[{"hash":"408682958567494157","title":"Mitochondrial Translation and Transport","description":"These proteins cluster around core mitochondrial metabolism and protein synthesis, as highlighted by translation and regulation of mitochondrial membrane permeability terms, plus multiple membrane transport terms (phosphate, thiosulfate, heme, and thiamine pyrophosphate). The co-occurrence of amino acid starvation response and cell division terms supports a growth/metabolic context often tied to mitochondrial function. A couple of terms appear noisy (female pregnancy, obsolete oxidation-reduction), but the core signal is mitochondrial translation and substrate transport.","confidence":"Medium","size":29,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0035435","count":3},{"id":"GO:0034198","count":3},{"id":"GO:0046902","count":3},{"id":"GO:0006412","count":3}]},{"hash":"1668821723981984208","title":"Bacterial Biosynthesis and Metabolism","description":"The top GO terms point to various biosynthetic pathways (antibiotic biosynthesis, menaquinone, biotin, and poly-hydroxybutyrate) and metabolic responses (amino acid starvation, response to toxic substances), suggesting proteins that contribute to microbial production of small molecules and storage polymers, with some stress adaptation roles. The presence of an outlier term related to endocannabinoid signaling likely reflects annotation noise, but the overall theme remains biosynthesis and metabolism in bacteria.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0042619","count":3}]},{"hash":"1888751253769008267","title":"DNA-binding transcriptional regulators","description":"This cluster is strongly enriched for transcription-related GO terms: DNA-templated transcription, positive/negative regulation of transcription by RNA polymerase II, and regulation of DNA binding, indicating these proteins function as transcription regulators. Additional terms related to redox regulation and nuclear export suggest regulatory modifications and localization features that commonly accompany transcription factors.","confidence":"High","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043388","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0000122","count":7},{"id":"GO:0098869","count":6},{"id":"GO:0080058","count":6}]},{"hash":"631588985989276064","title":"Cell Polarity and Synaptic Organization","description":"The cluster shows strong signals for epithelial cell polarity establishment/maintenance and tight junction assembly, alongside synaptic components such as protein localization to synapse and synaptic vesicle maturation, plus brain development. This points to proteins involved in organizing cellular interfaces and neuronal synapses. Some terms (photosynthesis, aging, cell cycle) are less aligned, possibly due to broad annotations or cross-species differences, but the core themes center on polarity and synaptic organization.","confidence":"Medium","size":29,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001302","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045197","count":2},{"id":"GO:0035418","count":2}]},{"hash":"909376597316831136","title":"Redox Homeostasis and Oxidative Stress Response","description":"Proteins in this cluster are dominated by GO terms related to detoxifying reactive species and maintaining redox balance, such as cellular oxidant detoxification, cellular response to oxidative stress, and redox homeostasis. The presence of protein deglutathionylation and oxidation-reduction processes further supports a redox-regulation theme. Some other terms (prostaglandin biosynthesis, methylamine metabolism, deoxyribonucleotide biosynthesis) are diverse, but the overarching signal is a coordination of redox state and oxidative stress response.","confidence":"High","size":29,"edges":405,"triangles":3627,"max_degree":28,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":12},{"id":"GO:0045454","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0001516","count":7},{"id":"GO:0030416","count":6}]},{"hash":"1119798062923891085","title":"Unknown","description":"The GO terms are broad and diverse (mRNA processing, ABA response, autophagy, multiple membrane transport processes, Golgi-related glycosylation, root hair development) with no single dominant function linking the proteins. There are no edges in the cluster, suggesting a lack of tight functional cohesion, so a specific, representative label cannot be confidently assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0009737","count":2},{"id":"GO:0032581","count":1},{"id":"GO:0097352","count":1},{"id":"GO:0032973","count":1}]},{"hash":"111631433315899844","title":"Transcription Regulation and Stress Response in Development","description":"The top GO terms cluster around DNA-templated transcription and transcription regulation, with notable stress-response (cadmium, heat) and developmental processes (brain development, embryonic pregnancy) plus mRNA decay, suggesting a gene-expression and signaling\u2013centric theme across development.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0071276","count":5},{"id":"GO:0061408","count":4},{"id":"GO:0000288","count":3},{"id":"GO:0043547","count":3}]},{"hash":"553024954816873782","title":"Developmental transcriptional regulation","description":"The GO terms center on DNA-templated transcription, regulation of gene expression, and multicellular development, suggesting proteins involved in controlling gene expression during development within the nucleus. The presence of smoothened signaling hints at developmental signaling interactions, reinforcing the developmental transcriptional regulation theme, even though a few entries reference epigenetic processes that can modulate transcription.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007224","count":2},{"id":"GO:0017186","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0051457","count":1},{"id":"GO:0007275","count":1}]},{"hash":"1255258972184659650","title":"Transcription Regulators and DNA Binding","description":"This cluster is dominated by GO terms about transcriptional control and DNA binding (DNA-templated transcription, negative regulation of transcription by RNA Pol II, regulation of DNA binding), suggesting the proteins are largely transcription regulators or DNA-binding factors. Other terms point to cell-cycle and stress-response roles, which can be shared by regulatory proteins, but the strongest signal is transcription regulation. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0000086","count":2}]},{"hash":"13797660800187549","title":"Unknown","description":"The top GO terms span diverse biological areas\u2014heart electrical activity, GPCR signaling, blood coagulation, calcium regulation, skin development, transcription, mRNA transport, digestion, and general development\u2014showing no single, coherent function tying the cluster. With no edges and no evident shared pathway, there isn't a unifying theme beyond broad organismal physiology, so 'Unknown' is appropriate.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0007596","count":3},{"id":"GO:0090281","count":3},{"id":"GO:0043588","count":3}]},{"hash":"725081549688270177","title":"Unknown","description":"The top GO terms span telomere maintenance, spindle assembly, and cell cycle, along with actin cytoskeleton organization, calcium transport, temperature sensation, and neural differentiation. This wide, heterogeneous mix suggests no single cohesive biological function or pathway tying the cluster together, and the lack of edges further indicates a non-specific or mixed set of roles. Therefore, a concise, meaningful label cannot be confidently assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000722","count":2},{"id":"GO:0071651","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0050960","count":2}]},{"hash":"1090873254063321809","title":"Methylation-Driven Biosynthesis Enzymes","description":"The cluster shows several methylation-related processes (N-terminal peptidyl-glycine methylation, tRNA methylation, arginine methylation, histone methylation) alongside biosynthetic processes (antibiotic, biotin, cobalamin). This suggests proteins involved in methyltransferase activity linked to biosynthesis and regulation of gene expression, hence a methylation-focused biosynthesis cluster.","confidence":"Medium","size":29,"edges":4,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":12},{"id":"GO:0009102","count":12},{"id":"GO:0018013","count":7},{"id":"GO:0030488","count":7},{"id":"GO:0016049","count":7}]},{"hash":"1236539346324188659","title":"Mitochondrial Transporters and Stress Response","description":"The cluster is enriched for transport-related GO terms across mitochondria (thiosulfate, heme, thiamine pyrophosphate, and pyrimidine nucleotide import) and mitochondrial stress or regulatory processes (response to superoxide, apoptotic mitochondrial changes, insulin/IGF signaling). This pattern suggests a cohesive module of mitochondrial carriers and regulators that coordinate metabolite import with redox balance and apoptotic signaling. The odd \u201cobsolete mitochondrial genome maintenance\u201d term likely reflects historical annotations rather than a conflicting function. Therefore, a mitochondrial transport and stress-response label best captures the cluster\u2019s shared biology.","confidence":"High","size":28,"edges":74,"triangles":67,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0015709","count":13},{"id":"GO:0015886","count":13},{"id":"GO:0030974","count":13},{"id":"GO:0007565","count":13},{"id":"GO:1990519","count":13}]},{"hash":"1269136023081152777","title":"Developmental transcriptional regulation and morphogenesis","description":"This cluster is dominated by GO terms for transcriptional regulation by RNA polymerase II (both positive and negative) and developmental processes such as midbrain development, cochlea morphogenesis, multicellular growth, post-embryonic development, and tissue remodeling, suggesting a cohesive role in controlling gene expression during development and morphogenesis. Immune-related terms like response to lipopolysaccharide and blood coagulation are present but appear secondary to the main developmental program.","confidence":"Medium","size":28,"edges":52,"triangles":3,"max_degree":18,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":8},{"id":"GO:0032496","count":7},{"id":"GO:0030901","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0035264","count":5}]},{"hash":"354214702904610949","title":"DNA Metabolism and Transcription/Repair","description":"This cluster is dominated by DNA-centric processes: DNA replication, regulation of DNA-templated transcription, nucleotide-excision repair, and rRNA methylation (RNA processing). While there are a few transport-related terms (amino acid/vitamin/xenobiotic transmembrane transport) and a nutrient/nodulation signal, the strongest shared function among members appears to be DNA metabolism and associated RNA processing activities.","confidence":"Medium","size":28,"edges":7,"triangles":0,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0031167","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0003333","count":2},{"id":"GO:0035461","count":2}]},{"hash":"2264267472025568801","title":"Developmental and stress-response proteins","description":"GO terms emphasize development (multicellular, forebrain, skin) and stress responses (ER stress\u2013related apoptosis, cadmium response), with supporting roles in mRNA transport and GTPase regulation. The cluster seems to group proteins involved in developmental programs that are modulated by cellular stress, rather than a single signaling module, so the label reflects a general developmental-stress theme.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007275","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0030900","count":7},{"id":"GO:0050830","count":7},{"id":"GO:0043588","count":7}]},{"hash":"469198227816396065","title":"Ribosome biogenesis and cell division","description":"This cluster is driven by GO terms for ribosomal subunit biogenesis and rRNA maturation (SSU/LSU/5.8S), i.e., ribosome assembly, together with cell cycle\u2013related processes such as cell division, meiotic spindle elongation, and microtubule polymerization. A secondary signal is transcriptional regulation by RNA polymerase II, suggesting coordination between ribosome production, transcription, and cell-cycle progression. The SOS response hints at DNA damage stress but appears less central to the core theme. Overall, the dominant theme ties ribosome biogenesis to cell division machinery.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009432","count":2},{"id":"GO:0046785","count":2},{"id":"GO:0045944","count":2}]},{"hash":"332807603166340358","title":"Stress-Responsive Transcription and Ribosome Biogenesis","description":"This cluster combines terms for DNA-templated transcription, intracellular signal transduction, and ribosome biogenesis (including LSU rRNA maturation), with several stress- and defense-related responses (cadmium, heat/mechanical stress, Gram-positive defense). The shared theme appears to be regulation of gene expression and ribosome assembly in response to cellular stress, rather than a single, cohesive pathway.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0061408","count":2}]},{"hash":"767768392496494624","title":"DNA replication and cell cycle regulation","description":"This cluster centers on DNA metabolism and cell-cycle-related processes: DNA repair, DNA replication, G1/S transition, and meiotic chromosome condensation, with supporting signals from ribosome biogenesis and nucleotide synthesis (folic acid biosynthesis). The combination of these GO terms suggests proteins collaborating in DNA synthesis and cell-cycle progression, despite some metabolic or stress-response terms present. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046656","count":3},{"id":"GO:0006281","count":3},{"id":"GO:0071549","count":2},{"id":"GO:0010032","count":2},{"id":"GO:0000082","count":2}]},{"hash":"427224202197770680","title":"Embryonic Organogenesis and Development","description":"This cluster centers on developmental processes and transcriptional control. Terms like DNA-templated transcription and DNA replication point to active gene regulation and proliferation, while embryonic organ development, spinal cord development, skin development, and seminiferous tubule development indicate broad organogenesis and tissue differentiation. The presence of a TGF-beta stimulus response and mitotic spindle orientation suggests morphogenesis and orderly cell division during development. Overall, the proteins appear to function together in embryonic development and tissue formation.","confidence":"Medium","size":28,"edges":11,"triangles":1,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0048568","count":4},{"id":"GO:0071560","count":3},{"id":"GO:0000132","count":3},{"id":"GO:0021510","count":3}]},{"hash":"606945406303631322","title":"Ribosome Biogenesis and Transcription Regulation in Germ Cells","description":"This cluster centers on ribosome biogenesis and translation, with multiple transcriptional regulation terms (RNA Pol II and Pol I-related) and germ cell development terms (oogenesis and spermatogenesis), suggesting coordinated control of protein synthesis and chromatin processes in germ-line contexts.","confidence":"Medium","size":28,"edges":3,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0048477","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0007283","count":2}]},{"hash":"1951401177563218438","title":"Bacterial vitamin biosynthesis and transport","description":"The top GO terms cluster around microbial metabolism: menaquinone biosynthetic process and biotin biosynthetic process point to vitamin biosynthesis, while nitrate assimilation and potassium ion transmembrane transport indicate nutrient processing and membrane transport. Cellular oxidant detoxification and a broad oxidation-reduction/green-redox signal further align with bacterial redox metabolism. A neuron-specific migration term appears to be noise. Overall, the cluster seems to reflect bacterial metabolic and transport functions rather than a single cohesive eukaryotic pathway.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009234","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0071805","count":2},{"id":"GO:0042128","count":2}]},{"hash":"754897846944420734","title":"Spliceosome-regulated mRNA splicing and translation initiation","description":"These proteins show strong signals for spliceosome-mediated splicing and its regulation (alternative splicing, and both positive/negative regulation), indicating a core theme of RNA processing. There is also a note of translation initiation factor complex assembly, suggesting coordination between mRNA processing and the beginning of translation. The phosphate transport term is minimal, so the main functional thread is RNA splicing regulation with a link to translation initiation.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0048025","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0048026","count":1}]},{"hash":"1660246896290748835","title":"Plant Light Sensing and Photosynthesis","description":"This cluster is dominated by GO terms about responses to specific light wavelengths (blue, red, far-red, UV-A) and light intensity, together with photosynthesis-related light harvesting in photosystems I and II, and chlorophyll-related biosynthesis. These co-occurring themes suggest proteins that participate in light perception/signaling and the assembly or regulation of the photosynthetic light-harvesting machinery.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009637","count":2},{"id":"GO:0018298","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0009769","count":2}]},{"hash":"1482036486873657650","title":"Developmental translation and polarity regulation","description":"Top GO terms reveal a strong emphasis on translation machinery (translation, preinitiation complex formation, translation reinitiation, ribosomal subunit biogenesis) along with developmental signals (brain development, exploration behavior) and cell polarity processes (epithelial polarity, tight junction assembly). This suggests a cluster of proteins involved in regulating protein synthesis during development and in establishing cellular polarity, with broader neural development implications. The diverse but connected terms imply a coherent theme of developmental translation control intertwined with cell polarity rather than a single, narrow function.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2}]},{"hash":"358439028568195176","title":"TLR-driven innate immune signaling","description":"The cluster is dominated by GO terms tied to toll-like receptor signaling (TLR4, TLR8, TLR10) and defense/inflammatory responses, suggesting a shared function in innate immune activation; other terms related to RNA transcription and ribosome biogenesis are present but likely represent background processes or annotation noise rather than core cluster function.","confidence":"Medium","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0001172","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0042797","count":2},{"id":"GO:0032722","count":2},{"id":"GO:0034166","count":2}]},{"hash":"121048205919688418","title":"Plant photoreception and light-stress signaling","description":"The top GO terms point to light perception and light-triggered responses in plants, including photoreception, blue light signaling, shade avoidance, photoreactive DNA repair, and light-induced defense pathways (systemic acquired resistance and singlet oxygen\u2013mediated PCD). The cluster thus seems enriched for photomorphogenesis and light-stress response functions, with related hormone signaling (strigolactone) and metabolic changes (lipid storage). This cohesive theme supports a label centered on plant light sensing and associated stress responses.","confidence":"High","size":27,"edges":14,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1901672","count":2},{"id":"GO:1902448","count":2},{"id":"GO:0006975","count":2},{"id":"GO:0019915","count":2},{"id":"GO:0045475","count":2}]},{"hash":"1840071784025000987","title":"DNA-templated transcription regulators","description":"This cluster is dominated by GO terms related to transcription and DNA-binding regulation (DNA-templated transcription; positive regulation of DNA binding; negative regulation of RNA polymerase II regulatory region DNA binding), pointing to a nuclear transcription regulatory theme. The presence of scattered terms like oxidant detoxification and deglutathionylation suggests some annotation noise or multifunctionality, and the lack of edges indicates the proteins are not forming a cohesive interaction module. Overall, it most likely represents transcription regulatory proteins working in the nucleus.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0042711","count":2},{"id":"GO:0098869","count":1},{"id":"GO:0080058","count":1},{"id":"GO:1903026","count":1}]},{"hash":"768622164419398146","title":"Nucleocytoplasmic and ER-Golgi Transport","description":"The top terms point to transport processes across nuclear pores (mRNA export, nuclear localization) and vesicle trafficking between the ER and Golgi (COPII budding, ER-to-Golgi and Golgi-to-ER transport). While some terms touch on replication or development, the dominant signal is intracellular transport and localization, linking nucleocytoplasmic export with ER-Golgi trafficking.","confidence":"Medium","size":27,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051028","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0031081","count":3},{"id":"GO:0036265","count":3}]},{"hash":"1057277461791788144","title":"Unknown","description":"The top GO terms are highly diverse (toxic/nutrient response, development, vitamin transport, ubiquitin-proteasome degradation, cell polarity) with no clear unifying function or pathway, and no edges between proteins. This prevents assigning a cohesive label beyond Unknown.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0007584","count":3},{"id":"GO:0001892","count":3},{"id":"GO:0031146","count":2},{"id":"GO:0051180","count":2}]},{"hash":"103720359097320178","title":"Genome maintenance and organelle quality control","description":"The cluster is enriched in DNA replication and repair-related terms (DNA replication, mitochondrial DNA replication regulation, UV-damage repair) and RNA quality control, plus processes tied to organelle maintenance (autophagosome maturation, peroxisomal protein import). This suggests a theme around genome maintenance together with organelle quality control mechanisms.","confidence":"Medium","size":27,"edges":19,"triangles":7,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":8},{"id":"GO:0016485","count":7},{"id":"GO:0001824","count":7},{"id":"GO:0034599","count":7},{"id":"GO:0070651","count":6}]},{"hash":"132136335227947333","title":"Ubiquitin-regulated cell death and transcription","description":"This cluster's GO terms center on ubiquitin pathways: ubiquitin-dependent protein catabolic process, deubiquitination (including H2A K63-linked and monoubiquitinated substrates), and necroptosis-related ripoptosome assembly, linking to activation-induced T cell death. While there are transcription and RNA processing terms, the strongest signal is ubiquitin signaling tied to cell death pathways, with supporting nuclear functions, so the label captures the dominant theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006924","count":2},{"id":"GO:0070537","count":1},{"id":"GO:0006511","count":1},{"id":"GO:0000289","count":1},{"id":"GO:1901026","count":1}]},{"hash":"852811711342023356","title":"Membrane transporters for diverse substrates","description":"This cluster shows a strong enrichment for transmembrane transport terms across a variety of substrates (nitrite, nitrate, phosphate, arabinose, potassium, sialic acid, fucose), suggesting a shared role in moving diverse molecules across membranes. A few non-transport terms are present, but the transport theme predominates, supporting the proposed label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010867","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0015707","count":1},{"id":"GO:0015706","count":1}]},{"hash":"812932279509228690","title":"Central metabolism and cofactor biosynthesis","description":"The top GO terms show glycolysis, TCA cycle, pyruvate and acetyl-CoA biosynthesis, plus biosynthesis of cofactors like thiamine and biotin and porphyrin/heme precursors. This indicates a cluster of proteins involved in core energy metabolism and the synthesis of essential cofactors, rather than a single specialized function.","confidence":"High","size":27,"edges":317,"triangles":2197,"max_degree":26,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0042866","count":7},{"id":"GO:0006099","count":7},{"id":"GO:0009228","count":7},{"id":"GO:0019483","count":7},{"id":"GO:0055114","count":6}]},{"hash":"169630888346013858","title":"Unknown","description":"This cluster lists very diverse GO terms, including cardiac conduction regulation, photosynthesis, ubiquitin-dependent protein degradation, sperm entry, and hormone signaling, with no single dominant biological theme tying most terms together. The spread across animals, plants, and different processes, plus lack of interactions (edges/triangles) among members, suggests the proteins do not share a cohesive function in this cluster. ","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903779","count":2},{"id":"GO:0019684","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0042787","count":1}]},{"hash":"2124961081533852165","title":"DNA-Templated Transcription and Cell Cycle","description":"The top GO terms center on DNA-templated transcription and cell cycle/mitosis (cell division, mitotic cell cycle), with related chromatin modification and ciliogenesis signals, suggesting a cluster of proteins involved in nuclear gene expression linked to cell proliferation and related processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0051301","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0060271","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1221088977315558769","title":"Membrane Transport and Xenobiotic Handling","description":"This cluster is dominated by GO terms for various transmembrane transport processes (potassium, vitamin, xenobiotic, antibiotic) and a related response to xenobiotics, suggesting a common theme around membrane transport and xenobiotic management. Some terms like transcription and ribosomal decay are present but appear less central to the cluster\u2019s main signal. Overall, a membrane transport/xenobiotic theme best fits the data.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070651","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0006855","count":2}]},{"hash":"93032390438671076","title":"Unknown","description":"The top terms include developmental and signaling processes (liver regeneration, placental morphogenesis, spindle assembly), calcium release, lipid catabolic and redox processes, plus some immune signaling terms, with several entries marked obsolete. The set is too heterogeneous to derive a single coherent function or pathway that ties all proteins together, so a concise, representative label cannot be assigned.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0051225","count":2},{"id":"GO:0051209","count":2},{"id":"GO:0046475","count":2},{"id":"GO:0070431","count":2}]},{"hash":"931813561237119353","title":"Light-Responsive Photosynthesis Components","description":"The top GO terms converge on light perception and photosynthetic light harvesting\u2014responses to blue, red, far-red, and UV-A light, along with photosystems I and II light harvesting and light intensity responses. This suggests a cohesive set of proteins involved in sensing light and driving photosynthetic light capture, including chlorophyll/phytol-related processes.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009637","count":2},{"id":"GO:0018298","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0009769","count":2}]},{"hash":"1047001126190126385","title":"Ion and Xenobiotic Transporters","description":"The top GO terms point to diverse membrane transport functions: potassium and chloride ion transport, membrane hyperpolarization, pH regulation, and transport of vitamins and xenobiotics, including detoxification of cadmium. This suggests a cohesive cluster of proteins involved in ion homeostasis and xenobiotic/detox transport, with a few organism-specific terms (sperm capacitation, teichoic acid transport) that reflect broader transport-related roles.","confidence":"Medium","size":26,"edges":38,"triangles":15,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":9},{"id":"GO:0060081","count":7},{"id":"GO:0051454","count":6},{"id":"GO:1902476","count":6},{"id":"GO:0035461","count":6}]},{"hash":"1510534638232725327","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":57,"triangles":60,"max_degree":11,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":6},{"id":"GO:0000463","count":6},{"id":"GO:0000466","count":6},{"id":"GO:0000462","count":5},{"id":"GO:0048026","count":5}]},{"hash":"748683620217035859","title":"Bacterial LPS core biosynthesis and envelope assembly","description":"Based on the strong representation of lipopolysaccharide biosynthetic terms, especially core region biosynthesis and the ADP-L-glycero-beta-D-manno-heptose biosynthetic process, the cluster seems centered on bacterial outer membrane envelope construction. Additional terms related to phospholipid processing and metal ion transport fit membrane-associated, envelope-related functions typical of Gram-negative bacteria, supporting a cohesive theme around LPS core formation and envelope biosynthesis.","confidence":"High","size":26,"edges":11,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0009103","count":8},{"id":"GO:0006564","count":5},{"id":"GO:0009244","count":5},{"id":"GO:0097171","count":5}]},{"hash":"286885988254935101","title":"RNA processing and gene expression regulation","description":"Based on the dominant GO terms\u2014siRNA processing, regulation of RNA splicing, mRNA deadenylation, and translation\u2014the cluster seems to group proteins involved in RNA metabolism and post-transcriptional control of gene expression. A couple of peripheral terms (DNA replication and immune-related processes) are present but less represented, suggesting the core signal is RNA processing and expression regulation.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0030422","count":2},{"id":"GO:0044829","count":1},{"id":"GO:0045347","count":1},{"id":"GO:0000289","count":1}]},{"hash":"1868331538696621431","title":"Unknown","description":"The GO terms are spread across neural development, synaptic plasticity, telomere maintenance, adipogenesis, and stress responses, with no dominant shared function tying all proteins; as such, there isn\u2019t a clear cohesive biological theme for this cluster.","confidence":"","size":26,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0060291","count":4},{"id":"GO:0035994","count":3},{"id":"GO:0032212","count":3},{"id":"GO:1904355","count":3},{"id":"GO:0016477","count":3}]},{"hash":"2049438830409231624","title":"Secondary metabolite biosynthesis","description":"The top GO terms cluster around biosynthesis and metabolism of small-molecule secondary metabolites (antibiotics, biotin, strigolactones, alkaloids) and related detox/response processes, with a few broad or potentially noisy terms (behavior, T cell costimulation). This points to a cohesive theme of secondary metabolite production and xenobiotic handling, despite some outliers.","confidence":"Medium","size":26,"edges":10,"triangles":4,"max_degree":5,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0009636","count":4},{"id":"GO:0019380","count":4}]},{"hash":"1462978153086667752","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0051301","count":3},{"id":"GO:1903071","count":2},{"id":"GO:0070059","count":2}]},{"hash":"1506616947890788495","title":"Cell cycle and developmental transcriptional regulation","description":"The cluster is dominated by GO terms related to cell division, cell cycle transitions (G1/S and G2/M), and cell population proliferation, along with transcriptional regulation (DNA-templated transcription and RNA Pol II regulation) and in utero embryonic development. This points to proteins coordinating cell cycle progression with transcriptional programs during development. Less central terms like viral life cycle and negative regulation of GTPase activity may reflect broader regulatory features rather than core cluster function.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0019058","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0034260","count":2},{"id":"GO:0000122","count":2}]},{"hash":"1631326317154628008","title":"Cardiac development and transcription regulation","description":"This cluster is enriched for transcription-related GO terms (DNA-templated transcription and transcription elongation by RNA Pol II) together with heart-specific processes (heart development, cardiac muscle contraction), suggesting coordinated transcriptional control linked to cardiac development/function. A few terms like thyroid hormone metabolism and leaf senescence appear as outliers.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0042403","count":2},{"id":"GO:0051489","count":2},{"id":"GO:0070493","count":2}]},{"hash":"1071807751889393657","title":"Light-Responsive Photosynthesis Components","description":"The cluster is enriched for GO terms detailing responses to multiple light wavelengths (blue, red, far-red, UV-A, high/low light) and for photosynthesis-related light harvesting in photosystems I and II, plus chlorophyll/chromophore\u2013related processes. This points to proteins involved in light perception and the photosynthetic light-harvesting machinery, with some terms reflecting chlorophyll/chromophore associations. Therefore, a concise label capturing light response and photosynthesis is appropriate.","confidence":"High","size":25,"edges":31,"triangles":8,"max_degree":17,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0071492","count":6},{"id":"GO:0009637","count":5},{"id":"GO:0018298","count":5},{"id":"GO:1904964","count":5},{"id":"GO:0010218","count":5}]},{"hash":"1935974858706153175","title":"Metabolism and Stress Signaling","description":"Top GO terms indicate multiple metabolic pathways (retinol/retinal, fructose, D-xylose, cholesterol metabolism) together with stress responses (cadmium ion response, daunorubicin metabolism, stress-activated protein kinase signaling) and apoptosis regulation, plus ion transport, suggesting a cluster that centers on cellular metabolism with an associated stress-response and homeostasis role.","confidence":"Medium","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":23},{"id":"GO:0042574","count":22},{"id":"GO:0046370","count":18},{"id":"GO:0042843","count":17},{"id":"GO:0043066","count":17}]},{"hash":"1597251316894257558","title":"Redox Homeostasis and Stress Response","description":"Many of the most represented GO terms relate to redox biology (oxidation-reduction, redox homeostasis, removal of superoxide radicals) and stress responses, with some auxiliary terms pointing to chloroplast/secretory pathway processes. The dominant pattern is cellular redox balance and defense against reactive oxygen species, so the label Redox Homeostasis and Stress Response fits best.","confidence":"High","size":25,"edges":22,"triangles":0,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006888","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0042128","count":2},{"id":"GO:0030091","count":2}]},{"hash":"687808647346358163","title":"Plant Development and Hormone Signaling","description":"The listed GO terms cluster around plant growth and development modulated by hormones, including cytokinin-activated signaling; ABA and salicylic acid responses; root meristem growth regulation; vegetative growth; trichome patterning; and secondary cell wall biogenesis. Together, these terms point to hormone-driven developmental regulation in plants rather than a single linear function.","confidence":"Medium","size":25,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":1},{"id":"GO:1900033","count":1},{"id":"GO:0010082","count":1},{"id":"GO:1905615","count":1},{"id":"GO:1901348","count":1}]},{"hash":"1866324160673488541","title":"Chitin-based Cell Wall Formation and Septation","description":"The top GO terms cluster around chitin biosynthesis and cell wall organization (chitin biosynthetic process, ascospore wall chitin biosynthetic process, cell wall organization), plus cytokinesis-related terms (actomyosin contractile ring contraction, division septum site selection, septum digestion after cytokinesis). This points to a cohesive theme of chitin-containing cell wall formation and septation, with some insect-development related terms (insect visual primordium formation, follicle epithelium polarity, follicle cell adhesion) that may reflect species-specific roles or context-specific functions within the same morphogenetic framework. Overall, the dominant signal is chitin-associated cell wall synthesis and septation processes.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006031","count":1},{"id":"GO:0001744","count":1},{"id":"GO:0000918","count":1},{"id":"GO:0075015","count":1},{"id":"GO:0007299","count":1}]},{"hash":"1216075611179283042","title":"Unknown","description":"The terms span chromatin/RNA processing, immune signaling, DNA repair, and several disparate developmental processes with only minimal connectivity, so there isn't a cohesive common function to label the cluster; thus it is Unknown.","confidence":"","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071044","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0010735","count":1},{"id":"GO:0042275","count":1},{"id":"GO:0060065","count":1}]},{"hash":"1913904936028812802","title":"Genome Replication and RNA Processing","description":"GO terms in this cluster cluster around DNA replication, genome maintenance (SOS response), transcription termination, viral genome replication, DNA topology changes, rRNA maturation, and mRNA decay. This mix points to a cohesive theme of nucleic acid metabolism and genome maintenance, justifying a label that combines replication and RNA processing functions.","confidence":"High","size":25,"edges":300,"triangles":2300,"max_degree":24,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0009432","count":8},{"id":"GO:0006369","count":8},{"id":"GO:0019079","count":7},{"id":"GO:0000463","count":7}]},{"hash":"805200749463141700","title":"RNA processing and ribosome biogenesis","description":"The dominant GO terms are RNA maturation and processing (rRNA maturation for 5.8S and LSU), translation, and RNA splicing (spliceosome assembly and mRNA splicing), which together point to RNA metabolism and ribosome production. A few terms relate to mitochondria (mitophagy regulation and ubiquinone biosynthesis), suggesting some mitochondrial context, but the core signal is RNA processing and ribosome assembly.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000466","count":1},{"id":"GO:1903146","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000463","count":1}]},{"hash":"815862425059908889","title":"Photosynthesis and Light Response","description":"The terms are dominated by photobiology: responses to blue light, far-red light, and UV-A, plus photosynthesis-related light harvesting in photosystem II and chlorophyll-related biosynthesis, which together point to chloroplast-associated light-driven processes. Some outlier terms (ergosterol biosynthesis, xenobiotic response, DNA replication) reduce coherence, so the label is representative but with Medium confidence.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006696","count":2},{"id":"GO:0090394","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0009637","count":2}]},{"hash":"1461209848659672300","title":"Photoperiodic flowering regulation","description":"Most of the leading GO terms point to plant responses to day length and flowering control (short-day photoperiodism, regulation of flower development) and related light signaling (far-red). While a couple of terms touch general cellular processes, the dominant theme is photoperiodic regulation of flowering and related circadian movement (circumnutation). This makes Photoperiodic flowering regulation a concise, representative label with High confidence.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006289","count":1},{"id":"GO:0006360","count":1},{"id":"GO:0070816","count":1},{"id":"GO:0010018","count":1},{"id":"GO:0000160","count":1}]},{"hash":"1046944088478366183","title":"Histone modification and transcription regulation","description":"The terms point to transcription control via chromatin state, with DNA-templated transcription, elongation regulation, heterochromatin formation, and multiple histone acetylation processes supporting chromatin-based transcription regulation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0043982","count":2},{"id":"GO:0043983","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0043968","count":2}]},{"hash":"292046725277179063","title":"Neuronal Calcium Transport and Synaptic Plasticity","description":"This cluster is dominated by GO terms for calcium ion transport and homeostasis across membranes (plasma and mitochondria) and by synaptic plasticity processes (long-term potentiation/depression), indicating a cohesive theme of calcium signaling in neuronal communication. The terms point to calcium import/export and mitochondrial calcium handling as core functions, with synaptic modulation as a downstream or associated function. Some outlier terms exist, but the central pattern is clear.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097369","count":2},{"id":"GO:0007154","count":2},{"id":"GO:0048022","count":2},{"id":"GO:0006851","count":2},{"id":"GO:0060292","count":2}]},{"hash":"800628892726503438","title":"Unknown","description":"The GO terms are highly heterogeneous (axonogenesis, adenohypophysis morphogenesis, thyroid hormone metabolism, cuticle development, autophagy-related processes, redox, cAMP response, etc.) and there are no shared functional pathways or a connected biological theme among the proteins (no edges or high-degree links). This makes it inappropriate to assign a cohesive functional label beyond Unknown.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0007409","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0042554","count":2}]},{"hash":"133496370108364822","title":"Fatty acid metabolism and energy regulation","description":"The cluster is dominated by GO terms related to lipid metabolism and energy control (malonyl-CoA catabolic process, regulation of fatty acid beta-oxidation and fatty acid oxidation, acetyl-CoA biosynthesis, and fatty acid biosynthetic process), with supporting terms on glucose metabolism; a couple of development terms appear but are less representative. Overall, the shared theme is lipid metabolism and energy homeostasis among the proteins.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051798","count":2},{"id":"GO:0043113","count":2},{"id":"GO:0030324","count":2},{"id":"GO:2001294","count":1},{"id":"GO:0010906","count":1}]},{"hash":"1603363581003592132","title":"Unknown","description":"The top GO terms span very disparate processes across different kingdoms (bacterial LPS and biosynthesis, plant sporopollenin and anthocyanin biosynthesis, animal lung development) plus redox and post-translational modification. There isn't a clear common function binding the 24 proteins, indicating heterogeneous or mixed annotations. Therefore, no single representative theme can be assigned.","confidence":"","size":24,"edges":6,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042619","count":4},{"id":"GO:0030324","count":3},{"id":"GO:0032364","count":3},{"id":"GO:1901874","count":3}]},{"hash":"1491658085320094203","title":"Diverse Transmembrane Transporters","description":"The top GO terms show a pattern of transmembrane transport across membranes for a variety of substrates\u2014vitamins, xenobiotics, ions (potassium, phosphate), sugars (galactose), nitrate, sialic acid, and even neurotransmitter loading into vesicles\u2014suggesting this cluster groups membrane transporter proteins with broad substrate specificity.","confidence":"High","size":24,"edges":26,"triangles":4,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":7},{"id":"GO:0006855","count":7},{"id":"GO:0042891","count":6},{"id":"GO:0071805","count":4},{"id":"GO:0098700","count":4}]},{"hash":"1382265115695629229","title":"RNA processing and translational regulation","description":"This cluster is enriched for spliceosome-mediated mRNA processing (cis splicing and alternative splicing) and for translation-related processes (preinitiation complex formation, translation) as well as post-transcriptional regulation (miRNA-mediated silencing and poly(A) tail regulation), indicating a cohesive group of RNA processing and control of protein synthesis factors.","confidence":"High","size":24,"edges":11,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0045292","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0048025","count":2}]},{"hash":"1451682838805989954","title":"Stress-responsive transcription","description":"The cluster is driven by transcription-related activity (DNA-templated transcription) and contains multiple GO terms tied to cellular responses to chemical and oxidative stress (cadmium, copper, nitroglycerin, singlet oxygen, heat). These patterns suggest a group of proteins involved in stress-induced transcriptional programs, even though a couple of terms are noisy or unrelated. Therefore, a label emphasizing transcription coupled with stress response fits best.","confidence":"Medium","size":24,"edges":55,"triangles":112,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060136","count":2},{"id":"GO:0043497","count":2},{"id":"GO:2001033","count":2},{"id":"GO:1904843","count":2}]},{"hash":"2155594282247268199","title":"Ubiquitin-Proteasome Regulation and Antigen Processing","description":"This cluster is enriched for ubiquitin-related processes (deubiquitination, SCF- and APC/C-dependent proteasomal degradation) and antigen processing/presentation via MHC I, with accompanying T cell receptor signaling. The common thread appears to be proteostasis via ubiquitin ligase regulation and proteasome-driven peptide generation for immune presentation, with some secondary stress-response signals.","confidence":"High","size":24,"edges":273,"triangles":1960,"max_degree":23,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":14},{"id":"GO:0031145","count":12},{"id":"GO:0031146","count":12},{"id":"GO:0050852","count":11},{"id":"GO:0002479","count":11}]},{"hash":"2172287615055798258","title":"Metal and oxidative stress response","description":"These GO terms cluster around cellular responses to stress, especially metal ions (cadmium, copper) and oxidative challenges (singlet oxygen, nitroglycerin), with a note of transcriptional regulation (DNA-templated transcription) that often accompanies stress responses. While some terms are outdated or peripheral, the dominant theme is metal/oxidative stress defense linked to transcriptional changes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0060136","count":2},{"id":"GO:0043497","count":2},{"id":"GO:2001033","count":2}]},{"hash":"155115943427700861","title":"Translation initiation complex formation","description":"The GO terms dominated by initiation of translation\u2014formation of the translation preinitiation complex, IRES-dependent translational initiation, and regulation/reinitiation of translation\u2014point to proteins that function in initiating protein synthesis, i.e., the translation initiation machinery. A few unrelated terms appear but are likely incidental noise.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001731","count":3},{"id":"GO:0075522","count":2},{"id":"GO:0006446","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0009608","count":1}]},{"hash":"2031945437762020033","title":"Synaptic Signaling and RNA Processing Proteins","description":"Top GO terms are dominated by neuronal synaptic functions (long-term potentiation, neurotransmitter secretion) with supporting roles in calcium signaling and PI pathways, plus mRNA transport and splicing. This points to a cluster enriched for synaptic signaling components and associated RNA processing factors, with some non-neuronal processes likely reflecting shared cellular machinery.","confidence":"Medium","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060291","count":2},{"id":"GO:0008284","count":2},{"id":"GO:0048015","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0071277","count":2}]},{"hash":"840794161015440963","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":114,"triangles":233,"max_degree":23,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":13},{"id":"GO:0006268","count":11},{"id":"GO:0045944","count":10},{"id":"GO:0010571","count":9},{"id":"GO:0048701","count":9}]},{"hash":"769601982495515998","title":"Ubiquitin-Dependent Proteolysis and Cell Cycle Regulation","description":"The dominant GO terms center on ubiquitin-dependent protein degradation (including K48-linked ubiquitination and ERAD pathways) and regulation of polyubiquitination, indicating a core role in targeted proteolysis. The presence of mitotic G1 DNA damage checkpoint signaling links this degradation activity to cell-cycle control, supporting a cohesive theme of protein turnover coordinating cell division. Peroxisomal import and transcription terms appear less central but may reflect broader ubiquitin involvement.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0000746","count":3},{"id":"GO:0070936","count":3}]},{"hash":"155305959840511038","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0046825","count":1},{"id":"GO:0045454","count":1}]},{"hash":"556025371118448889","title":"Plant growth regulation and chromatin maintenance","description":"This cluster centers on plant growth and development regulation (root meristem growth, vegetative growth, trichome patterning, secondary cell wall biogenesis) with chromatin/DNA structure maintenance signals (rDNA heterochromatin formation, G-quadruplex DNA, telomere RNA localization), suggesting a theme where chromatin state modulates growth programs.","confidence":"Medium","size":24,"edges":2,"triangles":0,"max_degree":2,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0000183","count":4},{"id":"GO:1990414","count":4},{"id":"GO:0009736","count":3},{"id":"GO:1900033","count":3},{"id":"GO:0010082","count":3}]},{"hash":"79042954590992959","title":"Bacterial Fatty Acid Metabolism and Bioluminescence","description":"The cluster shows strong representation of fatty acid biosynthesis, fatty-acyl-CoA metabolism, and retinoid metabolism terms, plus bioluminescence, which together point toward lipid-centric metabolism with light-emitting activity typical of certain marine bacteria. While some terms are obsolete, the recurring lipid pathways and occasional bioluminescence support this theme.","confidence":"High","size":24,"edges":23,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006633","count":4},{"id":"GO:0042572","count":4},{"id":"GO:0042574","count":3},{"id":"GO:0006069","count":2}]},{"hash":"1412751192485697313","title":"Amino acid and cofactor biosynthesis","description":"The cluster is dominated by GO terms for biosynthetic pathways of amino acids and cofactors (lysine, tyrosine, biotin, porphyrin/heme intermediates, and kynurenic acid), plus related metabolic processes such as fatty acid homeostasis. This suggests a cohesive role in the production and regulation of diverse metabolites rather than a single specific enzyme function. There are additional notes on metabolic regulation (insulin response, transcription) that align with broader metabolic control, but the strongest signal is biosynthesis across multiple pathways. ","confidence":"High","size":24,"edges":220,"triangles":1116,"max_degree":23,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":14},{"id":"GO:0006782","count":14},{"id":"GO:0009102","count":14},{"id":"GO:0033512","count":13},{"id":"GO:0034276","count":12}]},{"hash":"1329337413602592580","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0006458","count":3},{"id":"GO:0070843","count":3},{"id":"GO:0030433","count":3}]},{"hash":"466773552003909588","title":"Glial Ion Signaling and Transcription","description":"This cluster shows a pattern of glial cell proliferation regulation (positive and negative) together with multiple ion-related responses (zinc, manganese, calcium) and transcriptional activity (DNA-templated transcription, heat-stress transcription regulation). While not all terms fit a single pathway, the strongest common theme is ion signaling linked to transcriptional regulation in glial cells.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048265","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071294","count":1},{"id":"GO:0060253","count":1}]},{"hash":"460347444816863034","title":"Ubiquitin-Dependent Antiviral Signaling Regulation","description":"Most terms cluster around ubiquitination processes (ubiquitin-dependent protein catabolic process, protein ubiquitination, autoubiquitination, K63-linked ubiquitination) and antiviral/innate immunity signaling (defense response to virus, RIG-I pathway regulation, I-kappaB phosphorylation). This points to a group of proteins that regulate antiviral signaling through ubiquitin-mediated modification. Confidence: High","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0051865","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0033151","count":3},{"id":"GO:0070534","count":3}]},{"hash":"1039286005111329809","title":"Plant light perception and photosynthesis","description":"The top GO terms revolve around photosynthesis and responses to blue, red, far-red light, UV-A, and light intensity, along with light harvesting in photosystem II and phytol biosynthesis regulation. This pattern strongly points to proteins involved in light sensing/signaling and photosynthetic machinery, indicating a light-responsive photosynthesis cluster.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0009637","count":3},{"id":"GO:0018298","count":3},{"id":"GO:1904964","count":3},{"id":"GO:0010218","count":3}]},{"hash":"1825074621784919834","title":"Transcription Regulation and Neuronal Plasticity","description":"The top GO terms point to DNA-templated transcription and its regulation, with a notable link to long-term synaptic potentiation, suggesting a set of transcriptional regulators involved in neuronal signaling and plasticity. Additional terms like cellular response to cAMP, redox homeostasis, and apoptotic processes indicate broader cellular signaling and stress-response roles. The lack of edges implies these proteins may function as regulators rather than a tightly connected complex, consistent with a transcription- and signaling-focused cluster rather than a single pathway.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0006915","count":2}]},{"hash":"971578281062464532","title":"Intracellular trafficking and protein processing","description":"The cluster\u2019s top GO terms are dominated by vesicle transport and cargo processing: ER-to-Golgi vesicle transport, retrograde ER-to-cytosol transport, and endosome-to-lysosome transport via multivesicular bodies, along with general protein processing. While some terms relate to neuronal development or stress responses, the concentration of intracellular trafficking terms suggests a cohesive theme around vesicle trafficking and protein maturation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050775","count":2},{"id":"GO:0045470","count":1},{"id":"GO:0035617","count":1},{"id":"GO:0033314","count":1},{"id":"GO:0045463","count":1}]},{"hash":"558766689250564545","title":"Unknown","description":"The GO terms in this cluster cover a wide range of unrelated processes\u2014from mitotic progression and fungal sporulation (G2/M transition, prospore membrane formation, karyogamy) to neural development and memory (substantia nigra development, visual learning, long-term memory), as well as membrane trafficking (endocytic recycling, phagocytosis) and glycosylation. There is no single coherent function or pathway tying these terms together, so a concise, representative label cannot be assigned beyond Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0032120","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0060048","count":2}]},{"hash":"1132196696441624819","title":"Mitotic Spindle Checkpoint and Chromosome Segregation","description":"The top GO terms are dominated by mitosis-related processes\u2014mitotic spindle assembly checkpoint signaling, metaphase/anaphase transition, and sister chromatid cohesion\u2014indicating a cluster focused on mitotic progression and chromosome segregation. A few outliers (apoptotic signaling, ER-Golgi transport, histone phosphorylation) are present but do not define the cluster.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008631","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0002037","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0032837","count":1}]},{"hash":"1394160043181123165","title":"Actin Cytoskeleton Organization","description":"The top GO terms center on actin filament bundle assembly (mitotic contractile ring), microvillus organization, pigment granule transport, and regulation of GTPase activity, all reflecting actin cytoskeleton dynamics and related intracellular transport. Although some terms are obsolete or developmental, the common thread is cytoskeletal organization and trafficking.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903478","count":1},{"id":"GO:1902405","count":1},{"id":"GO:0048496","count":1},{"id":"GO:0070493","count":1},{"id":"GO:0032529","count":1}]},{"hash":"501848577170743328","title":"COPI-Mediated ER\u2013Golgi Transport","description":"The GO terms point strongly to components of the early secretory pathway, including COPI coating of Golgi vesicles, COPI-coated vesicle budding, ER-to-Golgi vesicle transport, and positive regulation of protein exit from the ER; Wnt secretion also fits with secretion through this pathway. Some terms (chromatin, placenta development, aggression) appear unrelated and may be incidental, but the dominant theme is COPI/ER\u2013Golgi vesicle trafficking.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":2},{"id":"GO:0061357","count":1},{"id":"GO:0001893","count":1},{"id":"GO:0048205","count":1},{"id":"GO:0002121","count":1}]},{"hash":"376481055556793308","title":"Unknown","description":"The proteins here have a scattered mix of GO terms (digestion, defense response to Gram-positive bacteria, transcription regulation, glucose response, angiogenesis, gland development, photoinhibition, sphingolipid metabolism), with several obsolete terms as well. There\u2019s no clear, cohesive theme or shared function linking them, making a concise, representative label inappropriate. ","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044130","count":4},{"id":"GO:0007586","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0071333","count":3},{"id":"GO:0050830","count":3}]},{"hash":"1337144442787064765","title":"RNA Methylation Machinery","description":"Top GO terms point to RNA guanine-N7 methylation for rRNA and tRNA, indicating the cluster centers on RNA modification enzymes; other terms are broader cellular processes that do not outweigh this signature. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":4},{"id":"GO:0051291","count":3},{"id":"GO:0008340","count":3},{"id":"GO:0006744","count":3},{"id":"GO:0070476","count":3}]},{"hash":"1440690533220201896","title":"Proteostasis and mitochondrial import under stress","description":"The top GO terms cluster around protein transport, ubiquitin-dependent protein degradation, and unfolded protein response, indicating a proteostasis-focused function. Additional terms for mitochondrial inner membrane protein insertion and centrosome maintenance suggest coordination of protein targeting and cell organization under stress. Cadmium response and some hormone signaling terms likely reflect broader stress signaling cross-talk in the organism. Overall, the dominant theme is protein quality control and stress response with emphasis on mitochondrial import pathways.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0051661","count":2},{"id":"GO:0032979","count":1}]},{"hash":"187853821881997910","title":"Metabolic Stress Response","description":"The top GO terms indicate energy metabolism regulation (gluconeogenesis, fructose metabolism, negative regulation of glycolysis) combined with cellular stress responses (respiratory burst, xenobiotic response, cobalt ion signaling) and mitochondrial quality control (mitophagy). A few terms touch on development (brain development, cardiac muscle apoptotic regulation), but the dominant signal lies in how metabolic pathways are modulated under stress. Thus, a concise label is \"Metabolic Stress Response\" to reflect metabolism intertwined with stress responses.","confidence":"Medium","size":23,"edges":28,"triangles":8,"max_degree":22,"top_function":"autophagy","top_go_terms":[{"id":"GO:0006094","count":5},{"id":"GO:0016032","count":3},{"id":"GO:0010666","count":3},{"id":"GO:0009410","count":3},{"id":"GO:0045730","count":3}]},{"hash":"380618914532206140","title":"Ribosome Biogenesis and rRNA Processing","description":"This cluster is primarily driven by GO terms for ribosome biogenesis and maturation of LSU rRNA, indicating a core function in ribosome assembly and RNA processing. Other terms like cell division and protein homooligomerization may reflect broad growth-related processes, while mitophagy and neuronal/apoptotic terms could reflect secondary or context-specific connections. Overall, the dominant signal supports a ribosome-focused cluster.","confidence":"Medium","size":23,"edges":6,"triangles":0,"max_degree":3,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0051260","count":4},{"id":"GO:0000747","count":4},{"id":"GO:0061734","count":3}]},{"hash":"130759669376330804","title":"Protein and RNA Methylation Cluster","description":"The top GO terms cluster around methylation processes (peptidyl-lysine dimethylation/trimethylation, N-terminal methylation, and rRNA methylation) with a link to chromatin regulation (rDNA heterochromatin formation), suggesting a group of proteins involved in methylation-based modification and chromatin control; a few terms are obsolete or atypical (behavioral signaling), but the core theme is methylation activity.","confidence":"Medium","size":23,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043497","count":2},{"id":"GO:0035641","count":2},{"id":"GO:0032259","count":1},{"id":"GO:0018027","count":1},{"id":"GO:0031167","count":1}]},{"hash":"805805865838715718","title":"Gene expression and metal stress response","description":"This cluster centers on core gene expression processes (DNA-templated transcription, translation, transcription antitermination, translational fidelity) and cellular responses to metal stress (cadmium, arsenite), with additional regulatory and metabolic terms. The combination suggests a module that ties gene expression machinery to environmental stress signaling, though some terms are broader or peripheral (e.g., cholesterol biosynthesis, visual learning).","confidence":"Medium","size":23,"edges":18,"triangles":5,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0006412","count":3},{"id":"GO:2001033","count":3},{"id":"GO:0071276","count":3},{"id":"GO:1903936","count":3}]},{"hash":"1518040655780246699","title":"TLR-driven macrophage activation and cytokine production","description":"The cluster is dominated by GO terms related to macrophage activation, defense against Gram-positive bacteria, and multiple Toll-like receptor signaling pathways (TLR4, TLR9, TLR10) with regulatory roles in cytokine and chemokine production, including IL-18. This points to innate immune signaling in macrophages as the core theme. One outlier term about floral meristem growth appears unrelated, likely noise. Overall, the proteins appear to coalesce around TLR-mediated macrophage responses and cytokine regulation.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042116","count":4},{"id":"GO:0050830","count":4},{"id":"GO:0043547","count":3},{"id":"GO:0050707","count":3},{"id":"GO:0032741","count":3}]},{"hash":"1940359358596497899","title":"Light-Responsive Photosynthesis","description":"The top GO terms cluster around photosynthesis and responses to various light conditions (blue, red, far-red, UV-A, high/low light) and light harvesting in photosystem II, plus chlorophyll-related biosynthesis. This suggests a cohesive group of proteins involved in light-regulated photosynthetic processes.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0009637","count":1},{"id":"GO:0018298","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0010218","count":1}]},{"hash":"284109213098188102","title":"Unknown","description":"The top terms are a scattered mix of immune development (B cell homeostasis, germinal center formation, monocyte differentiation), signaling, and translation/RNA processing, with no clear shared function and no edges connecting nodes, so there is no cohesive biological theme to label.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0060710","count":2},{"id":"GO:0002635","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0002181","count":2}]},{"hash":"23573878455833996","title":"Cell Stress Response and Proteostasis","description":"The cluster\u2019s top GO terms point to stress-related and protein quality control processes: unfolded protein response, heat response, ER-associated degradation, and gamma radiation response, all hinting at proteostasis under stress. There are also entries for DNA replication and transcription regulation, suggesting some coupling to cell-cycle or transcriptional control during stress. Some trafficking-related terms (receptor recycling, endosome size) imply broader cellular maintenance. Overall, the dominant theme is cellular stress response and proteostasis with ancillary connections to DNA processes and trafficking, making this a coherent, though not tightly focused, cluster.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060316","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1900490","count":2},{"id":"GO:0006986","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1471109246705420086","title":"Genome maintenance and cell-cycle machinery","description":"The top GO terms center on DNA repair via homologous recombination, telomere maintenance, spindle assembly, and broader genome stability processes, with supporting signals from RNA processing and cytoskeletal organization. This suggests a cluster of proteins involved in genome maintenance and cell division rather than a single narrow function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000724","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0051017","count":2}]},{"hash":"1858022880762251222","title":"Bacterial Transcription and Ribosome Biogenesis with Transport","description":"This cluster centers on DNA-templated transcription and ribosome biogenesis (including small subunit export) and a SOS response, complemented by multiple membrane transport and secretion-related GO terms (teichoic acid transport, amino acid transport, thiamine transport, glycerophosphodiester transport, and Type I secretion). Together these suggest a bacterial gene set coordinating gene expression, ribosome assembly, stress response, and envelope/transport functions.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0009432","count":3},{"id":"GO:0000056","count":3},{"id":"GO:0015777","count":2}]},{"hash":"880414340236467771","title":"Plant Hormone Signaling and Nutrient Transport","description":"The cluster shows enrichment for plant hormone-related processes (auxin signaling and gibberellin homeostasis), as well as nutrient transport/assimilation (nitrate transport and reduction) and vesicle trafficking (ER\u2013Golgi transport), pointing to combined roles in hormone regulation and nutrient movement in plants. Some pigmentation and herbicide-response terms also align with plant-specific cellular functions, reinforcing a plant-centered theme. Confidence: Medium","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0046784","count":2},{"id":"GO:0042938","count":1}]},{"hash":"738321495239687384","title":"Biosynthesis and Methylation Enzymes","description":"The top GO terms indicate a mix of biosynthetic processes (antibiotic, menaquinone, biotin, poly-hydroxybutyrate) and methylation-related activities (rRNA methylation, peptidyl/glycine methylation, N-terminal methylation). This suggests a set of proteins involved in various biosynthetic pathways and methylation modifications rather than a single, cohesive function. The diversity and lack of interaction support a broad biosynthesis/methylation theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009234","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0018027","count":4}]},{"hash":"2155604075897710654","title":"TLR Signaling and Inflammation","description":"Most terms describe Toll-like receptor pathways (TLR4/8/10), inflammatory signaling, and chemokine production, suggesting the proteins cluster around innate immune sensing and inflammation. A few unrelated terms appear in the list but do not alter the overall theme.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019800","count":1},{"id":"GO:0071726","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0034166","count":1},{"id":"GO:0010080","count":1}]},{"hash":"1875396064398269443","title":"Dopaminergic Neuron Development and Dopamine Metabolism","description":"The top GO terms are centered on dopaminergic neuronal biology, including synaptic transmission, neuron projection development, and dopamine metabolic processes, pointing to a shared function in dopamine signaling and neuron development. A few unrelated terms appear, but the dominant pattern supports a dopaminergic neuron development/signaling module. Confidence: Medium","confidence":"","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":1},{"id":"GO:0001963","count":1},{"id":"GO:0070050","count":1},{"id":"GO:0031175","count":1},{"id":"GO:0071542","count":1}]},{"hash":"1854694872945566983","title":"Stress-Induced Translational Regulation","description":"Top terms are dominated by cellular stress responses and translational regulation under stress (ER stress, UV response, nutrient starvation) including eIF2alpha phosphorylation and regulation of cytoplasmic translation, supporting a label for stress-induced translational control.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060765","count":1},{"id":"GO:1904803","count":1},{"id":"GO:0031953","count":1},{"id":"GO:0071232","count":1},{"id":"GO:0097201","count":1}]},{"hash":"1219520717757925804","title":"Membrane Transport and Signaling","description":"Proteins in this cluster are linked to transmembrane transport (sodium, nitrite/nitrate, xenobiotics) and related membrane activities such as ion-driven depolarization and neurotransmitter secretion (GABA). Although there are some regulatory/developmental and DNA repair terms, the dominant signal is membrane-associated transport and signaling across tissues, suggesting a membrane transport/secretory functional grouping.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0098912","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0035904","count":2}]},{"hash":"151628059736689584","title":"RNA processing and cell cycle regulation","description":"The top GO terms cluster around RNA processing and splicing (RNA splicing, mRNA processing, spliceosomal tri-snRNP complex assembly, miRNA transcription) and cell proliferation processes (mitotic cell cycle, cell division), with a note of ubiquitination (K11-linked). Some plant-development terms (inflorescence development, pollen maturation) may reflect organism-specific annotations or broader regulatory roles tied to development. Overall, the dominant signal points to coordination between post-transcriptional RNA processing and cell cycle regulation, justifying the label.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061614","count":1},{"id":"GO:0000278","count":1},{"id":"GO:0070979","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0010229","count":1}]},{"hash":"470721071012328789","title":"DNA Damage Response and Cell Cycle Regulation","description":"The terms cluster around DNA double-strand break repair (NHEJ) and cell cycle control, with related notes on nuclear envelope attachment and ncRNA-mediated gene silencing, plus some cytokine and macrophage activation signals; this points to a module focused on genome integrity maintenance and cell-cycle coordination, with ancillary immune signaling activity.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990683","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006471","count":2},{"id":"GO:0097680","count":2}]},{"hash":"1233089672351752006","title":"Unknown","description":"The top GO terms are scattered across development (ectoderm, renal structures, oviduct) and include unrelated items like chromatin remodeling and host-symbiont responses, with no shared function or interactions connecting the proteins. Since there is no clear common theme or enriched pathway, the cluster is best labeled Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071681","count":1},{"id":"GO:0048496","count":1},{"id":"GO:0080034","count":1},{"id":"GO:0008285","count":1},{"id":"GO:0007398","count":1}]},{"hash":"2239616976946203487","title":"Deubiquitination and ubiquitin-dependent proteolysis","description":"The cluster is enriched in deubiquitination terms (K48- and K11-linked) and ubiquitin-dependent protein catabolic processes, pointing to regulation of protein turnover by ubiquitin signaling. A few RNA processing and transcription terms appear but are less consistent with this core theme, so the label centers on proteostasis via ubiquitin modification.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071108","count":2},{"id":"GO:0035871","count":2},{"id":"GO:0070894","count":1},{"id":"GO:0070537","count":1},{"id":"GO:0006511","count":1}]},{"hash":"1624196971257853096","title":"Vesicle trafficking and mitosis","description":"The top GO terms point to endomembrane transport (Golgi-to-endosome, endosome-to-lysosome, vesicle docking) and positive regulation of GTPase activity, paired with cell division and mitotic spindle assembly. This suggests a cluster centered on coordinated vesicle trafficking with cell cycle progression, with some developmental signaling context (e.g., Smoothened pathway, kidney development). Overall, the dominant theme is vesicle trafficking linked to mitosis and developmental signaling.","confidence":"High","size":22,"edges":57,"triangles":52,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007224","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0006895","count":3}]},{"hash":"1110770653667076049","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms related to ubiquitination and ubiquitin-mediated proteolysis (ubiquitin-dependent protein catabolic process, autoubiquitination, various ubiquitin linkages including K48, K6, K11, and the ERAD pathway), with additional signals for histone ubiquitination affecting transcription and TNF signaling. This points to a cohesive module centered on ubiquitin signaling governing protein turnover and chromatin-related regulation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0051865","count":7},{"id":"GO:0016567","count":6},{"id":"GO:0070936","count":6},{"id":"GO:0030433","count":6}]},{"hash":"2292872989703537202","title":"Neural development and synapse regulation","description":"The cluster shows enrichment for neural-related processes such as visual perception, regulation of presynapse assembly, and sensory neuron axon guidance, alongside membrane trafficking (receptor recycling) and signaling modules (GTPase activity, Hippo signaling). While there are general cell cycle signals present, the strongest cohesive theme is neural development and synaptic assembly/maintenance coupled with signaling and trafficking. ","confidence":"Medium","size":22,"edges":224,"triangles":1413,"max_degree":21,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0000278","count":9},{"id":"GO:0000160","count":8},{"id":"GO:0019236","count":8}]},{"hash":"1046587727300278195","title":"Ribosome biogenesis and RNA pseudouridylation","description":"The cluster centers on RNA modification (pseudouridine synthesis in rRNA/tRNA), translation, and ribosome assembly, indicating a cohesive role in ribosome production and function; auxiliary processes like protein maturation and iron-sulfur cluster assembly may support ribosome biogenesis, while some terms (antibiotic response, nitrogen fixation) may reflect organism-specific contexts or indirect associations.","confidence":"High","size":22,"edges":231,"triangles":1540,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0000455","count":2},{"id":"GO:0031119","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0046677","count":1},{"id":"GO:0000448","count":1}]},{"hash":"771989290690727738","title":"Macrophage Activation and Cytokine Production","description":"This cluster is best characterized by terms related to immune signaling, including macrophage activation, positive regulation of interleukin-18 production, and positive regulation of chemokine production, suggesting a set of proteins involved in inflammatory response and cytokine secretion. Additional terms about secretion and trafficking (protein export from ER and nucleus, localization to the cell surface, lysosomal enzyme secretion) align with a broader theme of secretory pathways supporting immune signaling. Some items such as pseudohyphal growth and invasive growth in response to glucose limitation appear less connected to vertebrate immunity and may reflect cross-species annotation noise.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001403","count":2},{"id":"GO:2000010","count":2},{"id":"GO:0070863","count":2},{"id":"GO:0007124","count":2},{"id":"GO:0033299","count":2}]},{"hash":"1548088944435698362","title":"Cofactor Biosynthesis and DNA Metabolism","description":"This cluster is dominated by GO terms for biosynthesis of essential cofactors (menaquinone, thiamine, biotin) and by core nucleic acid processes (tRNA methylation, DNA-templated transcription, DNA replication) along with central metabolism (glucose metabolism). While a few stress-related terms (cadmium response, innate immune response) appear, the prominent theme ties vitamin/cofactor biosynthesis to nucleic acid metabolism, suggesting a metabolism\u2013DNA processing functional module.","confidence":"Medium","size":22,"edges":34,"triangles":25,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0009234","count":5},{"id":"GO:0030488","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0071276","count":4},{"id":"GO:0009228","count":4}]},{"hash":"520889254315178764","title":"Broad cellular processes","description":"Proteins in this cluster map to a variety of GO terms spanning cell growth, spindle assembly, calcium transport, RNA processing, telomere maintenance, neural differentiation, and thermoception. The lack of a single dominant pathway and the dispersion of terms suggest a broad, general set of cellular functions rather than a unified process.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0071651","count":1},{"id":"GO:0051225","count":1},{"id":"GO:0098703","count":1},{"id":"GO:0090503","count":1}]},{"hash":"146781787005758422","title":"Translation, Splicing, and Ubiquitination in Cell Division","description":"This cluster centers on core gene expression and protein regulatory processes active during cell division: translation is prominent, along with mRNA splicing via the spliceosome, and multiple ubiquitination-related processes (including autoubiquitination and histone ubiquitination, plus related ERAD pathway). These themes together point to a coordinated module of protein synthesis, RNA processing, and ubiquitin-mediated regulation that supports mitosis and cell-cycle progression, with occasional developmental signals reflected in terms like embryonic development and ABA response.","confidence":"High","size":21,"edges":62,"triangles":96,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0000278","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0001701","count":4},{"id":"GO:0051865","count":3}]},{"hash":"1717548742976680518","title":"Proteolysis and stress-responsive protein trafficking","description":"This label captures the prominence of proteolysis-related terms (proteolysis, collagen and bradykinin catabolism) alongside protein handling pathways (ER-to-Golgi transport; mitochondrial intermembrane space import) and cellular stress responses (oxidative stress, stress-related metabolic regulation, cardiac hypertrophy). Although transcription regulation and DNA replication appear among the terms, they appear less central to the main theme of proteolysis and trafficking under stress. ","confidence":"Medium","size":21,"edges":19,"triangles":1,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0030574","count":2},{"id":"GO:0010815","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0006888","count":2}]},{"hash":"818388814563248359","title":"Unknown","description":"The terms are scattered across transcription, transport, metabolism, and development with no single dominant function, suggesting either mixed proteins or noisy annotations rather than a coherent biological module.","confidence":"","size":21,"edges":15,"triangles":3,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0048240","count":4},{"id":"GO:0009103","count":4},{"id":"GO:0070574","count":4},{"id":"GO:0071577","count":4}]},{"hash":"1052324836375951784","title":"TLR Signaling and Inflammation","description":"The top GO terms center on Toll-like receptor signaling (TLR4, TLR8, TLR10), responses to bacterial lipopeptides, chemokine regulation, and inflammatory processes, pointing to a cluster of proteins involved in innate immune sensing and inflammatory signaling. Some unrelated terms appear as noise, but the core theme is TLR-mediated immune activation and inflammation.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019800","count":1},{"id":"GO:0071726","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0034166","count":1},{"id":"GO:0010080","count":1}]},{"hash":"1679861599653455898","title":"Unknown","description":"The GO terms span very diverse processes (vitamin K\u2013related carboxylation, photosystem II assembly, transcription elongation regulation, mRNA transport, nuclear pore assembly, ciliary docking, TORC1 signaling, and apoptotic regulation) with only a single edge connecting proteins, suggesting no cohesive, single-function theme for the cluster. Confidence in a single representative label is None.","confidence":"","size":21,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017187","count":1},{"id":"GO:0042373","count":1},{"id":"GO:0010207","count":1},{"id":"GO:0034244","count":1},{"id":"GO:0032968","count":1}]},{"hash":"655794174316718389","title":"Translational initiation and ribosome assembly","description":"This cluster is centered on the protein synthesis machinery and RNA-level regulation. Dominant GO terms include translation, formation of the translation preinitiation complex, regulation of translational initiation, and translation reinitiation, plus viral translation initiation/termination terms, indicating a core group of translation factors and initiation steps. Additional RNA regulatory processes appear, such as ncRNA-mediated gene silencing and regulation of mRNA splicing, suggesting broader RNA-based control of gene expression. A few outliers (e.g., transcription-coupled nucleotide-excision repair) are present but dilute the main theme. Overall, the label reflects a cohesive translation-focused cluster with RNA-regulatory roles.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0048026","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0075525","count":3},{"id":"GO:0075522","count":3}]},{"hash":"1707467919910131529","title":"Unknown","description":"The listed GO terms span diverse processes (DNA replication and telomerase assembly; plant secondary growth and phototransduction; hypoxia signaling and HIF-1alpha pathway; chemotaxis; xenobiotic response; immune regulation). There is no coherent single function tying the proteins together, so a specific label cannot be assigned.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006265","count":1},{"id":"GO:0080117","count":1},{"id":"GO:1905323","count":1},{"id":"GO:0009585","count":1},{"id":"GO:0070483","count":1}]},{"hash":"988005972771021067","title":"Cortical Neuron Development and Synaptic Signaling","description":"The top GO terms point to neural development and connectivity: cerebral cortex development, fasciculation of motor neuron axon, integrin-mediated signaling, long-term synaptic potentiation, and protein trans-autophosphorylation, all of which align with axon guidance, synaptic formation, and plasticity in cortical neurons. Some terms are obsolete or general, but the dominant signal is neuronal development and synaptic signaling.","confidence":"High","size":21,"edges":202,"triangles":1187,"max_degree":20,"top_function":"DNA repair","top_go_terms":[{"id":"GO:2001033","count":21},{"id":"GO:0097156","count":21},{"id":"GO:0007229","count":21},{"id":"GO:1990758","count":21},{"id":"GO:0021987","count":21}]},{"hash":"9701055964792394","title":"Translation initiation and mRNA turnover","description":"The cluster\u2019s top GO terms are dominated by cytoplasmic translation, formation of the translation preinitiation complex, translation reinitiation, and mRNA transport, along with deadenylation-dependent decay, pointing to a coherent theme around protein synthesis and RNA fate rather than a single signaling pathway. Some cell cycle terms appear, but the translation/mRNA processing terms are the strongest signal. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0001731","count":2}]},{"hash":"1400318683032810967","title":"Unknown","description":"The GO terms are highly diverse: protein ubiquitin-proteasome catabolic process, DNA repair, mRNA capping, and general stress responses appear alongside plant-specific processes such as sucrose transport, fructose export from vacuole, nectar secretion, and regulation of auxin signaling. The mixture lacks a single coherent biological function or pathway that would unify the cluster, so a universal label isn\u2019t possible beyond Unknown.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0090305","count":1},{"id":"GO:0006281","count":1},{"id":"GO:1902334","count":1},{"id":"GO:0015770","count":1}]},{"hash":"1389554666622802141","title":"Mitotic progression and cell division","description":"The cluster is dominated by mitosis- and cell cycle\u2013related GO terms: G1/S and G2/M transitions, cell division, spindle dynamics, and chromosome condensation, indicating proteins working together to regulate mitotic entry and progression. The presence of DNA-templated transcription supports coordinated gene expression for these processes, with mammary gland epithelial proliferation suggesting a proliferative context. Overall, a mitosis-centric cell cycle label best fits the enriched functions.","confidence":"High","size":21,"edges":17,"triangles":11,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":11},{"id":"GO:0000086","count":10},{"id":"GO:0000082","count":10},{"id":"GO:0051301","count":9},{"id":"GO:0033598","count":9}]},{"hash":"1402325899226460042","title":"Bacterial Methylation and Biosynthesis Enzymes","description":"The main GO terms point to methylation-related processes (tRNA methylation, rRNA methylation, peptidyl-arginine/glutamine methylation) along with vitamins and antibiotic biosynthesis (menaquinone, biotin, antibiotic biosynthetic process). This pattern suggests a cluster of enzymes involved in methylation modifications and biosynthetic pathways typical of bacterial metabolism. Other terms about xenobiotic response and tellurium ion response support a general stress/defense context rather than a single pathway, but the shared methylation/biosynthesis theme remains the strongest signal.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009234","count":2},{"id":"GO:0030488","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0017000","count":2}]},{"hash":"2236300520169378091","title":"ER-Golgi Vesicle Transport","description":"The top GO terms are dominated by COPII-coated vesicle budding and ER-Golgi transport (anterograde and retrograde), suggesting the cluster centers on secretory pathway components involved in vesicle trafficking between the ER and Golgi. While a few terms touch nuclear transport and transcription, the strongest signal is vesicle trafficking, supporting a cohesive label for secretory/trafficking machinery.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0031081","count":2},{"id":"GO:0090114","count":2}]},{"hash":"1755898401170145472","title":"Plant carbohydrate metabolism and detoxification","description":"Top terms indicate carbohydrate metabolism (cellulose and stilbene catabolism; raffinose biosynthesis) and detoxification (cellular oxidant detoxification; epoxygenase P450 pathway), with glycolysis also present. These collectively point to a cluster centered on carbohydrate processing and detox/ xenobiotic handling, with a plant biology bias suggested by the cellulose/raffinose/stilbene terms; a few outliers (receptor recycling, osteoblast development) are less representative but don't override the main theme.","confidence":"Medium","size":21,"edges":14,"triangles":2,"max_degree":12,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0030245","count":5},{"id":"GO:0097755","count":4},{"id":"GO:0046272","count":4},{"id":"GO:0046839","count":4},{"id":"GO:0098869","count":4}]},{"hash":"88947961307537868","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000472","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000056","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0006508","count":2}]},{"hash":"211815865004445346","title":"TLR signaling and macrophage inflammatory activation","description":"The cluster is dominated by GO terms tied to toll-like receptor signaling (TLR4/8/9/10), macrophage activation, and regulation of cytokine and chemokine production, all pointing to innate immune sensing and subsequent inflammatory responses. This cohesive theme suggests proteins involved in macrophage-driven inflammation triggered by TLR pathways. The floral meristem term appears irrelevant noise in this context. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050707","count":2},{"id":"GO:0032741","count":2},{"id":"GO:0032722","count":2},{"id":"GO:0042116","count":2},{"id":"GO:0034166","count":2}]},{"hash":"1946040256698794850","title":"Plant cell cycle and stress signaling","description":"This cluster centers on core cell cycle processes (cell division, APC-dependent catabolic process) and chromatin modification, while also including several stress- and hormone-related terms (unfolded protein response/ER stress, cadmium response, cytokinin signaling, and regulation of gibberellin signaling). The combination suggests proteins that connect cell cycle control with stress responses and hormone signaling in plants, so the name captures the main themes without being overly narrow.","confidence":"Medium","size":20,"edges":21,"triangles":13,"max_degree":8,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0016570","count":5},{"id":"GO:0006986","count":5},{"id":"GO:0009736","count":5},{"id":"GO:0071276","count":5}]},{"hash":"1088769901884773671","title":"Endocytic Transport and Organelle Dynamics","description":"The top GO terms are dominated by endocytosis-related processes (endocytosis, endocytic recycling, endosome to melanosome transport) and mitochondrial membrane organization, pointing to membrane trafficking and organelle maintenance. Additional terms on autophagy and cytoplasmic processes support a broader theme of organelle turnover and dynamics, while a few terms (locomotory behavior, phosphorylation regulation) are less central. Overall, the cluster seems best described by vesicle trafficking and organelle remodeling activities.","confidence":"Medium","size":20,"edges":18,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0008344","count":3},{"id":"GO:0006914","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0006972","count":2}]},{"hash":"226168864015567688","title":"RNA processing and mRNA export","description":"The cluster shows strong representation of RNA maturation and transport processes: mRNA capping (GO:0006370), poly(A)+ mRNA export (GO:0016973), splicing regulation (GO:0048026), and siRNA processing (GO:0030422). Although a couple of terms relate to plant development (trophectodermal differentiation, embryo sac development) which may be contextual or annotation noise, the dominant signal is RNA processing and export in the nucleus/cytoplasm.","confidence":"High","size":20,"edges":20,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0001829","count":1},{"id":"GO:0009553","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0016973","count":1}]},{"hash":"1081559784700401838","title":"Unknown","description":"The GO terms are a mix of development-related processes (face morphogenesis; embryonic process in female pregnancy) and oxidative/stress-response terms (cellular response to hydroperoxide, cadmium ion, nitroglycerin; regulation of S-nitrosylation), with no clear single function tying them together. The sparse connectivity (edges 2, triangles 0, max degree 1) suggests a lack of a cohesive biological theme, so a precise, representative label isn\u2019t feasible beyond Unknown.","confidence":"","size":20,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":1},{"id":"GO:1903204","count":1},{"id":"GO:0071447","count":1},{"id":"GO:1902083","count":1},{"id":"GO:0060136","count":1}]},{"hash":"862358142725136061","title":"TLR-Driven Innate Immune Signaling","description":"The cluster is dominated by GO terms for innate immune response, defense against viruses and Gram-positive bacteria, and multiple Toll-like receptor signaling pathways (TLR4, TLR8, TLR10), along with regulation of chemokine/cytokine production and inflammatory responses, indicating a cohesive theme of TLR-mediated innate immunity. The floral meristem term likely represents noise rather than a functional link to immunity.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":4},{"id":"GO:0051607","count":4},{"id":"GO:0032722","count":3},{"id":"GO:0034166","count":3},{"id":"GO:0010080","count":3}]},{"hash":"549866744817104851","title":"Vesicle trafficking and endocytosis","description":"The GO terms cluster around intracellular transport processes: endocytosis, retrograde Golgi-ER vesicle transport, protein targeting to vacuoles, tubulin-based trafficking, and regulation of vesicle exocytosis. These indicate a cohesive theme of vesicle trafficking and endomembrane sorting, despite a few noisy terms from unrelated contexts. ","confidence":"Medium","size":20,"edges":28,"triangles":10,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0031384","count":5},{"id":"GO:0010796","count":5},{"id":"GO:0007420","count":5},{"id":"GO:2000300","count":5},{"id":"GO:0051291","count":4}]},{"hash":"1364537976073836280","title":"Unknown","description":"The top GO terms describe many distinct processes across different biological contexts (RNA stability, metabolism, development, vesicle fusion, protein palmitoylation, fungal mating-type gene conversion, humoral immunity, DNA repair, immunoglobulin isotype switching, aging). There is no consistent pathway, process, or compartment linking these proteins, and the topology shows no connections (Edges 0, Triangles 0). Therefore, there isn't a coherent functional theme to name.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048255","count":2},{"id":"GO:0046168","count":1},{"id":"GO:0048733","count":1},{"id":"GO:0042144","count":1},{"id":"GO:0018230","count":1}]},{"hash":"1650883458873680018","title":"Intracellular transport and TORC1 signaling","description":"The top terms point to intracellular trafficking processes (mRNA transport; ER to Golgi vesicle transport; NLS-bearing protein import into nucleus) alongside regulation of signaling and phosphorylation (positive regulation of GTPase activity; serine/threonine kinase activity and autophosphorylation; TORC1 signaling), with a note of stress response (hypoxia) and cell cycle involvement. This suggests a theme of transport-linked growth/signaling regulation, centered on TORC1 pathways and vesicle trafficking.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051028","count":4},{"id":"GO:0043547","count":4},{"id":"GO:0038202","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0006888","count":3}]},{"hash":"149697434657055697","title":"Unknown","description":"The GO terms span immune signaling (TLR10 pathway, diacyl lipopeptide response, chemokine production), mechanosensing, neural synapse assembly, and diverse developmental processes (plant floral meristem growth, tooth mineralization), with no single unifying function apparent across the proteins.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0019800","count":2},{"id":"GO:0071726","count":2}]},{"hash":"1424898863898423594","title":"Nuclear transcription regulation and deubiquitination","description":"The top GO terms point to control of transcription from DNA (including regulation and general transcription) and processing of RNA, coupled with a set of ubiquitin-related processes (deubiquitination, monoubiquitinated protein deubiquitination, and ubiquitin-dependent proteolysis). This suggests a cohesive cluster centered on nuclear gene expression regulation and protein ubiquitination dynamics, with additional links to developmental and cell-death-related pathways.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0070537","count":2},{"id":"GO:0006511","count":2},{"id":"GO:1901026","count":2},{"id":"GO:0021551","count":2}]},{"hash":"835281558098137509","title":"Ammonium Transport and Nitrogen Utilization","description":"Based on the prominent GO terms for ammonium transmembrane transport and transepithelial ammonium transport, along with nitrogen utilization and its regulation, the proteins appear to cluster around ammonium/nitrogen transport and related metabolism. Additional terms like carbon dioxide transport and methylammonium transport support a transporter/metabolic theme, with developmental terms likely secondary. ","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0070634","count":3},{"id":"GO:0009791","count":3},{"id":"GO:0072488","count":2},{"id":"GO:0019740","count":2}]},{"hash":"1165271798088787257","title":"Metabolic Regulation and Stress Response","description":"Most terms point to metabolism (cobalamin biosynthesis, gluconeogenesis, fructose metabolism, glycolysis regulation, dephosphorylation). Additional entries show xenobiotic response and respiratory burst, i.e., stress responses. A couple of terms about brain development and cardiac apoptosis may be incidental. The common thread is metabolic regulation with associated stress-response functions.","confidence":"Medium","size":20,"edges":17,"triangles":0,"max_degree":17,"top_function":"autophagy","top_go_terms":[{"id":"GO:0009236","count":6},{"id":"GO:0016311","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0006094","count":4},{"id":"GO:0010666","count":4}]},{"hash":"1381826250844136744","title":"Integrin signaling and angiogenesis","description":"The cluster is enriched for integrin-mediated signaling, cell adhesion/spreading, and angiogenesis, along with PI3K/AKT pathway regulation and cholesterol biosynthesis, suggesting a cohesive set of adhesion-driven signaling proteins involved in vascular development and tissue remodeling. Some terms (cadmium response, pain) seem peripheral noise rather than core features.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0071276","count":3},{"id":"GO:0014850","count":3},{"id":"GO:0051897","count":3},{"id":"GO:0006695","count":3}]},{"hash":"1586390955525523835","title":"Unknown","description":"Top terms span diverse processes including energy metabolism (mitochondrial ATP synthase assembly; photosystem II assembly/repair), redox/homeostasis (glutathione biosynthesis/catabolism), proteolysis, leukotriene biosynthesis, and lipid signaling (phosphatidylinositol regulation). The lack of a single cohesive biological function tying these GO terms together suggests the cluster is heterogeneous, so a precise, representative name cannot be determined.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0033615","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0006750","count":1},{"id":"GO:1901750","count":1}]},{"hash":"1442953707880368821","title":"Mitochondrial dynamics and prenylated protein processing","description":"The top terms center on mitochondrial fusion regulation, CAAX-box protein processing, and prenylated protein catabolic processes, suggesting a functional link to organelle dynamics and post-translational modification. Some terms are obsolete in GO, but the recurring themes point to mitochondrial maintenance and prenylation pathways.","confidence":"Medium","size":19,"edges":14,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006998","count":2},{"id":"GO:0061077","count":2},{"id":"GO:0010637","count":2},{"id":"GO:0071432","count":2},{"id":"GO:0030327","count":2}]},{"hash":"957379433528646357","title":"Chromatin assembly and mitotic cell division","description":"The strongest signals are nuclear: DNA-templated transcription and CENP-A containing chromatin assembly, along with cell division and mitotic cell cycle, suggesting a core focus on chromatin organization and chromosome segregation. Protein homooligomerization may reflect complex formation tied to transcription/chromatin functions, while other terms appear less central. Thus the label highlights the predominant theme of chromatin assembly linked to mitosis.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0051260","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0015886","count":4}]},{"hash":"1459390065327916671","title":"General cellular signaling and gene expression","description":"This cluster combines core gene-expression processes (mRNA processing, transcription, cytoplasmic translation) with several signaling pathways (T cell receptor signaling, insulin receptor signaling) and other varied cellular processes, suggesting a broad, multi-functional set of proteins rather than a single specific function.","confidence":"Medium","size":19,"edges":5,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006397","count":4},{"id":"GO:0050852","count":4},{"id":"GO:0000278","count":4},{"id":"GO:0016032","count":3},{"id":"GO:0008286","count":3}]},{"hash":"126191790739308697","title":"Diverse Substrate Membrane Transporters","description":"This cluster ties together GO terms for transmembrane transport of a broad range of substrates\u2014ions (potassium), vitamins, sugars (galactose, arabinose), nitrate, phosphate, sialic acid, xenobiotics, and neurotransmitter loading into synaptic vesicles\u2014suggesting a common theme of membrane-spanning transport proteins with varied substrate specificities.","confidence":"High","size":19,"edges":20,"triangles":2,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0035461","count":3},{"id":"GO:0098700","count":3},{"id":"GO:0015739","count":3},{"id":"GO:0006855","count":3}]},{"hash":"915399726444393385","title":"Unknown","description":"The top GO terms span diverse biological areas (vitellogenesis, cobalamin biosynthesis, transcription regulation, rDNA heterochromatin, RNA/tRNA/rRNA methylation, spermidine biosynthesis, miRNA transcription, T helper 2 differentiation, muscle stretch response). There isn't a single coherent function linking the majority of terms, so a concise, representative label cannot be determined.","confidence":"","size":19,"edges":147,"triangles":724,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0007296","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0000183","count":3},{"id":"GO:0070476","count":3}]},{"hash":"1737044672175059891","title":"RNA Pol II Transcription Machinery","description":"Most frequent terms describe transcription by RNA polymerase II (GO:0006366, GO:0006367) and initiation at Pol II promoters (GO:0006367), plus related transcription processes such as termination and antitermination (GO:0006363, GO:0031564). The inclusion of transcription-coupled nucleotide-excision repair (GO:0006283) supports a transcription-centric functional theme. A few other terms (oxidation-reduction, prostaglandin biosynthesis, methylation) appear less connected and may be ancillary. Overall, the cluster centers on RNA Pol II transcription and its regulation.","confidence":"High","size":19,"edges":74,"triangles":174,"max_degree":14,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0001516","count":3},{"id":"GO:0032259","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0006379","count":3}]},{"hash":"3776845404475435","title":"Sugar and small-molecule transport","description":"The proteins are enriched for transmembrane transport of sugars and related solutes (glucose, xylose, fructose, lactose biosynthesis, organic anions, xenobiotics), plus cellular responses to osmotic stress and glucose starvation. This pattern points to a membrane transporter module handling sugar uptake and related solute transport, with regulatory ties to nutrient status. Therefore, \u201cSugar and small-molecule transport\u201d captures the shared function of the cluster.","confidence":"High","size":19,"edges":118,"triangles":335,"max_degree":18,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:1904659","count":3},{"id":"GO:0043252","count":3},{"id":"GO:0044381","count":3},{"id":"GO:0005989","count":3},{"id":"GO:0015753","count":3}]},{"hash":"350626937348941299","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":14,"triangles":2,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0006986","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0071374","count":3},{"id":"GO:0046825","count":3}]},{"hash":"906282373546782731","title":"Unknown","description":"The listed GO terms span splicing, plant sepal formation, leukocyte migration, lipid droplet organization, and several viral-related processes, with no clear common function binding them. This lack of a cohesive theme makes a specific label inappropriate.","confidence":"","size":19,"edges":22,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0050900","count":1},{"id":"GO:0034389","count":1},{"id":"GO:0075713","count":1}]},{"hash":"942169067884088953","title":"Chromatin remodeling and transcription regulation","description":"The cluster is enriched for DNA-templated transcription, chromatin remodeling, and heterochromatin formation, suggesting a shared function in regulating chromatin state and gene expression; histone modification terms (even if deprecated) reinforce chromatin regulation, with some auxiliary terms possibly reflecting broader cellular stress links.","confidence":"High","size":19,"edges":37,"triangles":5,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060195","count":2},{"id":"GO:0043984","count":1},{"id":"GO:0006338","count":1},{"id":"GO:0006342","count":1}]},{"hash":"334497666785865294","title":"Diverse Transmembrane Transporters","description":"The top GO terms all point to transmembrane transport activities for a wide range of substrates (xenobiotics, nitrite/nitrate, phosphate, sugars, and various ions), suggesting these proteins form a cluster of membrane transporters with broad substrate specificity.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":2},{"id":"GO:0015707","count":1},{"id":"GO:0015706","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0015751","count":1}]},{"hash":"2034004207816076305","title":"Ribosome Biogenesis and RNA Modification","description":"The terms are dominated by ribosome biogenesis and translation, plus RNA modification processes such as rRNA and snRNA pseudouridine synthesis and rRNA processing, pointing to a nucleolar/RNA maturation role. Telomere maintenance via telomerase and Cajal body localization add a nuclear RNA-processing dimension, while a few terms about viral assembly appear as peripheral signals. Overall, the core cluster represents ribosome assembly and RNA modification functions.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0031118","count":1},{"id":"GO:0000469","count":1}]},{"hash":"1772032566610282221","title":"Nucleolar RNA processing and ribosome biogenesis","description":"The dominant terms are nucleolus organization, rRNA processing, and ribosomal large subunit biogenesis, pointing to nucleolar RNA processing and ribosome production. Additional RNA-regulation terms (ncRNA-mediated silencing, splicing regulation) reinforce an RNA-centric nuclear function, with some development-related terms (eye-antennal disc) suggesting a developmental context. Overall, the cluster centers on nuclear RNA processing and ribosome biogenesis with related gene-regulatory roles.","confidence":"High","size":19,"edges":9,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0031047","count":2},{"id":"GO:0000381","count":2},{"id":"GO:0061408","count":2},{"id":"GO:0045572","count":1},{"id":"GO:0035214","count":1}]},{"hash":"1468083146271526788","title":"RNA splicing and mRNA processing","description":"This cluster is dominated by spliceosome-related mRNA splicing terms (including general splicing, via spliceosome, and regulatory ncRNA-mediated silencing), plus mRNA export and translation initiation/reinitiation, with supporting rRNA processing steps. Together these terms point to a cohesive role in RNA processing, maturation, and initiation of translation. ","confidence":"High","size":19,"edges":46,"triangles":54,"max_degree":11,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0006378","count":6},{"id":"GO:0006406","count":4},{"id":"GO:0045292","count":4}]},{"hash":"1539956220330368066","title":"Diverse membrane transporters and secretion proteins","description":"This cluster is dominated by GO terms related to transport across membranes and secretion systems (amino acid and thiamine transport, glycerophosphodiester and heme transport, long-chain fatty acid import into peroxisomes, branched-chain amino acid transport, teichoic acid transport, and protein secretion by the Type I secretion system). The presence of antibiotic response may reflect efflux-related resistance, reinforcing the membrane-associated theme across bacteria and possibly eukaryotes. Overall, these terms point to a cohesive function in membrane transport and secretion rather than a single substrate.","confidence":"High","size":19,"edges":20,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":3},{"id":"GO:0015777","count":2},{"id":"GO:0003333","count":2},{"id":"GO:0030253","count":2},{"id":"GO:0015910","count":2}]},{"hash":"1147457649397729096","title":"Metal and Oxidative Stress Transcriptional Response","description":"The cluster shows enrichment for DNA-templated transcription and several stress-related GO terms, including cellular response to cadmium and copper ions, singlet oxygen, and nitroglycerin, suggesting a coordinated transcriptional response to metal ion and oxidative stress. Some obsolete terms appear but the core theme is stress-induced transcriptional regulation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0060136","count":2},{"id":"GO:0043497","count":2},{"id":"GO:2001033","count":2},{"id":"GO:1904843","count":2}]},{"hash":"1687704941968196253","title":"Heat Stress Response and Protein Quality Control","description":"The top GO terms center on responding to heat, regulating heat responses, and organizing protein folding/targeting (including post-translational targeting to membranes and inclusion body regulation), which points to a cluster of proteins involved in quality control and maturation under heat stress. Additional terms for iron-sulfur cluster assembly and DNA replication suggest a broader role in maintaining essential processes during stress. Overall, the cluster likely reflects heat-induced protein quality control and maturation pathways.","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0031204","count":2},{"id":"GO:0009408","count":2},{"id":"GO:1900035","count":2},{"id":"GO:0070389","count":2}]},{"hash":"1425796613544057110","title":"Translation and RNA Metabolism","description":"This cluster is dominated by translation-related GO terms (translation, translational initiation, elongation, termination, and selenocysteine incorporation) and RNA turnover (deadenylation-dependent decay), pointing to a common function in protein synthesis and RNA processing/regulation. While a few terms touch on other processes (cell cycle, antibiotic response, glial proliferation), the core signal centers on gene expression machinery. ","confidence":"Medium","size":19,"edges":5,"triangles":0,"max_degree":4,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0009103","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0045901","count":3}]},{"hash":"2043595402770079774","title":"DNA-templated transcription and metal/oxidative stress responses","description":"The top term is DNA-templated transcription, supported by additional GO terms indicating responses to metals (cadmium, copper), oxidative stress (singlet oxygen), and related chemical stimuli, suggesting a cluster centered on transcriptional regulation linked to metal/oxidative stress responses. Some terms are obsolete, and there are no network edges, but the core theme appears to be transcriptional activity combined with environmental stress response.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0060136","count":2},{"id":"GO:0043497","count":2},{"id":"GO:2001033","count":2},{"id":"GO:1904843","count":2}]},{"hash":"158522522594869291","title":"Peroxisomal protein import","description":"The cluster is dominated by GO terms related to targeting and importing proteins into the peroxisome matrix (protein targeting to peroxisome, docking, and substrate release), pointing to a cohesive function in peroxisomal protein import machinery. Other single-term annotations appear incidental rather than defining the core function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009561","count":1},{"id":"GO:0034453","count":1},{"id":"GO:0006516","count":1},{"id":"GO:0006625","count":1},{"id":"GO:0016560","count":1}]},{"hash":"537186759534372496","title":"Vertebrate Developmental Signaling Regulators","description":"The top GO terms point to regulatory roles in vertebrate development and signaling (Wnt and TGF-\u03b2 pathways, neuron differentiation, lung development) with both positive and negative regulation of signaling, plus links to development and immune-related contexts. This suggests a cluster of proteins that modulate developmental signaling and differentiation rather than a single pathway. ","confidence":"Medium","size":19,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0043525","count":2},{"id":"GO:0030182","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0030512","count":2}]},{"hash":"1844376082425675410","title":"Core Gene Expression and Genome Maintenance","description":"The top GO terms cluster around ribosome biogenesis, translation, and translation initiation, with accompanying terms for transcription and DNA replication/repair, suggesting a central cellular machinery that coordinates gene expression and genome maintenance. Additional terms about ER-Golgi transport reflect general protein processing roles in biosynthetic pathways, supporting a broad but cohesive core of expression and genome-related functions.","confidence":"Medium","size":19,"edges":43,"triangles":69,"max_degree":12,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":4},{"id":"GO:0006412","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006283","count":3},{"id":"GO:0045053","count":3}]},{"hash":"1128822178283061747","title":"Heart Development and Cell Adhesion","description":"The cluster centers on cardiac morphogenesis and related cell adhesion processes, with terms like sinoatrial node cell development and cell migration in heart development, as well as epithelial adhesion and adhesion-dependent spreading. While translation and ER protein folding appear among the terms, the strongest signal is heart development and tissue adhesion, suggesting this group functions in cardiac tissue formation and morphogenesis with associated cell\u2013ECM/cell\u2013cell interactions.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0007519","count":1},{"id":"GO:0060931","count":1},{"id":"GO:0002244","count":1}]},{"hash":"1386198915098781579","title":"MAPK-Wnt-Hippo Signaling and Apoptosis","description":"The top GO terms indicate a strong leaning toward major cell signaling pathways (p38MAPK, ERK cascades, canonical Wnt, Hippo) and programmed cell death, suggesting the proteins function in signaling networks that govern cell fate and apoptosis. Other terms like keratinocyte differentiation and, to a lesser extent, DNA replication and ion transport, appear as ancillary processes but do not redefine the central theme. Therefore, a label emphasizing these signaling axes and apoptosis best describes the cluster.","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006915","count":9},{"id":"GO:0090263","count":9},{"id":"GO:0038066","count":9},{"id":"GO:0006260","count":9},{"id":"GO:0033129","count":9}]},{"hash":"256030309738306547","title":"Central Carbon Metabolism and Amino-Acid Catabolism","description":"This cluster centers on glycolysis and the TCA cycle with glyoxylate and various amino-acid catabolic pathways, indicating a cohesive energy-generation/metabolism module. The presence of Notch signaling is likely an annotation artifact or outliers, while the dominant metabolic terms support Central Carbon Metabolism as the core theme.","confidence":"High","size":19,"edges":164,"triangles":855,"max_degree":18,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006096","count":6},{"id":"GO:0006099","count":6},{"id":"GO:0009436","count":5},{"id":"GO:0033512","count":5},{"id":"GO:0097053","count":5}]},{"hash":"708419089003628864","title":"Lysosomal Transport and Autophagy","description":"This cluster is dominated by GO terms tied to lysosome targeting, Golgi-to-lysosome transport, and endosomal transport, with aggrephagy highlighting autophagic clearance. Together these point to a core lysosome/endosome trafficking and degradation function, with a secondary, less central association to specific metabolic processes. ","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006622","count":2},{"id":"GO:0090160","count":2},{"id":"GO:0000103","count":2},{"id":"GO:0046656","count":2},{"id":"GO:0016197","count":1}]},{"hash":"1731565531595870858","title":"Unknown","description":"The top GO terms cover a mix of oxygen homeostasis and prolyl hydroxylation, redox processes, plus developmental, ECM, trafficking, and metabolism functions, with no single coherent theme tying all 19 proteins together. The lack of edges and a unified pathway makes it unclear what high-level function defines this cluster, so an Unknown label is appropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032364","count":2},{"id":"GO:1901874","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0046712","count":1}]},{"hash":"255502222384216523","title":"Cell Cycle and Telomere Maintenance with TOR Signaling","description":"The cluster shows a coherent emphasis on cell division, telomere maintenance, and TOR pathway signaling (TORC1/2), along with mitotic DNA replication checkpoints and chromosome localization, suggesting coordination of cell cycle progression with genome integrity and growth signaling. A few terms like social behavior may be annotation noise, but the dominant theme supports a cell-cycle/genome maintenance function linked to TOR signaling.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0007004","count":2},{"id":"GO:0038202","count":2},{"id":"GO:0045945","count":2},{"id":"GO:0035176","count":2}]},{"hash":"522041545480863985","title":"Calcium signaling and mitochondrial regulation","description":"The cluster is dominated by terms tied to calcium handling and mitochondrial function: regulation of mitochondrial membrane potential, SR/ER-mediated calcium release, and negative regulation of RyR calcium-release channels, plus pathways linking calcium signaling to insulin secretion. Other terms like transport substrates or olfactory perception appear less coherent with this core theme, suggesting some noise but a clear calcium-mitochondrial regulation signal overall.","confidence":"High","size":18,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":3},{"id":"GO:0051881","count":3},{"id":"GO:0061179","count":3},{"id":"GO:0010880","count":3},{"id":"GO:0007608","count":3}]},{"hash":"1093039081011655885","title":"Unknown","description":"The top GO terms show a broad mix: apoptosis, responses to various stimuli (fungicide, selenium ion, lipopolysaccharide), neurotransmitter regulation, and even pituitary gland development; several terms are obsolete. There is no unifying biological process or pathway that clearly links these proteins, so a concise, representative label cannot be assigned.","confidence":"","size":18,"edges":11,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042135","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0014063","count":2},{"id":"GO:0060992","count":2}]},{"hash":"1729922397401930919","title":"RNA Splicing Regulation and mRNA Processing","description":"The cluster centers on spliceosome-mediated regulation of splicing (negative, positive, alternative) and related RNA-processing steps (poly(A) tail regulation, mRNA export), with ancillary signals of translation control (eIF4F complex assembly, miRNA-mediated silencing). This combination points to a cohesive theme of post-transcriptional RNA processing and gene expression regulation.","confidence":"High","size":18,"edges":10,"triangles":0,"max_degree":5,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048025","count":3},{"id":"GO:0000380","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0060211","count":3},{"id":"GO:1902625","count":3}]},{"hash":"618260107166386609","title":"Iron uptake and endocytosis","description":"This cluster centers on iron handling and membrane trafficking: terms for intracellular iron ion homeostasis, iron import across the plasma membrane, and transferrin transport suggest uptake and intracellular iron management. The presence of endocytosis and membrane-associated processing (receptor-mediated endocytosis; ERAD-related glycoprotein trimming; proteolysis) supports a theme of membrane trafficking and protein turnover linked to iron handling. A plant-specific term (stomatal complex morphogenesis) is noted but does not dominate the set.","confidence":"Medium","size":18,"edges":15,"triangles":0,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0006879","count":1},{"id":"GO:0010103","count":1},{"id":"GO:1904382","count":1},{"id":"GO:0031293","count":1},{"id":"GO:0035609","count":1}]},{"hash":"138339623181591236","title":"Transmembrane Transport of Ions and Metabolites","description":"The terms show multiple transmembrane transport processes for a variety of substrates including nitrite, nitrate, phosphate ion, sodium, potassium, arabinose, sialic acid, fucose, and xenobiotics, plus nitrate assimilation. This convergence on membrane transport across diverse substrates indicates a cluster of transport proteins acting in uptake/efflux of ions and metabolites. Therefore a broad transporter-related label is appropriate.","confidence":"High","size":18,"edges":22,"triangles":4,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":4},{"id":"GO:0015707","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0015751","count":3},{"id":"GO:0071805","count":3}]},{"hash":"710469803401129610","title":"ER-Golgi trafficking and protein quality control","description":"The cluster centers on processes in the secretory pathway, including ER-to-Golgi and Golgi-to-ER vesicle transport, ER protein folding, ER-associated degradation (ubiquitin-dependent), and general protein ubiquitination. These terms point to the ER-Golgi trafficking machinery and its quality-control functions, with additional relevance from related transport steps like Golgi to vacuole transport and even ribosome biogenesis as a broad cellular context. Some terms (pigmentation, defense response) appear less directly related and may reflect annotation noise in a small set. Overall, the dominant theme is ER-Golgi processing and protein quality control.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0030433","count":2}]},{"hash":"733142025107777700","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0035019","count":2},{"id":"GO:0043486","count":2},{"id":"GO:0048254","count":1},{"id":"GO:0000472","count":1}]},{"hash":"364814134775791871","title":"Unknown","description":"The GO terms are highly diverse\u2014xenobiotic and antibiotic responses, development (lung and spermatid nuclei), vesicle transport, apoptosis regulation, GTPase signaling, dephosphorylation, and metabolism\u2014offering no single dominant function; thus there is no unambiguous label for the cluster.","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0035690","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0007289","count":2},{"id":"GO:0006888","count":2}]},{"hash":"1672413772235899182","title":"Chromatin regulation and transcription control","description":"The top GO terms point to chromatin organization and transcription regulation, including DNA-templated transcription, heterochromatin formation/maintenance, nucleosome density regulation, and peptidyl-lysine deacetylation. These together suggest a cluster of proteins involved in chromatin remodeling and transcriptional control, with supportive signals from related processes like miRNA transcription regulation and immune gene regulation. Some terms are legacy/obsolete, but the core theme remains chromatin modification and transcriptional control.","confidence":"High","size":18,"edges":145,"triangles":694,"max_degree":17,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0045820","count":8},{"id":"GO:0060303","count":8},{"id":"GO:0000183","count":8},{"id":"GO:0034983","count":8}]},{"hash":"63731580495055829","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":5,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0033317","count":1},{"id":"GO:2001009","count":1},{"id":"GO:0009663","count":1},{"id":"GO:0009831","count":1}]},{"hash":"1058825945266598520","title":"TLR Signaling and Inflammation","description":"The dominant terms point to toll-like receptor signaling (TLR4, TLR8, TLR10) and related innate immune responses, including cellular response to diacyl bacterial lipopeptides, positive regulation of chemokine production, and inflammatory responses. This suggests the proteins cluster around TLR-driven innate immunity and inflammation, with a few outlier terms (e.g., floral meristem growth) likely to be annotation noise or cross-species artifacts.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019800","count":1},{"id":"GO:0071726","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0034166","count":1},{"id":"GO:0010080","count":1}]},{"hash":"1866103294567030647","title":"Neural development and synaptic signaling","description":"This cluster prominently features terms tied to nervous system development, synaptic potentiation, calcium-dependent exocytosis, and transcriptional regulation, pointing to a coordinated neural development/synaptic signaling theme. While DNA replication and transcription are broader, their presence alongside nervous system\u2013specific terms suggests cells undergoing developmental transcriptional programs that support neural differentiation and function; a few terms like pseudohyphal growth are outliers but do not override the core neural-related pattern.","confidence":"Medium","size":18,"edges":37,"triangles":28,"max_degree":10,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":8},{"id":"GO:0019233","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0060291","count":6}]},{"hash":"478920985141722375","title":"Histone modification and chromatin regulation","description":"This cluster is dominated by GO terms related to histone modification, including histone H3-K36 dimethylation and H3-K9 acetylation, as well as histone exchange and various acetylation/deacetylation activities. Although a few terms touch on unrelated processes, the recurring theme is chromatin remodeling and histone modification, suggesting these proteins function in regulating chromatin state. The signal is strong enough to assign this label with high confidence.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097676","count":2},{"id":"GO:0043970","count":1},{"id":"GO:0060765","count":1},{"id":"GO:0005987","count":1},{"id":"GO:1905524","count":1}]},{"hash":"17892556627885325","title":"Unknown","description":"The top GO terms include immune co-stimulation, melanocyte proliferation/apoptosis, neural/behavioral processes, host-symbiont entry, and detoxification, which don\u2019t converge on a single cohesive function; with only one edge and no clustering signal, a precise, representative label isn\u2019t discernible.","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell adhesion","top_go_terms":[{"id":"GO:0008284","count":5},{"id":"GO:0098869","count":5},{"id":"GO:0035641","count":4},{"id":"GO:0097325","count":4},{"id":"GO:1902362","count":4}]},{"hash":"1138479339529013964","title":"Central Metabolism and Lipid Biosynthesis","description":"This cluster shows enrichment for core metabolic and biosynthetic processes: TCA cycle, amino acid catabolism (L-alanine, L-kynurenine), and fatty acid/long-chain fatty acid biosynthesis, plus antibiotic biosynthetic activity, suggesting a group of proteins involved in fundamental metabolism and lipid production, with some regulatory or signaling terms (cAMP response, Notch) appearing as ancillary connections.","confidence":"Medium","size":18,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0097053","count":4},{"id":"GO:0042853","count":4},{"id":"GO:0007219","count":4}]},{"hash":"898605041193955818","title":"Neural Development and Genome Regulation","description":"The cluster contains neural development terms (cerebral cortex development, embryonic cranial skeleton morphogenesis, motor neuron axon fasciculation) alongside core genome regulation terms (DNA replication, DNA-templated transcription, regulation of nuclear export, and DNA repair), suggesting a set of regulatory proteins coordinating neural development with genome and cell-cycle control.","confidence":"Medium","size":18,"edges":113,"triangles":380,"max_degree":17,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":17},{"id":"GO:0048701","count":17},{"id":"GO:0006351","count":16},{"id":"GO:0046826","count":16},{"id":"GO:2001033","count":15}]},{"hash":"171065835884928587","title":"Ubiquitin-Dependent Proteolysis","description":"This cluster centers on ubiquitin-driven protein turnover, with multiple terms for ubiquitin-dependent degradation, autoubiquitination, K48-linked ubiquitination, and ERAD. Additional terms for Wnt receptor catabolic process and peroxisome import reflect regulated protein turnover and trafficking; dosage compensation and V(D)J recombination hint broader ubiquitin roles in chromatin and immune processes. Overall, the dominant theme is ubiquitin-mediated proteolysis and quality control.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0038018","count":4},{"id":"GO:0016558","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0060816","count":4}]},{"hash":"36395915087926301","title":"Diverse metabolite biosynthesis","description":"The Top Terms show biosynthetic processes for menaquinone, ectoine, biotin, antibiotics, and related compounds, plus related fatty acid metabolism terms. This suggests a theme of enzymes involved in producing a range of metabolites rather than a single pathway, so a label like Diverse metabolite biosynthesis captures the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009234","count":4},{"id":"GO:0019491","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0009102","count":3}]},{"hash":"18039425264344716","title":"Oxidative stress response and lignin metabolism","description":"GO terms indicate detoxification of oxidants and oxidative stress response and hydrogen peroxide catabolic processes, plus plant-type cell wall organization and lignin catabolic processes, suggesting a plant defense module involving ROS management and cell wall remodeling; some tRNA aminoacylation terms appear but are likely incidental and do not alter the main theme.","confidence":"High","size":18,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0006979","count":3},{"id":"GO:0042744","count":3},{"id":"GO:0009664","count":3}]},{"hash":"116440150997786188","title":"Unknown","description":"The top GO terms span sensory perception (pain, thermoception), germ-line and meiotic processes, metal-sulfur cluster metabolism, and neuronal differentiation, with no single unifying function for all proteins. Because the cluster lacks a coherent common theme, a specific, representative label cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050966","count":2},{"id":"GO:0048136","count":2},{"id":"GO:0010032","count":2},{"id":"GO:0016226","count":1},{"id":"GO:0031162","count":1}]},{"hash":"552461534786065489","title":"Unknown","description":"The GO terms span many unrelated processes (protein oligomerization, nutrient response, transcription, differentiation, ubiquitination, viral latency, etc.), with no clear, cohesive function linking the proteins. Several terms are obsolete or weakly connected, so a specific label isn\u2019t justifiable.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0007584","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0036268","count":1}]},{"hash":"1538901061272295714","title":"Unknown","description":"The GO terms are highly diverse and show no clear, single biological theme: redox homeostasis, mRNA stability regulation, fat pad development, chromatin-related methylation (obsolete terms), chaperone-associated refolding (obsolete), spindle assembly, glycogen regulation, hemolytic activity in another organism, and xenobiotic response. With zero edges and several obsolete annotations, there is no cohesive function tying the proteins together, so a meaningful, specific label cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0043488","count":2},{"id":"GO:0060613","count":2},{"id":"GO:0061087","count":2},{"id":"GO:0070389","count":2}]},{"hash":"90681288602916281","title":"Nuclear RNA Processing and Decay","description":"The GO terms are dominated by nuclear RNA processing, surveillance, and decay processes (nonsense-mediated decay, snoRNA processing, histone mRNA decay, rRNA decay pathways, and nuclear polyadenylation-dependent rRNA decay) along with regulation of transcription elongation by RNA Pol II, suggesting a function centered on nuclear RNA metabolism and transcription control. A couple of terms (embryonic placenta development, mitotic cell cycle traversal point) are less directly related to this core theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001892","count":2},{"id":"GO:0070651","count":1},{"id":"GO:0043144","count":1},{"id":"GO:0071028","count":1},{"id":"GO:0034244","count":1}]},{"hash":"2299998510302865629","title":"Lipid catabolism and endocannabinoid signaling","description":"Most prominent GO terms point to lipid metabolism: triglyceride catabolic process, monoacylglycerol catabolic process, phosphatidylserine catabolic process, and regulation of endocannabinoid signaling pathway appear with multiple annotations. A few transcription-related and developmental terms may reflect multifunctional roles or annotation noise, but the core signature is lipid catabolism and lipid signaling. Thus, a label 'Lipid catabolism and endocannabinoid signaling' captures the dominant theme with reasonable confidence.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0006660","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0052651","count":2},{"id":"GO:0019433","count":2}]},{"hash":"46735848061034403","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":73,"triangles":152,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:0000398","count":6},{"id":"GO:0000462","count":6},{"id":"GO:0048568","count":6},{"id":"GO:0000463","count":6}]},{"hash":"502242589294519928","title":"Organelle genome maintenance and oxidative proteostasis","description":"This cluster combines DNA replication and regulation of mitochondrial DNA replication with peroxisomal protein import, chaperone-mediated assembly, and oxidative stress response. The mix suggests a cohesive theme around maintaining organelle genome integrity while preserving organelle proteostasis under oxidative conditions. The network connectivity supports a functional grouping of organelle maintenance and stress-response processes.","confidence":"Medium","size":17,"edges":60,"triangles":70,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0090296","count":6},{"id":"GO:0016558","count":6},{"id":"GO:0051131","count":6},{"id":"GO:0034599","count":6}]},{"hash":"677549528232235898","title":"Cellular maintenance and stress responses","description":"GO terms include autophagosome maturation, peroxisome matrix import and receptor recycling, UV-damage repair, stress granule disassembly, plus cell division and cell wall organization, indicating a set of housekeeping and organelle quality-control functions under stress.","confidence":"Medium","size":17,"edges":9,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0070651","count":2},{"id":"GO:0090296","count":2},{"id":"GO:0000733","count":2}]},{"hash":"1384033288723555287","title":"Yeast mitosis, spindle dynamics, and RNA export","description":"This cluster's terms emphasize yeast-specific cell division and cytoskeletal functions (karyogamy, SPB separation, actomyosin ring assembly, plus-end microtubule activities) alongside RNA metabolism processes (mRNA export, transcription regulation, stress granule disassembly). The combined signals point to a cohesive theme of coordinating cell division with RNA processing/export in yeast.","confidence":"Medium","size":17,"edges":109,"triangles":367,"max_degree":16,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000742","count":7},{"id":"GO:0016973","count":6},{"id":"GO:0045944","count":6},{"id":"GO:0031535","count":6},{"id":"GO:0000073","count":6}]},{"hash":"980523352038897650","title":"Unknown","description":"The GO terms are diverse, spanning oxidative stress response and detoxification as well as plant/fungal metabolism (lignin breakdown, cell wall organization, and sterol/carotenoid biosynthesis), with no single cohesive function tying the proteins together.  ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":1},{"id":"GO:0006979","count":1},{"id":"GO:0042744","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0009664","count":1}]},{"hash":"653898273448389267","title":"RNA Processing and Stress Response","description":"This cluster centers on RNA metabolism and quality control under stress, with GO terms for transcription and several rRNA decay/catabolic processes, accompanied by stress responses (unfolded protein response, cadmium ion response) and a minor link to innate immunity, suggesting a module coordinating RNA processing with stress signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0008283","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0045087","count":2}]},{"hash":"275080544402810763","title":"Cardiac signaling and intracellular transport","description":"The cluster includes GO terms tied to cardiac muscle signaling (e.g., Purkinje-to-ventricular signaling, hypertrophy in response to stress, regulation of contraction), calcium handling (Ca2+ release from the sarcoplasmic reticulum), and vesicle trafficking/exocytosis, plus some broader intracellular transport and GTPase regulation. While there are a few terms about nuclear transport and mRNA transport, the strongest pattern centers on signaling and transport processes within cardiac and related cells, justifying a label around cardiac signaling and intracellular transport.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0006607","count":2},{"id":"GO:1900242","count":1},{"id":"GO:0086004","count":1}]},{"hash":"1017836831749032502","title":"Stress-Responsive Transcriptional Regulation","description":"These proteins show enrichment for transcriptional control (DNA-templated transcription; RNA polymerase II regulation) and cellular responses to stressors (dexamethasone, cocaine, cardiac hypertrophy in stress) plus dendrite development, suggesting a theme of transcriptional regulation linked to stress-induced differentiation and development.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070314","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0031060","count":1},{"id":"GO:0045944","count":1}]},{"hash":"1784614933505553549","title":"NF-\u03baB Activation and Transcription Control by Ubiquitin-Proteasome","description":"The GO terms center on transcriptional regulation and NF-\u03baB signaling, especially I-kappaB phosphorylation and proteasomal degradation, which together enable NF-\u03baB\u2013driven gene expression. Additional terms about ufmylation and ER-related regulation suggest broader protein quality control and signaling links to transcription. Overall, the cluster seems to represent transcriptional regulation coordinated by ubiquitin-proteasome\u2013mediated NF-\u03baB pathway control, with some ER-associated regulatory themes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071480","count":2},{"id":"GO:1903721","count":1},{"id":"GO:0033146","count":1},{"id":"GO:1990592","count":1}]},{"hash":"201805742001613993","title":"Cerebellar glutamatergic signaling and granule neuron differentiation","description":"The cluster is dominated by neural terms: glutamatergic synaptic transmission, excitatory postsynaptic potentials, and cerebellar granule cell differentiation, along with a note on visual learning. This combination points to a cerebellar neuron development and synaptic signaling theme, especially involving glutamatergic signaling at excitatory synapses. Some terms about telomere maintenance and cell cycle appear but do not define the primary function of the cluster.","confidence":"High","size":17,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0043113","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0008542","count":2},{"id":"GO:0021707","count":2}]},{"hash":"1118858870279201315","title":"Ribosome Biogenesis and Translation","description":"The cluster shows strong signals for ribosome-related processes: maturation of LSU rRNA and 5.8S rRNA, ribosomal large subunit biogenesis, and multiple translation-related terms (translation, cytoplasmic translation, and mRNA capping), along with nonsense-mediated decay. While a DNA replication term appears, the dominant pattern is RNA processing and ribosome assembly/translation, suggesting a core function in ribosome biogenesis and protein synthesis.","confidence":"Medium","size":17,"edges":12,"triangles":1,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0042273","count":2},{"id":"GO:0006283","count":2}]},{"hash":"1095589083257735757","title":"Protein Synthesis and Trafficking","description":"The top GO terms cluster around cytoplasmic translation, protein processing, and ER-to-Golgi vesicle transport, pointing to roles in protein production and intracellular trafficking. Additional terms touch on lipid transport and stress-related RNA dynamics, which fit under broader cellular homeostasis rather than a single specialized pathway. Overall, the strongest common theme is production/processing and routing of proteins (and related components) within the cell.","confidence":"Medium","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0015910","count":3},{"id":"GO:0035617","count":3},{"id":"GO:0001407","count":3},{"id":"GO:0015886","count":3}]},{"hash":"832209681221563566","title":"Innate Immune Response and Interferon Signaling","description":"The cluster shows strong enrichment for innate immune processes: lipopolysaccharide signaling, defense against bacteria, innate immune response, response to dsRNA, and positive regulation of interferon-beta production, indicating a cohesive immune signaling role. Some other terms appear unrelated (e.g., mesoderm formation), but the dominant theme is innate immunity and interferon pathways. ","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031663","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0045087","count":3},{"id":"GO:0043330","count":3},{"id":"GO:0045359","count":3}]},{"hash":"159585132398794337","title":"Androgen-signaling and male reproductive development","description":"Prominent GO terms include prostate gland development, male sex differentiation, and steroid hormone receptor complex assembly, which together point to a theme of androgen signaling and male reproductive development. However, the cluster also contains several broader or unrelated terms (nonsense-mediated decay, protein peptidyl-prolyl isomerization, cell division, axon regeneration, smooth muscle contraction), which weakens the cohesion and lowers confidence in the single-theme interpretation.","confidence":"Low","size":17,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":3},{"id":"GO:0032508","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0048680","count":2},{"id":"GO:0006939","count":2}]},{"hash":"15717376623525815","title":"Stress-Responsive Gene Expression and Metabolism","description":"This cluster centers on regulation of transcription and translation and includes multiple stress- and drug-response terms, plus several metabolic processes, suggesting coordinated gene expression changes and metabolic adaptation under stress.","confidence":"Medium","size":17,"edges":34,"triangles":38,"max_degree":8,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:1901407","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4}]},{"hash":"493555109844376628","title":"Cardiac development and transcription regulation","description":"This cluster is dominated by GO terms about DNA-templated transcription and transcriptional regulation, along with heart-related processes (heart development, cardiac muscle hypertrophy in response to stress, regulation of cardiac muscle cell contraction, Purkinje signaling). Together, these suggest proteins involved in cardiac gene regulation and heart development, including stress-induced changes in contraction. Xenobiotic response is present but secondary to the cardiac transcription theme.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0014898","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0035690","count":2}]},{"hash":"101519766647109566","title":"TLR Signaling and Inflammation","description":"The GO terms are dominated by Toll-like receptor signaling pathways (TLR4, TLR8, TLR10), responses to diacyl lipopeptides, and positive regulation of inflammatory responses and chemokine production, pointing to an innate immune signaling cluster. Some terms appear unrelated (plant/dental processes), likely noise, but the central theme is TLR-mediated immune sensing and inflammation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019800","count":1},{"id":"GO:0071726","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0034166","count":1},{"id":"GO:0010080","count":1}]},{"hash":"277686828974192694","title":"Unknown","description":"The top GO terms span disparate areas\u2014development (lung, brain, multicellular organism), metabolism (glycolysis, thiamine biosynthesis, tryptophan catabolism), cytoskeleton (actin depolymerization), redox homeostasis, and intracellular transport\u2014showing no single coherent biological theme tying the proteins together. Since no clear functional cluster emerges from these terms, the set is best labeled Unknown with no confidence.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006569","count":2},{"id":"GO:0009228","count":2}]},{"hash":"1393109596197620888","title":"Spliceosome-Mediated Splicing Regulation","description":"This cluster is dominated by GO terms for regulating mRNA splicing via the spliceosome (negative, alternative, and positive regulation), pointing to a core role in RNA processing and post-transcriptional control. Some adjacent terms (mRNA export, translation initiation) indicate broader RNA metabolism connections, but the primary theme is spliceosome-driven splicing regulation.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048025","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0060211","count":1},{"id":"GO:1902625","count":1}]},{"hash":"302560770578279683","title":"Sphingolipid biosynthesis and adipogenesis","description":"This cluster is driven by lipid-related processes: sphinganine metabolic process, sphingosine biosynthetic process, fatty acid response, and white fat cell differentiation, suggesting sphingolipid metabolism and adipogenesis as the unifying theme. Some terms are obsolete or species-specific, indicating some noise.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0044130","count":4},{"id":"GO:1903699","count":3},{"id":"GO:0010205","count":3},{"id":"GO:0006667","count":3},{"id":"GO:0046512","count":3}]},{"hash":"1857386808283428692","title":"Lipid metabolism and redox homeostasis","description":"This cluster is dominated by GO terms for triglyceride metabolic process, response to food, and oxidative stress-related activities (cellular oxidant detoxification, redox homeostasis, response to ozone). While some development terms appear (lung, skeletal muscle, uterus development), the core signal is lipid metabolism coupled with redox/detox processes, suggesting a metabolic-oxidative stress theme.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0032094","count":3},{"id":"GO:0006641","count":3},{"id":"GO:0030324","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0098869","count":2}]},{"hash":"116293227464192255","title":"Neuronal Signaling and Ion Transport","description":"This cluster centers on neuronal electrical activity and signaling, as shown by terms like neuronal action potential, membrane repolarization, and potassium ion export. It also includes optic nerve organization and sensory perception of pain, tying neural structure to sensation. A few terms (circadian regulation, stress fiber assembly) are less directly tied but may reflect broader cellular signaling contexts. Overall, the theme is neural excitability and ion transport across membranes.","confidence":"Medium","size":16,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021633","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0098914","count":1},{"id":"GO:0050966","count":1},{"id":"GO:0019228","count":1}]},{"hash":"1836030547081126700","title":"Small RNA Biogenesis and Silencing","description":"The terms point to RNA-based regulatory pathways: miRNA and ta-siRNA processing, RNAi antiviral responses, and ncRNA-mediated heterochromatin formation, plus development-related regulation (vegetative phase change). This suggests a cluster of proteins involved in small RNA biogenesis and gene silencing, with roles in RNA processing and chromatin regulation across plant contexts.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010050","count":1},{"id":"GO:0060145","count":1},{"id":"GO:0010501","count":1},{"id":"GO:0006413","count":1},{"id":"GO:1901224","count":1}]},{"hash":"132341124464054320","title":"Neural and Muscular Development with Metabolic Regulation","description":"The cluster centers on developmental programs in neural and muscular lineages (substantia nigra development, neuron differentiation, skeletal muscle fiber development, cardiac muscle hypertrophy in response to stress), with supporting roles in metabolism and regulatory signaling (glycogen metabolism, regulation of glycogen catabolic process, glucocorticoid signaling) and cellular transport processes (ER to Golgi). This suggests proteins jointly contribute to tissue development and metabolic control across neural and muscular contexts, rather than a single narrowly defined function.","confidence":"Medium","size":16,"edges":90,"triangles":310,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0021762","count":11},{"id":"GO:0048741","count":11},{"id":"GO:0001915","count":9},{"id":"GO:0014898","count":9},{"id":"GO:0000082","count":9}]},{"hash":"2211874977891453400","title":"Embryonic organogenesis across tissues","description":"This cluster features a broad collection of developmental GO terms across multiple organs and tissues (heart/muscle, thyroid, neurohypophysis, tooth, hindbrain rhombomere, etc.). There isn\u2019t a single shared pathway or function, but rather a general theme of embryonic organogenesis and tissue development across diverse systems. Labeling it as embryonic organogenesis across tissues reflects this wide-ranging developmental theme without overstating a specific mechanism.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003350","count":1},{"id":"GO:0072181","count":1},{"id":"GO:0045317","count":1},{"id":"GO:0035880","count":1},{"id":"GO:2000288","count":1}]},{"hash":"949775091439177847","title":"Neuronal stress response and signaling","description":"The top GO terms cluster around cellular responses to metal- and chemical-induced stress (cadmium, arsenite), transcription, apoptosis, and the p38 MAPK cascade, with neural-context processes like glutamatergic synaptic transmission and visual perception. This suggests a theme of stress-activated signaling in neurons/retina rather than a single specific pathway, hence a neuronal stress-response label.","confidence":"Medium","size":16,"edges":5,"triangles":2,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0006915","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0007601","count":6}]},{"hash":"136086974200827610","title":"Unknown","description":"GO terms are too diverse\u2014immune regulation (T cell homeostasis, cytotoxicity), neural development (neuron differentiation, dendrite morphogenesis), cardiac stress response, cell cycle (G1/S), and ER-Golgi transport\u2014without a unifying function. Thus, a single representative label cannot be assigned.","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070940","count":3},{"id":"GO:0010719","count":3},{"id":"GO:0050774","count":3},{"id":"GO:0043029","count":3},{"id":"GO:0007605","count":2}]},{"hash":"649380212267198870","title":"Actin-driven cytoskeletal remodeling and cytokinesis","description":"The GO terms point strongly to actin dynamics (positive regulation of actin polymerization, formin-nucleated actin cable assembly, filopodium regulation) and cytokinesis (mitotic cleavage furrow formation), as well as related morphogenesis and polarity processes (dendrite morphogenesis, maintenance of cell polarity). Vesicle trafficking terms (Golgi to endosome, phagosome acidification) can be linked to cytoskeletal remodeling during membrane trafficking. Overall, the cluster appears to represent proteins coordinating actin-driven remodeling during cell division and shape changes.","confidence":"High","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006895","count":3},{"id":"GO:0001822","count":3},{"id":"GO:0051489","count":3},{"id":"GO:0048813","count":3}]},{"hash":"1859485968790855159","title":"Unknown","description":"GO terms in this cluster span energy metabolism (mitochondrial ATP synthesis, proton transport) and diverse extracellular and signaling processes (ECM disassembly, fibrinolysis, blood coagulation, centrosome localization, synaptic depression, GTPase activation, and cation transport). There isn\u2019t a coherent, single biological theme uniting these functions, so the cluster appears heterogeneous rather than functionally cohesive. ","confidence":"","size":16,"edges":14,"triangles":0,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0042776","count":2},{"id":"GO:0022617","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0015991","count":2},{"id":"GO:0042730","count":2}]},{"hash":"434451921073089650","title":"TLR-driven inflammatory signaling","description":"The top GO terms overwhelmingly point to Toll-like receptor pathways (TLR4 and TLR10) and downstream inflammatory processes, including cellular response to diacyl bacterial lipopeptide, regulation of chemokine production, and positive regulation of inflammatory response, suggesting these proteins cluster around innate immune sensing and signaling. A couple of terms related to ribosome biogenesis and plant developmental processes appear as outliers and are likely noise or misannotations, but they do not override the central theme of TLR-mediated inflammation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0019800","count":1},{"id":"GO:0071726","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0034166","count":1}]},{"hash":"676780707128710324","title":"Integrin signaling and cell migration","description":"These terms point to integrin-mediated signaling coordinating cell adhesion, spreading, and migration, with overlaps in axon regeneration and cell survival (anoikis avoidance) and a background of proliferative signals (telomere maintenance and DNA replication). The strongest shared feature is adhesion signaling driving movement, hence Integrin signaling and cell migration.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007229","count":2},{"id":"GO:0032212","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0034446","count":2},{"id":"GO:1904355","count":2}]},{"hash":"1098099704605411239","title":"ER proteostasis and redox signaling","description":"Proteins show enrichment for ER-related folding and stress responses (protein folding in ER; response to ER stress), together with redox-related processes (deglutathionylation, redox homeostasis) and transcription regulation, implying a link between ER proteostasis and redox-regulated transcription.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0080058","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0018401","count":1},{"id":"GO:1903206","count":1}]},{"hash":"1872584220194445760","title":"Unknown","description":"The GO terms are highly diverse: transcription initiation, regulation of androgen receptor signaling, various development processes (tarsal gland and uterus morphogenesis), and a metabolic process (sucrose catabolic), plus some obsolete annotations. There is no single coherent functional theme tying these proteins together, so a specific, representative label cannot be justified.","confidence":"","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043970","count":1},{"id":"GO:0060765","count":1},{"id":"GO:0005987","count":1},{"id":"GO:0010971","count":1},{"id":"GO:1905524","count":1}]},{"hash":"1653355461802376497","title":"Cardiac muscle development and calcium signaling","description":"The cluster centers on cardiomyocyte development and signaling: left ventricular morphogenesis, outflow tract morphogenesis, SA node regulation, and Purkinje-to-ventricular signaling, plus a noted calcium release from the sarcoplasmic reticulum, which highlights excitation-contraction coupling in heart tissue. Some terms about protein kinase regulation and unfolded protein response may reflect ancillary stress/quality-control signaling related to cardiac development. Overall, the dominant theme is cardiac muscle development linked with calcium-mediated signaling.","confidence":"Medium","size":16,"edges":26,"triangles":22,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0086029","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0043588","count":2}]},{"hash":"1265457126942536922","title":"Antiviral Immune Signaling and Inflammatory Response","description":"The cluster's GO terms cluster around host defense against viruses and inflammatory signaling, including cellular response to virus, suppression of viral genome replication, p38 MAPK cascade regulation, interleukin-1 and interferon-related regulation, and apoptosis execution. A couple of terms are less directly related (e.g., RNase MRP-dependent mRNA decay, cardiac contraction regulation), but the dominant themes point to innate antiviral signaling and inflammatory control.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044828","count":1},{"id":"GO:1900745","count":1},{"id":"GO:0071347","count":1},{"id":"GO:1900119","count":1},{"id":"GO:0042307","count":1}]},{"hash":"497442658040401852","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is strongly enriched for ubiquitination and proteasome/ERAD pathway terms (K48-linked ubiquitination, ubiquitin-dependent protein catabolic process, autoubiquitination, and ERAD-related terms). Additional terms like Wnt receptor catabolic process and peroxisomal import hint at degradation/regulation of proteins via ubiquitin tagging. While a few terms (viral process, X-chromosome inactivation, molybdopterin biosynthesis) are less related, the dominant theme points to ubiquitin-mediated protein turnover.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045116","count":4},{"id":"GO:0006777","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0060816","count":3},{"id":"GO:0070936","count":3}]},{"hash":"1436471105923025598","title":"Light perception and neuronal morphogenesis","description":"The cluster's top GO terms cluster around visual processes (visual perception, detection of visible light) and neuronal development (dendrite morphogenesis), with potassium ion transport supporting neuronal signaling. This combination suggests proteins involved in light sensing and neural signaling/morphogenesis, potentially matching photoreceptor or retina-associated pathways. Some terms (mitotic cell cycle, transcription) are broader or less specific, likely reflecting general cellular roles or annotation noise, but the core theme is vision-related neural function.","confidence":"Medium","size":16,"edges":95,"triangles":295,"max_degree":15,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":9},{"id":"GO:0007601","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0048813","count":7},{"id":"GO:0006813","count":7}]},{"hash":"1820210967906084227","title":"Redox Homeostasis and Protein Quality Control","description":"The cluster's top GO terms center on redox biology and oxidative stress responses (cell redox homeostasis, cellular response to oxidative stress) along with protein maintenance processes (protein repair, protein deglutathionylation) and ER-associated folding. This suggests a theme of protecting and repairing proteins under oxidative conditions and ensuring proper folding via redox-regulated pathways. The presence of prolyl hydroxylation adds a redox-linked post-translational modification angle. Overall, the proteins appear connected to redox-driven protein quality control.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0030091","count":4},{"id":"GO:0045454","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0080058","count":2}]},{"hash":"1718354648303995565","title":"Transcriptional Regulation in Differentiation","description":"The top GO terms point to transcriptional control (negative regulation of transcription by RNA polymerase II; DNA-templated transcription) along with various differentiation processes across lineages (megakaryocytes, spermatid nucleus, noradrenergic neurons). The presence of apoptosis and immune-response signals suggests broader regulatory contexts, but the common theme appears to be regulation of gene expression during development. This makes \"Transcriptional Regulation in Differentiation\" a concise, representative label.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045654","count":5},{"id":"GO:0043046","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0007289","count":4},{"id":"GO:0006351","count":4}]},{"hash":"943755355755085152","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to translation, ribosome biogenesis, and ribosomal subunit assembly (cytoplasmic translation, tRNA modification, ribosome biogenesis), indicating a shared function in ribosome assembly and protein synthesis. Some cell cycle and stress-related terms appear, but they are secondary to the core ribosomal/translation theme.","confidence":"High","size":16,"edges":19,"triangles":12,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":6},{"id":"GO:0006400","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0002181","count":4}]},{"hash":"1037039468468304632","title":"Lipid and Carbohydrate Metabolism with Stress Response","description":"The cluster is dominated by lipid and carbohydrate metabolic processes (retinol, fatty acid, cholesterol biosynthesis/catabolism, fructose, D-xylose) and includes detox and stress-related terms (cadmium response, daunorubicin metabolism, apoptosis regulation) plus membrane transport. This points to a set of proteins involved in broad metabolic remodeling with coordinated stress resilience rather than a single pathway.","confidence":"Medium","size":16,"edges":118,"triangles":532,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0042572","count":6},{"id":"GO:0046370","count":6},{"id":"GO:0006633","count":6},{"id":"GO:0042843","count":5}]},{"hash":"1708389311298919919","title":"Lipid and Retinoid Metabolism","description":"The top GO terms are mainly lipid-related and retinoid/steroid in nature (retinal and retinol metabolism, sphingolipid biosynthesis, and C21-steroid hormone metabolism), suggesting a cohesive theme around lipid and retinoid/steroid metabolic pathways. A few terms (poly-hydroxybutyrate biosynthesis, antibiotic biosynthesis, acetoin catabolism, and drug response) appear more peripheral, which may reflect broader metabolic capabilities or annotation noise. Overall, the cluster most plausibly represents lipid/retinoid/steroid biosynthetic and metabolic processes.","confidence":"Medium","size":16,"edges":7,"triangles":2,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0042574","count":4},{"id":"GO:0042572","count":4}]},{"hash":"554885295432615694","title":"Lipid Metabolism and Adipogenesis","description":"The top terms cluster around lipid-related processes, including sphinganine/sphingosine metabolism, sphingolipid biosynthesis, cholesterol esterification, and response to fatty acids, with white fat cell differentiation pointing to adipogenesis. A noteable but general term is protein homooligomerization, suggesting oligomeric protein complexes rather than a single pathway. Overall, the cluster centers on lipid metabolism and adipocyte-related functions, with some protein-assembly features.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0006667","count":1},{"id":"GO:0034435","count":1},{"id":"GO:0046512","count":1},{"id":"GO:1903699","count":1}]},{"hash":"2097541911878145280","title":"Unknown","description":"Unknown. The top GO terms span phosphorylation, transcription, cell division, immune signaling (interleukin-4 response), redox processes, ion transport, and thiamine biosynthesis, with no clear unifying function or pathway; the cluster also shows low connectivity, suggesting heterogeneity rather than a coherent module.","confidence":"","size":16,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016310","count":3},{"id":"GO:0071353","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0048148","count":2}]},{"hash":"725110676841400914","title":"Steroid hormone and retinoid lipid metabolism","description":"Top terms indicate strong emphasis on steroid hormone metabolism (C21-steroid, androgen) and retinoid metabolism (retinol, retinal), along with lipid biosynthesis (sphingolipids). This suggests a cohesive theme of lipid and steroid metabolic processes driving the cluster, despite a few outlier terms that may reflect cross-species annotation noise.","confidence":"Medium","size":16,"edges":11,"triangles":1,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0042572","count":8},{"id":"GO:0017000","count":8},{"id":"GO:0008207","count":7},{"id":"GO:0045150","count":7}]},{"hash":"1330267570607736578","title":"Epigenetic transcription and chromatin regulation in development","description":"The cluster centers on nuclear processes: DNA-templated transcription, histone H3-K9 methylation, histone mRNA turnover, and DNA repair, plus several development-related terms (brain development, uterus development, oogenesis). This suggests proteins involved in epigenetic regulation of gene expression with roles in developmental contexts, even though some terms are flagged as obsolete.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0016049","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0010735","count":1}]},{"hash":"1613678132706812572","title":"Insect Developmental Organogenesis","description":"The terms strongly point to insect development and organ formation, with multiple entries for mushroom body development, Malpighian tubule morphogenesis, head involution, molting, and lymph gland development. While some terms are general cellular processes, the overall theme centers on insect developmental biology and organogenesis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071763","count":1},{"id":"GO:0010207","count":1},{"id":"GO:0009608","count":1},{"id":"GO:1903220","count":1},{"id":"GO:0008258","count":1}]},{"hash":"1999456843106116046","title":"Ciliary Transition Zone and Developmental Patterning","description":"The GO terms cluster around ciliary transition zone localization and assembly, plus development-related processes (eye development, neural tube closure, dorsal convergence, and related patterning). This implies a core function in ciliary biology with roles in embryonic development and organogenesis, making the theme distinct and representative, despite a minor outlier term. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":1},{"id":"GO:1904491","count":1},{"id":"GO:1901620","count":1},{"id":"GO:0043010","count":1},{"id":"GO:0001843","count":1}]},{"hash":"256557967066945980","title":"Unknown","description":"The top terms show a scattered mix of metabolism, transport, stress response, hormone signaling, and development across different organisms, with no clear, cohesive function uniting them (and the cluster has no edges), so there isn\u2019t a single interpretable theme to label it beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006012","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0016570","count":2},{"id":"GO:0006986","count":2}]},{"hash":"476064641485930401","title":"Secondary metabolite biosynthesis","description":"This cluster shows enrichment for diverse biosynthetic processes including biotin, antibiotic, strigolactone, menaquinone, alkaloid, and poly-hydroxybutyrate biosynthesis, plus related catabolic and detox-response terms. The common theme is production of specialized metabolites, suggesting the proteins function together in secondary metabolite biosynthesis pathways, with some involvement in related metabolism and detox responses.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0009636","count":4},{"id":"GO:0019380","count":3}]},{"hash":"2148886906684327014","title":"Calcium-Dependent Exocytosis and Synaptic Regulation","description":"This cluster is dominated by GO terms tied to calcium signaling controlling exocytosis and synaptic vesicle cycling, such as regulation of presynaptic cytosolic calcium concentration, positive regulation of exocytosis, and regulation of synaptic vesicle endocytosis. These points strongly suggest a shared function in calcium-driven neurotransmitter release. Some terms touch cardiac and thyroid-related processes, but the central theme remains calcium-regulated exocytosis and synaptic regulation.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042403","count":2},{"id":"GO:1900242","count":1},{"id":"GO:0086004","count":1},{"id":"GO:0045921","count":1},{"id":"GO:0014898","count":1}]},{"hash":"1589308798085509677","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":42,"triangles":77,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006986","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0071374","count":2}]},{"hash":"51861553217599492","title":"Transmembrane Transport","description":"The top GO terms strongly point to diverse membrane transport activities, including glucose, organic anions, potassium ions, sialic acid, vitamins, xenobiotics, and neurotransmitter loading into synaptic vesicles, plus insulin-stimulated glucose import. This suggests the cluster is enriched for membrane transporter functions and vesicular transport components rather than a single enzymatic activity.","confidence":"High","size":15,"edges":7,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":1},{"id":"GO:0043252","count":1},{"id":"GO:0071805","count":1},{"id":"GO:0044381","count":1},{"id":"GO:0035461","count":1}]},{"hash":"2133840846489969462","title":"Autophagy-Linked Cell Cycle Regulation","description":"The cluster centers on autophagy-related processes (macroautophagy and nucleophagy) and regulation of the cell cycle, including links to apoptotic signaling (negative regulation of mitochondrial outer membrane permeabilization). While transport and ufmylation are present, the strongest and most coherent signal is autophagy coupled with cell-cycle control, suggesting a focus on cellular stress responses and survival mechanisms that couple autophagy with cell-cycle regulation.","confidence":"Medium","size":15,"edges":32,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034635","count":1},{"id":"GO:0002229","count":1},{"id":"GO:1901029","count":1},{"id":"GO:0006810","count":1},{"id":"GO:0007113","count":1}]},{"hash":"1709183154126314726","title":"ER protein quality control and stress response","description":"This cluster centers on ER-associated degradation, unfolded protein response, and ER folding processes (protein folding in the ER, unfolded protein response, ERAD), with supporting roles for ubiquitin-related deubiquitination and proteolysis, all key to maintaining ER proteostasis under heat stress. The presence of related terms like response to heat and regulation of protein export from the nucleus aligns with a broader cellular stress and quality-control program rooted in the ER.","confidence":"High","size":15,"edges":49,"triangles":35,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0006508","count":1},{"id":"GO:0043392","count":1},{"id":"GO:0042981","count":1}]},{"hash":"2032993384575239636","title":"RNA processing and translation","description":"The cluster is dominated by GO terms related to RNA metabolism (spliceosomal snRNP assembly, RNA processing, snoRNA splicing) and protein synthesis (cytoplasmic translation, translational elongation). While a few terms touch on development or immune signaling, the strongest and most consistent signal is RNA processing and translation machinery.","confidence":"Medium","size":15,"edges":13,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0000387","count":1},{"id":"GO:0006396","count":1},{"id":"GO:0060710","count":1},{"id":"GO:0002635","count":1},{"id":"GO:0071364","count":1}]},{"hash":"2077950730599590559","title":"Neuronal Chromatin Regulation and RNA Processing","description":"The terms point to chromatin-level control of gene expression (histone methylation, chromatin binding, Pol II transcription regulation) coupled with neural development signals (cerebral cortex development, dopamine metabolism) and RNA processing activities (alternative splicing, tRNA wobble modification). Metabolic cofactors like 2-oxoglutarate and dihydrolipoamide link these processes to epigenetic enzyme activity, supporting a cohesive theme of neural gene regulation via chromatin state and RNA processing.","confidence":"Medium","size":15,"edges":36,"triangles":20,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0051572","count":5},{"id":"GO:0000122","count":4},{"id":"GO:0002098","count":4},{"id":"GO:0000380","count":4},{"id":"GO:0021987","count":4}]},{"hash":"415742599258681883","title":"RNA metabolism and gene expression regulation","description":"The cluster contains GO terms spanning transcription initiation/regulation, transcription antitermination, and transcription-related processes, alongside ribosome biogenesis (90S preribosome assembly), tRNA processing, and translation. This suggests a theme around RNA metabolism and multi-level gene expression control, from transcription to translation, rather than a single specialized function. Confidence: Medium","confidence":"","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006935","count":2},{"id":"GO:0034463","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0031564","count":1}]},{"hash":"1587388424172364256","title":"Cellular stress response and DNA repair","description":"The cluster is enriched for responses to xenobiotic stimulus, cadmium ion, redox homeostasis, and base-excision repair, pointing to a coordinated cellular stress response and maintenance of genomic integrity. Glycogen biosynthesis and its regulation suggest metabolic remodeling during stress, while a few terms are obsolete or peripheral. Overall, the dominant theme is stress response combined with DNA repair.","confidence":"Medium","size":15,"edges":16,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0006284","count":3},{"id":"GO:0071276","count":2},{"id":"GO:0005978","count":2}]},{"hash":"897464889418199551","title":"Nuclear transcription regulation and DNA binding","description":"The most represented GO terms cluster around DNA-templated transcription and regulation of DNA binding (RNA polymerase II), along with other nuclear processes such as positive regulation of DNA binding and transcription-related activities, indicating a core function in transcription control within the nucleus. Obvious redox-related and viral-process annotations appear as less central or secondary associations. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0080058","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903026","count":2}]},{"hash":"1625262601940480084","title":"Unknown","description":"The GO terms span very disparate biological areas, from abiotic and chemical stress responses (herbicide, aluminum, ethanol) to core metabolic processes (porphyrin biosynthesis, ferredoxin metabolism, thiamine biosynthesis) and even unrelated mammalian traits (lactation, endothelial differentiation). The lack of a single coherent biological theme suggests there isn\u2019t a clear, shared function tying these proteins together, so a confident, specific label cannot be assigned.","confidence":"","size":15,"edges":9,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009635","count":2},{"id":"GO:0010044","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006782","count":2}]},{"hash":"1604870544730837400","title":"Neuroendocrine dopamine and serotonin regulation","description":"This cluster centers on neuroendocrine functions and monoamine signaling: multiple top terms describe pituitary development, dopamine metabolism/catabolism, and serotonin secretion regulation, plus corticosterone response and stress-related environmental responses (ethanol, metal ions). Together these point to a coherent theme of neuroendocrine control of dopamine/serotonin signaling.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0021983","count":7},{"id":"GO:0045964","count":7},{"id":"GO:0051412","count":7},{"id":"GO:0043046","count":7},{"id":"GO:0019805","count":7}]},{"hash":"1239040319862610623","title":"Viral life cycle and virion assembly","description":"The top GO terms cluster around viral processes: viral life cycle, virion assembly, fusion of viral membranes with host membranes, and establishment of proviral latency, plus RNA-templated DNA biosynthesis. While some terms like sepal formation or leukocyte migration appear unrelated (likely noise), the dominant signal points to viral replication and particle assembly. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048453","count":1},{"id":"GO:0050900","count":1},{"id":"GO:0034389","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0019058","count":1}]},{"hash":"2167770377369262190","title":"Ribosome Biogenesis and Transcription","description":"This cluster is dominated by GO terms for DNA-templated transcription, maturation of SSU-rRNA, and ribosome biogenesis, indicating a core role in ribosome production and gene expression. Additional terms for mitotic cell cycle and multicellular organism development suggest coordination with growth and development, while stress- and immune-related terms appear but are less central. Overall, the proteins seem linked to transcription-dependent ribosome biosynthesis and development processes.","confidence":"Medium","size":15,"edges":5,"triangles":1,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0000462","count":5},{"id":"GO:0042254","count":5},{"id":"GO:0030900","count":5},{"id":"GO:0071276","count":5}]},{"hash":"29645927237758669","title":"Cardiac calcium signaling and contraction regulation","description":"The proteins cluster around calcium handling and excitation-contraction coupling in cardiac muscle, as shown by GO terms for SR calcium release, positive regulation of calcium release, cardiac muscle contraction regulation, Purkinje-to-ventricle signaling, and adrenergic signaling. While a couple of terms touch cell cycle or development, the dominant theme is calcium-mediated contraction and related signaling in the heart, suggesting a coherent cardiac functional module.","confidence":"High","size":15,"edges":12,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":3},{"id":"GO:0007275","count":3},{"id":"GO:1900242","count":2},{"id":"GO:0086004","count":2},{"id":"GO:0086029","count":2}]},{"hash":"904734025004372497","title":"Glucocorticoid- and stress-responsive transcription regulation","description":"This cluster\u2019s top terms emphasize positive regulation of transcription by RNA polymerase II and cellular responses to dexamethasone, cocaine, and stress, suggesting a role in glucocorticoid signaling and broader stress-induced transcriptional control. While some histone modification terms are listed as obsolete, the recurring theme centers on transcriptional regulation in stress contexts, with links to neuronal development and organ homeostasis such as liver and heart under stress. Therefore, a label focusing on glucocorticoid- and stress-responsive transcription regulation captures the shared function.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031060","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0071549","count":2},{"id":"GO:0071440","count":2},{"id":"GO:0071314","count":2}]},{"hash":"203242318833352826","title":"RNA Decay and Turnover","description":"Predominant GO terms describe deadenylation-dependent and -independent mRNA decay, exonucleolytic RNA degradation, and adenosine catabolic processes, indicating a cluster enriched for RNA turnover and processing. While a few terms touch transcription, DNA repair, and p53-mediated apoptosis, these are less represented, so the core signal aligns with RNA decay pathways rather than DNA repair.","confidence":"High","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0000290","count":1},{"id":"GO:0043928","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0006154","count":1}]},{"hash":"2286208686588539384","title":"Neural development and glutamatergic synaptic signaling","description":"The top GO terms cluster around brain development, dendrite morphogenesis, and regulation of glutamatergic synaptic transmission and excitatory postsynaptic potentials, pointing to a neural development/synaptic function theme. A few terms are more general cellular processes, but they do not outweigh the dominant neural-centric signals.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0003100","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0051966","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0060079","count":3}]},{"hash":"1960658734272042756","title":"Protein acetylation and chromatin modification","description":"This cluster is dominated by GO terms for acetylation events\u2014N-terminal acetylation, peptidyl-lysine N6 acetylation, histone H4 acetylation\u2014and a subtelomeric heterochromatin formation term, pointing to acetylation-driven regulation of chromatin and proteins. Melatonin biosynthesis and other terms likely reflect acetyltransferase activity and related metabolism that fuels acetyl-CoA availability. Overall, the common theme is acetylation-related processes influencing chromatin and protein modification.","confidence":"High","size":15,"edges":10,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":4},{"id":"GO:0045150","count":4},{"id":"GO:0061606","count":4},{"id":"GO:0018002","count":4},{"id":"GO:0010125","count":4}]},{"hash":"1807516100628700872","title":"Ribosome Biogenesis and rRNA Processing","description":"Most prominent terms are maturation of SSU, 5.8S, and LSU rRNA from tricistronic transcripts, and maturation steps for rRNA, which point to ribosome biogenesis. There are additional signals for DNA replication and chromosome condensation, suggesting coordination with the cell cycle, but the rRNA processing signal dominates the cluster\u2019s theme.","confidence":"Medium","size":15,"edges":17,"triangles":13,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":7},{"id":"GO:0006260","count":6},{"id":"GO:0000463","count":5},{"id":"GO:0019079","count":5},{"id":"GO:0000466","count":4}]},{"hash":"1009392989308591126","title":"Spliceosome-driven mRNA processing and silencing","description":"This cluster shows strong enrichment for spliceosome-mediated mRNA splicing, including alternative and regulated splicing (positive/negative regulation), along with regulation of polyadenylation and tail shortening, plus ncRNA/miRNA\u2013mediated translational silencing. Together, these terms point to a group of proteins involved in post-transcriptional mRNA processing and translational control. ","confidence":"High","size":15,"edges":14,"triangles":1,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006378","count":4},{"id":"GO:0006446","count":4},{"id":"GO:0045292","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4}]},{"hash":"930100554829194523","title":"Triglyceride catabolism and lipid remodeling","description":"The top GO terms are dominated by triglyceride catabolic processes and mobilization, along with remodeling of triglyceride acyl chains and related phospholipids, indicating a core lipid metabolism and breakdown theme. A few regulatory terms (negative regulation of protein kinase activity and transcription regulation) appear but are less represented, so the primary signal points to lipid catabolism and membrane lipid remodeling. This justifies a label focused on triglyceride breakdown and lipid remodeling.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:2000480","count":1},{"id":"GO:0010898","count":1},{"id":"GO:0046338","count":1},{"id":"GO:0034638","count":1}]},{"hash":"412428538203936766","title":"Genome maintenance and organelle turnover","description":"The cluster\u2019s top GO terms center on DNA replication, DNA-templated transcription, and mitochondrial DNA replication, pointing to genome maintenance. Additional terms like UV-damage excision repair reinforce genome integrity themes, while autophagosome maturation and peroxisome matrix import receptor recycling indicate concurrent organelle quality control. Together, they suggest a coordinated role in genome maintenance and organelle turnover.","confidence":"Medium","size":15,"edges":32,"triangles":20,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0006541","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0055114","count":3},{"id":"GO:0070651","count":3}]},{"hash":"1292343778144358023","title":"Retinoid and steroid metabolism in lung development","description":"The cluster centers on retinol/retinal metabolism and related lipid pathways (including sphingolipid biosynthesis and C21-steroid hormone metabolism) and lung development, suggesting a cohesive theme of retinoid/lipid signaling driving lung morphogenesis. Some terms like acetoin catabolic process and poly-hydroxybutyrate biosynthesis, along with general drug response terms, may reflect incidental or cross-species annotations, but the core pattern supports a retinoid/lipid metabolism\u2013driven lung development theme.","confidence":"Medium","size":15,"edges":2,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0046677","count":6},{"id":"GO:0030324","count":6},{"id":"GO:0042572","count":6},{"id":"GO:0008207","count":5}]},{"hash":"395733868459874251","title":"Immune and tissue remodeling signaling","description":"These proteins showGO terms centered on immune response, tissue remodeling, and signaling regulation (calcium release, lipid kinase activity), with additional development-related terms (trophoblast and astrocyte differentiation). This pattern suggests a cluster tied to immune-linked remodeling and developmental signaling rather than a single specific pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006955","count":2},{"id":"GO:0060707","count":1},{"id":"GO:0060665","count":1},{"id":"GO:0007596","count":1},{"id":"GO:0048771","count":1}]},{"hash":"877529978748077548","title":"Oxygen-sensing and prolyl hydroxylation","description":"The top GO terms center on intracellular oxygen homeostasis and proline hydroxylation, pointing to oxygen-dependent post-translational modification. Additional terms touch on redox and mitochondrial-associated processes (ion transport and ATP synthesis), suggesting a broader respiration/mitochondrial context. With limited connectivity and low term counts, the link is plausible but modest, hence a Medium confidence.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032364","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0099132","count":1}]},{"hash":"440961472291484765","title":"Mitochondrial Cofactor and Nucleotide Transport","description":"The GO terms show several transporter activities: thiosulfate transport, heme transport, thiamine pyrophosphate transmembrane transport, and pyrimidine nucleotide import into mitochondrion, indicating a core theme of metabolite/cofactor import into organelles. The presence of a superoxide response implies linkage to mitochondrial oxidative stress. Some terms are obsolete, but the dominant pattern is organelle transport of cofactors and metabolites, supporting the proposed label.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":4},{"id":"GO:0018298","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0015709","count":2},{"id":"GO:0015886","count":2}]},{"hash":"414556110413466908","title":"Unknown","description":"The GO terms span diverse processes (amino acid starvation response, neutrophil clearance, glycogen metabolism, transcription, Wnt signaling, redox, photosynthesis, and multiple transports) with no clear shared function, suggesting no coherent theme for a specific label.","confidence":"","size":14,"edges":15,"triangles":13,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":2},{"id":"GO:0097350","count":2},{"id":"GO:0045819","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0090090","count":2}]},{"hash":"98973146314619498","title":"Mitochondrial Translation and Electron Transport","description":"The cluster is dominated by terms tied to organellar energy production and protein synthesis: mitochondrial electron transport (respiratory chain, ubiquinol to cytochrome c) and proton transmembrane transport, plus mitochondrial-specific tRNA aminoacylation and translation. A few terms like photosynthesis and embryonic development appear, but the strongest signal is mitochondrial gene expression linked to respiration, suggesting a cohesive theme of mitochondrial translation coupled to oxidative phosphorylation.","confidence":"High","size":14,"edges":86,"triangles":307,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:1902600","count":2},{"id":"GO:0022904","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0006122","count":1},{"id":"GO:0015979","count":1}]},{"hash":"940350527767434712","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":61,"triangles":130,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0048701","count":9},{"id":"GO:0071031","count":6},{"id":"GO:0010501","count":6},{"id":"GO:0006605","count":6}]},{"hash":"82548904401419370","title":"Unknown","description":"The GO terms here are very diverse, spanning lipid/sterol transport, pancreatic endocrine functions (insulin secretion, pancreas development), general gene expression (splicing, translation, nuclear export), and immune signaling (IL-18/chemokine production, macrophage activation). There\u2019s no clear single biological theme tying these proteins together, so a cohesive, specific label isn\u2019t supported. Confidence: None","confidence":"","size":14,"edges":18,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032366","count":1},{"id":"GO:0035773","count":1},{"id":"GO:0031016","count":1},{"id":"GO:0045843","count":1},{"id":"GO:0006376","count":1}]},{"hash":"443302362674534130","title":"Nuclear DNA damage response and chromosome maintenance","description":"The top GO terms point to nuclear and genome-maintaining processes, including base-excision repair and mitotic chromosome condensation, suggesting genome integrity maintenance. Supporting terms involve nuclear transport regulation and stress responses to cadmium/xenobiotics, indicating a broader nuclear-centric stress response. Although some terms are obsolete, the core themes converge on nuclear genome maintenance and cellular stress adaptation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070058","count":2},{"id":"GO:0007076","count":2},{"id":"GO:0043066","count":1},{"id":"GO:0071276","count":1},{"id":"GO:1902800","count":1}]},{"hash":"1987776129955517895","title":"RNA Synthesis and Ribosome Biogenesis","description":"The terms point to a cohesive module involving transcription (RNAP II initiation/elongation and antitermination) together with RNA processing (rRNA and tRNA) and ribosome assembly (90S preribosome), indicating coordinated RNA production and ribosome biogenesis, with some connection to stress-responsive translational regulation.","confidence":"Medium","size":14,"edges":37,"triangles":47,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0031564","count":3},{"id":"GO:0006364","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0045899","count":2},{"id":"GO:0032968","count":2}]},{"hash":"462445155323997113","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":81,"triangles":265,"max_degree":13,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0042273","count":5},{"id":"GO:0048026","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0006369","count":4},{"id":"GO:0043044","count":4}]},{"hash":"2291070396930023401","title":"Ribosome biogenesis and translation","description":"The cluster is enriched for ribosome- and translation-related GO terms (cytoplasmic translation, translation, translational initiation, tRNA modification, ribosomal subunit biogenesis, and ribosomal subunit export from the nucleus), with a few cell cycle terms that may reflect growth coordination. This pattern points to proteins involved in ribosome assembly and protein synthesis machinery, justifying the label.","confidence":"High","size":14,"edges":4,"triangles":0,"max_degree":4,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0002181","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0007049","count":3}]},{"hash":"1480743086577819844","title":"Plant hormone signaling and stress responses","description":"The GO terms point to plant-specific biology, center on hormone signaling (cytokinin-activated, gibberellin-related pathways) and stress-related processes (response to hydrogen peroxide, unfolded protein response, cadmium exposure), with additional links to chlorophyll biosynthesis regulation and development. This suggests a cluster of proteins involved in coordinating hormone signaling with stress and growth responses in plants, despite some terms being obsolete or broad.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0006986","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0071276","count":1},{"id":"GO:0009938","count":1}]},{"hash":"1107269720997264899","title":"Mitotic cell division and vesicle trafficking","description":"The cluster shows strong enrichment for mitotic cell cycle, cell division, and spindle assembly terms, pointing to roles in proliferation; it also includes vesicle trafficking processes (COPII budding and Golgi-to-ER transport), suggesting coordination between cell division and intracellular transport, with additional hints from growth and brain development terms that align with developmental proliferation.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":7},{"id":"GO:0000278","count":6},{"id":"GO:0090307","count":5},{"id":"GO:0000747","count":5},{"id":"GO:0090114","count":5}]},{"hash":"1598738402114716221","title":"Unknown","description":"No edges or enriched GO terms to tie the 14 proteins together, so there is no clear shared function or theme to assign. The cluster cannot be meaningfully named beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"396202661186430846","title":"Unknown","description":"These terms are too diverse to reflect a single cohesive function; they include transcription-related processes, ribosome biogenesis, protein kinase activation, vesicle transport, autophagy, viral processes, neurotransmitter release, and adhesion, so a specific functional label isn't supported.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032147","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0001113","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006367","count":1}]},{"hash":"1045428175020408135","title":"Nuclear mRNA processing and decay","description":"The cluster centers on nuclear RNA metabolism: spliceosome-mediated mRNA splicing, regulatory ncRNA\u2013mediated gene silencing, and multiple mRNA decay pathways (deadenylation-dependent decapping, deadenylation-independent decay, and related RNA hydrolysis), plus transcription and DNA repair. This combination points to coordinated RNA processing, turnover, and gene expression regulation in the nucleus.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0000290","count":1},{"id":"GO:0043928","count":1}]},{"hash":"1384562457947067825","title":"Unknown","description":"The GO terms are highly diverse, covering vitamin biosynthesis, immune/chemical stress responses, various xenobiotic/metabolic pathways, gene expression regulation, splicing, and development. There is no coherent, single function that ties these terms together, so a specific functional label is not evident.","confidence":"","size":14,"edges":9,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":3},{"id":"GO:0043046","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0060992","count":2},{"id":"GO:0070276","count":2}]},{"hash":"1283106468710910593","title":"Unknown","description":"This cluster shows a highly diverse set of GO terms ranging from plant defense (systemic acquired resistance) to kidney development, renin-angiotensin regulation, antigen presentation, APP processing, and even xylan catabolism, with no clear shared pathway or function. The lack of connectivity (edges/triangles zero) and only single-term representations further suggest there is no cohesive biological theme to label beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009627","count":1},{"id":"GO:0016540","count":1},{"id":"GO:0001823","count":1},{"id":"GO:0042985","count":1},{"id":"GO:0030163","count":1}]},{"hash":"605115977084376960","title":"Unknown","description":"The top GO terms span metabolism (coenzyme A biosynthesis), phosphorylation, development and sensory processes (thermoception, cerebellar granule cell differentiation), calcium transport, telomere maintenance, cytoskeleton assembly, and cell cycle. This broad mix shows no single cohesive function or pathway linking the proteins, indicating a heterogeneous cluster without a clear shared biological role.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015937","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0051225","count":1},{"id":"GO:0098703","count":1}]},{"hash":"1965860234481032323","title":"Translation and ribosome biogenesis","description":"The cluster is dominated by GO terms tied to translation and ribosome-related RNA processing, including translation, tRNA processing, preinitiation complex formation, reinitiation, termination, and rRNA maturation/processing. This points to proteins involved in ribosome assembly and the translation machinery, with ancillary RNA surveillance and RNA-modifying activity. Overall, a cohesive theme of protein synthesis and ribosome biogenesis emerges.","confidence":"High","size":14,"edges":69,"triangles":174,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0008033","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0002188","count":2},{"id":"GO:0006415","count":2}]},{"hash":"1489541093623180588","title":"Plant Growth Regulation and Hormone Signaling","description":"The proteins cluster around hormone-mediated development in plants (cytokinin signaling, ABA and SA responses), growth regulation (root meristem and vegetative growth), and secondary cell wall biogenesis, with translation appearing as a general activity. This combination suggests a functional group involved in growth control and hormone response rather than a single biosynthetic process.","confidence":"Medium","size":14,"edges":29,"triangles":14,"max_degree":8,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0009736","count":5},{"id":"GO:1900033","count":5},{"id":"GO:0010082","count":5},{"id":"GO:1905615","count":5}]},{"hash":"68043636363950078","title":"Neurodevelopment and Skeletal Morphogenesis","description":"This cluster is enriched for neural development terms (brain development, forebrain development, neuron apoptotic process) and skeletal morphogenesis, suggesting a developmental program spanning nervous and skeletal tissues. The ER-to-Golgi vesicle transport term hints at secretory and membrane-trafficking needs during development, supporting a coordinated growth and patterning theme; while some terms reference histone acetylation (obsolete) and general cell division, the strongest cohesive signal is neurodevelopment with supporting skeletal morphogenesis.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0048705","count":3},{"id":"GO:0051402","count":3}]},{"hash":"126055346922180763","title":"Cytoplasmic Translation Initiation Complex","description":"The cluster is dominated by GO terms related to translation initiation and formation of the cytoplasmic translation initiation complex, including explicit mentions of translational initiation and translation. Although a handful of terms are unrelated or obsolete annotations, the core signal points to involvement in cytoplasmic protein synthesis initiation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001732","count":1},{"id":"GO:0006413","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0060136","count":1},{"id":"GO:0043497","count":1}]},{"hash":"447553035414811541","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000480","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0048568","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1195694573376130984","title":"Viral replication and host RNA processing","description":"This cluster is enriched with terms tied to viral RNA genome replication, viral protein processing, and RNA-related processes (transcription, RNA processing, rRNA methylation). The presence of host autophagy activation and cell-cycle terms suggests virus\u2013host interactions and manipulation of host pathways, reinforcing a theme around viral life cycle and host RNA metabolism.","confidence":"Medium","size":14,"edges":11,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0039694","count":3},{"id":"GO:0039520","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0006396","count":2}]},{"hash":"1144518942622434135","title":"TLR signaling and inflammatory response","description":"The top GO terms cluster around Toll-like receptor pathways (TLR4, TLR8, TLR10) and immune/inflammatory outputs, including response to diacyl lipopeptides and regulation of chemokine production, suggesting the core function is innate immune sensing and inflammatory signaling. Some outlier terms (plant development, mineralization) appear as noise but do not negate the central theme.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019800","count":2},{"id":"GO:0071726","count":2},{"id":"GO:0032722","count":2},{"id":"GO:0034166","count":2},{"id":"GO:0010080","count":2}]},{"hash":"2223258325081327223","title":"Polysaccharide and polymer biosynthesis cluster","description":"The GO terms cluster around biosynthetic processes for lipopolysaccharide components (core region, O antigen), GDP-mannose metabolism, and related sugar-derived polymers, plus plant polymer biosynthesis (sporopollenin, anthocyanin/phenylpropanoid) and polyhydroxybutyrate. This suggests a broad theme of carbohydrate- and polymer-based biosynthesis rather than a single specific function.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0097171","count":4},{"id":"GO:0042619","count":4},{"id":"GO:0080110","count":3}]},{"hash":"1585165715804702081","title":"Unknown","description":"The proteins in this cluster map to a highly diverse set of GO terms, spanning neural development, DNA replication/repair, cell morphogenesis, various signaling processes, glucose response, immune defense, and angiogenesis. With no evident shared pathway or function and no edges connecting them, there isn\u2019t a cohesive theme to name the cluster beyond Unknown.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0000902","count":2}]},{"hash":"1857864874283032740","title":"Ammonium Transport & Nitrogen Utilization","description":"The cluster is dominated by terms tied to ammonium transport and nitrogen metabolism (ammonium transport, transepithelial transport, nitrogen utilization and its regulation). Additional terms for carbon dioxide transport and related metabolic processes suggest a broader nutrient uptake/assimilation theme in a photosynthetic or nutrient-processing context, but the core signal is ammonium handling and nitrogen use. Confidence: Medium","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006730","count":3},{"id":"GO:0015995","count":3},{"id":"GO:0046835","count":2},{"id":"GO:0072488","count":2},{"id":"GO:0070634","count":2}]},{"hash":"458750439132561276","title":"Tyrosine and phenylalanine catabolism","description":"This cluster is dominated by GO terms for L-tyrosine catabolic process, L-phenylalanine catabolic process, and homogentisate catabolic process, pointing to involvement in the tyrosine/phenylalanine degradation pathway. The other terms appear more peripheral or obsolete, but the strongest signal ties the proteins to aromatic amino acid breakdown via homogentisate. Confidence is moderate because a few non-specific terms exist, but the core theme is clear.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006572","count":1},{"id":"GO:0006559","count":1},{"id":"GO:1902000","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0060136","count":1}]},{"hash":"380193507602617034","title":"Cofactor Biosynthesis and Central Metabolism","description":"The terms point to cofactors biosynthesis (thiamine, lipoate), central metabolism (2-oxoglutarate and glutamate pathways), and redox homeostasis, indicating a cluster of enzymes tied to energy metabolism and cofactor production rather than transcription or signaling.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042391","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0007568","count":2}]},{"hash":"1787773571379463812","title":"TLR signaling and inflammatory response","description":"The top GO terms center on Toll-like receptor pathways (TLR4, TLR8, TLR10) and immune activation (diacyl lipopeptide response, regulation of chemokine production, inflammatory response), indicating a cohesive theme of innate immune signaling and inflammation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019800","count":1},{"id":"GO:0071726","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0034166","count":1},{"id":"GO:0010080","count":1}]},{"hash":"643559682041303179","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0046825","count":1},{"id":"GO:0045454","count":1}]},{"hash":"754166496218307002","title":"Membrane Ion Transport and Osmoregulation","description":"The cluster centers on transport of ions across the plasma membrane (sodium, potassium, and proton) and mechanisms maintaining intracellular ion balance and cell volume, with accompanying salt-stress and osmotic response terms. This suggests a cohesive function in membrane ion transport and osmoregulation rather than disparate processes.","confidence":"High","size":13,"edges":12,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098719","count":3},{"id":"GO:1903281","count":3},{"id":"GO:0071805","count":3},{"id":"GO:1902600","count":3},{"id":"GO:0030007","count":3}]},{"hash":"1292221709627030666","title":"Membrane Transport and Signaling","description":"The cluster\u2019s top terms cluster around membrane-associated processes: export of calcium and amino acids across the plasma membrane, protein palmitoylation that aids membrane association, vesicle trafficking (vacuole fusion), and activation of signaling pathways (PKA, calcineurin-NFAT). While some terms touch on metabolism or development, the dominant theme is membrane transport and signal transduction, justifying this label.","confidence":"Medium","size":13,"edges":12,"triangles":2,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":1},{"id":"GO:0032973","count":1},{"id":"GO:0009117","count":1},{"id":"GO:0046677","count":1},{"id":"GO:0006772","count":1}]},{"hash":"1990522777148139631","title":"Transcription Regulation and miRNA Processing","description":"The cluster combines GO terms centered on DNA-templated transcription and its termination control with RNA processing activities related to miRNA (pre-miRNA processing and miRNA catabolic process) and mRNA stabilization, suggesting involvement in transcriptional regulation and RNA maturation/turnover. Minor links to stress responses and immune cell movement are present but less defining, so the core theme is transcription control plus miRNA processing.","confidence":"Medium","size":13,"edges":15,"triangles":9,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0031564","count":1},{"id":"GO:1901724","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0031054","count":1}]},{"hash":"1777638315141768663","title":"Proteolysis, Immune Response, and Angiogenesis","description":"These proteins show a strong signal for proteolytic processing (proteolysis, ectodomain proteolysis, peptide catabolic process, angiotensin maturation) together with inflammatory/immune activity (adaptive immune response, leukotriene biosynthesis) and developmental/angiogenic signaling (multicellular organism development, cell differentiation, positive regulation of angiogenesis). The common thread appears to be proteolysis-driven regulation of immune responses and vascular development/remodeling.","confidence":"Medium","size":13,"edges":10,"triangles":0,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0046718","count":2},{"id":"GO:0030154","count":2},{"id":"GO:0002250","count":2}]},{"hash":"2173674624123166022","title":"Steroid and lipid metabolism with transcription regulation","description":"This cluster is enriched for steroid and lipid-related processes (C21-steroid hormone metabolism, androgen metabolism, sphingolipid biosynthesis, retinal metabolism) suggesting a lipid/steroid metabolic theme. It also includes transcriptional regulation and miscellaneous metabolic biosynthesis/catabolic terms (PHB, acetoin, antibiotic) that support a broader metabolic/regulatory context rather than a single narrow pathway.","confidence":"Medium","size":13,"edges":10,"triangles":5,"max_degree":5,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0008207","count":5},{"id":"GO:0045150","count":5},{"id":"GO:0042619","count":5}]},{"hash":"2216796531141711579","title":"Unknown","description":"The top GO terms are highly diverse, covering transcription regulation (galactose-induced and RNA Pol II), various cell-cycle events (G1/S transition, re-entry into mitosis), meiosis, epithelial differentiation in both plant and animal systems (stomatal opening, multi-ciliated and mammary gland epithelium), and even host-virus interactions. There isn\u2019t a single coherent biological theme connecting these terms for this cluster, so a specific label isn\u2019t justifiable.","confidence":"","size":13,"edges":12,"triangles":0,"max_degree":12,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000411","count":8},{"id":"GO:0044828","count":8},{"id":"GO:1903251","count":8},{"id":"GO:0000082","count":8},{"id":"GO:0032026","count":8}]},{"hash":"1857693574968259013","title":"Unknown","description":"The set of GO terms spans redox biology (oxidation-reduction, redox homeostasis, selenium response), innate immune signaling (response to lipopolysaccharide), RNA processing (spliceosome), stem cell proliferation, development (pituitary gland), neurotransmitter regulation (serotonin), and epigenetic regulation, with several obsolete terms and no clear single theme tying all proteins together.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0032496","count":4},{"id":"GO:0000380","count":4},{"id":"GO:2000648","count":4},{"id":"GO:0060992","count":3}]},{"hash":"955049697979702131","title":"Unknown","description":"The top GO terms cover a wide range of processes (pteridine metabolism, polyphosphate breakdown, DNA recombination and repair, cell differentiation, translation, apoptosis regulation, oogenesis, ATP response, and synaptic plasticity), with only one edge linking proteins and no shared dominant function. This lack of a cohesive, single theme suggests no clear, common function characterizes the cluster, so it is labeled Unknown.","confidence":"","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019889","count":1},{"id":"GO:0006798","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0030154","count":1}]},{"hash":"2250032102537667456","title":"Golgi-ER Vesicle Trafficking","description":"Top GO terms are dominated by Golgi apparatus organization and vesicle trafficking within the secretory pathway, including Golgi ribbon formation, intra-Golgi and ER-to-Golgi transport, and retrograde endosome-to-Golgi transport. These indicate a core function in intracellular protein transport through the Golgi. Though a couple of terms touch on neural signaling and RNA processing, the strongest and most frequent themes center on Golgi- and vesicle-mediated transport, supporting a label focused on Golgi/ER trafficking rather than nuclear processes.","confidence":"Medium","size":13,"edges":15,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0090161","count":3},{"id":"GO:0035640","count":2},{"id":"GO:2000463","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0006886","count":2}]},{"hash":"2121691607386276259","title":"Cell Cycle Regulation and Growth Signaling","description":"The top GO terms center on cell division and growth control\u2014G2/M transition, the general cell cycle, and regulation of cytokinesis\u2014often intertwined with apoptosis and growth pathways like Hippo signaling. While some terms point to differentiation or synaptic organization, the core theme across the cluster appears to be control of proliferation and division, justifying a name focused on cell cycle and growth signaling.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1946992787489127186","title":"Unknown","description":"The top GO terms across these proteins are highly diverse, spanning nuclear transport (nuclear pore organization, import of NLS-bearing proteins, mRNA export), spindle checkpoint signaling, and various biosynthetic and lipid-modification processes (hopanoid and tuberculosinol biosynthesis, protein desumoylation, geranylgeranylation). With no clear, recurring functional theme or shared pathway among multiple proteins, there isn\u2019t a coherent cluster function to label, so Unknown is most appropriate.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072417","count":1},{"id":"GO:0031990","count":1},{"id":"GO:0006999","count":1},{"id":"GO:0006607","count":1},{"id":"GO:0060188","count":1}]},{"hash":"2187963866219783867","title":"Immune signaling and stress regulation","description":"These terms cluster around regulation of signaling pathways, particularly immune-related signaling (CD40 signaling, PGRP signaling, antibacterial peptide biosynthesis) and broader regulatory processes (positive regulation of GTPase activity, TGF-beta response). There are also elements of cellular stress and protein quality control (ERAD-related terms, calcium handling, necroptosis regulation). The mixed set suggests a group of proteins that modulate signaling in immune and stress contexts rather than a single, tight pathway.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0010880","count":2},{"id":"GO:0071560","count":2},{"id":"GO:0006516","count":1}]},{"hash":"583015701559292080","title":"Redox detox and oxidative stress response","description":"The cluster is dominated by redox-related functions: hydrogen peroxide response, removal of superoxide radicals, glutathione metabolism, and redox homeostasis, pointing to oxidative stress defense and detoxification. Some metabolism terms (glycolysis, propylene catabolism) are broader but do not outweigh the redox theme.","confidence":"Medium","size":13,"edges":13,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042542","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0070276","count":2},{"id":"GO:0006096","count":2}]},{"hash":"813780988032539130","title":"Mitotic Proliferation with ER-Golgi Trafficking","description":"The cluster is dominated by terms tied to mitosis (mitotic spindle assembly, mitotic cell cycle, cell division) and to ER-Golgi-related vesicle trafficking (COPII budding, Golgi-to-ER, Golgi-to-endosome), with additional growth and brain-development terms suggesting a proliferative developmental context. This combination points to proteins involved in dividing cells that also coordinate secretory pathway function during growth.","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0006888","count":6},{"id":"GO:0090114","count":5},{"id":"GO:0008283","count":5}]},{"hash":"337101511200368014","title":"Mitochondrial Apoptosis Regulation and Stress Response","description":"The GO terms point to regulation of both intrinsic and extrinsic apoptotic pathways, with involvement of mitochondrial inner membrane processes and ROS metabolism. Supporting terms include stress-responsive signaling (interferon-beta, retinoic acid) and proteostasis (protein folding, regulation of catalytic activity), suggesting a cohesive module that modulates apoptosis in response to mitochondrial stress and oxidative signals. ","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0050790","count":2},{"id":"GO:0035458","count":1},{"id":"GO:2001243","count":1},{"id":"GO:0045039","count":1}]},{"hash":"1134903107777300789","title":"Xenobiotic transport and redox detoxification","description":"This cluster centers on membrane transport of xenobiotics and nutrients (xenobiotic, nitrite, and vitamin transmembrane transport) alongside redox balance and detoxification (cell redox homeostasis, cellular oxidant detoxification, oxidation-reduction). The presence of antibiotic response and metabolic terms like glycerol catabolism and PQQ biosynthesis suggests a bacterial context where transport and redox metabolism coordinate detoxification and utilization of diverse substrates. The viral process term may be an outlier or annotation noise, but it does not dominate the theme. Overall, the label reflects the strongest common thread among the terms: transport of compounds across membranes coupled with redox-based detoxification. ","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0016032","count":2},{"id":"GO:0018189","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0035461","count":2}]},{"hash":"2173646646317895941","title":"Nuclear RNA processing and ribosome biogenesis","description":"This cluster centers on RNA processing and ribosome assembly, with strong representation for mRNA splicing via spliceosome, ribosome biogenesis, and maturation of rRNA transcripts, suggesting a shared nuclear machinery role. Some terms reflect broader cell cycle and genome maintenance processes (cohesion, homologous recombination, cell division), which are compatible with nuclear functions. Minor terms like brain development and cellular conjugation may be annotations spillover rather than core cluster functions.","confidence":"Medium","size":13,"edges":5,"triangles":0,"max_degree":4,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0007064","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0000724","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0000747","count":3}]},{"hash":"598270833818731487","title":"Lipid metabolism and organ development","description":"The cluster is dominated by lipid-related processes (fatty acid beta-oxidation, acetyl-CoA catabolic, cholesterol metabolism) and tissue development terms (liver, adipose, brain development), with a hormone response term suggesting regulatory signaling. A term on apoptosis regulation hints at links between metabolism and cell survival. Overall, the proteins appear tied to lipid handling in the context of organ development and hormonal control.","confidence":"High","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":7},{"id":"GO:0042619","count":5},{"id":"GO:0046356","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0030435","count":5}]},{"hash":"1958733951762901320","title":"Nitrogen fixation and Fe-S assembly with transporters","description":"The top terms center on nitrogen fixation and iron-sulfur cluster assembly, which are biologically linked because nitrogenase relies on Fe-S clusters. The presence of multiple transmembrane transport terms (for nitrite, nitrate, phosphate, arabinose, potassium, sialic acid, fucose) suggests accompanying transporter activity within the same protein set. Despite an obsolete oxidation-reduction term, the core theme appears to be nitrogen metabolism tied to Fe-S biology, with diverse transport capabilities. ","confidence":"Medium","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0009399","count":2},{"id":"GO:0015707","count":1},{"id":"GO:0015706","count":1}]},{"hash":"1916450343990953915","title":"Innate immune and neurovascular signaling","description":"The top terms converge on signaling themes that bridge immune response with neural development and blood vessel formation: innate immune response, integrin-mediated signaling, axon fasciculation, and angiogenesis. Cyclic nucleotide biosynthesis adds a broader signaling context. Although some GO terms are obsolete, the overall pattern fits a cluster of proteins involved in neuro-immune-vascular communication.","confidence":"Medium","size":13,"edges":45,"triangles":67,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":10},{"id":"GO:0097156","count":9},{"id":"GO:0007229","count":9},{"id":"GO:0009190","count":9},{"id":"GO:1901214","count":9}]},{"hash":"537668226900969432","title":"Epithelial junctions and organ morphogenesis","description":"Top signals point to epithelial cell-cell adhesion (adherens junction and desmosome assembly) and organ development (hair follicle placode, renal vesicle formation, inner medulla development), suggesting a cluster centered on epithelial junction formation and morphogenesis. Some terms (peroxisome import, DNA damage response, mitochondrial Ca2+ regulation) are broader or less directly connected, but do not override the dominant developmental adhesion theme. ","confidence":"Medium","size":13,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016558","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0071681","count":3},{"id":"GO:0072033","count":3},{"id":"GO:0072053","count":3}]},{"hash":"1624319621887690770","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0036265","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0030433","count":2}]},{"hash":"964900027229112718","title":"mRNA Capping and Translation Initiation","description":"The top GO terms are dominated by translation-related processes: initiation and reinitiation (including IRES-dependent initiation and translation preinitiation complex formation) and RNA guanine-N7 methylation (m7G capping), which collectively define mRNA maturation and the start of translation. The chlorophyll and porphyrin-related terms appear peripheral, not central to the cluster\u2019s main function. Therefore, the cluster is best described by mRNA capping and translation initiation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0075525","count":2},{"id":"GO:0075522","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0006446","count":2}]},{"hash":"1392068543033673889","title":"ER stress response and protein processing","description":"The top GO terms are dominated by endoplasmic reticulum\u2013related processes (ER to Golgi transport, ER unfolded protein response, misfolded protein catabolic process, protein processing), indicating a focus on ER function and quality control. Additional terms like response to hypoxia and stress granule disassembly point to general cellular stress responses, which supports labeling this cluster as ER stress\u2013related protein processing and quality control.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":3},{"id":"GO:0035617","count":2},{"id":"GO:0033314","count":2},{"id":"GO:0016485","count":2},{"id":"GO:0006888","count":2}]},{"hash":"328621089506023791","title":"Membrane Solute Transporters","description":"The top GO terms point to diverse membrane transport activities (antimonite, arsenite, sodium-dependent organic anion, and plasma membrane pyruvate transport), indicating a common theme of solute/ion movement across membranes. A few outlier terms (face morphogenesis, blood coagulation) are likelyNoise. Overall, the cluster appears to group proteins with transporter functions, justifying this label.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":1},{"id":"GO:0015699","count":1},{"id":"GO:0006849","count":1},{"id":"GO:0043251","count":1},{"id":"GO:0015700","count":1}]},{"hash":"675231942622405356","title":"Unknown","description":"The GO terms span translation/RNA modification and membrane transport/proteolysis, plus development, with no coherent single function tying the proteins together. No edges also reduce evidence for a unified pathway, so there isn't a clear, representative label.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046944","count":1},{"id":"GO:0006450","count":1},{"id":"GO:0002949","count":1},{"id":"GO:0015699","count":1},{"id":"GO:0006849","count":1}]},{"hash":"2151783732109448354","title":"Mitochondrial Nutrient Transport and Metabolic Signaling","description":"Most of the top GO terms describe transport of nutrients or substrates into mitochondria (thiosulfate, heme, thiamine pyrophosphate, pyrimidine nucleotides) and mitochondria-related stress/metabolic signaling (amino acid starvation, superoxide, insulin/IGF signaling). A few terms are tangential (female pregnancy, obsolete mitochondrial genome maintenance), but the dominant theme is mitochondrial nutrient import and metabolic regulation.","confidence":"High","size":12,"edges":12,"triangles":4,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0034198","count":10},{"id":"GO:0015709","count":9},{"id":"GO:0015886","count":9},{"id":"GO:0030974","count":9},{"id":"GO:0007565","count":9}]},{"hash":"1985019264345724325","title":"Developmental cell fate specification and signaling","description":"The top GO terms cluster around specifying cell fates during development (wing cell fate, cone cell fate commitment, spermatid differentiation) and EGFR ligand maturation, indicating a common theme of developmental differentiation and signaling. Some terms pertain to broader cellular processes, but the developmental/fate-specification theme is dominant.","confidence":"High","size":12,"edges":12,"triangles":2,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0035311","count":3},{"id":"GO:0032815","count":3},{"id":"GO:0034620","count":3},{"id":"GO:0042676","count":3},{"id":"GO:0048515","count":3}]},{"hash":"635151286208169362","title":"Developmental ECM Remodeling","description":"The terms cluster around extracellular matrix remodeling (collagen catabolic process, basement membrane disassembly, bone resorption, intramembranous ossification) and organ morphogenesis (lung branching), suggesting a shared theme of tissue remodeling during development. While immune/neuropeptide catabolism terms appear, they do not dominate the cluster, so the central emphasis appears to be ECM turnover in morphogenesis. ","confidence":"Medium","size":12,"edges":59,"triangles":157,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0060441","count":5},{"id":"GO:0030574","count":5},{"id":"GO:2000179","count":5},{"id":"GO:0034769","count":5},{"id":"GO:0045453","count":5}]},{"hash":"1373814332699951179","title":"Plant Photoreception and Light Harvesting","description":"The top GO terms point to responses to multiple light wavelengths (blue, red, far-red, UV-A) and to light intensity, together with GO terms for photosynthesis light harvesting in photosystems I and II and chlorophyll (phytol) biosynthesis. This pattern strongly suggests a cluster of proteins involved in photoreception and the light-harvesting machinery of photosynthesis in plants.","confidence":"High","size":12,"edges":10,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009637","count":2},{"id":"GO:0018298","count":2},{"id":"GO:1904964","count":2},{"id":"GO:0010218","count":2},{"id":"GO:0009769","count":2}]},{"hash":"1135238445830081420","title":"Unknown","description":"The top GO terms are spread across very different processes: acetylcholine secretion and biosynthesis with synaptic potentials (neural signaling), sieve element differentiation (plant vascular development), angiogenesis, plus DNA repair, mRNA processing, cellular cadmium response, and a G2/M cell cycle transition. This broad mix lacks a single cohesive function or pathway that ties the proteins together, and there are no edges or triangles to suggest a defined module. Therefore, no specific label can be confidently assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061526","count":2},{"id":"GO:0090603","count":2},{"id":"GO:0008292","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0006397","count":2}]},{"hash":"913373602456547938","title":"Ribosome biogenesis and translation","description":"The top terms are dominated by translation and ribosome-related processes (translation, translational initiation/termination, ribosome biogenesis, ribosomal subunit biogenesis, mitochondrial translation), indicating a cluster of proteins involved in the protein synthesis machinery and ribosome assembly. Some ancillary terms (response to antibiotic, viral genome replication) may reflect broader interactions with translation, but the core signal is the ribosome/translation apparatus.","confidence":"High","size":12,"edges":62,"triangles":184,"max_degree":11,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0046677","count":4},{"id":"GO:0042274","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0006413","count":3}]},{"hash":"1746349841251814049","title":"Plant cell wall biosynthesis and mucilage production","description":"The top GO terms cluster around plant-specific cell wall biogenesis: root hair cell development, cell wall organization, and the biosynthesis of pectic polysaccharides such as homogalacturonan and rhamnogalacturonan II, as well as mucilage biosynthesis. This points to proteins involved in assembling and modifying cell wall components and mucilage, with some related glycosylation processes, rather than general cytosolic functions. ","confidence":"High","size":12,"edges":11,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0080147","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0006486","count":2},{"id":"GO:0010306","count":2},{"id":"GO:0006049","count":1}]},{"hash":"2201060697486069832","title":"Unknown","description":"The GO terms span several unrelated processes (cell division/cell cycle; various metabolic pathways; innate immune and interferon responses; plant hormone signaling and sex differentiation; mitochondria distribution), with no single cohesive function linking them. Therefore a concise, representative label cannot be assigned.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0006574","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009820","count":2},{"id":"GO:0007049","count":2}]},{"hash":"424071601137069311","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006265","count":7},{"id":"GO:0045944","count":7},{"id":"GO:0071031","count":7},{"id":"GO:0010501","count":7},{"id":"GO:0071051","count":7}]},{"hash":"446360038705321034","title":"Plant stress signaling and hormone regulation","description":"This cluster centers on plant-specific stress responses and hormone signaling: regulation of leaf senescence, chlorophyll biosynthesis, cytokinin- and gibberellin-mediated pathways, cadmium response, and unfolded protein/ER stress responses. A few terms are non-plant (e.g., apoptotic process, T cell differentiation) suggesting some noise, but the predominant theme is plant stress signaling and growth regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":1},{"id":"GO:0033081","count":1},{"id":"GO:1900056","count":1},{"id":"GO:0006986","count":1},{"id":"GO:0009736","count":1}]},{"hash":"1668014574239961118","title":"Plant Hormone Signaling and Growth Regulation","description":"This cluster centers on plant hormone signaling terms (cytokinin-activated signaling; responses to abscisic acid and salicylic acid) and growth-related processes (regulation of root meristem growth, positive regulation of vegetative growth, and positive regulation of secondary cell wall biogenesis). Together they point to proteins involved in hormone-driven control of plant development and growth, with some telomere-related terms likely ancillary. Confidence: Medium","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009736","count":1},{"id":"GO:1900033","count":1},{"id":"GO:0010082","count":1},{"id":"GO:1905615","count":1},{"id":"GO:1901348","count":1}]},{"hash":"104732569162774857","title":"ER-Golgi trafficking and nuclear pore localization","description":"The top terms cluster around vesicle transport between the ER and Golgi (COPII budding, ER-to-Golgi, Golgi-to-ER retrograde) and nuclear pore localization, suggesting a functional group focused on intracellular trafficking and transport. A few developmental and defense terms appear less related, likely annotation noise. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031081","count":2},{"id":"GO:0090114","count":2},{"id":"GO:0072520","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2}]},{"hash":"2158332731722221598","title":"Diverse Transmembrane Transporters","description":"The dominant GO terms are transmembrane transport across a wide range of substrates (nitrite, nitrate, phosphate, arabinose, potassium, sialic acid, sodium, xenobiotic, etc.), indicating membrane transporter activity with diverse substrates.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":1},{"id":"GO:0015706","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0071805","count":1}]},{"hash":"2062564394074137982","title":"Osmotic stress response and phosphatidylinositol biosynthesis","description":"The cluster exhibits strong signals for osmotic stress response (hyperosmotic salinity) and ABA-activated signaling, together with phosphatidylinositol and inositol biosynthesis pathways, pointing to a module that links osmostress adaptation with membrane lipid signaling. Some other metabolic terms (gluconeogenesis, sulfate assimilation) may reflect broader cellular metabolism rather than core function, but the core theme remains osmostress response and phosphoinositide metabolism.","confidence":"High","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042538","count":3},{"id":"GO:0046855","count":3},{"id":"GO:0006661","count":3},{"id":"GO:0009738","count":3},{"id":"GO:0000103","count":3}]},{"hash":"692393144358368430","title":"Neuronal Development and Transcriptional Regulation","description":"The cluster is dominated by neural development terms (forebrain development, nervous system development, dendrite morphogenesis, sensory perception of pain) along with DNA-templated transcription, indicating a group of proteins that regulate neural development through transcriptional control. Some DNA maintenance terms are present, but the overall signal points to neurodevelopmental gene regulation.","confidence":"Medium","size":12,"edges":14,"triangles":7,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0006260","count":8},{"id":"GO:0006281","count":7},{"id":"GO:0007275","count":7},{"id":"GO:0048240","count":6}]},{"hash":"1686937348061227565","title":"Ribosome Biogenesis and Translation","description":"This cluster is strongly enriched for GO terms related to protein synthesis and ribosome assembly, including translation, cytoplasmic translation, ribosome biogenesis, and ribosomal small subunit biogenesis, as well as tRNA modification. While there are some cell cycle terms, the dominant theme is components and processes involved in making and operating ribosomes and translating mRNA, supporting a cohesive role in protein synthesis and ribosome assembly.","confidence":"High","size":12,"edges":10,"triangles":3,"max_degree":6,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0042254","count":3},{"id":"GO:0002181","count":2},{"id":"GO:1901001","count":2},{"id":"GO:0051301","count":2}]},{"hash":"70179011516554955","title":"DNA Replication and Centrosome Cycle Regulators","description":"The cluster is dominated by GO terms tied to DNA replication, regulation of nuclear DNA replication, the centrosome cycle, and mitotic chromatid dynamics, pointing to core cell cycle and DNA replication control. While a few terms relate to neural development and synaptic processes, the strongest signal centers on replication and cell-cycle machinery, with some annotations possibly reflecting broader roles in development. Confidence: High","confidence":"","size":12,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":11},{"id":"GO:0010571","count":10},{"id":"GO:0007098","count":10},{"id":"GO:2001033","count":9},{"id":"GO:1990758","count":9}]},{"hash":"860996545538462276","title":"Metal Ion and ROS Stress Response","description":"The terms cluster around cellular responses to metal ions (cadmium, copper), oxidative/ROS stress (singlet oxygen) and related chemical exposures (nitroglycerin), plus transcriptional regulation; together they suggest a coherent theme of stress signaling and transcriptional response, despite some obsolete annotations.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060136","count":2},{"id":"GO:0043497","count":2},{"id":"GO:2001033","count":2},{"id":"GO:1904843","count":2},{"id":"GO:0071276","count":2}]},{"hash":"1461078277877845871","title":"Protein acetylation and related metabolism","description":"This cluster is dominated by acetylation-related GO terms (N-terminal acetylation, various peptide lysine acetylations, histone acetylation) and acetyltransferase-linked processes, with supporting pathways such as melatonin biosynthesis and acetoin/putrescine/mycothiol biosynthesis, pointing to a common theme of acetylation chemistry and acetyl-CoA\u2013dependent metabolism.","confidence":"High","size":12,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":5},{"id":"GO:0045150","count":5},{"id":"GO:0061606","count":5},{"id":"GO:0018002","count":5},{"id":"GO:0010125","count":5}]},{"hash":"959859448618276100","title":"Detox and diverse secondary metabolite biosynthesis","description":"This cluster is characterized by GO terms related to toxin response and detoxification (response to toxic substance, cellular oxidant detoxification) alongside a range of biosynthetic processes for secondary metabolites and signaling molecules (alkaloids, antibiotics, strigolactones, menaquinone) and related regulatory pathways (endocannabinoid signaling, strigolactone response). The common thread appears to be detox/middle-layer metabolism and diverse biosynthetic capabilities, rather than a single, cohesive pathway, which supports a broad label like this. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":3},{"id":"GO:0098869","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0019380","count":2},{"id":"GO:0009820","count":2}]},{"hash":"1673660374592915694","title":"Ubiquitin-Dependent Protein Degradation & ERAD","description":"The top GO terms are centered on ubiquitination and proteasome-mediated turnover (ubiquitin-dependent protein catabolic process, K48-linked ubiquitination, ERAD). This points to a cohesive theme of proteostasis through ubiquitin-mediated degradation, with supporting notes on receptor turnover (Wnt receptor catabolic process) and autoubiquitination; a few other terms appear ancillary or outdated annotations. ","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0038018","count":5},{"id":"GO:0070936","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0016558","count":5}]},{"hash":"1319240063300270088","title":"Plant Golgi sugar and nucleotide transporters","description":"The dominant GO terms point to transmembrane transport of nucleotide sugars into the Golgi (UDP-Gal, GDP-fucose, UDP-N-acetylglucosamine) and related sugar/ion transport, suggesting a module of Golgi-based transport machinery in plants. Some terms reflect plant development processes (pollen exine formation, shoot apical meristem regulation), which can relate to Golgi-mediated glycosylation and wall biosynthesis in plants. Overall, the cluster appears to represent plant Golgi sugar/nucleotide transporters and associated membrane transport activities.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071260","count":2},{"id":"GO:0061408","count":2},{"id":"GO:1990569","count":1},{"id":"GO:0032973","count":1},{"id":"GO:1902183","count":1}]},{"hash":"656745875867484338","title":"Neuronal signaling and axonogenesis","description":"This cluster centers on neuronal processes, with GO terms for axonogenesis, synaptic potentiation, presynaptic calcium regulation, and exocytosis, pointing to proteins involved in neuronal signaling and axon growth. Minor cardiac-related terms appear but do not define the cluster's main function.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0086004","count":1},{"id":"GO:0045921","count":1},{"id":"GO:0014898","count":1}]},{"hash":"657832696637355594","title":"Neural development and potassium signaling","description":"This cluster shows a clear emphasis on neural development and function, with terms like axonogenesis, long-term synaptic potentiation, excitatory postsynaptic potential, and Schwann cell development, alongside potassium ion homeostasis and potassium transmembrane transport. These together point to proteins involved in neuronal maturation and activity governed by potassium signaling. Although heart development and angiogenesis appear, they seem less central to the core pattern, which is neural development plus ion-channel\u2013related signaling. ","confidence":"Medium","size":12,"edges":10,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0060291","count":2},{"id":"GO:0060079","count":2},{"id":"GO:0043065","count":2}]},{"hash":"1665196534033300165","title":"Serine-related amino acid metabolism","description":"This cluster is dominated by serine-related terms (L-serine catabolic process, D-serine biosynthetic process) and includes several other amino acid biosynthesis and central-carbon metabolism terms (tryptophan, threonine, 2-oxobutyrate, pyruvate, oxaloacetate, transsulfuration), indicating a serine-centric amino acid metabolism theme.","confidence":"High","size":12,"edges":66,"triangles":220,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006565","count":5},{"id":"GO:0006107","count":3},{"id":"GO:0000162","count":3},{"id":"GO:0009088","count":3},{"id":"GO:0046360","count":3}]},{"hash":"1988982696859333451","title":"Amino Acid Biosynthesis and Related Metabolism","description":"The terms show multiple amino acid biosynthetic processes (methionine, threonine, isoleucine, homoserine) and various other metabolic pathways (inositol, galactitol, galacturonate, GDP-L-fucose salvage, cholesterol biosynthesis), suggesting a cluster of proteins involved in general metabolism with a focus on amino acid production rather than a single specific pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009086","count":3},{"id":"GO:0009088","count":3},{"id":"GO:0009097","count":2},{"id":"GO:0019310","count":2}]},{"hash":"682838741111394772","title":"Nematode Molting and Cuticle Formation","description":"The top GO terms point to nematode-specific development, including molting cycles, collagen/cuticle formation, and head (face) morphogenesis, with a few general processes like pharyngeal pumping and oxygen homeostasis. This suggests a theme of nematode developmental remodeling and cuticle formation, though the terms are sparsely represented, yielding a moderate confidence. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901874","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0043050","count":1},{"id":"GO:0032364","count":1},{"id":"GO:0055114","count":1}]},{"hash":"826732844032287957","title":"RNA processing and tRNA modification; programmed cell death","description":"This cluster centers on RNA metabolism: RNA processing, tRNA wobble modification, and translational regulation, with supporting RNA repair and mRNA processing terms. A minority of terms relate to programmed cell death and mitochondrial membrane permeability, implying stress-response connections but a mixed, loosely linked set of roles. Overall, the RNA-processing signature is the strongest signal, though not exclusively.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006858","count":1},{"id":"GO:0006897","count":1},{"id":"GO:0035553","count":1},{"id":"GO:0012501","count":1},{"id":"GO:0006397","count":1}]},{"hash":"2179124545846526149","title":"Transcription Regulation and Cell Cycle Control","description":"This cluster includes GO terms tied to transcriptional regulation (DNA-templated transcription, transcription by RNA polymerase II) and cell cycle control (negative regulation of G1/S transition, mitosis without cytokinesis), suggesting a shared theme of coordinating transcriptional programs with cell cycle progression. Other terms point to broader developmental and stress-response roles, but the core signal appears to be transcription regulation linked to cell cycle control.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000134","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0060707","count":1},{"id":"GO:0045944","count":1},{"id":"GO:0008015","count":1}]},{"hash":"608374916156580932","title":"Plant Golgi sugar transporters and glycosylation","description":"The top GO terms cluster around transmembrane transport of sugars and nucleotide sugars (e.g., UDP-glucose, phosphoenolpyruvate into Golgi lumen) and glycosylation processes (fucosylation, N-/O-glycan fucosylation), which together point to Golgi-localized sugar transport and glycosylation pathways in plant cells. Some root-development terms may reflect downstream roles, but the shared theme is Golgi sugar transport and glycosylation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":1},{"id":"GO:0035436","count":1},{"id":"GO:0015713","count":1},{"id":"GO:0036066","count":1},{"id":"GO:0080147","count":1}]},{"hash":"1673205208771707299","title":"Small-molecule and lipid transport","description":"The proteins cluster around membrane transport activities, including ammonium transmembrane transport, organic cation transport, and polyol transmembrane transport, as well as glycolipid transport, with supporting glycosphingolipid metabolism. This points to a cohesive theme of moving small molecules and lipids across membranes, rather than a single enzymatic function. While a few redox-related terms appear, the dominant signal is transport/metabolism of lipids and small molecules. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032364","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0072488","count":1}]},{"hash":"662727187663824717","title":"Mitochondrial transport and stress signaling","description":"The cluster centers on mitochondrial transport activities (thiosulfate, heme, thiamine pyrophosphate, and nucleotide import into mitochondria) and mitochondrial stress/apoptotic responses, with accompanying signaling responses to insulin/IGF and oxidative stress. A reproductive term appears as an outlier, but the dominant pattern points to mitochondrial transport/metabolism and stress signaling. ","confidence":"Medium","size":11,"edges":14,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015709","count":4},{"id":"GO:0015886","count":4},{"id":"GO:0030974","count":4},{"id":"GO:0007565","count":4},{"id":"GO:1990519","count":4}]},{"hash":"482097725936129533","title":"Mitochondrial transport, metabolism, and stress signaling","description":"The cluster centers on transport of diverse cofactors into mitochondria (thiosulfate, heme, thiamine pyrophosphate, pyrimidine nucleotides) and mitochondrial-focused responses, including oxidative stress (superoxide), apoptotic mitochondrial changes, and signaling related to insulin/IGF pathways. This points to a cohesive theme of mitochondrial transport/metabolism intertwined with stress and signaling. The pregnancy term appears out of place and may reflect annotation noise; overall the core function is mitochondrial transport and stress-related signaling.","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015709","count":3},{"id":"GO:0015886","count":3},{"id":"GO:0030974","count":3},{"id":"GO:0007565","count":3},{"id":"GO:1990519","count":3}]},{"hash":"1581682441855180800","title":"Mitochondrial Cofactor and Nucleotide Transport","description":"The top terms cluster around transport of cofactors and nucleotides into/within mitochondria (thiosulfate, heme, thiamine pyrophosphate, pyrimidine nucleotides) and include mitochondrial-specific stress and apoptotic responses (superoxide, insulin-related signaling). This suggests a cohesive function in mitochondrial transport and related regulation, with some metabolic signaling context as secondary, hence a Medium confidence.","confidence":"Medium","size":11,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015709","count":4},{"id":"GO:0015886","count":4},{"id":"GO:0030974","count":4},{"id":"GO:0007565","count":4},{"id":"GO:1990519","count":4}]},{"hash":"1482940798962765869","title":"Glycolysis and TCA Cycle Core Metabolism","description":"The top GO terms cluster around central carbon metabolism: glycolytic process, the TCA cycle, and thiamine biosynthesis (a cofactor for pyruvate dehydrogenase), plus regulation of pyruvate decarboxylation to acetyl-CoA. This points to a shared role in energy production and carbon flux from sugar breakdown to the TCA cycle, with a minor note of oxidative stress response (paraquat) that does not define the core function.","confidence":"High","size":11,"edges":32,"triangles":39,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0006096","count":4},{"id":"GO:0006099","count":4},{"id":"GO:0061732","count":4}]},{"hash":"913198428983723992","title":"Lipid biosynthesis and sterol regulation","description":"The top GO terms cluster around lipid metabolism and sterol pathways: prostaglandin biosynthesis, unsaturated fatty acid biosynthesis, regulation of ergosterol biosynthetic process, and mannosyl-inositol phosphorylceramide metabolic process, suggesting a shared role in lipid/sterol production and membrane lipid homeostasis. A few terms (nitrate assimilation, sebaceous gland differentiation, CNS myelin maintenance, mitochondrion inheritance) appear as outliers or cross-species annotations but do not negate the central lipid/sterol theme. Overall, the proteins likely participate in lipid and sterol biosynthesis and regulation.","confidence":"Medium","size":11,"edges":18,"triangles":6,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0001516","count":3},{"id":"GO:0046232","count":3},{"id":"GO:0006809","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006675","count":2}]},{"hash":"219457333087521488","title":"Endosomal Transport Pathways","description":"GO terms indicate endosomal trafficking between compartments (endosome to lysosome, endosome to Golgi, endosome to late endosome) and CVT pathway targeting to vacuoles, defining a vesicular transport cluster; some unrelated terms may reflect pleiotropy or background noise, but the dominant theme is endosomal transport.","confidence":"Medium","size":11,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0034498","count":2},{"id":"GO:0032258","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0045022","count":2}]},{"hash":"71055900766416116","title":"Transcription Regulation and Redox Detox","description":"The cluster is enriched for DNA-templated transcription and negative regulation of transcription by RNA Pol II, plus redox-related processes like cellular oxidant detoxification and deglutathionylation, suggesting a group involved in transcriptional control that may be modulated by redox state.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0019310","count":2},{"id":"GO:0098869","count":2}]},{"hash":"137207771851192327","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":16,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":1},{"id":"GO:0000715","count":1},{"id":"GO:0038018","count":1},{"id":"GO:0016558","count":1},{"id":"GO:0033151","count":1}]},{"hash":"138298596597288741","title":"TLR-Mediated Antiviral Innate Immunity","description":"The cluster\u2019s prominent GO terms cluster around toll-like receptor signaling (TLR7/8) and downstream MyD88-dependent pathways, innate immune response, and defense against virus, including positive regulation of interferon-alpha production. This points to a cohesive innate antiviral signaling module driven by TLRs, despite a few unrelated terms present. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034158","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0002755","count":2},{"id":"GO:0045356","count":2},{"id":"GO:0034154","count":2}]},{"hash":"1670682628576771702","title":"RNA Processing and Splicing","description":"This cluster is enriched for RNA metabolism: tRNA processing, spliceosomal complex/snRNP assembly, and P-body assembly with related mRNA decapping. These RNA maturation and turnover activities provide the most coherent unifying theme across the GO terms, with a few other terms (osmotic stress, cell cycle) likely representing secondary aspects. ","confidence":"Medium","size":11,"edges":9,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0034220","count":1},{"id":"GO:0071470","count":1},{"id":"GO:0009992","count":1},{"id":"GO:0000290","count":1}]},{"hash":"623233429001904271","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0046825","count":1},{"id":"GO:0045454","count":1}]},{"hash":"777954621788670773","title":"Developmental Transcription and Chromatin Regulation","description":"The top GO terms point to transcription, multiple developmental processes, and chromatin dynamics (heterochromatin, DNA repair) with protein turnover, suggesting a module focused on regulating gene expression during development and genome maintenance. Some immune/viral terms are likely less central.","confidence":"Medium","size":11,"edges":32,"triangles":43,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0042787","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0007519","count":2}]},{"hash":"2267456864560945147","title":"Microtubule dynamics in mitosis and cytokinesis","description":"This cluster centers on GO terms describing microtubule behavior during cell division, including plus-end directed sliding, spindle pole separation, and actomyosin ring assembly. It also includes microtubule-based vesicle transport and cytoplasmic microtubule depolymerization, pointing to coordinated roles in mitosis, cytokinesis, and intracellular trafficking. Some terms touch on adhesion and RNA granule dynamics, but the dominant signal is cytoskeleton- and microtubule-driven cell division and organization.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":10},{"id":"GO:0031535","count":10},{"id":"GO:0000073","count":10},{"id":"GO:0035617","count":10},{"id":"GO:0001560","count":10}]},{"hash":"1516722600134018765","title":"Spliceosome Regulation and mRNA Silencing","description":"These proteins cluster around post-transcriptional RNA processing: multiple GO terms point to spliceosome-mediated splicing (cis and alternative) and its regulation, plus ncRNA- and miRNA-mediated gene silencing, mRNA stability control, and even translation initiation machinery assembly. Together, they suggest a module coordinating splicing and RNA-based regulation of gene expression.","confidence":"High","size":11,"edges":54,"triangles":156,"max_degree":10,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":7},{"id":"GO:0031047","count":7},{"id":"GO:0010610","count":7},{"id":"GO:0045292","count":7},{"id":"GO:0048025","count":6}]},{"hash":"223276751625751504","title":"Fatty acid and quinone biosynthesis","description":"This cluster shows strong representation of fatty acid metabolism terms (beta-oxidation, fatty acid elongation, short- and medium-chain fatty acid biosynthesis) along with quinone biosynthesis (phylloquinone and menaquinone), suggesting a cohesive theme around lipid and quinone/vitamin biosynthesis common in bacterial metabolic networks. The antibiotic biosynthetic term may reflect broader secondary metabolism, but the core signal appears to be lipid and quinone-related pathways.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0006574","count":4},{"id":"GO:0042372","count":4},{"id":"GO:0009234","count":4},{"id":"GO:0006635","count":4}]},{"hash":"1402962377950925871","title":"DNA Damage Response and Chromatin Regulation","description":"The GO terms cluster around DNA damage response (global genome nucleotide-excision repair, various DNA damage checkpoints, DNA damage tolerance) and chromatin regulation (histone H3-K79 methylation, subtelomeric heterochromatin formation), indicating a DDR-chromatin module; a few terms touch transcription regulation, while a triglyceride biosynthetic term seems like an outlier.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034729","count":2},{"id":"GO:0006348","count":1},{"id":"GO:0070911","count":1},{"id":"GO:0051598","count":1},{"id":"GO:0031573","count":1}]},{"hash":"1287846715031850361","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":27,"triangles":32,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0000462","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006605","count":2}]},{"hash":"938951315530528714","title":"Ribosome Biogenesis and Translation Machinery","description":"This cluster is dominated by GO terms related to protein synthesis: translation, cytoplasmic translation, ribosome biogenesis, and formation of the translation preinitiation complex, plus selenocysteine incorporation and translational fidelity. Additional RNA-processing connections (mRNA decay and spliceosome regulation) and antibiotic response terms fit within the broader context of RNA metabolism influencing translation, supporting a cohesive theme around the ribosome and the translation machinery.","confidence":"High","size":11,"edges":12,"triangles":10,"max_degree":5,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000288","count":3},{"id":"GO:0006407","count":2}]},{"hash":"1344076259149408819","title":"Nuclear RNA Processing and Ribosome Biogenesis","description":"The cluster is dominated by transcription, mRNA splicing, and rRNA maturation along with ribosomal subunit biogenesis and nuclear pore localization, suggesting a core function in nuclear RNA processing and ribosome assembly; weaker signals for COPII vesicle budding, cadmium response, and testis development likely reflect ancillary processes or noise.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042273","count":3},{"id":"GO:0071276","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0000463","count":3}]},{"hash":"2084576578840533845","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":10,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006986","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0046825","count":2}]},{"hash":"1623433540915435846","title":"Membrane transport of diverse substrates","description":"The top GO terms all point to transport across membranes for a wide range of substrates (amino acids, vitamins, lipids, heme, teichoic acid) and secretion. This indicates a functional cluster of proteins involved in transmembrane transport and export rather than a single substrate-specific function.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015777","count":3},{"id":"GO:0003333","count":3},{"id":"GO:0030253","count":3},{"id":"GO:0015910","count":3},{"id":"GO:0015888","count":3}]},{"hash":"1204808877014778704","title":"Neural and cardiac development and signaling","description":"The proteins in this cluster show enrichment for neural (neuronal signaling, axon regeneration) and cardiac (heart trabecula formation) development and signaling, along with transcriptional regulation and calcium signaling, suggesting a shared theme of signaling and regulation in excitable tissues. Confidence: Medium","confidence":"Medium","size":11,"edges":39,"triangles":63,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0051301","count":4},{"id":"GO:0007049","count":4},{"id":"GO:0000117","count":3},{"id":"GO:0030073","count":3}]},{"hash":"2256500200199335556","title":"ER-Golgi trafficking and protein folding","description":"Most enriched terms cluster around ER-Golgi vesicle transport and protein folding, with supporting cytoskeletal and transport-related processes. While a few terms touch on metabolism and transcription, the dominant theme is secretion pathway machinery and quality control.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007584","count":2},{"id":"GO:0006890","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0043473","count":2},{"id":"GO:0006457","count":2}]},{"hash":"277273924978343917","title":"Ribosome biogenesis and RNA processing","description":"The top GO terms converge on ribosome assembly and RNA processing, including rRNA maturation, ribosome biogenesis, large subunit export, tRNA processing, and translation, indicating a cohesive cluster devoted to ribosome formation and function.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0051568","count":2},{"id":"GO:0034729","count":2},{"id":"GO:0000055","count":2}]},{"hash":"1455234701571742526","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045730","count":3},{"id":"GO:0044205","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0010666","count":2},{"id":"GO:0009410","count":2}]},{"hash":"762754601654781317","title":"TGF-\u03b2/BMP signaling regulation","description":"The cluster is dominated by terms about negative regulation of BMP signaling and TGF-\u03b2 receptor signaling, SMAD complex assembly, and cellular responses to TGF-\u03b2. This points to a coherent theme of controlling TGF-\u03b2/BMP pathway activity, with broader development-related terms (e.g., meristem maintenance) appearing as context rather than the core signal. Overall, the GO terms coalesce around regulation of TGF-\u03b2/BMP signaling.","confidence":"High","size":11,"edges":37,"triangles":62,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000173","count":11},{"id":"GO:0046827","count":11},{"id":"GO:0061191","count":11},{"id":"GO:0042006","count":11},{"id":"GO:0010991","count":11}]},{"hash":"1783237874779742939","title":"Nucleotide, carbohydrate, and lipid biosynthesis","description":"The cluster has strong GO signals for several biosynthetic processes, including carbohydrate metabolic process, GTP and GMP biosynthesis, fatty acid biosynthesis, L-cysteine biosynthesis and related sulfur metabolism. These point to a core theme of biosynthetic metabolism. Some terms (protein homotetramerization, lymphocyte proliferation, retina development) are more peripheral or context-specific and may reflect broader protein roles or tissue-specific expression. Overall, the common thread is biosynthesis and related metabolism across macronutrients and nucleotides, justifying the label.","confidence":"Medium","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0005975","count":8},{"id":"GO:0006183","count":8},{"id":"GO:0019343","count":8},{"id":"GO:0006633","count":8},{"id":"GO:0006177","count":8}]},{"hash":"1966463675057431040","title":"Unknown","description":"These GO terms describe highly diverse, largely unrelated processes (behavioral phenotypes like locomotory and psychomotor behavior; melanocyte biology; apoptosis regulation; xenobiotic catabolism; T cell costimulation; ECM disassembly; host-symbiont entry). With edge count 0 and no clear shared functional theme, there isn't a coherent function linking the proteins into a single interpretive cluster.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035641","count":1},{"id":"GO:0097325","count":1},{"id":"GO:1900119","count":1},{"id":"GO:1902362","count":1},{"id":"GO:0046294","count":1}]},{"hash":"1891938548523575491","title":"Plant lipid metabolism and antioxidant biosynthesis","description":"Most terms point to lipid metabolism and antioxidant biosynthesis (ubiquinone/CoQ and tocopherol/vitamin E), plus lipid homeostasis and photosynthesis, which are characteristic of plant plastids/mitochondria. A few terms (Purkinje cell morphogenesis, responses to antibiotics/cocaine) seem like noise or broader stress annotations. Overall, the cluster appears to reflect plastid-associated lipid and antioxidant biosynthesis in plants.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":3},{"id":"GO:0016242","count":3},{"id":"GO:0021692","count":2},{"id":"GO:1902171","count":2},{"id":"GO:1901006","count":2}]},{"hash":"212277543424870446","title":"Unknown","description":"The GO terms are highly diverse, spanning metabolism (fructosamine, mycothiol), transcription/Chromatin organization, protein processing, signaling (platelet aggregation), enzyme charging of tRNA (isoleucyl, cysteinyl), and collagen catabolism, with a couple labeled as obsolete regulation steps. There is no single cohesive biological function or pathway that unifies these terms for this cluster, suggesting either a mix of unrelated proteins or broad annotations. Therefore, a specific, representative label cannot be confidently assigned beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030389","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0034724","count":1},{"id":"GO:0030574","count":1},{"id":"GO:0034396","count":1}]},{"hash":"2132613652079252936","title":"Redox Homeostasis and Stress Response","description":"The cluster centers on redox biology: cellular redox homeostasis, glutathione metabolism, protein glutathionylation, and detoxification, with supporting signals from oxidative stress responses and DNA repair; the inclusion of redox-regulated calcium channel activity and starvation-associated metabolism suggests a cohesive redox signaling and stress-response program.","confidence":"High","size":10,"edges":23,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":5},{"id":"GO:0060316","count":5},{"id":"GO:0006749","count":5},{"id":"GO:0060315","count":5},{"id":"GO:1902476","count":4}]},{"hash":"927586274650775155","title":"Fungal sphingolipid and sterol metabolism","description":"This cluster is anchored by lipid metabolism pathways typical of fungi: mannosyl-inositol phosphorylceramide (IPC) metabolism, regulation of ergosterol biosynthesis, and unsaturated fatty acid biosynthesis. While some terms are broader or animal-associated, the lipid-related terms predominate, suggesting a fungal lipid metabolism module.","confidence":"Medium","size":10,"edges":13,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:0000001","count":3},{"id":"GO:0042128","count":3},{"id":"GO:0032443","count":3},{"id":"GO:0006809","count":3}]},{"hash":"14619694358240479","title":"Neuronal mitochondria and synaptic vesicle dynamics","description":"This cluster centers on mitochondrial processes (fusion, membrane organization, localization) alongside synaptic vesicle trafficking (recycling, budding) and calcium signaling regulation, with a brain-related development term (substantia nigra). The combination suggests a cohesive neuronal function linking energy/mitochondrial maintenance to presynaptic vesicle dynamics and calcium-dependent signaling, potentially tied to neuronal maturation or function.","confidence":"High","size":10,"edges":6,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":3},{"id":"GO:1901387","count":3},{"id":"GO:0021762","count":2},{"id":"GO:1903423","count":2},{"id":"GO:0008053","count":2}]},{"hash":"1000188442106893411","title":"Fungal sporulation and cell wall remodeling","description":"This cluster's GO terms strongly point to a fungal-specific program: ascospore-type prospore membrane formation indicates sporulation, while chitin and polysaccharide (cell wall macromolecule) catabolic processes suggest remodeling/degradation of the fungal cell wall. Additional membrane trafficking terms (plasma membrane tubulation, intralumenal vesicle formation, pinocytosis) fit with the membrane dynamics seen during sporulation and wall remodeling. Together, these terms imply a focus on fungal sporulation coupled with cell wall remodeling.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031640","count":1},{"id":"GO:0072722","count":1},{"id":"GO:0006952","count":1},{"id":"GO:0016998","count":1},{"id":"GO:0000272","count":1}]},{"hash":"1215205153980390097","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":34,"triangles":57,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0006986","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0046825","count":1}]},{"hash":"942082516161620469","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0000463","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0042274","count":2}]},{"hash":"1020673105584353902","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0035753","count":2},{"id":"GO:0003203","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0000973","count":1}]},{"hash":"1099866123562469466","title":"Unknown","description":"The TopGO terms are broad and scattered across photosynthesis, ribosomal export, maltose transport, ER organization, development, and stress responses, with no clear shared function or pathway. The network has no edges, suggesting the proteins do not cluster around a single biological theme, so a single informative label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":1},{"id":"GO:1904751","count":1},{"id":"GO:0015768","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0007029","count":1}]},{"hash":"831537371339947328","title":"DNA replication, repair, and SOS response","description":"The top GO terms are dominated by DNA replication (initiation and general replication), nucleotide-excision repair, and SOS response, with cell division also featured. This points to a core cluster of genome maintenance and DNA damage response functions, possibly reflecting a replication/repair module. A few other terms (mRNA processing, competence, antibiotic response, viral replication) are less central and may reflect broader annotations or cross-species functions, but the main signal centers on DNA maintenance.","confidence":"Medium","size":10,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0051301","count":3},{"id":"GO:0006406","count":3}]},{"hash":"1788765312452117486","title":"Transcription and RNA Processing with Methylation","description":"This cluster centers on gene expression control, with GO terms for DNA-templated transcription, alternative splicing, and mRNA capping, alongside multiple protein methylation events (peptidyl-lysine/arginine/glutamine methylation) and histone demethylation, suggesting a module of transcriptional regulation and epigenetic modification. The cadmium ion response term adds a stress-response angle but the core theme appears to be regulation of transcription and post-translational modifications.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071276","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000380","count":2},{"id":"GO:0000413","count":2},{"id":"GO:0034720","count":2}]},{"hash":"1739898705401304528","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":38,"triangles":77,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0000398","count":5},{"id":"GO:1901407","count":4},{"id":"GO:0071031","count":4}]},{"hash":"1577814446503186826","title":"Epigenetic Regulation of Transcription","description":"The cluster is dominated by terms related to histone modifications (methylation/acetylation) and regulation of transcription by RNA polymerase II, indicating epigenetic control of gene expression as the unifying theme; additional terms reflect cellular responses to drugs and stress that may involve transcriptional changes, with some developmental and homeostasis contexts included.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031060","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0071549","count":2},{"id":"GO:0071440","count":2},{"id":"GO:0071314","count":2}]},{"hash":"1474122101327469535","title":"ER stress and unfolded protein response","description":"This cluster is dominated by GO terms related to ER stress and protein quality control, including unfolded protein response, cellular response to unfolded protein, and chaperone-assisted protein refolding, as well as negative regulation of apoptotic signaling in response to stress. These together point to a theme of ER stress management and protein folding under stress, with some secondary annotations like oxidative/heat stress regulation. A few outliers (karyogamy, iron-sulfur cluster assembly, DNA replication) may reflect broader housekeeping roles or annotation noise.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903382","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0006880","count":2},{"id":"GO:1903751","count":2},{"id":"GO:1900035","count":2}]},{"hash":"818798520993203087","title":"Chromatin Methylation and Transcription Regulation","description":"Based on GO terms, the cluster is enriched for DNA-templated transcription and rDNA heterochromatin formation, plus multiple peptidyl-lysine and rRNA methylation terms, indicating proteins involved in chromatin state and RNA/DNA methylation that regulate gene expression. Although a few entries mention bacterial cell wall biosynthesis, these do not define the core theme of the set, which is epigenetic/nucleic-acid modification and transcription control.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0018027","count":1},{"id":"GO:0031167","count":1},{"id":"GO:0018023","count":1}]},{"hash":"1513960248994872360","title":"Fungal/plant cell wall biosynthesis","description":"Top GO terms point to biogenesis and modification of cell walls in both fungi and plants (chitin and \u03b2-D-glucan synthesis, xyloglucan metabolism, fungal-type wall organization, and plant-type wall modification), with an additional reference to detection of fungal-origin molecules. This ensemble supports a cohesive theme of cell wall construction/remodeling across kingdoms, making \"Fungal/plant cell wall biosynthesis\" a concise, representative label.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006037","count":1},{"id":"GO:0031505","count":1},{"id":"GO:0009831","count":1},{"id":"GO:0006078","count":1},{"id":"GO:0032491","count":1}]},{"hash":"847518220906625384","title":"Developmental Gene Regulation","description":"This cluster mixes developmental processes (cerebral cortex development, primitive erythrocyte differentiation) with gene expression control (alternative splicing, chromatin binding) and signaling (cAMP response), suggesting a function in regulating development through transcriptional and post-transcriptional mechanisms.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":6},{"id":"GO:0071320","count":6},{"id":"GO:0000380","count":5},{"id":"GO:0021987","count":5},{"id":"GO:0035563","count":5}]},{"hash":"2264733712595929781","title":"Unknown","description":"These proteins show a highly heterogeneous set of GO terms (DNA repair, tRNA splicing, chromatin modification, signaling, centrosome cycle, metabolism, ubiquitination regulation, development, immune tolerance) with no clear shared function, and there are no edges linking them, so a cohesive cluster label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000012","count":1},{"id":"GO:0006388","count":1},{"id":"GO:0043970","count":1},{"id":"GO:0060765","count":1},{"id":"GO:0007098","count":1}]},{"hash":"1887308735107748263","title":"Translation and ribosome assembly","description":"Dominant GO terms center on translation, ribosomal large subunit assembly, and translational termination, indicating proteins involved in the ribosome-based protein synthesis machinery. While there are additional signals for biosynthetic and metabolic processes, these are less represented, suggesting they are ancillary features or context-specific associations within a translation-focused cluster.","confidence":"High","size":10,"edges":43,"triangles":105,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0022904","count":2},{"id":"GO:0000027","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0009236","count":2}]},{"hash":"796780143051362976","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0019079","count":4},{"id":"GO:0048701","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0071031","count":2}]},{"hash":"1551835100603071627","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051754","count":2},{"id":"GO:0099132","count":1},{"id":"GO:0015986","count":1},{"id":"GO:0039694","count":1},{"id":"GO:0006370","count":1}]},{"hash":"299097786763084108","title":"Bacterial amino acid biosynthesis and nutrient metabolism","description":"This cluster centers on metabolic processes related to amino acid biosynthesis (L-serine, L-tryptophan), phenylacetate catabolism, siderophore biosynthesis, and 5-phosphoribose diphosphate metabolism, plus a general response to nutrient conditions and regulatory lysine acetylation. While sporulation and bioluminescence appear among the terms, the dominant theme is metabolic pathways for building or breaking down small molecules and adapting to nutrient availability in bacteria. ","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006564","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0018393","count":2}]},{"hash":"1077665302517503169","title":"Diverse biosynthetic pathways","description":"Most top GO terms are biosynthetic processes, including lipopolysaccharide and O-antigen biosynthesis, GDP-mannose metabolism, anthocyanin and sporopollenin biosynthesis, and antibiotic biosynthesis, with a couple of unrelated terms (DNA-templated transcription and an obsolete oxidation\u2013reduction term). This suggests the cluster spans multiple, distinct biosynthetic activities rather than a single pathway, justifying a label of diverse biosynthetic pathways.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0042619","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0080110","count":3}]},{"hash":"752359017072847791","title":"Neuronal differentiation and survival regulation","description":"The top GO terms center on neuronal development and survival, including neuron differentiation and positive regulation of neuron apoptotic process, with supporting signals from GTPase signaling and ubiquitin-dependent endocytosis, suggesting roles in neuronal signaling and receptor trafficking. Some terms are broader (tRNA processing, nuclear localization), but the strongest cohesive theme appears to be neuronal development and regulation of signaling/survival.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043525","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0035331","count":1},{"id":"GO:0070534","count":1},{"id":"GO:2000235","count":1}]},{"hash":"59526273141557231","title":"Unknown","description":"The top terms cover highly diverse processes (pheromone response, GPCR signaling, androgen receptor regulation, histone acetylation, salicylic acid response, megakaryocyte development, cell fate commitment, lysine acetylation, protein binding regulation, and tubulin deacetylation) with no clear common function or pathway. The cluster has no edges and low term coherence, so there is no representative, cohesive label to assign.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019236","count":1},{"id":"GO:0007186","count":1},{"id":"GO:0060765","count":1},{"id":"GO:0043967","count":1},{"id":"GO:0009751","count":1}]},{"hash":"1546892423067787129","title":"Cardiac calcium signaling and Ca2+ handling","description":"The cluster centers on calcium dynamics in heart muscle, with terms about Ca2+ transport and release from the sarcoplasmic reticulum, calcium import, and cardiac action potential, plus Purkinje-to-ventricular signaling\u2014together forming a cohesive cardiac calcium-coupled contraction module. Some terms appear unrelated (thermoception, skin development) but do not detract from the main pattern.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0086029","count":1},{"id":"GO:0051928","count":1},{"id":"GO:0014808","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0034767","count":1}]},{"hash":"132815400552707545","title":"Mitochondrial Transport and Stress Response","description":"This cluster is dominated by GO terms for transport of metabolites across mitochondrial membranes (thiosulfate, heme, thiamine pyrophosphate, and pyrimidine nucleotides) along with indicators of mitochondrial stress and apoptosis (response to superoxide, apoptotic mitochondrial changes). Insulin/IGF signaling responses suggest metabolic regulation linked to mitochondria. An obsolete term about mitochondrial genome maintenance may reflect historical annotation but does not weaken the coherent mitochondrial transport/stress/metabolism theme. ","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015709","count":3},{"id":"GO:0015886","count":3},{"id":"GO:0030974","count":3},{"id":"GO:0007565","count":3},{"id":"GO:1990519","count":3}]},{"hash":"1693377250162869198","title":"Nuclear transcriptional regulation","description":"Most terms center on nuclear, DNA-templated transcription and its regulation (DNA-templated transcription, negative regulation of transcription initiation) with a note on nuclear localization. A couple terms touch on development and N-terminal acetylation, and several terms are obsolete. Overall, the cluster seems to reflect nuclear transcriptional regulation rather than a single precise process, so the name fits.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017196","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0051457","count":1},{"id":"GO:0007275","count":1},{"id":"GO:0006349","count":1}]},{"hash":"1495128963406274361","title":"Lipid metabolism and adipogenesis","description":"Top GO terms point to lipid biosynthesis and fat cell development (sphingosine biosynthetic/metabolic processes, response to fatty acids, cholesterol esterification, white fat cell differentiation). Despite a few unrelated or obsolete terms, the dominant theme among the annotations is lipid metabolism and adipogenesis, suggesting these proteins participate in lipid pathways and fat differentiation.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0006667","count":1},{"id":"GO:0034435","count":1},{"id":"GO:0046512","count":1}]},{"hash":"313676238832492949","title":"Chemical Stress and Neurotransmitter Regulation","description":"The GO terms cluster around monoamine metabolism and regulation (dopamine/dopamine catabolic process, negative regulation of serotonin secretion) plus responses to various chemicals and stress signals (corticosterone, aluminum, herbicide, ethanol) and redox/homeostasis and apoptosis, suggesting a cohesive theme of neurotransmitter handling under chemical stress.","confidence":"Medium","size":9,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":4},{"id":"GO:0010044","count":4},{"id":"GO:0006915","count":3},{"id":"GO:0009635","count":3},{"id":"GO:0045964","count":3}]},{"hash":"2105972928461360227","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":18,"triangles":15,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1904707","count":1},{"id":"GO:1900122","count":1},{"id":"GO:0030574","count":1},{"id":"GO:2001268","count":1},{"id":"GO:0051549","count":1}]},{"hash":"763839879759073125","title":"Ribosome biogenesis and translation initiation","description":"The cluster\u2019s top GO terms are dominated by translation-related processes: maturation of SSU rRNA, formation of the translation preinitiation complex, and cytoplasmic translation, along with regulation of translational initiation. This points to a group of proteins involved in ribosome assembly and the initiation of translation, with a few unrelated terms present likely due to noise. ","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0006446","count":1},{"id":"GO:0060136","count":1}]},{"hash":"2142196434200028622","title":"Ribosome Biogenesis and Translation","description":"Top GO terms indicate translation-centric processes: translation, cytoplasmic translation, translation initiation, formation of the cytoplasmic translation initiation complex, and ribosome biogenesis, plus tRNA modification, pointing to a core theme of protein synthesis machinery; additional cell cycle/division terms may reflect growth-linked coordination with translation.","confidence":"High","size":9,"edges":21,"triangles":23,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0006400","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0001732","count":2},{"id":"GO:0006413","count":2}]},{"hash":"1748212899123871572","title":"Ribosome Biogenesis and Translation","description":"The top GO terms are dominated by translation and ribosome-related processes (translation, cytoplasmic translation, ribosome biogenesis, ribosomal small subunit biogenesis, tRNA modification), indicating these proteins mainly participate in ribosome assembly and protein synthesis. Additional terms about cell cycle and division may reflect coordination with growth, but the core signal is the ribosome/translation machinery.","confidence":"High","size":9,"edges":31,"triangles":55,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0042254","count":6},{"id":"GO:0042274","count":4},{"id":"GO:0002181","count":3},{"id":"GO:1901001","count":3}]},{"hash":"2300396928722181676","title":"Ribosome biogenesis and translation","description":"This cluster is dominated by GO terms directly tied to protein synthesis and ribosome assembly (translation, ribosome biogenesis, cytosolic ribosome assembly), with supporting hints from mitochondrial translation and rRNA processing steps, and a few stress-related translation regulation terms (UV/gamma radiation). The recurring theme is ribosome production and overall translation activity.","confidence":"High","size":9,"edges":33,"triangles":66,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":8},{"id":"GO:0042254","count":3},{"id":"GO:0070126","count":2},{"id":"GO:0031564","count":2},{"id":"GO:0006353","count":2}]},{"hash":"1488369176203544212","title":"Unknown","description":"The top GO terms cover a wide range of biological contexts, including plant root meristem regulation, mitochondrial translation, wing cell fate, NK cell regulation, unfolded protein response, eye cone cell fate, spermatid differentiation, ER-to-cytosol proteolysis, EGFR ligand maturation, and hyperosmotic salinity response. With only one annotation per term and no shared process or pathway evident, the proteins do not cohere around a single function or cellular theme. Because of this lack of a clear common function, I assign the label Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010082","count":1},{"id":"GO:0070131","count":1},{"id":"GO:0035311","count":1},{"id":"GO:0032815","count":1},{"id":"GO:0034620","count":1}]},{"hash":"186609401039466694","title":"RNA processing and translation","description":"This cluster is driven by GO terms for 7-methylguanosine mRNA capping, maturation of rRNA, and translation, pointing to proteins involved in gene expression and ribosome biogenesis. Mixed terms like protein localization and mitochondrial regulation are present but less informative for the main theme, so the label reflects the core function.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0000466","count":1},{"id":"GO:1903146","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0006412","count":1}]},{"hash":"1607348232611249899","title":"Ubiquitin-Dependent Protein Degradation","description":"Based on the top GO terms, this cluster is strongly enriched for ubiquitin-related degradation processes: ubiquitin-dependent protein catabolic process, autoubiquitination, and ubiquitin chain linkages (K48 and K6). These terms point to proteasomal targeting and turnover of various substrates, including histones and signaling components (e.g., Wnt receptor catabolic process, TNF signaling regulation). While a few outliers mention peroxisomal import and V(D)J recombination, the dominant theme is ubiquitin tagging to promote protein degradation, which justifies naming it \"Ubiquitin-Dependent Protein Degradation.\"","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0070936","count":5},{"id":"GO:0036205","count":5},{"id":"GO:1903265","count":5}]},{"hash":"370869944540952865","title":"Lymphocyte development and T cell regulation","description":"The GO terms point to lymphoid development and immune control, including V(D)J recombination, spleen and germinal center regulation, and negative regulation of T cell proliferation and differentiation, along with NF-kappaB signaling and ubiquitination-related signaling that modulates immune responses. Taken together, these terms suggest a cluster centered on lymphocyte development and T cell\u2013mediated immune regulation.","confidence":"High","size":9,"edges":7,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":1},{"id":"GO:0050999","count":1},{"id":"GO:0046007","count":1},{"id":"GO:1901224","count":1},{"id":"GO:0033151","count":1}]},{"hash":"623734297759436838","title":"Diverse Biosynthesis Pathways","description":"The top GO terms cluster around various biosynthetic processes\u2014fatty acid, retinol, lipopolysaccharide, and other metabolite biosynthesis, plus antibiotic and pigment biosynthesis\u2014suggesting the proteins share a broad biosynthetic/metabolic role rather than a single, narrow pathway. Some non-biosynthesis terms appear, but the central theme is widespread biosynthesis activity.","confidence":"Medium","size":9,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0006633","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0009103","count":2}]},{"hash":"538513157214870187","title":"Redox Homeostasis and Transcriptional Regulation","description":"The term set is dominated by redox-related processes (oxidation-reduction, cellular oxidant detoxification, redox homeostasis, deglutathionylation, mitochondrial membrane potential) and transcription-related terms (DNA-templated transcription, regulation of RNA polymerase II regulatory region). This suggests a cluster of proteins involved in maintaining cellular redox balance while coordinating transcriptional responses, with additional links to organelle function (vacuolar acidification) and signaling (prostaglandin biosynthesis). Some terms appear peripheral (e.g., odor perception) but do not override the central redox/transcription theme.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0007608","count":2}]},{"hash":"400383425224424459","title":"DNA Replication and Cell Cycle","description":"This cluster is dominated by DNA replication, chromosome separation, centrosome cycle, and DNA repair terms, consistent with proteins involved in DNA replication and cell-cycle control; a few outliers (embryonic skeleton morphogenesis, potassium transport) exist but do not define the core function.","confidence":"High","size":9,"edges":4,"triangles":0,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0010571","count":2},{"id":"GO:0006269","count":2},{"id":"GO:0007098","count":2},{"id":"GO:0048701","count":2}]},{"hash":"205312511387590482","title":"tRNA Aminoacylation and Translation","description":"This cluster is dominated by aminoacyl-tRNA synthetases (isoleucyl-, leucyl-, methionyl-, valyl-) and translation-related terms (translation, translational fidelity), indicating a cohesive set of proteins involved in protein synthesis. While there are hints of RNA processing (Group I intron splicing) and a melatonin biosynthetic term, the strongest signal ties to tRNA charging and the translation machinery, with only a minor connection to metabolism (TCA cycle).","confidence":"Medium","size":9,"edges":20,"triangles":19,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006099","count":2},{"id":"GO:0006355","count":1},{"id":"GO:0006428","count":1},{"id":"GO:0000372","count":1},{"id":"GO:0006450","count":1}]},{"hash":"1785310941142041063","title":"Ribosome biogenesis and cell division","description":"This cluster shows strong enrichment for protein synthesis and growth-related processes (cytoplasmic translation, ribosome biogenesis, cell division, mitotic spindle assembly, multicellular growth, and proliferation). Although trafficking-related terms (COPII budding, endocytic recycling) and GTPase regulation are present, the dominant theme centers on ribosome biogenesis and cell cycle progression, suggesting a module coordinating growth with division.","confidence":"Medium","size":9,"edges":4,"triangles":0,"max_degree":3,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0002181","count":3},{"id":"GO:0032456","count":3},{"id":"GO:0090307","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0090114","count":3}]},{"hash":"549842000394191490","title":"Cytoskeletal motility and intracellular transport","description":"The top GO terms cluster around cytoskeletal dynamics and movement\u2014spindle orientation, muscle filament sliding, uropod organization, cell gliding, and pigment granule transport\u2014plus processes like vacuole inheritance and Fc-gamma signaling in phagocytosis that rely on cytoskeletal tracks and motors. This points to a cohesive theme of cytoskeleton-driven motility and cargo trafficking rather than a single tissue-specific function.","confidence":"Medium","size":9,"edges":15,"triangles":10,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000132","count":3},{"id":"GO:0014728","count":2},{"id":"GO:0030049","count":2},{"id":"GO:0032796","count":2},{"id":"GO:0032529","count":2}]},{"hash":"997791360816889421","title":"Cell Cycle Regulation and Redox Stress Response","description":"The cluster is dominated by GO terms related to regulating the cell cycle and inhibiting cell proliferation, with supporting terms for stress signaling (MAPK cascade regulation) and redox/homeostasis (protein oxidation, redox homeostasis). Additional terms about protein maturation and a few tissue-specific processes (spermatogenesis, erythrocyte homeostasis) may reflect broad expression, but the core theme ties to cell-cycle control intertwined with oxidative and stress-response regulation.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0022417","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0007050","count":2},{"id":"GO:0032461","count":1},{"id":"GO:1904808","count":1}]},{"hash":"484892884544678236","title":"Redox Metabolism and RNA Regulation","description":"Top GO terms indicate a blend of redox/metabolic processes (redox homeostasis, quinolinate and glutamine metabolism) with RNA-centric regulation (tRNA wobble modification, endoribonuclease activity, translation regulation) and transcriptional control (DNA-templated transcription/termination), suggesting a cohesive cluster where metabolic redox state links to RNA processing and gene expression regulation, potentially under stress.","confidence":"Medium","size":9,"edges":24,"triangles":38,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0019805","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0006541","count":2}]},{"hash":"1328660104229446119","title":"Unknown","description":"The top terms are a mix of metabolism (amino acid and nucleotide processes) and broad developmental/physiological processes (differentiation, angiogenesis, myelination, chemotaxis, gastric motility), with no cohesive shared function and no edges among the proteins. This heterogeneity means there isn\u2019t a clear, single theme to label the cluster confidently. ","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000162","count":1},{"id":"GO:0030154","count":1},{"id":"GO:0006935","count":1},{"id":"GO:0007275","count":1},{"id":"GO:0000002","count":1}]},{"hash":"1407526687145843353","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098789","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0034414","count":2},{"id":"GO:0019243","count":2},{"id":"GO:0031126","count":2}]},{"hash":"323946585569523403","title":"Diverse metabolite biosynthesis","description":"The top GO terms point to multiple biosynthetic pathways across diverse metabolite classes (poly-hydroxybutyrate, sphingolipid, retinal, antibiotic, melanin, steroid hormones, androgens), plus related redox and catabolic processes. This suggests a cluster enriched for enzymes involved in various biosynthetic processes rather than a single, cohesive pathway. Confidence: Medium.","confidence":"","size":8,"edges":14,"triangles":11,"max_degree":7,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0042619","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0008207","count":4},{"id":"GO:0045150","count":4},{"id":"GO:0031427","count":4}]},{"hash":"676581556294833850","title":"Unknown","description":"The listed GO terms cover stress responses (unfolded protein response, ER stress, cadmium), hormone signaling (cytokinin, gibberellin), and disparate processes (ciliary motility, photoreceptor localization, organ identity). There is no clear shared function tying the proteins together, so a generic Unknown label is appropriate.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016570","count":1},{"id":"GO:0006986","count":1},{"id":"GO:0060296","count":1},{"id":"GO:0009736","count":1},{"id":"GO:0009938","count":1}]},{"hash":"760527128103986716","title":"TORC1-Driven Nutrient Growth Signaling","description":"The top GO terms center on TORC1 signaling and response to amino acids, pointing to a nutrient-sensing growth control theme. Additional terms about mRNA transport, nuclear pore assembly, and chromatin assembly suggest a link between growth signaling, gene expression, and DNA replication. This indicates a cluster of proteins involved in coordinating nutrient sensing with growth and transcriptional regulation.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051028","count":1},{"id":"GO:0051292","count":1},{"id":"GO:0097711","count":1},{"id":"GO:0038202","count":1},{"id":"GO:2001241","count":1}]},{"hash":"1459779942637049877","title":"Cytoplasmic translation and tRNA modification","description":"The protein cluster is strongly enriched for core translation processes: translation, cytoplasmic translation, initiation, elongation regulation, termination, and tRNA modification, indicating involvement in the protein synthesis machinery and RNA modification steps. Some auxiliary terms like antibiotic response and salt-stress regulation appear but are secondary to the dominant translation-focused signals.","confidence":"High","size":8,"edges":19,"triangles":19,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":6},{"id":"GO:0006413","count":2},{"id":"GO:0045901","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0006415","count":2}]},{"hash":"1203958891632441019","title":"Spliceosome-Mediated mRNA Splicing Regulation","description":"The top GO terms are tightly centered on mRNA splicing via the spliceosome, including positive/negative regulation of splicing, alternative splicing, and related RNA-processing steps such as poly(A) tail regulation and mRNA stability in response to stress. The presence of ncRNA- and miRNA-mediated silencing terms suggests these proteins participate in broader RNA regulatory networks, consistent with a cluster of splicing factors and RNA-processing regulators.","confidence":"High","size":8,"edges":21,"triangles":26,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":4},{"id":"GO:0000398","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0031047","count":3},{"id":"GO:1901407","count":3}]},{"hash":"16327666342043450","title":"RNA Splicing and Processing","description":"The cluster is heavily enriched for RNA metabolism and splicing-related terms: tRNA processing, spliceosomal complex and snRNP assembly, mRNA splicing via the spliceosome, P-body assembly, deadenylation-dependent decapping, and maturation of rRNA, plus transcription termination. These collectively point to coordinated RNA processing, splicing, and mRNA turnover functions, with some ancillary links to transcription and chromatin processes. Overall, a coherent RNA processing/splicing cluster with associated RNA decay.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0008033","count":5},{"id":"GO:0000290","count":4},{"id":"GO:0000245","count":4},{"id":"GO:0033962","count":4},{"id":"GO:1990141","count":4}]},{"hash":"1430703848773219561","title":"TLR Signaling and Inflammatory Response","description":"The top GO terms cluster around toll-like receptor signaling pathways (TLR4, TLR10), cellular response to diacyl bacterial lipopeptide, regulation of chemokine production, and inflammatory response, pointing to a shared function in innate immune signaling. A couple of more divergent terms appear as artifacts, but the majority supports a TLR-driven inflammatory module.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043486","count":2},{"id":"GO:0019800","count":1},{"id":"GO:0071726","count":1},{"id":"GO:0032722","count":1},{"id":"GO:0034166","count":1}]},{"hash":"1319151075762498439","title":"Synaptic vesicle cycling and neuronal signaling","description":"The top GO terms are dominated by regulation of synaptic vesicle exocytosis and endocytosis, plus excitatory postsynaptic potential, indicating a primary function in neuronal neurotransmission and synaptic plasticity. While there are outliers related to cell cycle and other growth processes, the strongest and most cohesive signal is vesicle trafficking at synapses, with incidental nods to neuronal development. ","confidence":"Medium","size":8,"edges":10,"triangles":5,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0051291","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006469","count":3}]},{"hash":"17731146753470631","title":"Ion Transport and Membrane Potential","description":"This cluster is dominated by GO terms related to transport across membranes and ion handling, including potassium, calcium, and manganese ion transport, amino acid transport, and long-chain fatty acid import into peroxisomes, as well as membrane hyperpolarization and intracellular pH changes. While there are outliers (teichoic acid transport, protein secretion, cell division), the overall theme points to membrane transport processes and ion homeostasis driving the cluster's function.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0060081","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0006828","count":2}]},{"hash":"2242769048837450891","title":"Proteostasis via ubiquitination and ERAD","description":"The terms point to protein quality control: ubiquitin-dependent degradation, ER-associated degradation (ERAD), and trafficking/localization to Golgi and membranes, indicating a proteostasis module that manages misfolded or excess proteins through ubiquitination and degradation, with support from chaperone-assisted folding pathways. Some terms are obsolete, but the core signal is clear.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0006511","count":2},{"id":"GO:0000042","count":2},{"id":"GO:1900035","count":2},{"id":"GO:0070389","count":2}]},{"hash":"532081420689951877","title":"RNA metabolism and organelle quality control","description":"This cluster combines GO terms tied to transcription and translation with RNA processing and stress response (DNA-templated transcription, translation, nonfunctional rRNA decay, UV-damage excision repair, stress granule disassembly) and to organelle maintenance/trafficking (protein import into peroxisome matrix, receptor recycling; regulation of mitochondrial DNA replication; autophagosome maturation). The mix suggests a theme of coordinating RNA metabolism with organelle protein handling and stress-induced quality control.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0070651","count":1},{"id":"GO:0090296","count":1},{"id":"GO:0000733","count":1}]},{"hash":"1002217015992586726","title":"Cholinergic signaling in sieve elements","description":"The top GO terms point to acetylcholine biosynthesis and secretion, plus sieve element differentiation, suggesting a possible link between cholinergic activity and phloem (sieve element) biology. However, with only three low-count terms and no network connectivity, the assignment is provisional. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061526","count":1},{"id":"GO:0090603","count":1},{"id":"GO:0008292","count":1}]},{"hash":"1759437408181203124","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0071042","count":4},{"id":"GO:0071035","count":4},{"id":"GO:0031047","count":4}]},{"hash":"1996490949502494942","title":"Unknown","description":"The top GO terms are a mix of ribosomal biogenesis, multiple metabolic pathways (inositol, heme, galactose, sorbitol), and regulatory activities, with several entries marked obsolete. This scattered mix does not point to a single cohesive function or pathway for the cluster, so a unifying label cannot be confidently assigned.","confidence":"","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042273","count":1},{"id":"GO:0043433","count":1},{"id":"GO:0019310","count":1},{"id":"GO:0042167","count":1},{"id":"GO:0033673","count":1}]},{"hash":"1622225832120980790","title":"Ribosome Biogenesis and Translation","description":"Most GO terms point to translation and ribosome biogenesis (translation; ribosomal large subunit assembly; preribosome assembly; ribosomal large subunit biogenesis), indicating a cluster of proteins involved in ribosome production and protein synthesis. A few terms related to retina/optic nerve development and mitotic cell cycle processes are present but less represented, suggesting these are secondary annotations rather than the cluster\u2019s primary function.","confidence":"High","size":8,"edges":17,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000027","count":2},{"id":"GO:0060041","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0007093","count":1}]},{"hash":"1215957919063211649","title":"Synaptic Exocytosis and Calcium Signaling","description":"GO terms center on neuronal signaling: exocytosis, excitatory postsynaptic potential, and long-term potentiation, combined with calcium ion regulation and protein dephosphorylation, suggesting a role in synaptic transmission and calcium-dependent signaling. While terms like retinal cone development and cardiac hypertrophy appear, they reflect broader signaling contexts rather than dominant themes in this cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045921","count":1},{"id":"GO:0014898","count":1},{"id":"GO:0046549","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0090281","count":1}]},{"hash":"1951093323025909592","title":"Fungal Stress Response and Metabolism","description":"This cluster features GO terms tied to fungal biology (fungal-type beta-glucan biosynthesis) and broad stress/metabolic processes (ER stress response, apoptosis regulation, hydrogen peroxide response, methionine salvage, iron-sulfur cluster assembly, DNA replication). The mix suggests a set of proteins involved in general fungal cell physiology, encompassing stress responses and core metabolism, rather than a single, tightly defined pathway. Confidence: Medium","confidence":"","size":8,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0019509","count":2},{"id":"GO:0019284","count":2},{"id":"GO:1903382","count":1},{"id":"GO:0000742","count":1},{"id":"GO:0006880","count":1}]},{"hash":"2019621525030237328","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0009258","count":1},{"id":"GO:0009245","count":1},{"id":"GO:0006730","count":1},{"id":"GO:0006413","count":1}]},{"hash":"273857764311513279","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042347","count":2},{"id":"GO:0046929","count":2},{"id":"GO:0098789","count":2},{"id":"GO:0050884","count":2},{"id":"GO:0046677","count":2}]},{"hash":"1985780894262095746","title":"Cytoskeleton-driven motility and intracellular transport","description":"The cluster is enriched for movement- and transport-related GO terms, including cell gliding, uropod organization, muscle filament sliding and contraction, pigment granule transport, and vacuole inheritance. Additional terms on microvillus organization and spindle orientation point to cytoskeletal organization as the unifying thread, linking motility with organelle trafficking and division-related processes.","confidence":"High","size":8,"edges":6,"triangles":1,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000132","count":4},{"id":"GO:0014728","count":3},{"id":"GO:0030049","count":3},{"id":"GO:0032796","count":3},{"id":"GO:0032529","count":3}]},{"hash":"2018296655311577684","title":"Rab GTPase signaling and protein geranylgeranylation","description":"The Top Terms show strong enrichment for Rab protein signal transduction, activation of GTPase activity, and protein geranylgeranylation (including positive regulation), which are hallmark features of Rab-driven vesicle trafficking and membrane targeting. While redox-related terms appear, the dominant signal centers on Rab GTPase activity and its prenylation, supporting a cohesive label focused on Rab signaling and prenylation.","confidence":"High","size":8,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0045454","count":2},{"id":"GO:0009409","count":2},{"id":"GO:0032482","count":1},{"id":"GO:0015031","count":1}]},{"hash":"119083738182721181","title":"Ubiquitin-Proteasome Regulation and Translesion Synthesis","description":"This cluster centers on ubiquitin-related processes: K48- and K63-linked ubiquitination, polyubiquitination involved in proteasomal degradation, and enrichment for positive regulation of ubiquitin-protein transferase activity, plus a TLS/dna damage context (error-prone translesion synthesis). Some terms also indicate immune signaling and apoptosis, consistent with ubiquitin's role in signaling and cell fate decisions. Therefore the proteins likely function in ubiquitin-mediated protein turnover and DNA damage response, possibly including TLS regulation.","confidence":"High","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:1901044","count":8},{"id":"GO:0042276","count":8},{"id":"GO:0051965","count":8},{"id":"GO:0070534","count":8},{"id":"GO:0070936","count":8}]},{"hash":"2164987156581785064","title":"Steroid and retinoid metabolism","description":"The cluster is dominated by GO terms for retinol and retinal metabolic processes and for androgen/testosterone biosynthesis, suggesting a core theme of lipid-derived metabolite processing and steroid biosynthesis. Other terms (antibiotic and lipopolysaccharide biosynthesis, phospholipid dephosphorylation, calcium and cadmium transport) appear as secondary annotations and do not override the central signal of steroid/retinoid metabolism.","confidence":"Medium","size":8,"edges":19,"triangles":17,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0042572","count":4},{"id":"GO:0042574","count":3},{"id":"GO:0008209","count":3},{"id":"GO:0061370","count":3},{"id":"GO:0055114","count":3}]},{"hash":"2031856328011784522","title":"Chromatin methylation and RNA modification","description":"The GO terms center on transcription control (negative regulation of transcription by RNA Pol II, DNA-templated transcription) and various methylation processes, including histone lysine methylation and RNA methylation (rRNA and tRNA). This suggests proteins in a cluster focused on transcription regulation via chromatin modification together with RNA modification activities. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0018027","count":1}]},{"hash":"304816253371186090","title":"Unknown","description":"The GO terms span cell division, ribonucleoprotein assembly, sex differentiation, cell cycle, metabolism, and hormone signaling with no dominant shared process, and there are no edges linking the proteins; thus no cohesive theme emerges to justify a specific label.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0000492","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0009749","count":2}]},{"hash":"251315482645759420","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080156","count":1},{"id":"GO:0090502","count":1},{"id":"GO:0009451","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0031425","count":1}]},{"hash":"1925998200081709395","title":"Cellular stress response and transcription","description":"The top GO terms point to cellular responses to metal ions (cadmium, copper) and chemical stress (nitroglycerin), suggesting a stress-response theme. Mitochondrial complex IV assembly hints at mitochondrial maintenance under stress, while DNA-templated transcription indicates transcriptional regulation linked to these responses. Although some terms are obsolete and the cluster is small with no interactions, the common thread appears to be cellular stress response coupled with transcriptional control.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033617","count":1},{"id":"GO:0060136","count":1},{"id":"GO:0043497","count":1},{"id":"GO:2001033","count":1},{"id":"GO:1904843","count":1}]},{"hash":"1604966096866001690","title":"Triglyceride mobilization and phospholipid catabolism","description":"The cluster shows strong representation of triglyceride-related terms (triglyceride catabolic process, triglyceride mobilization, triglyceride acyl-chain remodeling) and phospholipid catabolism (phosphatidylethanolamine and phosphatidylcholine catabolic processes), suggesting a core theme of lipid catabolism and membrane lipid remodeling. While a heme transport term appears, the lipid-focused GO terms predominate, supporting a function in lipid mobilization and membrane lipid turnover.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":2},{"id":"GO:2000480","count":2},{"id":"GO:0010898","count":2},{"id":"GO:0046338","count":2},{"id":"GO:0034638","count":2}]},{"hash":"1555687412108038093","title":"Diverse Transmembrane Transporters","description":"The top GO terms are all related to transporting various substrates across membranes (nitrite, nitrate, phosphate, arabinose, potassium, sodium, sialic acid, xenobiotics) with an additional metabolic link (fucose). This pattern points to a cluster of membrane transporter proteins with broad substrate specificity, rather than a single substrate-specific function. ","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0071805","count":2}]},{"hash":"98736329526542967","title":"Viral life cycle and virion assembly","description":"The top GO terms include viral life cycle, virion assembly, and proviral latency, which together strongly point to virus-related processes and virus-host interactions. While there are also general host-cell processes (protein folding, transcription regulation) and other miscellaneous terms, the viral-related annotations form the most coherent theme for this cluster. Confidence: Medium","confidence":"","size":7,"edges":7,"triangles":3,"max_degree":4,"top_function":"protein folding","top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0006457","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0048453","count":2},{"id":"GO:0050900","count":2}]},{"hash":"1047005192593157070","title":"Cochlear synaptic signaling and neural development","description":"The terms center on neural signaling and synaptic organization (receptor clustering, long-term synaptic depression, regulation of opioid receptor signaling) and on inner ear development (cochlea morphogenesis). While there are a few broader cellular functions like polarity and centrosome localization, the predominant theme is neural synaptic activity linked to cochlear development, supporting this label as representative.","confidence":"Medium","size":7,"edges":6,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000474","count":1},{"id":"GO:2000009","count":1},{"id":"GO:0007266","count":1},{"id":"GO:0051660","count":1},{"id":"GO:0045199","count":1}]},{"hash":"1795134443364967535","title":"Calcium-signaling and vesicle trafficking regulators","description":"This cluster is enriched for calcium-dependent signaling (NFAT regulation, calcium release), cAMP signaling, GTPase regulation, and regulation of synaptic vesicle endocytosis/exocytosis, pointing to proteins that modulate membrane trafficking and calcium- or second-messenger\u2013dependent pathways. Some context-specific terms (retinal development, nurse cell transport) appear, but the core theme centers on signaling linked to vesicle dynamics.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0051531","count":2},{"id":"GO:1900242","count":1},{"id":"GO:0086004","count":1},{"id":"GO:0014898","count":1}]},{"hash":"2280929037424596087","title":"Neuronal Mitochondrial Dynamics","description":"The top GO terms point to mitochondrial membrane organization, fission, inheritance, and intracellular distribution, indicating a core role in mitochondrial dynamics. Additional trafficking-related terms (endocytic recycling, protein targeting to vacuole) suggest broader cellular trafficking functions that can intersect with organelle maintenance. The brain development and GABAergic synaptic transmission terms imply neuronal context, where mitochondrial dynamics are crucial for energy supply and signaling. Overall, the cluster appears to center on mitochondrial dynamics with neuronal relevance.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":2},{"id":"GO:0007006","count":2},{"id":"GO:0006623","count":2},{"id":"GO:0048312","count":2},{"id":"GO:0060047","count":2}]},{"hash":"332085418557675467","title":"Cilium Assembly and Centrosome Maintenance","description":"The top GO terms are dominated by ciliogenesis and centrosome-related processes (non-motile cilium assembly, regulation of cilium beat frequency, maintenance of centrosome location), suggesting the proteins cluster around ciliary structure and centrosome positioning. Other terms reference stress responses and signaling, but the cilium/centrosome theme is the strongest cohesive signal for this cluster.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":3},{"id":"GO:0006486","count":2},{"id":"GO:0060296","count":2},{"id":"GO:0036494","count":2},{"id":"GO:0051661","count":2}]},{"hash":"516705104083851000","title":"Ubiquitin-mediated transcription and innate immune signaling","description":"This cluster centers on ubiquitination-related processes (autoubiquitination, ubiquitin-dependent proteolysis, sumoylation, K63-linked ubiquitination) and transcriptional regulation by RNA polymerase II, with links to innate immune signaling (MyD88-dependent TLR pathway) and viral processes. The combination suggests a theme where ubiquitin/SUMO modifiers regulate transcriptional responses and immune signaling, possibly in infection or developmental contexts.","confidence":"Medium","size":7,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0030154","count":2}]},{"hash":"299447925592334185","title":"ESCRT/MVB Vesicle Formation and Trafficking","description":"The cluster includes GO terms for multivesicular body assembly, intralumenal vesicle formation, and protein transport to vacuole via MVB sorting, plus viral budding via host ESCRT, all pointing to ESCRT-dependent vesicle formation and cargo trafficking. A few terms (ion transport, nucleus organization, viral life cycle) are peripheral, but the central theme is ESCRT/MVB\u2013mediated membrane trafficking.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006814","count":1},{"id":"GO:0042777","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0039702","count":1},{"id":"GO:0036258","count":1}]},{"hash":"193518510264119047","title":"ER stress\u2013driven translation and innate antiviral response","description":"GO terms cluster around innate immunity (innate immune response, defense response to virus) and ER-stress\u2013related translation control (cytoplasmic translation, translation initiation in response to ER stress), with RNA processing cues, suggesting a set of proteins coordinating ER stress responses with immune signaling.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0002181","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006986","count":2}]},{"hash":"771074843850576589","title":"Unknown","description":"The top GO terms span distinct domains\u2014plant leaf senescence, apoptotic process, and somatic diversification of immunoglobulins\u2014each represented by a single protein and with no edges connecting cluster members, providing no coherent functional theme to justify a more specific label.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1900056","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0016445","count":1}]},{"hash":"1079540581462021627","title":"Oxidative Stress and Transcription Regulation","description":"This cluster centers on redox balance and oxidative stress response (oxidant detoxification, redox homeostasis) and includes GO terms for DNA-templated transcription and regulation of DNA binding, suggesting a link between redox state and transcriptional control. The presence of peptidyl-proline hydroxylation hints at oxygen-sensing and post-translational regulation of transcription factors, reinforcing a cohesive redox-regulated transcription theme, despite a few peripheral terms such as viral process.","confidence":"High","size":7,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0080058","count":2},{"id":"GO:0006351","count":2},{"id":"GO:1903026","count":2},{"id":"GO:0018401","count":2}]},{"hash":"1224805410805551476","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0000398","count":5},{"id":"GO:1990416","count":5},{"id":"GO:0000388","count":5},{"id":"GO:0071031","count":4},{"id":"GO:0010501","count":4}]},{"hash":"1920210810504654938","title":"Unknown","description":"The top GO terms are spread between glycoprotein processing (glycoprotein catabolic process, post-translational modification, and glycosylation) and several unrelated terms (S-layer organization, embryonic pregnancy, stress responses, and obsolete annotations). With zero edges and diverse themes, there isn\u2019t a clear, single function that ties the cluster together, so a coherent, specific label cannot be confidently assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006516","count":1},{"id":"GO:0043686","count":1},{"id":"GO:0043687","count":1},{"id":"GO:0018279","count":1},{"id":"GO:0045232","count":1}]},{"hash":"408147435901058030","title":"TGF-\u03b2 signaling in vascular development","description":"This cluster centers on GO terms related to response to transforming growth factor beta stimulus, endothelial cell proliferation, and blood vessel morphogenesis, indicating a vascular development theme driven by TGF-\u03b2 signaling. Other terms like DNA-templated transcription and vesicle transport reflect supporting roles in regulation and trafficking, but the vascular development signals appear most salient, justifying a vascular-development label despite some neural/immune-associated terms appearing as noise.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0070262","count":2},{"id":"GO:1902262","count":1}]},{"hash":"768811617479412743","title":"Transcription Regulation with Redox Modifications","description":"The cluster centers on DNA-templated transcription and RNA polymerase II regulatory region control, suggesting a transcription-regulatory role. It also includes redox/mitochondrial-related terms (oxidant detoxification, deglutathionylation, mitochondrial permeability/potential regulation, proline hydroxylation), implying possible coordination between transcription and mitochondrial redox state. Some terms (viral process, necrotic cell death) may reflect annotation noise. Overall, the proteins may link transcription regulation with redox/post-translational modification processes.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0035794","count":1},{"id":"GO:0010917","count":1},{"id":"GO:0010940","count":1},{"id":"GO:0098869","count":1}]},{"hash":"433220561657558715","title":"Unknown","description":"The terms mix metabolism, DNA/chromatin processes, and developmental signals with obsolete items, showing no single cohesive function for the cluster.","confidence":"","size":7,"edges":20,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0006541","count":2},{"id":"GO:1904182","count":1},{"id":"GO:1905555","count":1},{"id":"GO:0071572","count":1}]},{"hash":"246122066462522786","title":"Ribosome biogenesis and rRNA processing","description":"The dominant GO terms are RNA guanine-N7 methylation and maturation of 5.8S and LSU rRNA, plus ribosome biogenesis, which together point to the core process of assembling functional ribosomes. While there are additional terms related to vesicle trafficking and cell division, the strongest signal across the cluster is ribosome production and rRNA processing, justifying a label centered on ribosome biogenesis. This reflects a cohesive biological theme of preparing the protein synthesis machinery, with peripheral links to growth-related processes.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036265","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0039694","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0000463","count":2}]},{"hash":"1529214080085392626","title":"Core Cellular Machinery","description":"The cluster centers on essential, broad cellular processes: cell division and centromere/chromatin assembly, microtubule dynamics, translation and ribosome biogenesis, and vesicle transport, with supportive roles in protein homooligomerization and cell fusion. This combination points to a set of fundamental cellular functions necessary for growth and division, rather than a single specialized pathway. Therefore, the label reflects a general housekeeping cluster of core cellular machinery.","confidence":"Medium","size":7,"edges":17,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0006412","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0051013","count":2}]},{"hash":"737079370008231763","title":"ER stress and protein folding","description":"The terms center on endoplasmic reticulum functions: protein folding in the ER, ER unfolded protein response, and ER stress\u2013related apoptotic signaling; chaperone regulation of autophagy also ties to ER quality control. Some terms such as insulin processing and extracellular matrix organization reflect secretory pathway involvement. A few annotations (phytochelatin biosynthesis) appear as noise. Overall, the cluster seems to represent ER-associated protein maturation and stress response.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904715","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0046938","count":1},{"id":"GO:0070059","count":1}]},{"hash":"810234102406675086","title":"Cell Division and Cytoskeletal Dynamics","description":"The dominant GO terms point to spindle assembly, actin filament bundle assembly, and cell cycle, suggesting a core theme of cell division and cytoskeletal remodeling. Additional terms like maturation of SSU-rRNA and telomere maintenance reflect fundamental cellular housekeeping and genome maintenance that support division. Other terms (inflammatory response to wounding, calcium import, thermoception, cerebellar differentiation) are more peripheral noise relative to the core theme. The combination implies a cluster anchored in division and structural organization rather than a single coherent pathway.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0090594","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0051225","count":1},{"id":"GO:0098703","count":1}]},{"hash":"504459388831917764","title":"Developmental signaling and cell cycle regulation","description":"The cluster's GO terms cluster around DNA replication and nuclear cell cycle regulation, apoptotic process, mesoderm formation, and signaling pathways such as Wnt and Hippo, along with keratinocyte differentiation. This combination points to proteins involved in coordinating developmental signaling with proliferation and differentiation. While some terms are peripheral (parathyroid hormone response, negative regulation of Smoothened signaling), the overarching theme is growth signaling coupled with development and cell cycle control, justifying the label.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006915","count":4},{"id":"GO:0071374","count":4},{"id":"GO:0035329","count":4},{"id":"GO:0030216","count":4}]},{"hash":"885180058830784472","title":"Neural and cardiac signaling and stress response","description":"This cluster features terms related to neural signaling (action potential, axon regeneration), cardiac development (heart trabecula formation), calcium signaling (SR Ca2+ release), secretory processes (insulin secretion), and stress responses (hydrogen peroxide, APP catabolism), suggesting a broader theme of signaling and cellular stress in excitable or secretory tissues.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2000648","count":3},{"id":"GO:0030073","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0019227","count":2},{"id":"GO:0060347","count":2}]},{"hash":"5932929573382638","title":"Innate antiviral signaling and interferon response","description":"The cluster\u2019s GO terms are dominated by innate antiviral functions: cellular response to exogenous dsRNA, cellular response to type I interferon, innate immune response, and defense response to virus, indicating core antiviral signaling and interferon-related activity. Additional terms like intracellular signal transduction and regulation of GPCR signaling suggest participation in broader signaling networks. A couple of terms (gibberellin signaling regulation, asymmetric neuroblast division) appear less connected and may reflect annotation noise. Overall, the theme centers on innate antiviral signaling and interferon responses.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035556","count":2},{"id":"GO:0009938","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0048312","count":1}]},{"hash":"1781491687724635499","title":"Diverse Membrane Transporters","description":"The top GO terms cluster around transport across membranes for a wide range of substrates (amino acids, lipids, vitamins, heme, drugs, etc.), with no single dominant pathway, suggesting a group of proteins broadly involved in membrane transport rather than a specific process.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015777","count":1},{"id":"GO:0003333","count":1},{"id":"GO:0030253","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0015888","count":1}]},{"hash":"1535498276792144038","title":"Ubiquitin-Dependent NF-\u03baB Signaling and Apoptosis Regulation","description":"The terms concentrate on ubiquitin-mediated proteolysis (ubiquitin-dependent protein catabolic process, autoubiquitination), TNF-mediated signaling, and I-kappaB phosphorylation, all pointing to NF-\u03baB pathway activation and regulation of apoptosis. While there are related chromatin modification terms, the dominant theme ties ubiquitin-proteasome control to inflammatory signaling and cell fate decisions, with some immune system context via V(D)J recombination.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":3},{"id":"GO:0033151","count":3},{"id":"GO:2000620","count":3},{"id":"GO:0051865","count":3},{"id":"GO:1903721","count":3}]},{"hash":"1221059479667066755","title":"RNA splicing and gene silencing","description":"The cluster is dominated by GO terms for spliceosome-mediated mRNA processing and RNA silencing (siRNA processing, miRNA-mediated translation repression, and both positive/negative regulation of mRNA splicing via the spliceosome). A translation initiation factor term is present but peripheral, suggesting a primary theme of post-transcriptional regulation through splicing and RNA silencing. The outlier calcium-release term is likely noise. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030422","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0051209","count":1}]},{"hash":"1124268278053985293","title":"Unknown","description":"The GO terms include coenzyme A biosynthesis, phosphorylation, histone acetylation, flavonoid and sucrose metabolism, hormone signaling regulation, estrogen catabolic process, protein ubiquitination regulation, tarsal gland development, and heparan sulfate proteoglycan biosynthesis. These cover disparate metabolic, signaling, epigenetic, developmental, and biosynthetic processes with no clear shared function or pathway for the cluster. Therefore a single intuitive label cannot be confidently assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015937","count":1},{"id":"GO:0016310","count":1},{"id":"GO:0043970","count":1},{"id":"GO:0009812","count":1},{"id":"GO:0060765","count":1}]},{"hash":"1555336101855315608","title":"Carotenoid metabolism and light perception","description":"These proteins seem linked by carotenoid-derived signaling: plants use carotene/xanthophyll catabolism and strigolactone biosynthesis, while vertebrates manage light sensing through visual perception and retina-related processes. The overlap suggests a shared theme: carotenoid metabolism feeding light-response pathways across species, connecting carotenoid-derived signals to both plant development and retinal function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901601","count":1},{"id":"GO:0007601","count":1},{"id":"GO:0010223","count":1},{"id":"GO:0016121","count":1},{"id":"GO:0007604","count":1}]},{"hash":"1118630510854813702","title":"RNA splicing and post-transcriptional regulation","description":"The GO terms show a clear emphasis on mRNA splicing via the spliceosome (including alternative splicing and regulation of splicing) and post-transcriptional control such as miRNA-mediated silencing. A couple of transport-related terms are present, but the dominant signals point to RNA processing and regulation of gene expression after transcription. This supports a label focused on RNA processing/regulation rather than a single transport function. ","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0065002","count":1},{"id":"GO:0043953","count":1},{"id":"GO:1902458","count":1},{"id":"GO:0009306","count":1},{"id":"GO:0048025","count":1}]},{"hash":"1730080351285469668","title":"RNA processing and transcription control","description":"The proteins in this cluster are linked primarily through RNA metabolism and transcriptional regulation: DNA-templated transcription, transcription antitermination, and negative regulation of termination of transcription, along with post-transcriptional RNA processing such as pre-miRNA processing and miRNA catabolic process, and CRD-mediated mRNA stabilization. Mitochondrial-related terms (protein import into the mitochondrial intermembrane space, cristae formation) appear as less cohesive outliers, suggesting some multifunctionality or broader roles, but the dominant signal points to RNA processing and transcription control. ","confidence":"Low","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0031564","count":1},{"id":"GO:1901724","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0031054","count":1}]},{"hash":"1681120269001840725","title":"Unfolded protein response and chaperone activity","description":"This cluster is dominated by GO terms related to chaperone-assisted protein folding, refolding, and cellular responses to unfolded proteins and heat stress, suggesting a cohesive theme around protein quality control and stress responses. Some terms (e.g., DNA replication, fungal cell wall biosynthesis) appear as outliers, but do not override the central chaperone/stress signal, so the label captures the core function of the group.","confidence":"Medium","size":6,"edges":7,"triangles":3,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0070389","count":3},{"id":"GO:1903382","count":2},{"id":"GO:0000742","count":2},{"id":"GO:0006880","count":2}]},{"hash":"1118803778743006833","title":"DNA Damage Repair and Xenobiotic Stress Response","description":"The cluster is enriched for base-excision repair and DNA-damage related responses (including depurination, response to xenobiotic stimulus, and cellular response to cadmium), plus negative regulation of apoptotic processes. These patterns point to proteins involved in sensing environmental stress and activating DNA repair while modulating cell survival, despite some older/obsolete terms present that are less informative. ","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0043066","count":3},{"id":"GO:0071276","count":3},{"id":"GO:1902800","count":3},{"id":"GO:0072421","count":3},{"id":"GO:0033158","count":3}]},{"hash":"771556909584730062","title":"Metal Ion Transport and Homeostasis","description":"The strongest recurring GO terms involve copper, zinc, and cadmium ion transport and intracellular calcium ion homeostasis, suggesting a core function in metal ion handling and calcium signaling. The remaining terms appear less coherent and may reflect annotation noise or broader associations, but the metal ion transport theme remains the most representative for the cluster.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0006825","count":2},{"id":"GO:0019373","count":2},{"id":"GO:0071577","count":2}]},{"hash":"2248499629715168784","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0006450","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0009561","count":1},{"id":"GO:0042274","count":1}]},{"hash":"2183980915720443813","title":"Mitochondrial membrane signaling and neuronal adhesion","description":"This cluster centers on mitochondrial membrane potential regulation and cardiolipin-related lipid handling, with strong signals for membrane localization (lipid rafts), cadherin-mediated cell adhesion, and dopaminergic synaptic transmission. The combination suggests proteins that coordinate mitochondrial function with membrane signaling at neural synapses and cell\u2013cell interfaces, with a minor immune signaling signal (IL-2 production) that may reflect cross-talk or broader roles. Overall, the label captures mitochondria-associated membrane signaling in neural/adhesive contexts.","confidence":"Medium","size":6,"edges":9,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0010918","count":2},{"id":"GO:0032623","count":2},{"id":"GO:0001302","count":2},{"id":"GO:2000049","count":2},{"id":"GO:1903044","count":2}]},{"hash":"208524570911554531","title":"Unknown","description":"The listed GO terms cover widely separate processes (protein stabilization, photosynthesis, polysaccharide transport, mitochondrial ATP synthesis, DNA repair, and purine metabolism) with no clear shared function or pathway. This diversity makes it hard to assign a single, representative label, so Unknown is appropriate.","confidence":"","size":6,"edges":9,"triangles":4,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0050821","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0015774","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0006281","count":1}]},{"hash":"972926127705826371","title":"Unknown","description":"The top GO terms are highly heterogeneous: cell division, viral genome replication, flagellum organization, SRP-dependent cotranslational targeting to membrane, and various pentose/quinolinate metabolism terms. There is no single cohesive biological process or pathway linking these terms, suggesting the cluster may contain proteins with diverse, unrelated functions or an assembly with mixed annotations. Confidence: None","confidence":"","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0019079","count":2},{"id":"GO:0044781","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0006616","count":1}]},{"hash":"359489965005426030","title":"Muscle and heart development with neuromuscular signaling","description":"The cluster is driven by muscle/heart development terms (myoblast fusion, heart development, angiogenesis, multicellular organism development) and neuromuscular signaling indicators (long-term synaptic potentiation, excitatory postsynaptic potential), suggesting a developmental program tied to muscle and cardiovascular tissues with associated neuromuscular activity. Some terms (e.g., cell cycle, apoptosis, plant signaling) are less central but do not override the core muscle/vascular development theme.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0014850","count":3},{"id":"GO:0060079","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0007520","count":3}]},{"hash":"1836843066485711759","title":"Unknown","description":"The GO terms are diverse, spanning apoptosis in different cell types, cell migration, epithelial polarity, spindle assembly, calcium transport, temperature sensation, and neural differentiation, with no single cohesive theme to anchor a concise, representative label.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097284","count":3},{"id":"GO:0033028","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0090162","count":3},{"id":"GO:0007205","count":3}]},{"hash":"753927883910445273","title":"Genome maintenance and stress response","description":"This cluster combines GO terms tied to DNA replication and repair (mitotic DNA replication checkpoint signaling, UV-damage excision repair), chromatin assembly (CENP-A containing chromatin assembly), and RNA quality control (nonfunctional rRNA decay) with processes related to cellular stress responses (stress granule disassembly) and organelle quality control (autophagosome maturation, peroxisomal protein import). The collection suggests proteins involved in maintaining genome integrity while managing cellular stress and organelle turnover, hence a label centered on genome maintenance and stress response.","confidence":"Medium","size":6,"edges":12,"triangles":9,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070651","count":5},{"id":"GO:0090296","count":5},{"id":"GO:0000733","count":5},{"id":"GO:0097352","count":5},{"id":"GO:0016562","count":5}]},{"hash":"821407518455956484","title":"Small-molecule and lipid metabolism","description":"This cluster shows diverse catabolic and biosynthetic processes for small carbon sources (ethanol, sorbitol, xylitol, formaldehyde) and fatty acids (omega-oxidation and biosynthesis), pointing to a broad metabolic theme rather than a single pathway. The presence of lipopolysaccharide and antineoplastic agent response terms suggests linked stress or xenobiotic responsiveness that often accompanies metabolic reprogramming.","confidence":"Medium","size":6,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0043458","count":2},{"id":"GO:0032496","count":2},{"id":"GO:0006069","count":2},{"id":"GO:0006062","count":2},{"id":"GO:0010430","count":2}]},{"hash":"56159563942746042","title":"DNA-templated transcription in development","description":"The top GO term is DNA-templated transcription (GO:0006351) with 3 proteins, suggesting a core transcription-related function; the remaining terms show a broad set of developmental processes (axis specification, uterus morphogenesis, blastocyst formation) and some obsolete annotations, indicating a general developmental regulation signal rather than a single pathway.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0071041","count":1},{"id":"GO:0033169","count":1},{"id":"GO:0007290","count":1}]},{"hash":"1220478551553494842","title":"Unknown","description":"There isn\u2019t a single cohesive function tying these GO terms together: immune signaling and antigen presentation terms coexist with ER stress, hormone signaling, development, and fertilization terms, suggesting no clear common biological theme for this cluster.","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033144","count":1},{"id":"GO:0048916","count":1},{"id":"GO:0048387","count":1},{"id":"GO:0030968","count":1},{"id":"GO:0002502","count":1}]},{"hash":"1245942169252419378","title":"Purine nucleotide metabolism and salvage","description":"The proteins in this cluster are annotated with GO terms centered on nucleotide metabolism: ADP and CDP biosynthesis, AMP salvage, nucleoside monophosphate phosphorylation, and purine ribonucleotide interconversion. These recurring themes indicate a shared role in purine nucleotide turnover and energy phosphate cycling. Two terms about development (liver/brain) appear but are less representative of the core function and may reflect broader or tissue-context annotations. Overall, the dominant pattern is purine nucleotide metabolism and salvage.","confidence":"Medium","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0001889","count":3},{"id":"GO:0046041","count":3},{"id":"GO:0006172","count":3},{"id":"GO:0046705","count":3},{"id":"GO:0046940","count":3}]},{"hash":"947215457691927198","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0030433","count":3},{"id":"GO:0006295","count":2},{"id":"GO:0006296","count":2},{"id":"GO:0042769","count":2}]},{"hash":"2267701852521023953","title":"Genome Maintenance and Chromatin Assembly","description":"Dominant GO terms describe DNA replication/repair and chromatin assembly (mitotic DNA replication checkpoint signaling, UV-damage excision repair, CENP-A containing chromatin assembly) with supporting RNA processing terms (nonfunctional rRNA decay, stress granule disassembly). A few terms relate to organelle import/autophagy, which are less representative. Overall, genome maintenance and chromatin dynamics best explain the cluster.","confidence":"Medium","size":5,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070651","count":3},{"id":"GO:0090296","count":3},{"id":"GO:0000733","count":3},{"id":"GO:0097352","count":3},{"id":"GO:0016562","count":3}]},{"hash":"206371300773057006","title":"Unknown","description":"The listed GO terms are heterogeneous, spanning oxidative stress response (hydrogen peroxide), protein repair/modification, chromatin organization, collagen breakdown, and several obsolete terms. With no edges or shared functional signal, there isn't a clear common function uniting these proteins, so the cluster is best labeled Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":1},{"id":"GO:0030091","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006464","count":1},{"id":"GO:1990355","count":1}]},{"hash":"680526847369020529","title":"Unknown","description":"There are no shared GO terms or interactions among the five proteins (no edges, no triangles, and no Top Terms listed), so there is no functional signal to derive a meaningful label. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"915249888270048855","title":"Unknown","description":"This cluster contains a set of GO terms that span disparate biological areas (vision, endothelial proliferation, protein folding, ubiquitin-dependent catabolic regulation, tRNA biosynthesis, G-protein assembly, ureteric bud morphogenesis, circadian gene expression, and pregnancy). With no network edges and only singleton annotations, there is no coherent common function tying the proteins together, so a singular, meaningful label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":1},{"id":"GO:0001938","count":1},{"id":"GO:0061084","count":1},{"id":"GO:2000059","count":1},{"id":"GO:0007329","count":1}]},{"hash":"1136257122936533079","title":"Transmembrane transporters","description":"The top GO terms indicate a collection of membrane transport activities across diverse substrates (teichoic acid, amino acids, ions, vitamins, lipids) and even secretion, pointing to proteins that move substances across membranes or mediate secretion. Despite some context variation, the unifying theme is transmembrane transport functions, rather than signaling or metabolism.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015777","count":1},{"id":"GO:0003333","count":1},{"id":"GO:0051454","count":1},{"id":"GO:0030253","count":1},{"id":"GO:0071805","count":1}]},{"hash":"1291452638736587492","title":"Unknown","description":"The GO terms are scattered across cardiac development, regulation of cardiac conduction, embryonic pregnancy, and various cellular responses to chemicals and metals, with no clear shared function or pathway and no interactions observed among the proteins; thus there is no coherent label to assign.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003231","count":1},{"id":"GO:1903779","count":1},{"id":"GO:0060136","count":1},{"id":"GO:0043497","count":1},{"id":"GO:2001033","count":1}]},{"hash":"1746270812470432974","title":"Ubiquitin-Mediated Immune Signaling and Apoptosis","description":"Top GO terms center on ubiquitin-dependent protein catabolic process and protein autoubiquitination, implying involvement of the ubiquitin-proteasome system. Additional terms reference negative regulation of transcription and I-kappaB phosphorylation, TNF-mediated signaling, and cell cycle regulation, pointing to signaling control and cell fate decisions. The presence of V(D)J recombination hints at lymphocyte-related immune processes. Together, these terms suggest a cluster of proteins participating in ubiquitin-driven regulation of immune signaling and apoptosis.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0033151","count":1},{"id":"GO:2000620","count":1},{"id":"GO:0051865","count":1}]},{"hash":"118320408673170427","title":"Tissue Development and Morphogenesis","description":"This cluster centers on developmental and tissue-organization processes, with terms like eye pigmentation, renal vesicle formation, renal inner medulla development, female germline ring canal formation, and adherens junction assembly pointing to morphogenesis and cellular architecture. Other terms (tRNA processing, DNA damage response, mitochondrial calcium regulation) are more general cellular maintenance but do not override the developmental theme. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015991","count":2},{"id":"GO:0048069","count":1},{"id":"GO:0071681","count":1},{"id":"GO:0008033","count":1},{"id":"GO:0072033","count":1}]},{"hash":"1871572598635461570","title":"Bacterial flagellar assembly and secretion system","description":"This cluster is dominated by GO terms for bacterial-type flagellum-dependent motility and flagellum assembly, with another prominent term for protein secretion by the type III secretion system, pointing to components of the flagellar apparatus and secretion machinery. The remaining terms may reflect associated membrane transport and energy processes, but the core theme is bacterial flagellar structure and T3SS-related secretion.","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0071973","count":3},{"id":"GO:0044780","count":3},{"id":"GO:0006629","count":2},{"id":"GO:0090463","count":2},{"id":"GO:0030254","count":2}]},{"hash":"1010881983135051818","title":"Neuronal Signaling and Development","description":"This cluster appears to be dominated by signaling-related GO terms (integrin-mediated signaling, protein trans-autophosphorylation, and references to PI3K signaling/angiogenesis) plus neural development cues (fasciculation of motor neuron axons and cerebral cortex development). The remaining terms (glucose response, immune defense, and DNA repair) are less cohesive with the main theme and may reflect broader annotations or multi-function proteins. Overall, the strongest coherent theme is signaling processes intertwined with neural development, justifying the label, albeit with some ambiguity.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045766","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0014068","count":2},{"id":"GO:2001033","count":1}]},{"hash":"1598494091479678541","title":"Redox Homeostasis and Stress Response","description":"The top GO terms cluster around oxidation-reduction processes and redox-related metabolism (oxidation-reduction, redox homeostasis, NAD+ biosynthesis, anaerobic respiration) and stress responses (fungicide, LPS, selenium ion). While a couple of terms point to neuroendocrine processes, the strongest common theme is redox balance and metabolic adjustment under stress, which suits a small, sparsely connected protein cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0060992","count":2},{"id":"GO:0014063","count":2},{"id":"GO:0010269","count":2},{"id":"GO:0009435","count":2}]},{"hash":"1264573294188014538","title":"Metabolic Stress Response Network","description":"This cluster shows many GO terms tied to cellular responses to diverse stimuli (insulin, heat, hypoxia, epinephrine, nutrients, and cAMP) and to core metabolic processes (pyruvate biosynthesis, lipopolysaccharide biosynthesis), plus seed maturation and programmed cell death. The common thread is an integration of stress signaling with metabolic regulation, rather than a single, tightly defined pathway.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0012501","count":2},{"id":"GO:0042866","count":2},{"id":"GO:0009408","count":2}]},{"hash":"1596862809987439401","title":"Protein acetylation and chromatin regulation","description":"The dominant GO terms point to acetylation events (N-terminal acetylation, peptidyl-lysine acetylation, histone H4 acetylation) and heterochromatin formation, suggesting a cluster centered on protein acetylation and chromatin-like regulation, with other metabolism-related terms appearing peripheral.","confidence":"Medium","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006348","count":5},{"id":"GO:0030187","count":4},{"id":"GO:0045150","count":4},{"id":"GO:0061606","count":4},{"id":"GO:0018002","count":4}]},{"hash":"259502622661263453","title":"Translation Machinery and Regulation","description":"Dominant GO terms describe various stages of translation (initiation, elongation, termination, general translation) and their regulation, including mitochondrial translation. The cluster thus appears to represent components of the protein synthesis machinery and its regulation. A few non-translation terms (skeletal muscle differentiation, antibiotic response, heterochromatin formation) are peripheral and do not define the core theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006413","count":1},{"id":"GO:0035914","count":1},{"id":"GO:0045901","count":1},{"id":"GO:0002184","count":1},{"id":"GO:1902802","count":1}]},{"hash":"426754046208095525","title":"Unknown","description":"The GO terms cover a broad mix: neural development (cerebral cortex development, negative regulation of axonogenesis), reproductive processes (sperm capacitation), development of glands (pituitary development), RNA processing (alternative splicing), redox/homeostasis, and stress-related responses, with no clear, single biological theme. The cluster also has no edges, indicating dispersed annotations or heterogeneous function among proteins. Therefore, there isn\u2019t a coherent function to name beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0045793","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0050771","count":2}]},{"hash":"275880501181838750","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0035975","count":1},{"id":"GO:0009435","count":1},{"id":"GO:0006561","count":1},{"id":"GO:0009089","count":1}]},{"hash":"136868526707811704","title":"Nutrient and stress signaling responses","description":"Based on the GO terms, this cluster is enriched for cellular responses to metabolic cues (glucose stimulus, insulin stimulus, amino acid starvation) and dsRNA, pointing to nutrient/energy stress signaling and innate response pathways. Some terms also touch on broader signaling and developmental or mitotic processes, which may reflect background noise, but the dominant theme is nutrient- and stress-related signaling.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071333","count":2},{"id":"GO:0043330","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0032869","count":2},{"id":"GO:2001033","count":1}]},{"hash":"1108588754066559053","title":"Endosomal trafficking and MVB sorting","description":"The cluster is dominated by GO terms for vesicle transport involving the Golgi, endosomes, and vacuoles, including Golgi-to-endosome and endosome-to-Golgi transport, endocytosis, and late/early endosome routing via multivesicular body sorting. This indicates a cohesive endosomal/lysosomal trafficking module with MVB sorting and vacuolar targeting. Actin cortical patch assembly aligns with cytoskeletal involvement in vesicle movement, while a couple of terms (female pregnancy, cardioblast fate regulation) likely reflect annotation noise.","confidence":"High","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006895","count":1},{"id":"GO:0009997","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0007565","count":1},{"id":"GO:0006897","count":1}]},{"hash":"2072474011909347075","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0006986","count":1},{"id":"GO:0034975","count":1},{"id":"GO:0071374","count":1},{"id":"GO:0046825","count":1}]},{"hash":"237731846032330660","title":"Vesicle trafficking and receptor signaling","description":"The cluster is driven by GO terms for vesicle fusion with the ER and Golgi, plus receptor clustering and signaling-related processes (Rho signaling, opioid receptor pathway regulation) and cell polarity/localization, suggesting a theme of membrane trafficking linked to signaling and organization at the cell surface. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048279","count":1},{"id":"GO:0016320","count":1},{"id":"GO:0048280","count":1},{"id":"GO:2000474","count":1},{"id":"GO:2000009","count":1}]},{"hash":"2140877365111182187","title":"Inflammation and cellular stress response","description":"The GO terms cluster around immune activation and inflammatory signaling (positive regulation of inflammatory response, TNF production, response to ischemia, response to ATP) along with anti-apoptotic regulation and protein-folding stress (chaperone-mediated protein complex assembly). Some nuclear processes (pore complex assembly, telomerase RNA localization to Cajal body) may reflect broader cellular stress responses. Together these suggest a module coordinating immune/inflammatory signaling with cellular stress survival, hence the name.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0014823","count":4},{"id":"GO:0051131","count":4},{"id":"GO:0050729","count":4},{"id":"GO:0071866","count":4},{"id":"GO:0002931","count":4}]},{"hash":"269983441153965671","title":"DNA Repair and Damage Response","description":"The terms cluster around multiple DNA repair pathways (NER, BER, cross-link repair) and DNA damage\u2013triggered apoptotic signaling, suggesting proteins focused on sensing, repairing DNA damage and coordinating cell fate; a growth term appears incidental.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000715","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0008630","count":1},{"id":"GO:1901255","count":1},{"id":"GO:0070914","count":1}]},{"hash":"1660732280318481144","title":"Epithelial Cytoskeletal Remodeling","description":"The terms converge on actin- and contractile-filament\u2013based processes (muscle contraction regulation, actin filament bundles, microvillus organization, contractile-ring-related localization) and epithelial-specific structures (follicle cell microvilli, apical bud growth, uropod-related organization). This suggests a cluster of proteins involved in cytoskeletal remodeling and surface structure organization in epithelial contexts. Confidence: Medium","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007118","count":2},{"id":"GO:0006620","count":2},{"id":"GO:0014728","count":1},{"id":"GO:1903478","count":1},{"id":"GO:0030049","count":1}]},{"hash":"555481477403082741","title":"Plant growth and environmental stress signaling","description":"The top GO terms cluster around growth regulation (cell size, secondary growth) and various environmental responses (lipopolysaccharide response, hypoxia detection, red/far-red phototransduction), with supporting metabolism and genome maintenance processes (pyruvate to acetyl-CoA regulation, branched-chain amino acid catabolism, DNA topology, telomerase assembly). This suggests a theme of coordinating growth with environmental cues and stress, rather than a single, narrow pathway. Confidence: Medium","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":3},{"id":"GO:0010510","count":3},{"id":"GO:0032496","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009083","count":2}]},{"hash":"1203590406599794280","title":"Unknown","description":"The terms are highly heterogeneous (developmental processes, detoxification/metabolism, redox homeostasis, RNA splicing, epigenetic regulation, and membrane potential), with no single process dominating. Consequently, there is no clear, confidence-justified label that represents the cluster\u2019s shared function.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060992","count":2},{"id":"GO:0070276","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0021983","count":2},{"id":"GO:0000380","count":2}]},{"hash":"2186004006583622646","title":"Unknown","description":"The terms span ion homeostasis, membrane potential, vesicle trafficking, microvillus regulation, muscle contraction, sensory and immune processes, showing no single cohesive function or pathway to bind the proteins together; with zero edges/triangles, the cluster appears functionally diverse and not easily labeled.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006883","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0086009","count":1},{"id":"GO:0030007","count":1},{"id":"GO:0010248","count":1}]},{"hash":"424380517503207909","title":"Amino acid biosynthesis and metabolism","description":"The terms show a clear emphasis on biosynthesis and catabolism of L- and D-amino acids (leucine, isoleucine, valine, D-amino acids) and related metabolic processes, with additional signals for folic acid biosynthesis; overall, it points to a cluster of proteins involved in amino acid metabolism, despite some unrelated terms that may reflect broader metabolic roles or annotation noise.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0010817","count":1},{"id":"GO:0046437","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0046656","count":1},{"id":"GO:0009098","count":1}]},{"hash":"2129903267654029767","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0098507","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0006370","count":1},{"id":"GO:1900182","count":1},{"id":"GO:0019988","count":1}]},{"hash":"437668998322419818","title":"Mitotic spindle assembly and chromosome segregation","description":"This cluster is dominated by mitosis- and spindle-related GO terms such as cell cycle, positive regulation of sister chromatid biorientation, localization to the mitotic spindle pole body, and attachment of spindle microtubules to the kinetochore, indicating a role in mitotic spindle function and chromosome segregation. Some metabolic terms appear but do not define the primary function. ","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006098","count":1},{"id":"GO:0006006","count":1},{"id":"GO:0042952","count":1},{"id":"GO:0098783","count":1}]},{"hash":"488089328220211434","title":"Methyltransferases (RNA and protein)","description":"Based on the top GO terms, the cluster is strongly enriched for methylation-related activities: peptidyl-lysine dimethylation, N-terminal peptidyl-glycine methylation, and rRNA methylation. These point to enzymes that transfer methyl groups to proteins or RNA, suggesting the proteins are methyltransferases or closely related factors. The other terms are less coherent with this theme, but do not overpower the clear methylation signal. Overall, the cluster likely represents methylation-related enzymes.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":2},{"id":"GO:0018013","count":2},{"id":"GO:0031167","count":2},{"id":"GO:0000411","count":1},{"id":"GO:0044828","count":1}]},{"hash":"658712465836486523","title":"ER-to-Golgi Vesicle Transport","description":"This cluster\u2019s top GO annotation is ER-to-Golgi vesicle-mediated transport (GO:0006888), indicating involvement in cargo movement from the endoplasmic reticulum to the Golgi in the early secretory pathway. The four proteins are connected via vesicle trafficking consistent with COPII-mediated transport. Given the single, specific function dominating the terms, this name succinctly captures the cluster\u2019s shared activity.","confidence":"High","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":1}]},{"hash":"745365672925813484","title":"Unknown","description":"The GO terms are highly diverse\u2014mechanosensory response, pain perception, chemokine production, vascular differentiation, spindle assembly, chromatid cohesion, development, cell growth, and calcium transport\u2014showing no single shared function for the four proteins.","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035994","count":1},{"id":"GO:0050968","count":1},{"id":"GO:0071651","count":1},{"id":"GO:0060843","count":1},{"id":"GO:0051225","count":1}]},{"hash":"1519072085006834948","title":"Nuclear transport and centrosome regulation","description":"The top GO terms point to nuclear trafficking (tRNA export from nucleus; import of NLS-bearing proteins) and centrosome-related processes (centrosome cycle; regulation of protein localization to centrosome; chromosome attachment to the nuclear envelope), with additional links to nucleus size and spermatogenesis. This suggests a cohesive theme around nuclear transport and centrosome/nuclear envelope dynamics as the cluster\u2019s core function.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006409","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0007283","count":1},{"id":"GO:0097298","count":1},{"id":"GO:0007098","count":1}]},{"hash":"1108710460321822813","title":"Unknown","description":"The Top Terms span development, apoptosis, transcription, cell size regulation, chemotaxis, neurotransmitter regulation, and diverse environmental responses, with no clear shared function or pathway. The cluster shows no edges or interactions, suggesting these proteins do not cluster by a single cohesive function. ","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0006935","count":2}]},{"hash":"9129359399311702","title":"RNA Pol II/III Transcription Regulation","description":"The top GO terms are dominated by transcription-related processes, including RNA polymerase II promoter regulation, preinitiation complex assembly, and RNA polymerase III transcription regulation, suggesting the proteins cluster around transcription initiation machinery. Some entries (SMAD signaling, detoxification) are peripheral, but the core theme is transcription control, so this label reflects the main function of the cluster.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075297","count":1},{"id":"GO:0070898","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0060261","count":1},{"id":"GO:0045945","count":1}]},{"hash":"1869006367241435463","title":"Mitotic spindle dynamics and cytokinesis","description":"This cluster shows strong representation of microtubule-driven processes (plus-end directed microtubule activities, vesicle transport along microtubules, microtubule depolymerization) and components of the cytokinetic machinery (actomyosin contractile ring assembly, spindle pole separation). While there are related terms about cell adhesion and stress granules, the dominant theme is mitotic spindle dynamics and the execution of cytokinesis, with linked cytoskeletal regulation at the cell cortex.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":3},{"id":"GO:0031535","count":3},{"id":"GO:0000073","count":3},{"id":"GO:0035617","count":3},{"id":"GO:0001560","count":3}]},{"hash":"2258266331601465662","title":"Cytoskeletal dynamics during cell division","description":"This cluster centers on microtubule-driven activities and mitotic events: plus-end directed microtubule sliding and vesicle transport along microtubules, spindle pole separation, and actomyosin contractile ring assembly, indicating coordinated cytoskeletal rearrangements during cell division. Additional terms on stress granule dynamics and adherens maintenance reflect broader cytoskeletal and signaling contexts but do not override the core mitotic/microtubule theme. Overall, the proteins are best grouped as factors involved in cytoskeletal remodeling and mitosis.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000743","count":3},{"id":"GO:0031535","count":3},{"id":"GO:0000073","count":3},{"id":"GO:0035617","count":3},{"id":"GO:0001560","count":3}]},{"hash":"1542399721293803962","title":"Immune activation and inflammatory signaling","description":"The top GO terms point to inflammation and immune processes (positive regulation of inflammatory response, TNF production, IgG isotype switching) alongside stress responses (ischemia, ATP response) and protein quality control (chaperone-mediated assembly), suggesting a cluster of proteins involved in immune/inflammatory signaling with supporting cellular stress responses.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0014823","count":2},{"id":"GO:0051131","count":2},{"id":"GO:0050729","count":2},{"id":"GO:0071866","count":2},{"id":"GO:0002931","count":2}]},{"hash":"1059987005737595820","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0044830","count":1},{"id":"GO:1902416","count":1},{"id":"GO:0070935","count":1},{"id":"GO:0090503","count":1}]},{"hash":"1662217856634463657","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006986","count":3},{"id":"GO:0034975","count":3},{"id":"GO:0071374","count":3},{"id":"GO:0046825","count":3},{"id":"GO:0045454","count":3}]},{"hash":"664544176079359728","title":"Unknown","description":"The GO terms are highly diverse, including metal ion responses (cadmium, copper), oxidative stress (singlet oxygen), DNA-templated transcription, and an embryonic development process. With no clear, shared function tying these proteins together, a precise label is not identifiable.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060136","count":1},{"id":"GO:0043497","count":1},{"id":"GO:2001033","count":1},{"id":"GO:1904843","count":1},{"id":"GO:0071276","count":1}]},{"hash":"750220817474518705","title":"Neuronal development and synaptic signaling","description":"The top GO terms cluster around neuronal development and synaptic processes: cerebral cortex development, fasciculation of motor neuron axons, integrin-mediated signaling in neurons, and long-term synaptic potentiation, with supporting signaling-related terms like protein trans-autophosphorylation and cyclic nucleotide biosynthesis. A few terms relate to generic cell cycle/DNA repair, which may reflect broader roles or annotation noise, but the dominant signal is neuronal development and synaptic signaling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001033","count":1},{"id":"GO:0097156","count":1},{"id":"GO:0007229","count":1},{"id":"GO:1990758","count":1},{"id":"GO:0021987","count":1}]},{"hash":"148219030085025938","title":"Photosynthesis proteins","description":"Based on the singleGO term present (photosynthesis), the cluster appears to be centered on photosynthetic function. The small size and lack of additional relations limit confidence, but the dominant term supports this as the representative theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":1}]},{"hash":"2153104516298690477","title":"Co-translational membrane targeting and secretion","description":"The terms point to translation and targeting of nascent proteins to membranes, especially SRP-dependent cotranslational targeting and Sec-mediated transport, as well as protein secretion. This indicates a cohesive group of proteins involved in directing ribosome-bound polypeptides to the secretory pathway and membrane insertion.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006605","count":1},{"id":"GO:0043952","count":1},{"id":"GO:0009306","count":1},{"id":"GO:0006616","count":1}]},{"hash":"1983022918611400202","title":"Peroxisomal Matrix Protein Import","description":"The top GO terms strongly point to import of proteins into the peroxisome matrix and receptor recycling, indicating a coherent peroxisomal import function for this cluster (GO:0016558 and GO:0016562, each with two associations). Other terms present are sparse or unrelated (transcription, cell division, stress responses), suggesting some annotation noise but not overriding the core peroxisomal import signal. Overall, the cluster is best described as involving peroxisomal matrix protein import, with moderate confidence due to some conflicting terms.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016562","count":2},{"id":"GO:0016558","count":2},{"id":"GO:0070987","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0030433","count":2}]},{"hash":"842743076372170474","title":"Neural development and axon fasciculation","description":"This cluster is driven by terms related to neural development, notably fasciculation of motor neuron axons and cerebral cortex development, with integrin-mediated signaling supporting neuron-ECM interactions during axon guidance. While there are some general terms (translation, kinases), the strong neural development signals suggest the core theme is neuronal development and axon pathfinding.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:2001033","count":1},{"id":"GO:0097156","count":1},{"id":"GO:0007229","count":1},{"id":"GO:1990758","count":1}]},{"hash":"900288731188627715","title":"Circadian Transcription Regulation","description":"The top GO terms include circadian rhythm, entrainment of circadian clock, and regulation of DNA-templated transcription, pointing to a cluster centered on transcriptional control within circadian timing. Additional DNA maintenance terms (DNA replication, recombinational repair) appear but are secondary to the circadian-regulated transcription theme.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":1},{"id":"GO:0006276","count":1},{"id":"GO:0016539","count":1},{"id":"GO:0032508","count":1},{"id":"GO:0042754","count":1}]},{"hash":"2091877514902014568","title":"Neural Axonogenesis and Muscle Development","description":"The top GO terms cluster around neural development (long-term synaptic potentiation, axonogenesis, Schwann cell development) and muscle-related processes (myoblast fusion, response to muscle activity), with additional cell cycle and signaling terms that reflect general developmental contexts. This suggests a theme of development and differentiation in neural/glial and muscle lineages, rather than a single pathway. Note that some terms (like abscisic acid signaling) may arise from broad or cross-species annotations, but the dominant pattern points to neural and muscle development.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060291","count":3},{"id":"GO:0007520","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0043065","count":3}]},{"hash":"2064763187769703583","title":"RNA Methylation Enzymes","description":"The GO terms point strongly to RNA modification: multiple entries for rRNA/tRNA guanine-N7 methylation and general rRNA modification, indicating methyltransferase activity. Additional biosynthetic terms (ubiquinone, antibiotic biosynthesis) fit a broader context of metabolism and cofactor production, but the core signal is RNA methylation enzymes. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006744","count":1},{"id":"GO:0070476","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0017000","count":1},{"id":"GO:0036265","count":1}]},{"hash":"1911162013151006249","title":"Unknown","description":"The top GO terms span photosynthesis-related processes and transcription regulation, but also sporulation, immune, and neural functions. This mix shows no single coherent biological theme for the cluster, suggesting heterogeneous annotations or functionally unrelated proteins grouped together.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048564","count":1},{"id":"GO:0015979","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0009408","count":1}]},{"hash":"1525972813888055996","title":"ER Protein Folding and Redox Homeostasis","description":"This cluster is enriched for terms tied to endoplasmic reticulum protein folding, ER stress response, deglutathionylation, and redox homeostasis. Although a couple of transcription-related terms appear, the dominant signals point to ER quality control and oxidative regulation, suggesting proteins involved in folding and maintaining redox balance in the ER.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080058","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0018401","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0045454","count":2}]},{"hash":"2283909146949761482","title":"Post-transcriptional Regulation: Splicing and Translation","description":"The terms are dominated by regulation of mRNA splicing via the spliceosome (positive/negative and alternative splicing) and components involved in translation initiation and miRNA-mediated silencing, indicating a cluster centered on post-transcriptional control of gene expression. Some unrelated terms may reflect broader annotations, but the core theme is RNA processing and translation regulation.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048453","count":1},{"id":"GO:0048025","count":1},{"id":"GO:0000380","count":1},{"id":"GO:0048026","count":1},{"id":"GO:0050900","count":1}]},{"hash":"2165424461183271877","title":"Ubiquitination and Cell Cycle Regulation","description":"This cluster centers on protein ubiquitination with multiple linkage types (K48, K63, K6) and autoubiquitination, pointing to ubiquitin-proteasome\u2013regulated functions. The inclusion of cell division and APC-dependent catabolic processes reinforces a role in cell cycle control. Some viral process and peroxisomal import terms may reflect broader regulatory contexts or annotation overlap, but the dominant theme is ubiquitin-mediated regulation linked to cellular proliferation.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":3},{"id":"GO:0070936","count":3},{"id":"GO:0016032","count":3},{"id":"GO:0051092","count":3},{"id":"GO:0070911","count":3}]},{"hash":"699908603183654387","title":"Transcription and metal/oxidative stress response","description":"The top GO terms include DNA-templated transcription and cellular responses to cadmium, copper, and singlet oxygen, suggesting proteins in this cluster link transcriptional activity with responses to metal and oxidative stress; however, some terms are unrelated or obsolete, indicating a loosely connected set of functions centered on transcription and stress signaling.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0060136","count":1},{"id":"GO:0043497","count":1},{"id":"GO:2001033","count":1},{"id":"GO:1904843","count":1}]},{"hash":"1605300429502761975","title":"N-terminal and Lysine Protein Acetylation","description":"The top GO terms are dominated by acetylation-related processes on proteins, including N-terminal acetylation and lysine/peptidyl acetylation variants, which strongly suggests a cluster centered on protein acetylation regulation or execution. There are other metabolic terms present, but the acetylation theme is the most coherent and representative. ","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030187","count":2},{"id":"GO:0045150","count":2},{"id":"GO:0061606","count":2},{"id":"GO:0018002","count":2},{"id":"GO:0010125","count":2}]}]