved in neural development and neurotransmitter release rather than non-neural processes.","confidence":"High","size":14,"edges":79,"triangles":237,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0031384","count":3},{"id":"GO:0010796","count":3},{"id":"GO:2000300","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0034517","count":3}]},{"hash":"1428820886554715509","title":"Golgi\u2013ER vesicle transport","description":"The prominent terms include retrograde vesicle-mediated transport from Golgi to ER, Golgi organization, and endocytosis, pointing to a core intracellular trafficking theme. Other terms (hippocampus development, endothelin regulation, NF-kappaB signaling, mitotic cell cycle) are broader or secondary, reflecting overlaps rather than a single primary function. Thus, a concise label capturing the dominant trafficking role is appropriate.","confidence":"Medium","size":14,"edges":50,"triangles":60,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":5},{"id":"GO:0003100","count":4},{"id":"GO:0000056","count":4},{"id":"GO:0006897","count":4},{"id":"GO:0007030","count":4}]},{"hash":"18923870177255812","title":"Ubiquitin-Dependent Proteolysis and Cell Cycle Regulation","description":"The GO terms overwhelmingly point to ubiquitin-mediated degradation pathways (ERAD, autoubiquitination, free ubiquitin chains, N-end rule), coupled with cell cycle-related processes (exit from mitosis, cell division) and regulatory signaling (NF-kappaB). This indicates a cohesive theme of ubiquitin-dependent protein turnover influencing cell cycle and transcriptional signaling.","confidence":"High","size":14,"edges":91,"triangles":364,"max_degree":13,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0030433","count":14},{"id":"GO:0051865","count":14},{"id":"GO:0070911","count":14},{"id":"GO:0010994","count":11},{"id":"GO:0051301","count":11}]},{"hash":"1700348931233045220","title":"Viral life cycle and latency","description":"This cluster is enriched for viral-related processes: viral life cycle, uncoating, proviral latency, and viral release, indicating proteins involved in viral infection and replication. The presence of translation and protein folding terms suggests host machinery engagement during viral processes as well.","confidence":"High","size":14,"edges":66,"triangles":155,"max_degree":13,"top_function":"protein folding","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0019061","count":3},{"id":"GO:1901407","count":3},{"id":"GO:2000276","count":3},{"id":"GO:0010849","count":3}]},{"hash":"782300270091647664","title":"DNA replication and cell cycle regulation","description":"The terms cluster around DNA replication, mitotic cell cycle, DNA repair, and centrosome/microtubule\u2013associated processes, with transcription-related activity. This points to a cohesive group of proteins involved in DNA replication and cell-cycle progression, including centrosome dynamics and related nuclear events.","confidence":"High","size":14,"edges":13,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0007275","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0035372","count":7}]},{"hash":"51963294494550613","title":"RNA transcription and processing","description":"The dominant GO terms center on transcription and RNA processing: transcription by RNA polymerases I/II/III, including rRNA transcription, elongation, and termination, plus mRNA splicing via the spliceosome and RNA-templated transcription. A few terms reference lipopolysaccharide response or obsolete annotations, but the core pattern points to nuclear gene expression machinery focused on transcription and RNA processing.","confidence":"Medium","size":14,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0042790","count":1},{"id":"GO:0006362","count":1}]},{"hash":"1788443067395756421","title":"RNA processing and translation initiation","description":"The GO terms are dominated by RNA metabolism activities: mRNA splicing via the spliceosome, mRNA stability and modification, rRNA maturation, and formation of translation preinitiation complexes with translation reinitiation. This points to a cluster of proteins involved in RNA processing and the early stages of protein synthesis, even though there are no direct interaction edges observed in this dataset.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0002188","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0000462","count":3}]},{"hash":"1533502492980571661","title":"Nuclear DNA replication and chromatin assembly","description":"This cluster is driven by GO terms for cell division, DNA replication, CENP-A\u2013containing chromatin assembly, and nucleus organization, pointing to core nuclear functions in genome maintenance and chromatin dynamics. A few terms touch on RNA decay and ER-Golgi transport, but the dominant theme remains nuclear processes.","confidence":"High","size":13,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0070651","count":3},{"id":"GO:0061641","count":2},{"id":"GO:0070676","count":2},{"id":"GO:0006260","count":2}]},{"hash":"785143191214821713","title":"Unknown","description":"The top GO terms span DNA damage response (DNA strand invasion, SOS response, cellular response to camptothecin, response to toxic substance), ribosome biogenesis, and various developmental processes (germarium-derived oocyte fate determination, ovarian follicle development, and polarity specification), with no single cohesive function linking all terms. This diversity suggests no clear, shared biological theme for a concise label.","confidence":"","size":13,"edges":5,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0007294","count":2},{"id":"GO:0042148","count":2},{"id":"GO:0009636","count":2}]},{"hash":"1791567980743564942","title":"Developmental morphogenesis and genome maintenance","description":"The terms show both DNA repair/replication (genome maintenance) and developmental processes like root hair development, cell morphogenesis, and gastrulation regulation, along with cell migration, indicating a cluster spanning genome maintenance and developmental/cell-movement functions.","confidence":"Medium","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0045666","count":2},{"id":"GO:0000902","count":2}]},{"hash":"1765109759210496499","title":"Amino acid metabolism and vitamin biosynthesis","description":"The top terms cluster around amino acid turnover (L-alanine and L-kynurenine catabolism, L-tyrosine biosynthesis, obsolete L-lysine pathways) plus central metabolism (oxaloacetate) and cofactor-related processes (cobalamin biosynthesis) as well as fatty acid homeostasis. The Notch signaling term seems unrelated noise. Overall, this points to a metabolic module focused on amino acid metabolism and vitamin cofactor biosynthesis rather than signaling.","confidence":"Medium","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042853","count":6},{"id":"GO:0007219","count":5},{"id":"GO:0097053","count":5},{"id":"GO:0019878","count":4},{"id":"GO:0006571","count":3}]},{"hash":"1395636953124221555","title":"RNA maturation and translational regulation","description":"The cluster shows strong enrichment for RNA processing and translation-related GO terms, including translation, tRNA processing, rRNA maturation, primary miRNA processing, and regulation of translation initiation via eIF2\u03b1 phosphorylation. Although one term (hypoglossal nerve morphogenesis) seems unrelated and likely noise, the dominant theme ties RNA maturation to control of protein synthesis, justifying the label.","confidence":"High","size":13,"edges":12,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0021618","count":1},{"id":"GO:0031053","count":1},{"id":"GO:0009636","count":1}]},{"hash":"1631486893324836651","title":"Core DNA replication and proteostasis network","description":"This cluster centers on essential cellular maintenance: DNA replication is prominent, and several terms point to protein handling and trafficking (SRP-dependent targeting to membranes, unfolded protein response, inclusion body regulation), plus supporting roles in cofactor assembly (iron-sulfur clusters) and general morphology and stress responses. The combination suggests a broad housekeeping module integrating genome duplication with protein homeostasis rather than a single specialized pathway. ","confidence":"Medium","size":13,"edges":31,"triangles":45,"max_degree":12,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0000742","count":6},{"id":"GO:0000902","count":6},{"id":"GO:1903382","count":5},{"id":"GO:0006616","count":5}]},{"hash":"1693108423576438323","title":"Unknown","description":"The top GO terms are a random mix of metabolic, signaling, and development-related processes with only singleton occurrences, and there are no links between proteins (no edges or triangles). This lack of a cohesive functional theme makes it impossible to assign a concise, representative label beyond Unknown.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009744","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0035878","count":1},{"id":"GO:0051291","count":1},{"id":"GO:0045859","count":1}]},{"hash":"723655042917872932","title":"RNA processing and translational regulation","description":"These proteins appear to participate in RNA biogenesis and the control of protein synthesis, with terms covering snRNA processing, snoRNA splicing, and polyadenylation, together with initiation/termination/reinitiation of translation (including IRES-mediated viral initiation and viral termination-reinitiation) and regulation of translational initiation. This suggests a cohesive theme of RNA maturation coupled to translation control, albeit with some legacy/obsolete terms. ","confidence":"Medium","size":13,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006378","count":5},{"id":"GO:0001731","count":4},{"id":"GO:0006369","count":4},{"id":"GO:0075522","count":3},{"id":"GO:0075525","count":3}]},{"hash":"688757067786456926","title":"Unknown","description":"The GO terms are highly diverse, including intracellular protein transport, kinetochore assembly, left-right asymmetry, metal ion response, male sex differentiation, organ identity maintenance, cell division, and interferon response. There is no single dominant function or shared pathway across the cluster, and most terms appear only once. With no cohesive theme, a meaningful, cohesive label cannot be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0051382","count":1},{"id":"GO:0071908","count":1},{"id":"GO:0010288","count":1},{"id":"GO:0046661","count":1}]},{"hash":"1854301223360281568","title":"Cardiac and muscle differentiation with chromatin remodeling","description":"The cluster is enriched for GO terms related to heart and muscle development (cardiac atrium morphogenesis, pericardium morphogenesis, muscle cell differentiation) and chromatin regulation (CENP-A chromatin assembly, transcription initiation-coupled chromatin remodeling, histone methylation regulation). This combination suggests proteins linked to differentiation of cardiac/muscle lineages coordinated with chromatin dynamics; other terms like ER-Golgi transport are ancillary. ","confidence":"Medium","size":12,"edges":4,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0003344","count":2},{"id":"GO:0001649","count":2},{"id":"GO:0045815","count":2}]},{"hash":"2294570934321824448","title":"Xenobiotic Stress and Gene Expression Regulation","description":"The top GO terms cluster around how cells respond to chemical stress (response to xenobiotic stimulus, response to toxic substance) and adjust gene expression (regulation of DNA-templated transcription, negative regulation of translation), with signaling involvement (positive regulation of nitric oxide biosynthesis). Some metabolic terms appear, but the dominant theme is stress-induced regulation of transcription/translation and xenobiotic signaling, suggesting a label focused on stress-responsive gene regulation. Confidence: Medium","confidence":"","size":12,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0017148","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045429","count":2},{"id":"GO:0006355","count":2}]},{"hash":"1472987632352303002","title":"Cell Cycle and Genome Maintenance","description":"Multiple top GO terms cluster around cell division processes (mitotic cell cycle, centrosome cycle, cell division) and genome maintenance (DNA replication, DNA repair). Secondary terms point to general growth-related processes (ribosomal biogenesis, ER\u2013Golgi transport), but the dominant theme is cell cycle progression and genome integrity. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000902","count":4},{"id":"GO:0001893","count":3},{"id":"GO:0007098","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0006260","count":3}]},{"hash":"163946827098044359","title":"Vesicle trafficking and secretory pathway regulation","description":"The cluster shows a strong focus on vesicle transport processes: positive regulation of ER to Golgi vesicle-mediated transport, late endosome to lysosome transport, exocytosis modulation, and small GTPase-mediated signaling (typical of Rab/Arf regulators). Lipoprotein particle assembly also ties to secretory pathways. While a couple terms relate to development or apoptosis, the dominant signal is vesicle trafficking and secretory pathway regulation, justifying this label.","confidence":"High","size":12,"edges":20,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0045956","count":2},{"id":"GO:0007264","count":2},{"id":"GO:1902824","count":2}]},{"hash":"1688213672410501358","title":"Neuronal development and synapse assembly","description":"The top GO terms point to neuronal development, synapse formation, and cell adhesion (homophilic adhesion, brain development, synapse assembly), with supporting signals for cytoskeletal remodeling (GTPase activity, actin filament capping) and growth signaling (TGF-beta response). This combination is characteristic of processes governing neuronal differentiation, adhesion between cells, and synapse establishment.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007156","count":3},{"id":"GO:0043547","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0007416","count":2},{"id":"GO:0050731","count":2}]},{"hash":"2010521961458203732","title":"Unknown","description":"The GO terms are highly heterogeneous, including metabolic processes (xanthine and phenylacetate catabolic processes, ATP synthesis via electron transport), ion transport, lactation, nitrogen fixation, and several negative regulators of vascular development (endothelial differentiation, VEGF signaling, vasculogenesis). This lack of a single cohesive function or pathway makes it unclear how these proteins form a coherent cluster with a specific, representative function.","confidence":"","size":12,"edges":29,"triangles":39,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0045602","count":3},{"id":"GO:0009115","count":3},{"id":"GO:0042773","count":3}]},{"hash":"754650249355381202","title":"TGF-\u03b2/BMP Signaling Regulation","description":"Most terms point to regulation of Transforming Growth Factor beta and Bone Morphogenetic Protein signaling (negative regulation of BMP signaling, negative regulation of TGF-\u03b2 receptor signaling, cellular response to TGF-\u03b2 stimulus) with peptidyl-threonine dephosphorylation suggesting phosphatases modulating this pathway. Some outlier terms refer to plant-specific processes or obsolete annotations, but the central theme is clear: modulation of TGF-\u03b2/BMP signaling (SMAD-associated). Confidence: Medium","confidence":"","size":12,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030514","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0035970","count":3},{"id":"GO:0080005","count":3},{"id":"GO:0010991","count":3}]},{"hash":"752018863027516584","title":"Cross-tissue developmental signaling","description":"The top GO terms cluster around developmental processes in multiple tissues (midgut, olfactory pit, blood vessel) and signaling responses (retinoic acid, cAMP), with some metabolism terms present but not defining the group. This suggests a cross-tissue developmental signaling theme.","confidence":"Medium","size":12,"edges":18,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007494","count":3},{"id":"GO:0060166","count":2},{"id":"GO:0051591","count":2},{"id":"GO:0009258","count":2},{"id":"GO:0055129","count":2}]},{"hash":"120135455826994444","title":"Redox homeostasis and glutathione metabolism","description":"This cluster is dominated by GO terms related to redox balance and glutathione pathways (cell redox homeostasis, cellular oxidant detoxification, glutathione metabolic process, protein glutathionylation), suggesting a module focused on protecting against oxidative stress and managing redox chemistry. The presence of translation and spliceosome terms may reflect broader cellular stress or housekeeping processes that co-occur, but the strongest shared function centers on redox regulation and glutathione turnover.","confidence":"Medium","size":12,"edges":26,"triangles":23,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0045292","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0098869","count":2}]},{"hash":"459971294980704810","title":"Unknown","description":"The GO terms span diverse processes (peroxisomal protein import, mitochondrial DNA metabolism, tRNA aminoacylation and translation, embryonic development, DNA biosynthesis, and even a bacterial sugar transport system) with no clear, cohesive functional theme binding all proteins together. This diversity makes it hard to assign a specific, representative label beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":2},{"id":"GO:0045836","count":2},{"id":"GO:0009401","count":1},{"id":"GO:0006433","count":1},{"id":"GO:0001701","count":1}]},{"hash":"883182752233014483","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0010019","count":1},{"id":"GO:0001682","count":1}]},{"hash":"137812204496223510","title":"DNA replication and cell cycle proteins","description":"Based on the GO terms, the cluster is enriched for core genome maintenance and division processes\u2014DNA replication (GO:0006260), mitotic cell cycle (GO:0000278), DNA repair (GO:0006281), and DNA recombination (GO:0006310)\u2014along with cell division (GO:0051301). A few terms related to development or perception (visual perception, embryonic cranial skeleton morphogenesis) appear but seem peripheral to the dominant DNA replication/repair/cell cycle theme. Overall, the proteins appear to function together in genome maintenance and progression through the cell cycle.","confidence":"High","size":12,"edges":9,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0007118","count":3},{"id":"GO:0006813","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0000278","count":3}]},{"hash":"311543361714316660","title":"Macromolecular Assembly and Organelle Organization","description":"This cluster is dominated by terms about assembling and organizing cellular structures and organelles, including mitochondrial complex III assembly, CENP-A chromatin assembly, intralumenal vesicle formation, gas vesicle organization, cilium movement, and microtubule severing. While there are a couple of outlier processes (DNA damage tolerance and FAD catabolism), the overarching theme centers on the construction and maintenance of macromolecular assemblies and organelle dynamics.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":2},{"id":"GO:0034551","count":2},{"id":"GO:0031412","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0032979","count":2}]},{"hash":"820202226694526819","title":"ER-Golgi vesicle trafficking","description":"Most of the top GO terms are about vesicle-mediated transport between the endoplasmic reticulum and Golgi (ER to Golgi and Golgi to ER), indicating proteins in the cluster participate in the secretory pathway. Other terms (cell division, metabolism) are less central, but the strongest pattern is ER-Golgi trafficking.","confidence":"High","size":12,"edges":4,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0000920","count":2}]},{"hash":"1591896980273771439","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000447","count":4},{"id":"GO:0000480","count":4},{"id":"GO:0000472","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0051301","count":3}]},{"hash":"1511061936436029736","title":"Mitochondrial Membrane Transport and Dynamics","description":"The cluster is dominated by GO terms related to mitochondrial membranes\u2014regulation of mitochondrial membrane potential, apoptotic mitochondrial changes, various transmembrane transports (NAD, coenzyme A, citrate), and mitochondrial fission. This points to a cohesive function around mitochondrial membrane regulation and dynamics, with a few outliers (e.g., pregnancy term) that do not alter the overall theme. ","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":3},{"id":"GO:0007565","count":3},{"id":"GO:0008637","count":3},{"id":"GO:0035349","count":3},{"id":"GO:0034198","count":3}]},{"hash":"218102333640108199","title":"Unknown","description":"Top terms are highly diverse, spanning metabolism (glycolysis, sucrose response, cobalamin biosynthesis), RNA methylation, chromosome and spindle dynamics (CENP-A assembly, cell division, microtubule severing), protein oligomerization, and secretory/quality-control pathways (ER to Golgi transport, ERAD). This scattered mix provides no clear common function binding the cluster, so a single coherent label is not evident. ","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009744","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0051013","count":2},{"id":"GO:0061641","count":2}]},{"hash":"511833607765268942","title":"Unknown","description":"The GO terms are highly heterogeneous (autophagy, peroxisome matrix import, JNK regulation, histone modification, V(D)J recombination, development-related processes). The lack of a unifying function and the absence of protein\u2013protein interactions (edges) suggest these proteins do not form a cohesive functional cluster, and several terms are obsolete.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0030433","count":6},{"id":"GO:0051301","count":5},{"id":"GO:0016558","count":5},{"id":"GO:0090073","count":5},{"id":"GO:0006914","count":4}]},{"hash":"1873930052895202949","title":"Amino Acid Metabolism and Cofactor Biosynthesis","description":"The cluster centers on multiple amino acid-related processes (histidine, alanine, tyrosine, lysine) and related metabolic activities (oxaloacetate metabolism, fatty acid homeostasis) plus cobalamin biosynthesis, suggesting a coherent theme around amino acid metabolism and cofactor biosynthesis. Notch signaling appears as an outlier term and does not define the core function of the cluster, so the label emphasizes metabolic pathways rather than signaling. ","confidence":"Medium","size":11,"edges":24,"triangles":27,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000105","count":4},{"id":"GO:0007219","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0033512","count":4}]},{"hash":"1863218402955166996","title":"Unknown","description":"The terms span diverse processes including multiple biosynthetic pathways (glycolate, serine, glycerol, cardiolipin, ADP-L-glycero-manno-heptose) along with copper ion transport and actin rod assembly, giving no single, cohesive function to label. Therefore, a distinct, confident cluster name cannot be assigned.","confidence":"","size":11,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0046295","count":1},{"id":"GO:0031247","count":1},{"id":"GO:0006564","count":1}]},{"hash":"590856764526686062","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":51,"triangles":133,"max_degree":10,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0031118","count":4},{"id":"GO:0031120","count":4},{"id":"GO:2000623","count":3},{"id":"GO:0046330","count":3}]},{"hash":"1915650401527496542","title":"ER Proteostasis and Protein Targeting","description":"These proteins cluster around processes that ensure proper protein maturation and handling in the secretory pathway: SRP-dependent targeting to the ER, unfolded protein response, ER stress-related apoptosis regulation, and deubiquitination/quality-control mechanisms. Iron-sulfur cluster assembly fits as part of broader protein maturation, reinforcing a proteostasis theme. Some terms (e.g., karyogamy, Fc\u03b5 receptor signaling, epinephrine response) are less connected, but the dominant signal is ER-associated protein synthesis, folding, and quality control.","confidence":"Medium","size":11,"edges":25,"triangles":25,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:2000378","count":3},{"id":"GO:0071872","count":3},{"id":"GO:0038095","count":3},{"id":"GO:0016579","count":3}]},{"hash":"112344792334756709","title":"ER Stress and Protein Quality Control","description":"This cluster is dominated by GO terms related to handling misfolded/older proteins (cellular response to unfolded protein, SRP-dependent cotranslational targeting to membrane, protein targeting to membrane), and protective regulation of apoptosis under stress, indicating a cohesive theme of proteostasis and ER-associated quality control. Some terms like DNA replication and iron-sulfur cluster assembly appear as peripheral connections, not overriding the main stress/protein-homeostasis thread.","confidence":"Medium","size":11,"edges":18,"triangles":6,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0000742","count":6},{"id":"GO:1903382","count":5},{"id":"GO:0006616","count":5},{"id":"GO:0090084","count":5}]},{"hash":"1367789595132539525","title":"Cell growth, division, and ribosome biogenesis","description":"GO terms indicate roles in cell growth, cell division, mitotic cohesion, and ribosome biogenesis, pointing to proteins involved in proliferative machinery and protein synthesis. Some terms are obsolete or less central, but the dominant theme centers on growth and division processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:2001275","count":3},{"id":"GO:0031954","count":2},{"id":"GO:1902510","count":2},{"id":"GO:0070734","count":2}]},{"hash":"1318441846636704599","title":"Mitochondrial transport and membrane dynamics","description":"The cluster centers on mitochondrial processes: regulation of membrane potential, mitochondrial membrane fission, and transmembrane transport of metabolites such as CoA, NAD, and citrate. These terms together imply a mitochondria-focused role in energy metabolism and organelle remodeling, with a few peripheral metabolic signals (insulin secretion, amino acid starvation) that may reflect broader cellular energy status. Thus the label highlights the core theme of mitochondrial transport and dynamic membrane processes.","confidence":"High","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":2},{"id":"GO:0007565","count":2},{"id":"GO:0008637","count":2},{"id":"GO:0035349","count":2},{"id":"GO:0034198","count":2}]},{"hash":"1942625394248280336","title":"Diverse cell signaling and differentiation cues","description":"This cluster centers on signaling and stimulus-response processes, with GO terms for small GTPase\u2013mediated signaling, JNK cascade regulation, and cellular responses to nerve growth factor, nitric oxide, and retinoic acid. Immune differentiation terms (adaptive immune response, B cell differentiation) and osteoclast fusion suggest additional context-specific outcomes of signaling pathways. Overall, it points to a set of regulators of signaling that influence development and immune-related differentiation rather than a single, cohesive pathway.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1990090","count":2},{"id":"GO:0007264","count":2},{"id":"GO:0072675","count":2},{"id":"GO:1903356","count":2}]},{"hash":"621173643461404221","title":"DNA replication and cell cycle proteins","description":"The top GO terms cluster around DNA replication, DNA repair, mitotic/meiotic cell cycles, centrosome cycle, and cell division, suggesting a cohesive group involved in genome maintenance and cell cycle progression. Peripheral terms like ribosomal subunit assembly and mitochondrial protein import are less central, and the cocaine response term appears as noise rather than defining the cluster. Confidence reflects the strong alignment to cell cycle/replication processes.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0032092","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0042220","count":3}]},{"hash":"2133392034702368096","title":"Unknown","description":"The top GO terms are scattered across diverse processes (transport, glycosylation, immune and neural functions, development, and behavior) with only 1 hit each, and there are no edges connecting the proteins. This lack of a shared biological theme or pathway means there is no coherent function tying the cluster together, so the appropriate label is Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060905","count":1},{"id":"GO:0034488","count":1},{"id":"GO:0006488","count":1},{"id":"GO:0015811","count":1},{"id":"GO:0080144","count":1}]},{"hash":"462353466455892194","title":"mRNA Splicing and Processing","description":"Most of the GO terms point to RNA processing and spliceosome-mediated splicing (mRNA splicing via spliceosome, mRNA cis splicing, via spliceosome, positive regulation of mRNA splicing via spliceosome, mRNA modification, and mRNA polyadenylation). Although several terms are obsolete, the recurring theme is mRNA maturation and spliceosome regulation, suggesting these proteins function in RNA processing rather than other pathways. A minor link to translation initiation (IRES-dependent viral translational initiation) and blastocyst formation is present but less represented.","confidence":"High","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0001825","count":1},{"id":"GO:0006378","count":1}]},{"hash":"1663806109370538538","title":"Bacterial cell wall polysaccharide biosynthesis and glycosylation","description":"The top GO terms cluster around sugar nucleotide metabolism (UDP-glucose), various glycosylation pathways (O-linked and N-acetyl-galactosamine), and the synthesis/organization of cell wall polysaccharides (hyaluronan-like polymers, cellulose) with transport and teichoic acid biosynthesis, indicating a coherent theme of building and modifying bacterial cell wall glycopolymers. The immunoglobulin production term likely reflects noise or misannotation.","confidence":"Medium","size":10,"edges":8,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006011","count":1},{"id":"GO:0002378","count":1},{"id":"GO:0030213","count":1},{"id":"GO:0018243","count":1},{"id":"GO:0016266","count":1}]},{"hash":"773721071202304526","title":"Developmental growth and ER-Golgi trafficking","description":"This cluster includes GO terms related to development (brain and male gonad), cell proliferation and apoptosis, ER-to-Golgi transport and protein targeting to the ER, and cytoskeletal regulation (actin capping). Although there are no reported edges among the proteins, the common theme ties developmental processes with intracellular trafficking and cytoskeletal dynamics, justifying a label that emphasizes both development and vesicle transport/cytoskeleton coordination.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043981","count":3},{"id":"GO:0008584","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0051301","count":3}]},{"hash":"596709265635896219","title":"Glycolysis and TCA cycle","description":"This cluster is dominated by GO terms tied to central carbon metabolism and energy production: glycolytic process, glucose metabolic process, tricarboxylic acid cycle, and regulation of pyruvate decarboxylation to acetyl-CoA. These recurring themes point to cellular energy metabolism as the unifying function, with other terms like translation or immune response likely incidental annotations. Overall, the cluster represents metabolic processes feeding energy production.","confidence":"High","size":10,"edges":31,"triangles":38,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034340","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0061034","count":2}]},{"hash":"45098730967858174","title":"Unknown","description":"The GO terms span very diverse contexts (transcription regulation, plant UV-B response, animal endocannabinoid signaling, arachidonic acid metabolism, trehalose response, pectin catabolism, nuclear microautophagy, vesicle trafficking, and lipid remodeling). They do not reveal a single cohesive function or pathway tying the proteins together, suggesting the cluster represents a heterogeneous set of roles rather than a common theme.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0071493","count":2},{"id":"GO:0071926","count":2},{"id":"GO:0019369","count":2},{"id":"GO:0098921","count":2}]},{"hash":"969526464218470767","title":"Nuclear quality control and DNA replication","description":"This cluster shows enrichment for nuclear-associated processes: nuclear protein quality control by the ubiquitin-proteasome system, tRNA import into the nucleus, and DNA replication, suggesting a shared nuclear function. Other terms indicate broader regulation and stress responses that may intersect with these core activities, but the strongest signals point to nuclear quality control and genome maintenance.","confidence":"Medium","size":10,"edges":7,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0031204","count":3},{"id":"GO:0090084","count":3},{"id":"GO:1900035","count":3}]},{"hash":"1526863329589954250","title":"DNA replication and repair with neural development signals","description":"The top GO terms strongly center on nuclear functions\u2014DNA repair, DNA-templated transcription, and DNA replication\u2014with supporting processes like protein stability and apoptosis signaling, suggesting a core DNA maintenance cluster. The neural and muscle-related terms (cerebellum development, dendritic spine morphogenesis, response to muscle activity, regulation of cardiac muscle proliferation) imply additional signaling or developmental roles, but these appear secondary to the DNA maintenance theme.","confidence":"Medium","size":10,"edges":7,"triangles":1,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006281","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0014850","count":8},{"id":"GO:0060997","count":8}]},{"hash":"252073164235885400","title":"Developmental ECM remodeling","description":"The GO terms point to extracellular matrix interactions and remodeling (basement membrane disassembly, cell adhesion) with accompanying bone development processes (ossification, resorption). While some terms touch reproductive or neural contexts, the strongest coherence is ECM dynamics driving tissue morphogenesis, justifying a label focused on developmental extracellular matrix remodeling.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046697","count":2},{"id":"GO:2000179","count":2},{"id":"GO:0007156","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0045453","count":1}]},{"hash":"329982670036383142","title":"Neural development and RNA processing","description":"The cluster is dominated by neural development terms (positive regulation of neural precursor cell proliferation; positive regulation of neuron projection development) and RNA-related processes (tRNA wobble uridine modification; alternative mRNA splicing via spliceosome), suggesting a core theme around neuronal development supported by RNA processing mechanisms. Additional terms related to inflammatory response and oxidative stress are present but seem less central to the main theme.","confidence":"Medium","size":10,"edges":9,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000179","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0000380","count":2},{"id":"GO:0032496","count":2}]},{"hash":"2286980018413610800","title":"DNA Replication and Centrosome Cycle","description":"The cluster is dominated by GO terms for DNA replication, the centrosome cycle, and positive regulation of nuclear cell cycle DNA replication, pointing to a core function in cell cycle control and genome duplication. Neural development terms (cerebellum/hippocampus) and differentiation (chondrocyte) are less central and likely reflect broader roles in some proteins, but do not define the main theme. ","confidence":"High","size":10,"edges":11,"triangles":4,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0000902","count":9},{"id":"GO:0010571","count":9},{"id":"GO:0007098","count":9},{"id":"GO:0021549","count":8}]},{"hash":"839241252621515866","title":"Transmembrane Ion and Metabolite Transport","description":"The top GO terms indicate multiple transmembrane transport activities across diverse substrates (potassium, nitrate/nitrite, phosphate, sialic acid, xenobiotics) and vesicular neurotransmitter loading, pointing to a cohesive theme of membrane transporters and vesicle packaging. A few nuclear RNA processing terms appear as outliers and may reflect annotation noise, but the dominant signal is transport across membranes. ","confidence":"Medium","size":10,"edges":15,"triangles":2,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0015706","count":2}]},{"hash":"2282661268052926981","title":"Ribosome biogenesis and assembly","description":"This cluster is enriched for GO terms related to ribosome production: ribosome biogenesis, large subunit biogenesis, and maturation of LSU-rRNA, as well as ribosome assembly. These consistently point to a shared role in making and assembling ribosomes. The other terms (mitotic chromatid segregation, protein folding, forebrain development) are less represented and likely represent secondary associations or noise.","confidence":"High","size":10,"edges":6,"triangles":2,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042273","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0042255","count":2},{"id":"GO:1902626","count":2}]},{"hash":"238030738038275286","title":"Unknown","description":"The top GO terms span transcription, translation initiation, development (forebrain and skeletal), DNA-templated transcription, cell cycle, ER-stress\u2013related apoptosis, immune defense, and general growth responses. This broad mix lacks a single cohesive function or pathway tying the proteins together, so a specific, concise label is not clearly supported.","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0001501","count":2}]},{"hash":"1868729572283688045","title":"Growth-Linked Metabolism and Cytoskeleton Dynamics","description":"The cluster includes genes involved in energy metabolism (glycolysis, glycogen breakdown, fructose-6-phosphate pathways) and ribosome biogenesis, alongside actin filament depolymerization, which together point to cellular growth and structural remodeling. Additional regulatory terms hint at signaling influence on growth and survival, though the presence of diverse processes (and one obsolete term) means there isn\u2019t a single tightly defined function. Overall, it suggests a broad growth/metabolism\u2013related cluster with cytoskeleton remodeling.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0030042","count":2},{"id":"GO:0046835","count":1},{"id":"GO:0093001","count":1},{"id":"GO:0006002","count":1}]},{"hash":"1501600047498243484","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0000389","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0000350","count":1}]},{"hash":"112517040318784071","title":"Angiogenesis and vascular signaling","description":"This cluster centers on endothelial tube morphogenesis and regulation of endothelial migration, pointing to angiogenesis and vascular development. Supporting GO terms (Wnt signaling, activin receptor signaling, adiponectin signaling) reflect broader signaling crosstalk that modulates vascular formation and tissue regeneration, including liver regeneration, with additional diverse signaling inputs like testosterone response and protein phosphorylation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":1},{"id":"GO:0033574","count":1},{"id":"GO:0097421","count":1},{"id":"GO:0032927","count":1},{"id":"GO:0033211","count":1}]},{"hash":"716019880620594004","title":"DNA replication and mitotic cell cycle regulation","description":"Predominant GO terms include DNA replication, meiotic cell cycle, G1/S transition, and kinetochore localization, all pointing to cell cycle progression and chromosomal maintenance. A few terms (cocaine response, Schwann cell development, ascospore formation, sphingomyelin catabolic process) appear unrelated to the core theme and may reflect annotation noise, but the dominant signal supports a DNA replication/mitosis-focused cluster.","confidence":"High","size":9,"edges":11,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0042220","count":3},{"id":"GO:0051321","count":3},{"id":"GO:0014044","count":3},{"id":"GO:0034501","count":3}]},{"hash":"699726976475843931","title":"Carbohydrate and Lipid Biosynthesis","description":"The GO terms point to multiple biosynthetic pathways for energy-storage molecules (trehalose, starch, amylopectin, glycogen) and lipids (ubiquinone, sterol biosynthesis), indicating a metabolic synthesis-focused cluster. Vacuolar acidification and a couple of tRNA modification terms are present but represent a smaller portion of the annotations, so the central theme is biosynthesis of carbohydrates and lipids with overall metabolic significance.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":2},{"id":"GO:0005992","count":1},{"id":"GO:0019252","count":1},{"id":"GO:0010021","count":1},{"id":"GO:0005980","count":1}]},{"hash":"1317855584911698553","title":"Unknown","description":"The annotated processes are highly diverse, from lipid catabolism and cholesterol regulation to sporulation, DNA damage response and repair, muscle and lung development, drug response, and calcium signaling. No single shared function stands out across all terms, so Unknown.","confidence":"","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006685","count":9},{"id":"GO:0030437","count":9},{"id":"GO:1905213","count":9},{"id":"GO:2000002","count":9},{"id":"GO:0042220","count":9}]},{"hash":"1515564128073308047","title":"Neurodevelopment and DNA Regulation","description":"The cluster is dominated by brain development terms (cerebellum development, hippocampus development) together with DNA-related processes (DNA replication, DNA-templated transcription), suggesting proteins that participate in gene expression and proliferation during neurodevelopment. The other terms (Wnt signaling regulation, apoptosis, nitric oxide response, sterol import, glycogen metabolism, neutrophil clearance) indicate broader roles, but the strongest signal is neurodevelopment linked to nuclear gene regulation.","confidence":"Medium","size":9,"edges":9,"triangles":3,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0097350","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0045819","count":3}]},{"hash":"78942435031924562","title":"Unknown","description":"The GO terms are too diverse to support a single cohesive function. A couple suggest RNA modification (tRNA wobble thiolation, tRNA seleno-modification) and ubiquitin-related protein modification (urmylation, ubiquitin-dependent proteolysis), but other terms (spinal cord development, PPAR signaling, glycerol metabolism, pseudohyphal growth) appear unrelated. Because of this heterogeneity, a concise, representative label cannot be justified.","confidence":"","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0035357","count":2},{"id":"GO:0035335","count":1},{"id":"GO:0070329","count":1}]},{"hash":"543771323220173953","title":"Unknown","description":"The listed GO terms span nuclear processes (DNA replication, spliceosome dynamics) and organelle-related activities (mitochondrion/vacuole targeting, ion transport), with no single, cohesive function linking all proteins. There isn\u2019t a clear shared theme to name a specific cluster, so the label is Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000388","count":2},{"id":"GO:0031453","count":2},{"id":"GO:0000393","count":2}]},{"hash":"1667470979129406829","title":"Cellular stress and metabolic signaling","description":"The co-listed GO terms point to a module centered on cellular sensing and response to metabolic and environmental cues\u2014mitochondrial membrane potential regulation, amino acid starvation response, insulin signaling, redox homeostasis, toxin exposure, LPS, and hormone stimuli. The presence of DNA replication and mesoderm formation terms suggests ancillary links to growth and development. Overall, this cluster seems best described as a stress and metabolic signaling group rather than a single precise pathway.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0031100","count":2}]},{"hash":"2087499679598614","title":"Nuclear gene expression and cell cycle","description":"Proteins here are enriched for transcription (DNA-templated), RNA processing (mRNA splicing), ribosome biogenesis, and chromatin regulation (histone methylation), with accompanying cell cycle roles (mitotic cohesion and cell division). The combination suggests a core nuclear machinery cluster involved in gene expression and chromosome-based processes, rather than a single signaling pathway. Some development-related terms appear but are less representative of the main theme, which aligns with fundamental nuclear function and cell cycle control.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0007338","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0031954","count":2}]},{"hash":"591388453548509404","title":"Ribosome biogenesis and mRNA surveillance","description":"Dominant GO terms center on rRNA maturation (5.8S, SSU/LSU), translation processes (initiation, termination, translation), and RNA surveillance/decay pathways (non-stop decay, no-go decay), indicating a cluster of proteins involved in ribosome assembly and mRNA quality control.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0035167","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0071025","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006415","count":1}]},{"hash":"827722101285071330","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000472","count":2}]},{"hash":"144666050053397255","title":"COPI-Dependent ER-Golgi Vesicle Trafficking","description":"Based on the GO terms, the cluster centers on COPI-coated Golgi vesicles, ER exit site localization, and ARF-regulated trafficking, indicating ER-Golgi vesicle formation and transport as the core function. Endomembrane organization and Golgi-to-endosome transport terms further support a secretory/trafficking theme, with some polarity-related localizations that can reflect specialized trafficking in different cell types. Overall, there is a cohesive link to vesicle trafficking and membrane transport within the secretory pathway.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048205","count":2},{"id":"GO:0070863","count":2},{"id":"GO:0070973","count":1},{"id":"GO:0032012","count":1},{"id":"GO:2000114","count":1}]},{"hash":"331474110520059252","title":"Mitochondrial Transport and Dynamics","description":"Most of the top GO terms point to mitochondrial membrane transport (NAD, CoA, citrate transmembrane transport) and membrane-related processes (regulation of mitochondrial membrane potential, mitochondrial membrane fission, apoptotic mitochondrial changes). This suggests a cohesive theme around mitochondrial transport activities coupled to mitochondrial morphology/dynamics and energetic regulation, with a few terms likely representing noise from unrelated annotations.","confidence":"High","size":9,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051881","count":2},{"id":"GO:0007565","count":2},{"id":"GO:0008637","count":2},{"id":"GO:0035349","count":2},{"id":"GO:0034198","count":2}]},{"hash":"433788686815326734","title":"Unknown","description":"The top GO terms are highly diverse (ER-Golgi transport, actin nucleation, protein autophosphorylation, apoptosis regulation, histone methylation, development, mitosis, ribosome biogenesis), including several obsolete terms. This set doesn't reveal a single coherent function or pathway that ties all proteins together, so a specific, representative label cannot be assigned with confidence.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0034316","count":3},{"id":"GO:0031954","count":2},{"id":"GO:1902510","count":2},{"id":"GO:0070734","count":2}]},{"hash":"983696035418464583","title":"Translation machinery and mRNA decay","description":"The cluster is dominated by GO terms tied to protein synthesis and RNA turnover, including translation (initiation, elongation, termination), and the deadenylation-dependent mRNA decay pathway, with additional hints from selenocysteine incorporation. This points to a cohesive group of factors involved in the core translational apparatus and its regulation. Terms like endosome localization may reflect associated trafficking roles of some factors; glial proliferation and antibiotic response appear peripheral.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":3},{"id":"GO:0014009","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0001514","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1471101938319213074","title":"Mitotic cell division and ER-Golgi trafficking","description":"The cluster is enriched for mitosis-related terms (mitotic cell cycle, mitotic spindle assembly, cell division) and secretory pathway processes (ER\u2013Golgi and COPII vesicle budding), implying proteins involved in proliferative cell cycles coordinated with membrane trafficking.","confidence":"High","size":8,"edges":14,"triangles":7,"max_degree":5,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0006890","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0008283","count":6},{"id":"GO:0035264","count":6}]},{"hash":"1087099077275265989","title":"Developmental differentiation and calcium signaling","description":"This cluster shows multiple developmental terms across tissues (ascospore formation, skeletal muscle fiber development, lung epithelial differentiation, Schwann cell development, branching morphogenesis) along with several calcium-related terms (detection of calcium ion, regulation of calcium-release channel activity, postsynaptic calcium concentration). While there are also terms for DNA replication and cell budding, the dominant pattern is developmental processes with a recurring role for calcium signaling, suggesting proteins coordinating differentiation with calcium dynamics.","confidence":"Medium","size":8,"edges":15,"triangles":14,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030437","count":4},{"id":"GO:0048741","count":4},{"id":"GO:0060487","count":4},{"id":"GO:0005513","count":4},{"id":"GO:0060316","count":4}]},{"hash":"578269800429257769","title":"DNA Damage Response & Repair","description":"This cluster is dominated by GO terms for DNA strand invasion, double-strand break repair via synthesis-dependent strand annealing, SOS response, and cellular responses to DNA-damaging agents like camptothecin and cisplatin, indicating a cohesive theme of DNA damage sensing and homologous recombination repair.","confidence":"High","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042148","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0009432","count":2},{"id":"GO:0072757","count":2},{"id":"GO:0072719","count":2}]},{"hash":"954670146151935752","title":"Nuclear transcriptional regulation and chromatin control","description":"Most top terms center on RNA polymerase II\u2013mediated transcription and chromatin processes (negative regulation of Pol II, DNA-templated transcription, rDNA heterochromatin formation, and regulation of Pol II regulatory region binding). A few terms point to defense/immune responses, which may reflect broader stress signaling cross-talk rather than a defining theme. Thus, the cluster is best described as nuclear transcriptional regulation with chromatin control.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000183","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0016032","count":2}]},{"hash":"792442606062740569","title":"DNA replication proteins and chaperone interactions","description":"The strongest signals are DNA replication and protein heterooligomerization, plus chaperone-cofactor-dependent refolding, suggesting a theme of replication complex assembly and associated protein folding. The other terms appear sporadic or obsolete, likely annotation noise, so the core theme remains replication-related assembly and folding functions.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0051291","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0005985","count":1},{"id":"GO:0007631","count":1}]},{"hash":"1582892616656057291","title":"tRNA charging and translation","description":"This cluster is dominated by GO terms for tRNA aminoacylation (prolyl-, glutamyl-, glutaminyl-tRNA) and translation, with supporting tRNA modification terms, indicating involvement in tRNA charging and protein synthesis. Other terms are less represented, so the main theme is translation machinery.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":1},{"id":"GO:0006433","count":1},{"id":"GO:0006424","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006425","count":1}]},{"hash":"1942311430102776159","title":"Genome maintenance and nuclear transport","description":"GO terms center on DNA replication and nucleotide-excision repair (DNA maintenance), plus kinetochore localization and nuclear export, pointing to nuclear genome maintenance coordinated with protein trafficking. Additional terms for protein phosphorylation and targeting suggest regulatory control over these processes. A few items on ribosome biogenesis and ubiquitin-dependent protein catabolic regulation may reflect broader nuclear functions, yet the dominant theme remains genome maintenance and nuclear transport.","confidence":"Medium","size":8,"edges":14,"triangles":13,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032092","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006468","count":2},{"id":"GO:0034501","count":2}]},{"hash":"388959448276240797","title":"Ribosome Biogenesis and Translation","description":"The cluster is strongly enriched for ribosome-related processes: translation (GO:0006412), large ribosomal subunit biogenesis (GO:0042273), large subunit assembly (GO:0000027), and maturation of LSU-rRNA (GO:0000463), pointing to a group of ribosome biogenesis/translation proteins. A few eye-development terms are present but much less represented, suggesting incidental annotations rather than a cohesive eye-specific function.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0000027","count":3},{"id":"GO:1902626","count":3},{"id":"GO:0000463","count":3}]},{"hash":"1025891903748581402","title":"Nucleolar RNA Synthesis and Ribosome Biogenesis","description":"The cluster shows clear enrichment for nucleolar-associated processes: rRNA processing and ITS1 cleavage, nucleolar/rRNA transcription by RNA polymerases I\u2013III, ribosome biogenesis, and nucleologenesis, plus related RNA processing (spliceosome) and ncRNA-mediated chromatin regulation, all tying to nucleolar RNA production and ribosome assembly.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000464","count":3},{"id":"GO:0009307","count":2},{"id":"GO:0000388","count":2},{"id":"GO:0042790","count":2},{"id":"GO:0001172","count":2}]},{"hash":"156242846600191162","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006046","count":2},{"id":"GO:0007010","count":2},{"id":"GO:0006207","count":2},{"id":"GO:0006147","count":2},{"id":"GO:0006146","count":2}]},{"hash":"1842129404127437242","title":"Cell cycle and DNA replication","description":"Dominant signals are DNA replication and mitotic cell cycle terms (DNA replication, G1/S transition, meiotic cell cycle, kinetochore localization, mitotic control), suggesting a cohesive cell-division module; other terms point to broader development or neural signaling but are secondary.","confidence":"High","size":8,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042220","count":5},{"id":"GO:0051321","count":5},{"id":"GO:0014044","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0034501","count":5}]},{"hash":"55094554151397984","title":"Unknown","description":"The GO terms span ribosome biogenesis, kinase activation, various viral lifecycle steps (release and capsid envelopment), intracellular trafficking, abscission, and general protein transport, with no clear single function uniting them. The mix of virus-related processes and basic cellular processes suggests no cohesive theme for a confident label.","confidence":"","size":8,"edges":7,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0019076","count":1},{"id":"GO:0048672","count":1},{"id":"GO:0009838","count":1}]},{"hash":"1974060870311917990","title":"Stress-Activated Signaling and Trafficking","description":"These proteins cluster around cellular stress responses, especially heat and light stress (heat and high light/UV-A responses) and the MAPK signaling cascade, with additional links to intracellular transport and cytoskeletal dynamics (endosome-to-vacuole trafficking, axonal transport, and microtubule remodeling). This suggests a theme of stress signaling integrated with trafficking/structural responses. ","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032511","count":2},{"id":"GO:0070141","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0051403","count":2},{"id":"GO:0009644","count":2}]},{"hash":"2149291340420517303","title":"Mitotic chromatin organization and heterochromatin maintenance","description":"The top GO terms cluster around chromatin state regulation (nucleosome assembly, heterochromatin formation, histone methylation regulation, transcription regulation) and cell division (centrosome cycle, spindle assembly), suggesting a module linking chromatin remodeling/maintenance with mitosis. This combination supports a cohesive theme of chromatin state during cell division.","confidence":"High","size":8,"edges":11,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007098","count":4},{"id":"GO:0061188","count":3},{"id":"GO:0030466","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0061086","count":3}]},{"hash":"89603032187187806","title":"TGF-beta/BMP Signaling Regulation","description":"This cluster\u2019s GO terms converge on BMP and TGF-beta signaling and their downstream SMAD-related regulation (negative regulation of BMP signaling, negative regulation of TGF-beta receptor signaling, and cellular response to TGF-beta). While there are miscellaneous terms related to mitochondria or photosystems that may be peripheral or cross-talk, the core pattern points to regulation of the TGF-beta/BMP pathway, suggesting a cohesive cluster around this signaling axis.","confidence":"Medium","size":8,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0032543","count":1},{"id":"GO:0030514","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0035970","count":1},{"id":"GO:0080005","count":1}]},{"hash":"1713946095326656316","title":"Unknown","description":"The GO terms are from many unrelated domains (development, physiology, metabolism, and ion transport) with no single coherent theme, suggesting a mixed or noisy cluster rather than a specific functional module.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0003081","count":1},{"id":"GO:0045453","count":1},{"id":"GO:0009590","count":1},{"id":"GO:0051591","count":1}]},{"hash":"431611002200155862","title":"Developmental Morphogenesis","description":"Several top GO terms center on developmental processes in different tissues (bone development, ganglion development, bronchus morphogenesis), suggesting a theme of morphogenesis and tissue development. While other terms point to basic metabolism and transcription, the shared pattern is development-related functions across diverse tissues, supporting a developmental morphogenesis label. ","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060348","count":2},{"id":"GO:0044209","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0061548","count":1}]},{"hash":"1240527209094073752","title":"Central Carbon Metabolism and Energy Production","description":"This cluster centers on core energy-yielding pathways: the TCA cycle, pyruvate decarboxylation to acetyl-CoA, and assembly of the mitochondrial respiratory chain complex II, all pointing to central carbon flux into respiration. It also includes methanogenesis and formate metabolism, which are energy-generation processes in microbes and archaea, supporting an overarching energy metabolism theme across domains. A few terms related to tRNA biosynthesis and processing are present but more peripheral to the main energy-focused signal. ","confidence":"Medium","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0006086","count":2},{"id":"GO:0034553","count":2},{"id":"GO:0015948","count":1},{"id":"GO:0042426","count":1}]},{"hash":"635648595534277972","title":"Unknown","description":"The annotated terms span highly diverse biological areas (DNA replication, viral genome replication, translesion synthesis, mitochondrial assembly/insertion, gas vesicle organization, aggresome formation, microtubule severing, chromatin assembly, and vesicle formation) with no single cohesive function tying the proteins together. This appears to be a heterogeneous or fragmented cluster rather than a specific pathway or process, so I label it Unknown with None confidence. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0019079","count":3},{"id":"GO:0070987","count":2},{"id":"GO:0034551","count":2},{"id":"GO:0031412","count":2}]},{"hash":"100132506882124534","title":"Stress-Linked Metabolism and Hormone Biosynthesis","description":"This cluster lacks a single dominant function but centers on metabolic regulation intertwined with stress responses. It includes stress-related regulation of mRNA stability and stress-activated kinase signaling, along with diverse biosynthetic and xenobiotic metabolism processes (pyridoxal, bile acids, testosterone; daunorubicin/doxorubicin), and membrane-associated potassium transport. Taken together, it points to metabolic control under stress with hormonal biosynthesis involvement.","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0010610","count":2},{"id":"GO:0044597","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0097066","count":2},{"id":"GO:0042821","count":2}]},{"hash":"919072940770691796","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006094","count":2},{"id":"GO:0032889","count":2},{"id":"GO:1903298","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0061621","count":2}]},{"hash":"2114221000061296714","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009089","count":1},{"id":"GO:0051402","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006006","count":1},{"id":"GO:0035606","count":1}]},{"hash":"2182235801599954298","title":"ER-Golgi vesicle transport and mitotic signaling","description":"Explanation: The terms cluster around ER-to-Golgi and Golgi-to-ER vesicle transport, regulation of GTPase and serine/threonine kinase activities, and cell-cycle processes including mitosis. This pattern suggests a module coordinating intracellular trafficking in the secretory pathway with signaling that drives cell division.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0051028","count":2}]},{"hash":"1247843611709553961","title":"Mitochondrial Inner Membrane Protein Insertion","description":"The strongest non-obsolete term among the top terms is GO:0045039, which points to protein insertion into the mitochondrial inner membrane, suggesting a mitochondrial import/assembly theme. Other terms are sparse or obsolete and cover varied areas (e.g., snoRNP assembly, general catalytic regulation), making the connection weaker overall. So the label reflects the most distinctive signal, but with limited confidence.","confidence":"Low","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0072321","count":1},{"id":"GO:0045039","count":1},{"id":"GO:0017196","count":1},{"id":"GO:0000492","count":1}]},{"hash":"1141263391776708481","title":"Neuronal signaling and brain development","description":"Several top terms indicate synaptic signaling and plasticity (JNK cascade, long-term potentiation) and brain structure formation (cerebellum and hippocampus development), along with related stress signaling (NO response) and protein turnover. While there are some peripheral terms (B cell differentiation, chondrocyte differentiation, sterol import), the dominant pattern points to neuronal signaling and brain development.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007254","count":4},{"id":"GO:0060291","count":4},{"id":"GO:0032436","count":4},{"id":"GO:0071550","count":3},{"id":"GO:0021549","count":3}]},{"hash":"145798773276562531","title":"Bacterial fatty acid and cell envelope biosynthesis","description":"The top GO terms cluster around lipid metabolism and cell-envelope components typical of bacteria: fatty acid biosynthesis (medium- and long-chain), menaquinone biosynthesis, lipoteichoic acid biosynthesis, siderophore biosynthesis, and related metabolic processes. Bioluminescence can be linked to bacterial systems that interface with these pathways. Some plant-related terms like seed germination appear as noise, but the dominant signal points to bacterial lipid metabolism and cell-surface biosynthesis.","confidence":"Medium","size":7,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010030","count":5},{"id":"GO:0006633","count":5},{"id":"GO:0008218","count":5},{"id":"GO:0036112","count":5},{"id":"GO:0008206","count":5}]},{"hash":"689097140836159550","title":"Chromatin Assembly and Genome Maintenance","description":"Proteins in this cluster are centered on chromatin organization and genome maintenance: CENP-A\u2013containing chromatin assembly, nucleosome assembly, heterochromatin formation (pericentric and rDNA), transcription-coupled chromatin remodeling, DNA replication, and nucleotide-excision repair. A couple of outlier terms (pericardium morphogenesis, osteoblast differentiation) are unlikely to define the core function.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061641","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006289","count":2}]},{"hash":"568378375939742050","title":"Unknown","description":"The GO terms span diverse, largely unrelated processes (cell division and cycle; tRNA modification and ribosome biogenesis; mitochondrial organization; synaptic GABAergic transmission and neuron apoptosis regulation). There is no single cohesive function tying these proteins together, so a specific, representative label cannot be assigned. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006400","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0000747","count":2}]},{"hash":"1257292243586469409","title":"Ubiquitin-Mediated Regulation of Cellular Processes","description":"The top GO terms center on ubiquitination (K48-linked and polyubiquitination) and ubiquitin-dependent ERAD, indicating a link to targeted protein turnover. Additional terms reference regulation of the cell cycle, transcription, and various signaling and cell death pathways (TLR signaling, Wnt catabolic process, necroptosis), suggesting these proteins participate in broader ubiquitin-driven regulatory functions across cellular processes.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070936","count":1},{"id":"GO:0000209","count":1},{"id":"GO:0071157","count":1},{"id":"GO:1900095","count":1},{"id":"GO:0034121","count":1}]},{"hash":"1280954382423399374","title":"DNA Replication and Repair","description":"The terms are dominated by DNA replication and repair processes: translesion synthesis (both error-free and error-prone), nucleotide excision repair, DNA replication, proofreading, replication initiation, lagging-strand elongation, and UV-damage\u2013related synthesis. A single outlier term on fatty acid homeostasis likely reflects noise rather than a true cluster theme. This coherence supports labeling the cluster as DNA replication and repair machinery.","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070987","count":1},{"id":"GO:0055089","count":1},{"id":"GO:0006297","count":1},{"id":"GO:1902975","count":1},{"id":"GO:0042276","count":1}]},{"hash":"1747461106691897988","title":"Chromatin modification and transcriptional regulation","description":"This cluster shows enrichment for arginine methylation and histone-related methylation, plus negative regulation of transcription by RNA polymerase II, pointing to an epigenetic mechanism controlling gene expression. While a few terms (like cobalamin biosynthesis or root hair development) are less related and may reflect annotation noise, the dominant theme is chromatin modification linked to transcriptional control.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019919","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0009236","count":2}]},{"hash":"981724465211637010","title":"Neural development and signaling","description":"The cluster is enriched for nervous system-related terms such as nervous system development, hippocampus development, and visual perception, along with signaling activities like dopamine response, calcium-dependent exocytosis, JNK pathway regulation, and GTPase activity regulation. While mitotic cell cycle and cell division appear, the more dominant theme centers on neuronal development and synaptic signaling, suggesting these proteins collectively participate in neuron formation and communication rather than general cell proliferation.","confidence":"Medium","size":6,"edges":4,"triangles":1,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0007601","count":3},{"id":"GO:0021766","count":2}]},{"hash":"246805589331554754","title":"Vesicle trafficking and GTPase signaling","description":"Top GO terms cluster around membrane trafficking and small GTPase\u2013regulated processes: endocytosis, regulation of exocytosis (including synaptic vesicle exocytosis), and protein transmembrane transport. The presence of a mating projection growth regulation term aligns with Cdc42/Rho-family GTPases driving polarized membrane dynamics, reinforcing the theme. Together, these suggest a functional group focused on vesicle trafficking and GTPase-driven membrane signaling across cell types, including osteoclast-like vesicle activity reflected in bone resorption. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031384","count":2},{"id":"GO:0010796","count":2},{"id":"GO:2000300","count":2},{"id":"GO:0010762","count":1},{"id":"GO:0045453","count":1}]},{"hash":"2237314635321384788","title":"Proteostasis and developmental signals","description":"This cluster centers on core cellular maintenance (proteostasis) such as protein folding in ER and autophagy, as well as redox balance, with additional development- and differentiation-related terms (chaeta development, neuron remodeling, spermatid nucleus elongation) and some gene expression/transport terms. The functions are broad and only loosely cohesive, so the label aims to capture the strongest recurring theme (proteostasis) while acknowledging developmental signals; confidence is Low.","confidence":"Low","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006914","count":1},{"id":"GO:0022416","count":1}]},{"hash":"352597688541760785","title":"Membrane lipid biosynthesis and actin remodeling","description":"This cluster shows a notable emphasis on lipid-related processes, including cardiolipin biosynthesis, glycerol biosynthesis, serine biosynthesis (a precursor for lipid metabolism), and phospholipid dephosphorylation, alongside actin cytoskeleton dynamics (actin rod assembly and regulation of actin filament depolymerization). While some terms touch on energy, transport, or development and are less directly connected, the common thread appears to be lipid metabolism with concurrent remodeling of the actin cytoskeleton.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006564","count":2},{"id":"GO:0021987","count":2},{"id":"GO:0031247","count":1},{"id":"GO:0071318","count":1},{"id":"GO:0006825","count":1}]},{"hash":"387542346731109908","title":"Unknown","description":"The terms include rRNA maturation and translation, which could suggest a ribosome-associated cluster, but the majority of terms describe distinct metabolic and developmental processes (chitin/chitobiose catabolism, pro-B cell and neuron differentiation, DNA repair, transcription regulation). With no consistent functional theme and no edges tying the proteins together, there is no clear, cohesive label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0052777","count":1},{"id":"GO:0006032","count":1},{"id":"GO:0000272","count":1}]},{"hash":"1127620781036696036","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms tied to ribosome production and function: translation (cytoplasmic), ribosome biogenesis, and small subunit biogenesis/export, along with prolyl-tRNA aminoacylation. This suggests proteins that participate in assembling ribosomes and carrying out protein synthesis in the cytoplasm. A few low-frequency terms (TNF response, embryonic development) are incidental and do not define the core function of the cluster.","confidence":"High","size":6,"edges":8,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":2},{"id":"GO:0042274","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0061481","count":1}]},{"hash":"707528820850727146","title":"Neural Development and Signaling","description":"The top GO terms point to brain and neural development (mesoderm formation, cerebellum and hippocampus development, neural tube patterning) and Hedgehog pathway regulation, suggesting a group of proteins involved in developmental signaling and CNS patterning. While other terms (DNA replication, microtubule organization, DISC assembly, hormone response, lipid-related processes) reflect general cellular functions present in developing cells, the prevalent theme centers on neural development and signaling. Confidence: Medium","confidence":"","size":6,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001707","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0071374","count":3},{"id":"GO:0031122","count":2}]},{"hash":"1516850056680129393","title":"Proton Transport and Vesicle Acidification","description":"The top GO terms center on protons and acidification across membranes\u2014proton transmembrane transport, vacuolar and endosomal acidification, and proton motive force\u2013driven ATP synthesis\u2014with Type III secretion often powered by PMF. While a couple terms are more distant (bone differentiation, cocaine response), the dominant theme is proton-gradient\u2013driven membrane processes that regulate vesicle function and secretion.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001649","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0006353","count":1},{"id":"GO:0015991","count":1},{"id":"GO:0090464","count":1}]},{"hash":"96975291528678439","title":"RNA processing and export","description":"The cluster is characterized by GO terms tied to mRNA maturation\u2014export from the nucleus, splicing via the spliceosome, and RNA modification\u2014indicating a core theme around RNA processing and export. While there are a couple of terms related to DNA replication, the strongest signals are in RNA processing events, justifying this label. ","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1901407","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0016556","count":1}]},{"hash":"1683243811660462034","title":"Nuclear transport and perinuclear chromatin tethering","description":"The terms cluster around nucleocytoplasmic transport (mRNA, tRNA, and ribosomal subunit export) and nuclear pore organization, plus several periphery-related chromatin/telomere tethering events and perinuclear localization, indicating a cohesive theme of nuclear transport coupled with chromatin tethering at the nuclear periphery.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071390","count":1},{"id":"GO:0016973","count":1},{"id":"GO:0034398","count":1},{"id":"GO:0006999","count":1},{"id":"GO:0006409","count":1}]},{"hash":"347371945600500012","title":"Unknown","description":"The top GO terms span translation, development (oogenesis and cell differentiation), cell death regulation (necroptotic and apoptotic processes), and basic metabolism (glycogen/\u03b1-glucan catabolism and PRPP biosynthesis). With no edges and only a few terms represented, there is no clear, cohesive functional theme linking the proteins, so Unknown is the most appropriate label.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0048477","count":1},{"id":"GO:0030154","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0070266","count":1}]},{"hash":"2166902768355913773","title":"DNA replication and chromosome maintenance","description":"The cluster is dominated by GO terms for DNA replication, mitotic sister chromatid cohesion, cell division, and homologous recombination repair, pointing to genome maintenance and mitotic progression as the core theme. Secondary associations with ribosome biogenesis and ER-Golgi trafficking likely reflect broader cellular housekeeping rather than a primary function of these proteins. ","confidence":"High","size":6,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0007064","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042254","count":2}]},{"hash":"595643146208522925","title":"Zinc Ion Homeostasis and Transport","description":"The cluster is dominated by GO terms about zinc handling: intracellular zinc ion homeostasis, response to zinc ion, zinc ion transmembrane transport, and negative regulation of zinc ion import. While there are some tissue-development terms (hippocampus/cerebral cortex development and keratinocyte differentiation), these likely reflect zinc\u2019s broad role in development and differentiation rather than a single tissue-specific function. Overall, the shared function appears to be regulation of zinc ion availability and transport within and across membranes, which cohesively ties the proteins together.","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021766","count":2},{"id":"GO:0006977","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0010839","count":2},{"id":"GO:0046827","count":2}]},{"hash":"1842064663345444186","title":"Vacuolar autophagy and Cvt pathway","description":"Top terms point to autophagy-related processes (macroautophagy, nucleophagy) and cytoplasm-to-vacuole targeting (Cvt pathway), plus vacuolar transport, suggesting a cluster of proteins involved in autophagic degradation and delivery to the vacuole. Some metabolism-related terms are present but secondary to the autophagy signal.","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006777","count":3},{"id":"GO:0032447","count":3},{"id":"GO:0009229","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0002143","count":3}]},{"hash":"691744090302754022","title":"Developmental Transcription and Fate Specification","description":"This cluster centers on transcription-related GO terms (DNA-templated transcription; transcription elongation fidelity) and several development/differentiation processes (cardiac cell fate, myoblast fate, mesenchymal differentiation, digestive tract/ureter morphogenesis). While immune signaling terms appear (T-helper 1 activation, IL-1\u03b2 production), the common thread appears to be transcriptional control guiding developmental fate decisions, justifying the label Developmental Transcription and Fate Specification.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0048546","count":1},{"id":"GO:2000043","count":1},{"id":"GO:0072197","count":1},{"id":"GO:2000741","count":1}]},{"hash":"439199939638334422","title":"Proteostasis and ER Stress Regulation","description":"The terms cluster around protein folding and quality control: SRP-dependent targeting to the ER, cellular response to unfolded proteins, chaperone-related folding, and regulation of stress-induced apoptosis, all pointing to maintenance of proteostasis and ER function. Some terms may reflect broader stress responses or unrelated processes, but the dominant theme is ER-associated proteostasis and stress regulation.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903382","count":1},{"id":"GO:0006616","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0090084","count":1},{"id":"GO:0034620","count":1}]},{"hash":"1619897345914858704","title":"DNA damage response and cell cycle control","description":"This cluster centers on GO terms for DNA replication, DNA-templated replication, mitotic cell cycle, and error-free translesion synthesis, together with apoptosis and proliferation regulation. These features point to a cohesive theme of responding to replication stress and coordinating cell cycle progression and growth signaling (including Wnt pathway regulation). Some terms like innate immune response and cadmium response may reflect broader stress signaling, but the core pattern is DNA damage response and cell-cycle control.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0006260","count":2}]},{"hash":"583725696167736201","title":"Ribosome Biogenesis and Nuclear Export","description":"Dominant terms are ribosome biogenesis and ribosomal small subunit export from nucleus, each with two occurrences, indicating the core function of this cluster centers on ribosome assembly and export. The other GO terms appear less consistently and likely reflect ancillary processes rather than a cohesive module. Therefore, the label cleanly captures the primary shared function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000056","count":2},{"id":"GO:0010738","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0043124","count":1},{"id":"GO:0021766","count":1}]},{"hash":"2175288033550116290","title":"Unknown","description":"The GO terms span a multitude of unrelated processes (DNA-templated transcription, DNA repair, mitochondrial assembly, vesicle formation, microtubule dynamics, chromatin assembly, etc.), with no clear shared function linking the proteins. This appears to be a heterogeneous cluster without a cohesive theme, so Unknown with None. ","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070987","count":1},{"id":"GO:0034551","count":1},{"id":"GO:0031412","count":1},{"id":"GO:0070842","count":1}]},{"hash":"860422338173144017","title":"Developmental RNA Processing","description":"The GO terms point to development (multicellular organism development, blastocyst formation) and RNA processing (mRNA splicing, modification), suggesting a role in regulating gene expression during development via RNA-level mechanisms. The presence of obsolete terms and lack of interactions among proteins means this label emphasizes broad functional themes rather than a tight complex.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:1901407","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0001825","count":1}]},{"hash":"2276073914530542356","title":"Glycan biosynthesis and nucleotide-sugar metabolism","description":"The GO terms point most strongly to production and activation of nucleotide sugars (UDP-glucose, UDP-glucuronate) and polysaccharide biosynthesis (alginate, enterobacterial common antigen), suggesting a shared function in glycan assembly. Other terms reflect general cellular stress responses ( xenobiotic response, redox homeostasis) or broad metabolic processes, which are less specific to this cluster but may accompany glycan biosynthesis. Overall, the dominant theme is glycan-related biosynthesis with supporting sugar metabolism signals.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0006813","count":2},{"id":"GO:0071375","count":2},{"id":"GO:0006915","count":2}]},{"hash":"859854437327386041","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":7,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0061000","count":3},{"id":"GO:0007264","count":2},{"id":"GO:0010227","count":2},{"id":"GO:1903527","count":2},{"id":"GO:1902307","count":2}]},{"hash":"588820580585265567","title":"DNA replication and photosynthesis proteins","description":"The top GO terms are dominated by DNA replication, DNA repair, transcription, and ribosome-related assembly, alongside bacteriochlorophyll biosynthesis and photosynthesis, suggesting a cluster of proteins involved in genetic information processing in photosynthetic bacteria. Some discordant terms (gas vesicle organization, mitotic cell cycle, neuronal vesicle transport) likely reflect noisy or broad annotations rather than a single cohesive function.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0030494","count":3},{"id":"GO:0015979","count":3},{"id":"GO:0030163","count":3},{"id":"GO:0006281","count":2}]},{"hash":"891612733097627088","title":"Neuronal Synapse Localization and Signaling","description":"The top GO terms feature synapse-related localization (protein/receptor localization to synapse, immunological synapse formation) and signaling components (calcium transport, phosphorylation, JNK cascade), with related behavioral terms pointing to neural functions. While a few terms are less synapse-focused, the strongest cohesive theme is synapse localization and neuronal signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903760","count":1},{"id":"GO:2000821","count":1},{"id":"GO:0035641","count":1},{"id":"GO:0046328","count":1},{"id":"GO:0001771","count":1}]},{"hash":"196178152982571444","title":"RNA processing and transcription regulation","description":"The cluster\u2019s GO terms are dominated by RNA processing and transcription-related activities, including mRNA modification, mRNA splicing via the spliceosome, and transcription from RNA polymerase II promoters (with some dosage compensation context). Even though several terms are obsolete, the remaining annotations point to a core theme of RNA processing and transcription regulation, with additional hints of translation initiation control. Confidence: Medium","confidence":"","size":5,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009048","count":2},{"id":"GO:1901407","count":1},{"id":"GO:1905663","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0001825","count":1}]},{"hash":"1548637095781603392","title":"Mitotic spindle and cytokinesis components","description":"The top GO terms strongly point to cell division machinery: spindle orientation, spindle midzone assembly, mitotic spindle elongation, and actomyosin contractile ring assembly, which together suggest roles in mitosis and cytokinesis. The other terms (cell adhesion, bud site selection, chloroplast movement, ureteric bud invasion) appear less central and may reflect broader developmental or polarity-related contexts. Overall, the cluster seems best described by core mitotic/cytokinesis functions with some peripheral associations.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007156","count":1},{"id":"GO:0007120","count":1},{"id":"GO:0009904","count":1},{"id":"GO:0060404","count":1},{"id":"GO:0051296","count":1}]},{"hash":"812288590331151474","title":"Unknown","description":"The GO terms are highly diverse, spanning transcription, lipid metabolism, inflammatory signaling, and neural processes, with no clear single function tying all five proteins together. This makes it hard to assign a coherent, specific label beyond Unknown.","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0008203","count":1},{"id":"GO:0042632","count":1},{"id":"GO:0034128","count":1},{"id":"GO:0006954","count":1}]},{"hash":"472939340600151996","title":"Plant cell wall biosynthesis and glycosylation","description":"Most GO terms point to plant cell wall components and assembly (homogalacturonan, glucuronoxylan, mucilage) and general cell wall organization, especially plant-type secondary cell wall biogenesis. A subset also indicates protein O-linked glycosylation, suggesting modification of wall-related proteins. Together, these terms imply a shared role in plant cell wall polysaccharide biosynthesis and protein glycosylation.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035269","count":1},{"id":"GO:0010289","count":1},{"id":"GO:0009834","count":1},{"id":"GO:0010417","count":1},{"id":"GO:0016266","count":1}]},{"hash":"905799511310426217","title":"Transmembrane Ion and Small Molecule Transport","description":"Based on the top GO terms, the cluster is dominated by transmembrane transport activities for various ions and small metabolites (potassium, phosphate, nitrate/nitrite, sialic acid) and xenobiotics, as well as related neurotransmitter loading into synaptic vesicles. A couple of regulatory RNA-related terms are present but the most representative shared function across proteins appears to be membrane transport. Thus the label highlights the primary theme of ion/solute transport across membranes.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048026","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0071805","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0015706","count":1}]},{"hash":"1571884815883459603","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0071630","count":1},{"id":"GO:0035719","count":1},{"id":"GO:0071374","count":1}]},{"hash":"1914504238891849739","title":"Skeletal muscle actin filament assembly and development","description":"The GO terms cluster around skeletal muscle biology, notably skeletal muscle fiber development/adaptation and thin filament (actin) assembly, with supporting actin cytoskeleton localization signals, suggesting a focus on actin-driven muscle fiber formation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":1},{"id":"GO:0051654","count":1},{"id":"GO:0016344","count":1},{"id":"GO:0043503","count":1},{"id":"GO:0000011","count":1}]},{"hash":"1656068474585156907","title":"Proteasome- and Wnt-signaling cluster","description":"The GO terms cluster around proteasomal degradation and ubiquitin-related processes (SCF-dependent ubiquitination, proteasomal ubiquitin-dependent and independent catabolic processes, and proteasome core complex assembly), alongside multiple Wnt signaling terms (canonical and planar cell polarity). Immune signaling terms (inflammatory response regulation and C-type lectin receptor signaling) appear as additional connections, but the dominant theme links protein turnover to signaling pathways. Confidence: Medium","confidence":"","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0002862","count":2},{"id":"GO:0051437","count":2},{"id":"GO:0010363","count":2},{"id":"GO:0010499","count":2}]},{"hash":"196961184838272107","title":"Heterochromatin Regulation and Proteostasis","description":"The cluster features GO terms largely tied to heterochromatin formation and regulation (DNA methylation-dependent constitutive heterochromatin formation, pericentric heterochromatin formation, and related regulation of rDNA heterochromatin), complemented by terms on protein quality control (aggresome assembly and polyubiquitinated misfolded protein transport). While some terms touch on differentiation and angiogenesis, the dominant theme is epigenetic/chromatin regulation paired with proteostasis, making this a coherent single-cluster label.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045668","count":4},{"id":"GO:0060766","count":4},{"id":"GO:0048742","count":3},{"id":"GO:0090050","count":3},{"id":"GO:0070845","count":3}]},{"hash":"703048854158357532","title":"Viral lifecycle and entry","description":"Dominant GO terms center on viral processes: uncoating, fusion of viral membranes, viral release, and the overall viral life cycle, with latency as a proviral state. A few general terms like protein folding or secretion appear incidental. The cluster appears to group proteins involved in the viral infection cycle. ","confidence":"High","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0019061","count":1},{"id":"GO:1901407","count":1},{"id":"GO:2000276","count":1},{"id":"GO:0010849","count":1},{"id":"GO:0075713","count":1}]},{"hash":"1235000552714154506","title":"Unknown","description":"The cluster shows diverse GO terms spanning translation, RNA processing, mitochondrial assembly, vesicle formation, cell division, and differentiation, with no dominant shared function. The presence of obsolete terms and single-count items reinforces that there is no coherent theme tying the proteins together.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006407","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0033119","count":1},{"id":"GO:0060543","count":1},{"id":"GO:0034551","count":1}]},{"hash":"1308177788901748968","title":"DNA replication licensing and MCM assembly","description":"The GO terms show a coherent theme around initiation/licensing of DNA replication: pre-replicative complex assembly, MCM complex assembly, and mitotic DNA replication initiation. These point to replication machinery. The other terms appear incidental noise given the small cluster, so the core signal is replication licensing and assembly.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0031412","count":1}]},{"hash":"1444603530834534549","title":"Sugar and vitamin membrane transporters","description":"This cluster centers on GO terms describing transmembrane transport of sugars (glucose, fructose, trehalose) and vitamins, plus related transport processes, suggesting a shared function as membrane transport proteins for sugars and vitamins. Some peripheral terms about adhesion or epithelial structure are present but less representative of the core theme. ","confidence":"Medium","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900026","count":2},{"id":"GO:0033144","count":2},{"id":"GO:0071805","count":1},{"id":"GO:0015739","count":1},{"id":"GO:0060731","count":1}]},{"hash":"1526526164770970466","title":"Nuclear Chromatin and Ribosome Biogenesis","description":"The terms point to chromatin-level processes (nucleosome assembly, chromosome condensation) alongside ribosome biogenesis, suggesting nuclear-centric functions. Activation of protein kinase activity provides a regulatory hook that could coordinate these nuclear processes. The cluster likely represents proteins involved in nuclear/chromatin regulation and ribosome production rather than cytosolic signaling. ","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0030261","count":1},{"id":"GO:0006334","count":1}]},{"hash":"2077176369683096199","title":"Mitochondrial dynamics during the cell cycle","description":"The cluster is dominated by GO terms for mitochondrial fission, mitochondrial membrane organization, and cell cycle, suggesting proteins involved in mitochondrial dynamics linked to cell division; a small GTPase signaling term supports regulated membrane remodeling, with other terms being secondary. ","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000266","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0007006","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0007264","count":2}]},{"hash":"1464791087965911988","title":"Mitochondrial Membrane and Lipid Regulation","description":"The proteins in this cluster are enriched for mitochondrial-related processes (inner mitochondrial membrane organization, regulation of mitochondrial membrane potential, mitochondrial DNA replication) and lipid-related localization and signaling (lipid localization, protein localization to membrane raft, SREBP signaling pathway, cholesterol biosynthesis regulation). This combination points to a coherent theme of mitochondrial membrane maintenance coupled with lipid homeostasis, with a secondary, less central link to immune signaling via T cell polarity. Confidence: Medium","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903905","count":3},{"id":"GO:0007007","count":3},{"id":"GO:1903044","count":3},{"id":"GO:0052547","count":3},{"id":"GO:0045541","count":3}]},{"hash":"1469902297357751891","title":"Mitochondrial membrane organization and lipid homeostasis","description":"Based on the top GO terms, the cluster centers on inner mitochondrial membrane organization, lipid localization, and lipid/cholesterol regulatory pathways (SREBP signaling and cholesterol biosynthesis). These converge on mitochondrial membrane integrity and lipid metabolism, with a few less-connected terms (e.g., a T cell polarity term) that are likely peripheral noise. Therefore, the label focuses on mitochondria-associated membrane and lipid regulation as the core theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:1903905","count":2},{"id":"GO:0007007","count":2},{"id":"GO:1903044","count":2},{"id":"GO:0052547","count":2}]},{"hash":"1888644260469640119","title":"TCA Cycle and Glyoxylate Metabolism","description":"The GO terms cluster around central carbon metabolism and energy production, with explicit references to the TCA cycle (GO:0006099), malate and oxaloacetate metabolism (GO:0006108, GO:0043627), and the glyoxylate cycle (GO:0006097). Additional terms touch on related pathways such as photorespiration and signaling responses, which aligns with a plant-associated metabolic network that channels carbon through the TCA and glyoxylate shunt. Overall, the proteins appear linked by metabolic flux through respiration and organic-acid pathways rather than a single signaling or structural function.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043627","count":1},{"id":"GO:0006107","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0051591","count":1},{"id":"GO:0080093","count":1}]},{"hash":"480546581624688161","title":"Ribosome biogenesis and translation","description":"The terms cluster strongly around ribosome production and function: maturation and assembly of the small ribosomal subunit, ribosome biogenesis, nucleolar rRNA transcription by RNA polymerase I, and translation, with related regulation by Pol I. This pattern points to proteins involved in ribosome assembly and protein synthesis, with a minor, off-target term present. ","confidence":"High","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1900153","count":2},{"id":"GO:0030490","count":2},{"id":"GO:0006407","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0042254","count":2}]},{"hash":"2142785501615242096","title":"Skeletal muscle fiber development and actin assembly","description":"The GO terms center on skeletal muscle biology, including muscle fiber development, thin filament (actin) assembly, and actin localization, suggesting the proteins function in muscle cytoskeleton organization and filament assembly. Some terms are obsolete or peripheral, but the strongest signal ties to muscle actin architecture.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":3},{"id":"GO:0051654","count":3},{"id":"GO:0016344","count":3},{"id":"GO:0043503","count":3},{"id":"GO:0000011","count":3}]},{"hash":"1935452552041839201","title":"Telomere/Cajal body RNA localization","description":"This cluster centers on GO terms about localizing RNA and proteins to telomeres and Cajal bodies (e.g., telomerase RNA localization to Cajal body, scaRNA localization to Cajal body, and positive regulation of protein localization to telomere), indicating a theme of nuclear RNA processing and telomere maintenance. A few terms appear unrelated and may reflect annotation noise, but the core signal points to nuclear RNA localization linked to telomere biology.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1904851","count":1},{"id":"GO:0044053","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0090666","count":1}]},{"hash":"1529198654541594748","title":"Nuclear RNA Processing and Splicing","description":"The GO terms cluster around nuclear RNA maturation and splicing activities: maturation of SSU-rRNA, tRNA processing, mRNA splicing via spliceosome, spliceosomal complex assembly, and nuclear import, with deadenylation-dependent decapping of nuclear-transcribed mRNA also pointing to RNA turnover in the nucleus. While some terms (hair cycle, ABA response) are less directly related and may reflect annotation noise, the core signal points to RNA processing and spliceosome machinery within the nucleus.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042633","count":1},{"id":"GO:0009414","count":1},{"id":"GO:1990141","count":1},{"id":"GO:0030490","count":1},{"id":"GO:0045292","count":1}]},{"hash":"1117116917134902403","title":"Histone modification and chromatin regulation","description":"The top GO terms point to regulation of histone deacetylase activity, heterochromatin formation, and other histone modification processes, suggesting a shared role in controlling chromatin state and transcription. Some terms are obsolete or developmental in nature, which may reflect annotation noise for a small cluster, but the core theme remains chromatin regulation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901726","count":1},{"id":"GO:0061188","count":1},{"id":"GO:1904388","count":1},{"id":"GO:1901097","count":1},{"id":"GO:0002458","count":1}]}]